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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of {{ project }} nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ============================================================================== JSME Molecular Editor 2024-04-29 Licence: BSD-3-Clause (Novartis Institutes for BioMedical Research and Bruno Bienfait); this copy is MODIFIED: the code that opens other websites is taken out Source: https://jsme-editor.github.io/ (the original); the change is lib/mol3d_web/jsme_patch.py ============================================================================== MODIFIED COPY (2026-10-10): the code that opens other websites was taken out of this copy of JSME. Its menu entry "Search chemical structure (through InChIKey)" (a Google search), and the Help and JSME home buttons of its About box, no longer open a window, and the three addresses (the Google search and two pages of the editor's own website) are blank in the files. Nothing else was changed: the editor draws, reads and writes structures as before, and its About box still shows its version and this licence. The change is made by lib/targetid/web/jsme_patch.py, which counts what it replaces in each file, and is described in lib/targetid/web/static/VENDOR.md. The original is available from the JSME project's website. Copyright (c) 2024, Novartis Institutes for BioMedical Research Inc and Bruno Bienfait All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Novartis Institutes for BioMedical Research nor the names of the authors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. JSME uses code from the following libraries: - Apache Harmony - Apache License v2.0 http://www.apache.org/licenses/ - gwt-mosaic - Apache License v2.0 http://www.apache.org/licenses/ - gwt-exporter - Apache License v2.0 http://www.apache.org/licenses/ - gwt - Apache License v2.0 http://www.apache.org/licenses/ - OpenChemLib - https://github.com/Actelion/openchemlib/blob/master/LICENSE - InChI 1.05 - http://www.inchi-trust.org/ - emscripten - https://kripken.github.io/emscripten-site/index.html ============================================================================== Sobol' direction numbers, dimensions 1 to 64 (web/sobol.js: the starting points of the conformer search) Licence: BSD-style (Copyright (c) 2008, Frances Y. Kuo and Stephen Joe); the text is below, word for word Source: https://web.maths.unsw.edu.au/~fkuo/sobol/ (the file new-joe-kuo-6.21201, the D(6) set: 63 of its lines, as scipy 1.17.1 ships them) Credit: S. Joe and F. Y. Kuo, Constructing Sobol sequences with better two-dimensional projections, SIAM J. Sci. Comput. 30 (2008) 2635-2654. ============================================================================== ----------------------------------------------------------------------------- Licence pertaining to sobol.cc and the accompanying sets of direction numbers ----------------------------------------------------------------------------- Copyright (c) 2008, Frances Y. Kuo and Stephen Joe All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of the copyright holders nor the names of the University of New South Wales and the University of Waikato and its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ============================================================================== Data ============================================================================== Data served by this site: the lists behind the Random buttons (ChEMBL and PDB) and behind the PDB codes (the rest of the PDB ligands, and which ligands each PDB entry holds). Each list is a text file of this site, served unchanged; the page reads it in the visitor's browser and shows a molecule from it. ====================================================================================== ChEMBL 37: a random sample of 20,000 molecules (chembl-sample.tsv: SMILES and ChEMBL identifier) ====================================================================================== Licence: CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/) Source: ChEMBL release 37 (https://www.ebi.ac.uk/chembl/), prepared on 01/05/2026; doi:10.6019/CHEMBL.database.37 The sample is a selection from ChEMBL 37: compounds with at least one Ki, Kd, IC50 or EC50 value (nM) on a single protein or protein complex (assay confidence 7 to 9), each structure standardised (largest organic fragment, neutralised, no metal; stereo kept), then 12 to 50 heavy atoms, one fragment, only the elements H C N O F P S Cl Br I. The SMILES are therefore those of that standardisation, not ChEMBL's own canonical_smiles character for character. Only the structure and the ChEMBL identifier are in the file; none of ChEMBL's calculated acd_* columns is. Share-alike: this file is a derivative database of ChEMBL and is licensed CC BY-SA 3.0 as well: whoever receives it may copy, adapt and redistribute it, also commercially, if they credit ChEMBL and keep the same licence on what they share. Attribution: Molecule examples: a random sample of ChEMBL 37 (https://www.ebi.ac.uk/chembl/), CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0/); Zdrazil B et al., Nucleic Acids Res 2024, doi:10.1093/nar/gkad1004. ====================================================================================== Protein Data Bank ligands: a random sample of 15,000 ligands (pdb-sample.tsv: SMILES, component identifier, one entry that holds it, and the component's name) ====================================================================================== Licence: CC0 1.0 (https://creativecommons.org/publicdomain/zero/1.0/); the PDB archive's data files are in the public domain, and we credit them anyway Source: wwPDB Chemical Component Dictionary and RCSB PDB (https://www.rcsb.org, https://www.wwpdb.org/), snapshot 2026-09-26; the entry codes are those of an RCSB harvest of 2026-09-30, limited to the entries Pocket2D can open Ions, water, solvents, buffers, detergents, polymer residues and chain ends, obsolete components, anything under 12 heavy atoms, and anything with an element outside H C N O F P S Cl Br I are not in it. Attribution: PDB ligand examples: wwPDB Chemical Component Dictionary and RCSB PDB (https://www.rcsb.org), CC0 1.0; Burley SK et al., Nucleic Acids Res 2023, doi:10.1093/nar/gkac1077. This product uses data from the RCSB Protein Data Bank (RCSB.org), a member of the wwPDB, which archives the PDB under CC0 1.0. ====================================================================================== Protein Data Bank ligands, all of them: pdb-more.tsv (the other 20,790 of the 35,790 ligands, same columns) and pdb-entries.tsv (76,031 entries and their ligands) ====================================================================================== pdb-sample.tsv followed by pdb-more.tsv (without its header line) is the whole list of 35,790 ligands, from the same draw and the same sources and filter as above; the Random PDB button draws from the first 15,000 only. pdb-entries.tsv has, for each PDB entry that the pages of Pocket2D can open and that holds at least one of those ligands, the entry code and the component identifiers of its ligands (identifiers only: no structure, name or other resource's data). The page reads them when a PDB ligand code or a PDB entry code is typed in the Text box. Licence: CC0 1.0 (https://creativecommons.org/publicdomain/zero/1.0/); sources and attribution as above. ============================================================================== OpenFF Sage 2.3.0 (the force field's parameters) ============================================================================== Copyright (c) 2016, Open Forcefield Group Attribution 4.0 International ======================================================================= Creative Commons Corporation ("Creative Commons") is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an "as-is" basis. 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Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at creativecommons.org/policies, Creative Commons does not authorize the use of the trademark "Creative Commons" or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses. Creative Commons may be contacted at creativecommons.org. OpenFF Sage 2.3.0 as Mol3D ships it is NOT the unmodified force field. Licence: CC BY 4.0, Copyright (c) 2016, Open Forcefield Group (LICENSE.txt, as the openforcefields package ships it). https://creativecommons.org/licenses/by/4.0/ Source: openff_unconstrained-2.3.0.offxml of the Python package openforcefields 2026.01.0 (sha256 65b926cf38ae4bc2f6f9cac907c3cadba154cc84988dd10ab2c3895aaf2dd995). What was changed (the licence asks for it to be said): 1. The force field was converted from its offxml to JSON for the page (openff-2.3.0.json). Its numbers are exact (every one is compared with what the OpenFF toolkit parses). 2. Three angle terms were APPENDED at the end of the Angles section, so that they take precedence over the generic terms before them. Their numbers are Sage 2.2.1's own, from openff-2.2.1.offxml (sha256 1b24deb47970bae2d179a5b4e023d4a57c9c78614fe431f1670e3f75e0012c3a); the SMIRKS are new: a32-sulfonyl-N [#7X3:1]-[#16X4:2]~[#8X1:3] angle 107.2123 degrees, k 239.2024 kcal/mol/radian^2 a32-sulfamide [#7X3:1]-[#16X4:2]-[#7X3:3] angle 107.2123 degrees, k 239.2024 kcal/mol/radian^2 a31-sulfonyl-N [#8X1:1]~[#16X4:2](-[#7X3])~[#8X1:3] angle 120.4698 degrees, k 188.6314 kcal/mol/radian^2 They apply only to the angles of a sulfur with four neighbours that carries a nitrogen with three neighbours and an oxygen with one: N-S-O and N-S-N of a sulfonamide or sulfamide, and the O-S-O of such a group. Sulfones, sulfonates, sulfoxides, thioethers and every molecule without a sulfonamide or sulfamide keep Sage 2.3.0 exactly (a test holds it). 3. Four proper-torsion terms were APPENDED at the end of the ProperTorsions section, so that they take precedence over the generic terms before them (the last parameter that matches wins); the SMIRKS are new: t2-chain [#6X4:1]-[#6X4;!r3:2]-!@[#6X4;!r3:3]-[#6X4:4] n=3 phase 0 k 0.3350000000, n=2 phase 180 k 0.0890000000, n=1 phase 180 k 0.2290000000 t2-ring6 [#6X4:1]-[#6X4;r6:2]-@[#6X4;r6:3]-[#6X4:4] n=3 phase 0 k 0.0922387404, n=2 phase 180 k 0.3159935922, n=1 phase 180 k 0.3247796807 t3-chain-ch [#1:1]-[#6X4;!r3;!$(*~[!#1;!#6]):2]-!@[#6X4;!r3;!$(*~[!#1;!#6]):3]-[#1:4] n=3 phase 0 k 0.1530000000 t4-chain-ch [#1:1]-[#6X4;!r3;!$(*~[!#1;!#6]):2]-!@[#6X4;!r3;!$(*~[!#1;!#6]):3]-[#6X4:4] n=3 phase 0 k 0.0830000000 t2-chain applies to the C-C-C-C torsions of sp3 carbons about a bond that is in no ring and has no cyclopropane carbon in it; t2-ring6 to those about a bond of a six-membered ring (the ring's own and the bonds of an exocyclic carbon on it); t3-chain-ch to the H-C-C-H and t4-chain-ch to the H-C-C-C torsions about such a bond between two carbons whose neighbours are all carbon or hydrogen (a carbon that bears O, N, S or a halogen keeps Sage 2.3.0's own H terms). The numbers of t2-ring6 are Sage 2.0.0's own t2, from openff-2.0.0.offxml (sha256 ebb7eeff28dc513a5c5480a0f820b9a0a242053dfbda9ccc8e8db4a258bdeeda). The numbers of t2-chain, t3-chain-ch and t4-chain-ch are NOT Sage's: they were FITTED for Mol3D, the five constants together, to alkane conformer energies, saddle points and C-C rotation barriers (the data are listed below; the fitted rows are alkane-v2-lab.json, sha256 a70c377159d24f9fe6933a6893f5ba06c5db972979916656df62f63d6e58823d). The torsions of three-, four-, five-, seven- and eight-membered rings, of cyclopropyl bonds, and every torsion that has an atom that is not an sp3 carbon in it (the H-C-C-H and H-C-C-C ones above apart) keep Sage 2.3.0 exactly (a test holds it). 4. Three van der Waals terms were APPENDED at the end of the vdW section, so that they take precedence over the generic terms before them (the last parameter that matches wins); the SMIRKS are new: n-acidH-COOH [#1:1]-[#8X2H1]-[#6X3]=[#8X1] epsilon 0.046 kcal/mol, Rmin/2 0.2245 angstrom n-acidH-SO3H [#1:1]-[#8X2H1]-[#16X4]=[#8X1] epsilon 0.046 kcal/mol, Rmin/2 0.2245 angstrom n-acidH-PO3H [#1:1]-[#8X2H1]-[#15X4]=[#8X1] epsilon 0.046 kcal/mol, Rmin/2 0.2245 angstrom They apply only to the hydrogen of an acid group: an O-H hydrogen whose oxygen is bonded to a carbon, a sulfur or a phosphorus that carries a terminal oxygen by a double bond (a carboxylic, a sulfonic or a phosphoric or phosphonic acid, and the acid hydroxyls of the mono-esters of sulfuric and phosphoric acid). The hydrogen of an alcohol, a phenol, an oxime, a hydroxamic acid or water keeps Sage 2.3.0's n12 exactly (a test holds it), as does every molecule without such a group. The numbers are NOT Sage's: they are the polar hydrogen of the CHARMM force fields (CHARMM22 and CHARMM36 type H: MacKerell AD Jr et al., J. Phys. Chem. B 1998, 102, 3586-3616; CGenFF's HGP1 has the same pair: Vanommeslaeghe K et al., J. Comput. Chem. 2010, 31, 671-690, doi:10.1002/jcc.21367, which was not re-read; the pair of type H was checked in OpenMM 8's charmm36.xml, generated from CHARMM's par_all36_prot.prm: epsilon 0.192464 kJ/mol = 0.0460 kcal/mol, sigma 0.0400014 nm = Rmin/2 0.22450 A. No CHARMM, CGenFF or OpenMM file is copied: two published numbers, used as a model choice and cited), as given in the file acidh-v1-lab.json (sha256 e7385c2bebff806b06414e06ee9a8eacaa1c39fc2e36bf3f7b4169e59590ceca). 5. Five proper-torsion terms were APPENDED at the end of the ProperTorsions section, after the four above (the last parameter that matches wins); the SMIRKS are new: t78-amideNH-alkyl [#1:1]-[#7X3:2](-[#6X4])-!@[#6X3:3](=[#8X1:4])-[#6,#1] n=2 phase 180 k 1.5330438981, n=1 phase 0 k 2.4325639442 t78-amideNH-aryl [#1:1]-[#7X3:2](-[#6X3a])-!@[#6X3:3](=[#8X1:4])-[#6,#1] n=2 phase 180 k 1.5330438981, n=1 phase 0 k 3.0314209744 t79-ureaNH-alkyl [#1:1]-[#7X3:2](-[#6X4])-!@[#6X3:3](=[#8X1:4])-[#7X3;!$([#7](-[#6X3]=[#8,#16])-[#6X3]=[#8,#16]);!$([#7]-[#16X4])] n=2 phase 180 k 1.0551435903, n=1 phase 0 k 2.3085974941 t79-ureaNH-aryl [#1:1]-[#7X3:2](-[#6X3a])-!@[#6X3:3](=[#8X1:4])-[#7X3;!$([#7](-[#6X3]=[#8,#16])-[#6X3]=[#8,#16]);!$([#7]-[#16X4])] n=2 phase 180 k 1.0551435903, n=1 phase 0 k 2.4821600158 t79-thioureaNH [#1:1]-[#7X3:2](-[#6X4,#6X3a])-!@[#6X3:3](=[#16X1:4])-[#7X3;!$([#7](-[#6X3]=[#8,#16])-[#6X3]=[#8,#16]);!$([#7]-[#16X4])] n=2 phase 180 k 1.0551435903, n=1 phase 0 k 1.5966404538 Each applies only to the H-N-C=X torsion of an N-H whose other substituent is an sp3 carbon (alkyl) or an aromatic carbon (aryl), across an acyclic C-N bond: a secondary amide (t78-amideNH-alkyl, -aryl), a urea (t79-ureaNH-alkyl, -aryl: the second nitrogen is not acylated and not sulfonylated) or a thiourea (t79-thioureaNH). The numbers of the periodicity-2 term of each are Sage 2.3.0's own, those of the row it overrides (t78 or t79, from openff_unconstrained-2.3.0.offxml); the periodicity-1 term is NOT Sage's: it was FITTED for Mol3D, to wB97X-3c gas-phase energy differences between the cis and the trans state of 16 small molecules (44 states; the rows as given are in amidenh-v1-lab.json, sha256 47d3e7fdbe7df3976c2ba74718c4ac5e159f1b673c583be40f0a8049da4b897f). Tertiary amides, lactams, cyclic ureas and carbamates, N-acylureas, sulfonylureas, imides, hydrazides, hydroxamic acids, thioamides, amidines, carbamic acids, esters, N-vinyl amides and every carbamate keep Sage 2.3.0 exactly, as does every molecule without such an N-H (a test holds it, bit for bit). 6. Nothing else: no bond, improper, other van der Waals parameter or library charge differs from Sage 2.3.0. Sage Open (experimental), an entry of the force field choice, uses the parameters above and changes the ENERGY FUNCTION, not a parameter, for that entry only: the Lennard-Jones attraction between two atoms whose shortest path along the bonds is six or more bonds long (or that are in different fragments) is switched off. The repulsion of such a pair is kept by splitting its Lennard-Jones energy at its minimum distance (Weeks JD, Chandler D, Andersen HC, J. Chem. Phys. 1971, 54, 5237-5247, doi:10.1063/1.1674820): below that distance the energy is the Lennard-Jones energy plus epsilon, beyond it nothing. Every other term is Sage's. The energy shown is then added to the implicit water of docs/water-notice.txt, as a single point at the minimum. Sage Unfold (experimental), another entry of the force field choice, is Sage Open (experimental) with one more change of the ENERGY FUNCTION, not of a parameter: the Coulomb attraction between a polar hydrogen (a hydrogen bonded to N or O) and any N or O atom with a negative partial charge is removed when the shortest path along the bonds from the hydrogen is six or more bonds long (or the two atoms are in different fragments): the term K q(H) q(A) / r is taken off whole below 2.5 angstrom and not at all beyond 3.5 angstrom, and between the two it is multiplied by the CHARMM energy switching function (Brooks et al., J. Comput. Chem. 1983, 4, 187-217, doi:10.1002/jcc.540040211), which falls from 1 to 0. The pairs depend on the charges of the page (OpenFF's NAGL network, as for every entry), and sulfur, fluorine and chlorine are never partners. Every other term is Sage Open's, and its energy is added to the implicit water of docs/water-notice.txt in the same way. A hydrogen bond whose hydrogen is five bonds or fewer from the atom it bonds to (a ring of six atoms or fewer, counting the hydrogen) is untouched; one whose hydrogen is six or more bonds from it (a ring of seven or more, such as the C7 gamma-turn of a peptide) loses its contact attraction, and so does the far H-bond salt bridge of a larger zwitterion; the contact opens to about 3.5 angstrom (the attraction that remains, (1 - S) K q q / r, is lowest at 3.46 angstrom; not measured against reference data). A salt is allowed: no ligand with several fragments was measured; in a salt the ions still attract, and only the contact attraction of its polar hydrogens to the other ion's N and O is removed, so the contact is a little longer (not measured). What was measured (199 public ligands of the Platinum set, a pilot subset stratified by rotatable bonds, Mol3D 0.22.0; the ranking against the crystal poses is in llms.txt): physically cleaner, NOT more accurate. None of the conformers checked is flagged as overlapping: 0 of the 136 stored lowest conformers, 0 of the 1,783 Kept rows and 0 of the 199 best-matching rows of all 199 ligands, and 0 of the 202 rows of four complete test lists (only stored conformers were checked). A far intramolecular hydrogen bond in the lowest conformer: 0 % with Sage Unfold (0 of 136 stored water-scored lowest conformers, and 0 of 199 by the search's own lowest), 9 % with Sage Open (132 stored water-scored lowest), 28 % for Sage in vacuum with Mol3D 0.21.1 (the lowest conformer of all 199), 4 % in the crystal poses (crystal poses: heavy atoms only). Hydrogen bonds closing a 6- or 7-membered ring: 13 % of the 136 stored lowest conformers, 19 % of the crystal poses (heavy atoms only); the term removes the 7-membered ones (the hydrogen six bonds from the partner) and keeps the 6-membered ones, which is why the share is below the crystal's 19 %. Its lowest conformer is folded (the page's flag) for 1 % of the ligands, against 6 % for Sage Open (same version) and 36 % for Sage in vacuum (Mol3D 0.26.2, whose search and energies are those of 0.22.0 and later); the flag is relative to each list's own least-folded conformer, so the comparison between methods is approximate. Only the ranking was measured; the energies and the shares shown for Sage Unfold are our choice and untested. The entries that are not experimental are as they were. What the four terms do not fix (Mol3D's own benchmark runs of 2026-10-13): the cyclohexane chair-to-half-chair barrier stays about 1.3 kcal/mol too low (error -1.33 against the reference 12.25) and the twist-boat about 0.8 too high (6.81 against about 5.97), methylcyclohexane's axial/equatorial difference is 1.37 against about 1.75 and cis-trans decalin 1.90 against about 2.7 (the ring C-C-C-C torsions move the barrier and the twist-boat together); the rotation barriers of C-C bonds that carry O, N or S (ethanol, ethylamine, ethanethiol) stay 0.5 to 0.7 kcal/mol too high, as in Sage 2.3.0; t2-chain also acts on polyol chains (riboflavin's ribityl chain: Folmsbee MAE 2.08 -> 2.41); t2-ring6 makes ring geometries a little worse against B3LYP-D3BJ/DZVP (RMSD p90 of molecules whose only change is in a six-ring 0.95 -> 1.01 angstrom) while their energies improve. The data the constants were fitted to (22 references; none of the data is part of Mol3D, only the numbers fitted to it are; all are published under CC BY 4.0, read at source): the conformer energies of n-butane and n-pentane in ACONF (Gruzman D, Karton A, Martin JML, J. Phys. Chem. A 2009, 113, 11974-11983, doi:10.1021/jp903640h; as collected in GMTKN55: Goerigk L et al., Phys. Chem. Chem. Phys. 2017, 19, 32184-32215, doi:10.1039/C7CP04913G); the three minima and ten saddle points of n-pentane in Pentane13 (Martin JML, J. Phys. Chem. A 2013, 117, 3118-3132, doi:10.1021/jp401429u; as collected in GSCDB137: Liang J, Head-Gordon M, J. Chem. Theory Comput. 2025, 21, 12601-12621, doi:10.1021/acs.jctc.5c01380); and the C-C rotation barriers of ethane, propane, butane (syn), tert-butyl-CMe2Cl and adamantyl-CMe2Cl in Stylianakis I et al., J. Comput.-Aided Mol. Des. 2023, 37, 607-656, doi:10.1007/s10822-023-00513-5 (DLPNO-CCSD(T)/CBS). Held out of the fit and used to check it: the 11 n-hexane conformers of ACONF; ACONFL (n-dodecane, n-hexadecane, n-icosane: Ehlert S, Grimme S, Hansen A, J. Phys. Chem. A 2022, 126, 3521-3535, doi:10.1021/acs.jpca.2c02439, with the references revised by Santra G, Martin JML, J. Phys. Chem. A 2022, 126, 9375-9391, doi:10.1021/acs.jpca.2c06407; CC BY 4.0); the barriers of ethanol, ethylamine, ethanethiol and bicyclooctyl-CMe2Cl and 65 conformational energies of Stylianakis et al.; and, for damage only, the torsion profiles of TorsionNet206 (Rai BK et al., J. Chem. Inf. Model. 2022, 62, 785-800, doi:10.1021/acs.jcim.1c01346; data on Zenodo 8215107, CC BY) and of the MACE-OFF re-drive of TorsionNet500 (Zenodo 11385284, CC0), Drug20 (Kong L, Bryce RA, ChemPhysChem 2025, 26, e202400992; data on Figshare 27136077, CC BY 4.0), Folmsbee and Hutchison's conformer set (Int. J. Quantum Chem. 2021, 121, e26381; MIT) and the OpenFF Industry Benchmark v1.2 (Zenodo 15801401, CC BY 4.0). What the terms were checked against (kcal/mol; mean absolute error against CCSD(T)-level references unless stated, with the heavy-atom dihedrals restrained; Sage 2.3.0 with the sulfonyl terms as Mol3D 0.15.0 had it -> the two terms of Mol3D 0.16.0 -> these four). HELD OUT of the fit: ACONF hexanes (11 conformer energies, CCSD(T)) 0.60 -> 0.78 -> 0.11; ACONFL (n-dodecane, n-hexadecane and n-icosane, 50 conformers, PNO-LCCSD(T)-F12) 1.45 -> 0.88 -> 0.20; the rotation barrier about the quaternary C-C bond of bicyclooctyl-CMe2Cl (error) +0.16 -> -2.50 -> +0.36; the six-membered-ring axial/equatorial energies of Stylianakis et al. (43) 1.19 -> 0.78 -> 0.80. IN the fit, so a check of the fit and not of the terms: Pentane13 (13 stationary points of n-pentane, CCSD(T)-F12b) 0.80 -> 1.00 -> 0.18; the rotation barriers about the quaternary C-C bonds of tert-butyl-CMe2Cl and adamantyl-CMe2Cl (errors; two of the three quaternary barriers were in the fit) -0.52 / -0.59 -> -3.10 / -3.18 -> -0.23 / -0.32; Stylianakis et al. 2023 (153 scored of its 157 conformational energies and barriers: those every method has) 1.31 -> 1.22 -> 1.16 overall, which includes the five barriers that were fitted (1.33 -> 1.20 -> 1.19 without them), barriers (33) 1.83 -> 1.95 -> 1.69. For damage only: TorsionNet500 (drug-fragment torsion profiles, wB97M-D3(BJ)/def2-TZVPPD, 86 profiles reached) mean RMSE 1.535 -> 1.528 -> 1.526, none worse; TorsionNet206 1.463 -> 1.461 -> 1.460; Drug20 median R^2 0.776 -> 0.783 -> 0.788; Folmsbee-Hutchison (350 molecules, DLPNO-CCSD(T)) mean error 1.211 -> 1.198 -> 1.197; Industry Benchmark v1.2 mean absolute ddE 2.194 -> 2.142 -> 2.137 over the 4,778 molecules the terms can touch (39,677 conformers, with NAGL charges: not the whole benchmark, and not comparable with the OpenFF runs published with AM1-BCC charges). Why (sulfonyl): Sage 2.3.0 halved the stiffness of its generic sulfur angle terms (a31 k 188.6 -> 112.8, a32 k 239.2 -> 113.2 kcal/mol/rad^2); with NAGL's charges a sulfonamide's N-S-O closes to about 92 degrees and a sulfamide folds (N-S-N 78 degrees); Sage 2.2.1's terms, for the sulfonamide and sulfamide angles only, give 101-104 degrees (QM 103-108). Why (alkane): Sage 2.3.0's C-C-C-C torsion t2 favours gauche from 2.1.0 on: it puts n-butane gauche 0.11 kcal/mol above anti (MMFF94 0.78, GFN2 0.60, experiment ~0.67), the all-gauche helix lowest for n-pentane to n-octane, methylcyclohexane's axial methyl 0.11 above equatorial (experiment ~1.74) and cis-decalin 0.06 above trans (experiment ~2.7). Four terms, for acyclic C-C bonds and six-membered-ring C-C bonds only, give butane gauche 0.51, all-trans lowest, 1.37 and 1.90: t2-chain's three constants and two threefold H terms (H-C-C-H, H-C-C-C, only between carbons bonded to C and H alone) are fitted to alkane minima, saddles and C-C rotation barriers (ACONF, ACONFL, Pentane13, Stylianakis' ethane to adamantyl-CMe2Cl), t2-ring6 is Sage 2.0.0's t2. Known limit of the alkane terms: the rotation of a methyl group on a quaternary carbon (a tert-butyl) is 0.5-1.0 kcal/mol too easy with these terms (OpenFF's alkane torsion drives, QCArchive dataset 390); Sage 2.3.0 had it right. On the 164 single-bond drives of that set the mean error is 0.56 kcal/mol with Sage 2.3.0 and 0.33 with the four alkane terms (better for 92 drives, worse for 10). Why (amide N-H): Sage 2.3.0 ranks the cis N-H state of a secondary amide, urea or carbamate 2 to 4 kcal/mol too low against wB97X-3c (NMA cis -0.03 against +2.00, acetanilide cis -0.81 against +2.06), its sign wrong for anilides and N-aryl ureas; the n1 term of its H-N-C=X torsions t78 and t79 is too small. Five terms for the H-N-C=X torsion of an N-H amide, urea or thiourea (an alkyl or aryl carbon on the nitrogen, an acyclic C-N bond), with Sage's own n2 and a fitted n1, bring the state gaps toward wB97X-3c: held-out RMS 1.76 -> 0.66 kcal/mol (the five terms that ship; carbamates stay as Sage has them). What the five terms were checked against (Mol3D's own benchmark runs of 2026-10-14, all with the five terms that ship; Sage 2.3.0 with the sulfonyl, alkane and acid-hydrogen terms -> with the five terms; gas-phase wB97X-3c as the reference of the state gaps). STATE GAPS (each state's best conformer of the page's search re-optimised with GFN2, the force field minimised at that geometry with every heavy-atom dihedral held, each state's energy above the lowest state of the same method, error against wB97X-3c): the 21 held-out states of 7 models, none of them in the fit, RMS 1.76 -> 0.66 kcal/mol, largest 3.75 -> 1.87; the 44 states of the fit, RMS 1.78 -> 0.74, largest 4.70 -> 2.20; by class (the held-out states other than the lowest, above the lowest state of wB97X-3c) N-methylacetamide 2.03 -> 0.48, acetanilide 2.88 -> 0.15, N-alkyl ureas 3.97 -> 0.22, N-aryl ureas 4.63 -> 0.64, thioureas 2.08 -> 1.09, carbamates 1.44 -> 1.44 and an ester 0.40 -> 0.40 (both as Sage has them: the carbamate term was held back); a urea with a lactam, whose cis states have an intramolecular hydrogen bond, 4 states, 4.67 -> 2.91. N-methylacetamide's cis state is +1.51 above trans (wB97X-3c +2.00; before the terms -0.03) and acetanilide's +1.91 (+2.06; before -0.81). RELAXED SCANS about the C-N bond (GFN2 geometries, 15-degree steps, the lower envelope of a forward and a backward scan, the force field minimised at each with only that dihedral held): the cis end of N-methylacetamide +1.71 (wB97X-3c +2.01; before +0.19) and of acetanilide +1.87 (+2.01; before -0.87). CONFORMER ENERGIES, the restrained protocol (heavy-atom dihedrals held, each force field also started from the other's minimum), only the molecules that carry a typed group: Industry Benchmark v1.2 1,629 molecules mean absolute error 1.918 -> 1.842 kcal/mol (415 better, 201 worse), Folmsbee-Hutchison 131 molecules 1.373 -> 1.325 (17 better, 2 worse), TorsionNet500 47 profiles 1.416 -> 1.361 (4 better, none worse), TorsionNet206 24 profiles 1.836 -> 1.741 (2 better, none worse). CRYSTAL POSES (Platinum 2017-01, each pose and each single flip of each amide-like bond minimised freely; the share of groups whose crystal state is the lowest): ureas 17 -> 28 % of 121 groups, thioureas 81 -> 88 % of 16, N-aryl secondary amides 54 -> 81 % of 28, N-alkyl 85 -> 89 % of 82. What the five terms do not fix: they are a torsion fix only. The rotation barriers about the C-N bond are raised by 0.6 to 1.4 kcal/mol and stay too low: the highest point of the relaxed scan, wB97X-3c; before the terms; with them (kcal/mol): N-methylacetamide 14.40; 5.25; 6.29, acetanilide 13.12; 5.59; 6.47, N,N'-dimethylurea 7.40; 4.21; 5.53, 1-methyl-3-phenylurea 6.28; 3.44; 4.82, N,N'-dimethylthiourea 6.74; 3.74; 4.78, that is 6 to 8 too low for amides and 1.5 to 2 for ureas and thioureas. No term for the barriers is offered (one H-N-C=X term cannot carry them), and nothing is claimed for molecular dynamics. Thioureas are half fixed (N,N'-dimethylthiourea's cis,cis state +1.88 against wB97X-3c +3.75). N-aryl ureas keep a floor of about 1 kcal/mol (RMS 0.83 to 1.00 in the fit). A cis state that has an intramolecular hydrogen bond stays overbound by Sage's fixed charges (a lactam urea's tc and ct states, -1.09 and -3.99 against +1.92 and +3.17; the page's step that sets the amide states to trans before a search and its check of them, which hold such a molecule in its trans,trans state, stay). A carbamate's N-H is NOT touched: its term was fitted and held back because it made Folmsbee-Hutchison 0.035 kcal/mol worse (the rule allows 0.02); Boc-NHMe's and Cbz-NHMe's cis N-H states stay below trans (-0.06 and -0.62 kcal/mol against wB97X-3c +1.62 and +1.66), and the crystal state is the lowest for 36 % of 70 carbamate groups, with and without the five terms (50 % with the held-back one). Nor are touched a tertiary amide (the crystal state is the lowest for 56 -> 60 % of 25, through its other groups), a lactam, a cyclic urea, an N-acylurea, a sulfonylurea, an imide, a hydrazide, a hydroxamic acid, a thioamide, an amidine, a carbamic acid, an ester or an N-vinyl amide. Why (acid hydrogen): Sage's hydrogen on an oxygen has no van der Waals wall (epsilon 0.0000123 kcal/mol); the hydrogen of an acid group (the NAGL charges of 7XB7's sulfonic acid: oxygens -0.67 to -0.76 e, hydrogen +0.48 e) can then fall onto an oxygen of its own group, 1.04 A from it, and stay: the 1-4 Coulomb attraction of the two is 42.3 kcal/mol stronger there (-85.0 against -42.6), paid for by 38.8 kcal/mol of angle strain and 4.4 of bond strain, a minimum that is not the molecule (the sulfonic acid of 7XB7: wB97X-3c puts it 172.6 kcal/mol above the clean one, and every medium tried keeps it, water included). A small Lennard-Jones term on the acid hydrogen, and only there, with the CHARMM polar hydrogen's numbers, takes the collapsed minima away. What the three terms were checked against (Mol3D's own benchmark runs of 2026-10-14; the force field before the terms -> with them). The 73 acid ligands of the Platinum and LigBoundConf sets (neutral, 80 starts of the toolkit's conformer generator and the crystal pose each): ligands with a collapsed minimum (an acid hydrogen under 1.3 A from an oxygen of its own group) within 15 kcal/mol of the lowest 3 -> 0, with the lowest minimum collapsed 2 -> 0, with the crystal pose's minimum collapsed 2 -> 0; collapsed minima 38 of 2,920 -> 0 of 2,947; the strain of the crystal pose, median 4.65 -> 4.78 kcal/mol (the median of the paired changes 0.00: the medians differ through a few ligands, the largest change being a nucleotide's (3HZA) 23.6 -> 4.2-5.7, which is the collapse disappearing). The acid of PDB entry 7XB7: the collapsed structure (H...O 1.04 A, -241.94 kcal/mol) stays there before and minimises to H...O 2.08 A (-243.39) with the terms. Conformer energies, the restrained protocol of the Folmsbee-Hutchison and Industry Benchmark sets, their acids only: mean absolute error 1.233 -> 1.228 kcal/mol (123 molecules, 1,076 references) and 2.208 -> 2.190 (182 molecules, 1,396 references); 1 molecule better by more than 0.2, none worse. What they cost: an intramolecular N...H-O hydrogen bond of an acid gets weaker (5-aminovaleric acid's hydrogen-bonded conformer: +0.29 kcal/mol above the best open one, -0.05 before; DFT -1.11; N...H 1.62 -> 1.69 A; one molecule was tested against DFT), and an acid dimer pushed together is too stiff (an acetic acid dimer at 0.9 of its distances loses 2.71 kcal/mol of binding with the terms, 1.11 before, 1.23 in wB97X-3c: about 1.5 too stiff). Binding at the equilibrium distance is unchanged (-15.50 -> -15.54 kcal/mol for the acetic acid dimer, wB97X-3c -20.19: Sage underbinds it by about 4 with or without the terms). So the name of this force field is OpenFF Sage 2.3.0 with three sulfonyl angle terms from Sage 2.2.1, four alkane torsion terms (t2-ring6 is Sage 2.0.0's t2, the other three were fitted for Mol3D), three acid-hydrogen van der Waals terms (CHARMM's polar hydrogen) and five N-H torsion terms of amides, ureas and thioureas (Sage's own n2, a fitted n1; the page's tooltip calls them the amide terms; the file's name field says "openff_unconstrained-2.3.0+sulfonyl+alkane2+acidh+amidenh"). The changes are Mol3D's, not the Open Force Field Initiative's. Sage's partial charges are not in this folder: the charge model is nagl/ (its own NOTICE.txt). ============================================================================== OpenFF NAGL (the charge model: configuration and weights) ============================================================================== Copyright (c) 2023, Open Forcefield Group Attribution 4.0 International ======================================================================= Creative Commons Corporation ("Creative Commons") is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an "as-is" basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. 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Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at creativecommons.org/policies, Creative Commons does not authorize the use of the trademark "Creative Commons" or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses. Creative Commons may be contacted at creativecommons.org. OpenFF NAGL partial charges (openff-gnn-am1bcc-1.0.0), Open Forcefield Group, CC BY 4.0 (Copyright 2023 Open Forcefield Group; the licence text is the file LICENSE beside this one). WHAT THE FILES ARE. nagl-config.json and nagl-weights.f16 are a conversion of the model file openff-gnn-am1bcc-1.0.0.pt (openff-nagl-models 2026.09.0, sha256 7981e7f5b0b1e424c9e10a40d9e7606d96dcd3dd2b095cb4eeff6829f92238ee, the charge model of OpenFF Sage 2.3.0): the network's configuration, and its 22 tensors as little-endian float16 (the largest rounding error is 0.0019). Made on the host by scripts/nagl-export.py (which reads the file without running anything from it) and scripts/nagl-slim.py. The conversion changes the numbers' precision and nothing else. WHAT IS NOT SHIPPED. The model file also carries a lookup table: the reference charges (OpenEye AM1-BCC) of 13,944 small molecules, keyed by InChI (10.2 MB of JSON). It is left out: a visit that chooses OpenFF Sage 2.3.0 would load 10 MB more for fourteen thousand molecules. The page's charges are the NETWORK's for every molecule, so they are the network's estimate of AM1-BCC charges, never AM1-BCC charges calculated for the molecule. nagl-config.json records what was dropped (its `slim` part: the count, the size and the sha256 of the dropped table in canonical JSON). THE CODE. The page runs the network with its own code (web/nagl.js, web/nagl-features.js, web/nagl-resonance.js), written from NAGL's algorithms (openff-nagl 0.6.0) and tested against NAGL's own numbers. No code of NAGL is shipped. NAGL's licence: MIT License Copyright (c) 2022 Lily Wang Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ============================================================================== Implicit water (GB-OBC): the model of the water entry, written for this site ============================================================================== The water of the "OpenFF Sage 2.3.0, water" entry is written for this site from published equations: there is no data file and no code of another program in it. What it is: the generalized-Born model OBC II (alpha 1.0, beta 0.8, gamma 4.85) with Hawkins, Cramer and Truhlar's pairwise descreening integral, a dielectric offset of 0.09 A, solvent 78.5 and solute 1, and a surface term of ACE form (0.0054 kcal/mol/A^2, that is 2.25936 kJ/mol/nm^2, probe 1.4 A), added to the energy of OpenFF Sage 2.3.0 with the partial charges of the NAGL model. Its code is web/gbobc.js. The papers, and what each gives: - Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 55:383-394 (2004): the OBC II rescaling and its three constants, the offset, the mbondi2 radii. - Hawkins GD, Cramer CJ, Truhlar DG. Chem Phys Lett 246:122-129 (1995) and J Phys Chem 100:19824-19839 (1996): the pairwise descreening integral and the screening factors (H 0.85, C 0.72, N 0.79, O 0.85, F 0.88, P 0.86, S 0.96). - Bondi A. J Phys Chem 68:441-451 (1964): the van der Waals radii the mbondi2 radii are built on (H 1.2, or 1.3 on a nitrogen; C 1.7, N 1.55, O 1.5, F 1.5, P 1.85, S 1.8, Cl 1.7). - Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 100:1578-1599 (1996): the form of the surface term. The numbers are published scientific constants. They were read where OpenMM 8.6.0 states them (its Python source for the OBC II model: the constants and the form of the rescaling, the offset, the mbondi2 radii, the screening factors, the surface term) and checked against the papers; OpenMM (MIT and LGPL-3.0-or-later) is the independent reference the tests compare with, and none of its code or files, and none of Amber's, is used or served here. Our own choices, because the published tables have no entry: bromine 1.85 A and iodine 1.98 A (Bondi's van der Waals radii) with the screening factor 0.8, and 0.8 for chlorine too (the default of the screening table). Lithium, sodium, potassium, rubidium, caesium and xenon have no water parameters (no radius means anything for an ion): a structure that has one is refused, by name, by the entries that need water parameters (the water entry, Sage Open (experimental) and Sage Unfold (experimental)); nothing falls back to vacuum by itself. What was checked: over 112 structures of 29 molecules (ions, a zwitterion, a salt, a sulfonic acid, an iodide, the 65-atom example, strained geometries) the energy and the analytic gradient agree with OpenMM's GBSAOBCForce (Reference platform, double precision) to 7.1e-13 kcal/mol and 8.0e-13 kcal/mol/A, and with finite differences. What it is not: the water is not fitted with Sage's parameters or the charge model, and its energy is the model's estimate, not a measurement. Sage Open (experimental) and Sage Unfold (experimental) add this water's energy, once, at a geometry that was minimised without it (nothing is minimised in water by those entries). Energies of the water entry, of Sage Open, of Sage Unfold and of the vacuum entry are never compared (a charged molecule is lower in water by tens of kcal/mol).