Quantifying steric effects based on LJ energy difference between conformers using this script. Openmm An openmm system is created and energy decomposition is decomposed into several contributions based on forcegroups. There are four force groups in smirnoff FFs:
'HarmonicAngleForce'
'HarmonicBondForce'
'NonbondedForce' (electrostatics + vdW)
'PeriodicTorsionForce'
The partial charges are made to zero to zero out zeroed to remove the electrostatics contributions and from the ‘NonbondedForce’, which then gives the LJ energy. The absolute difference in LJ energy between the highest energy conformer and lowest energy conformer (highest and lowest based on QM energies) is considered as a metric. The list below shows molecules that have this LJ difference less than 0.01 kcal/mol and greater than 8 kcal/mol.
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Molecules are sorted from highest difference to lowest difference in LJ energies.
DLM: Change the threshold and check for more sterics, make a list and exclude from future fits
Record info | Structure | QM-MM relative energies (kcal/mol) |
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TD record: 2703380 , LJ energy diff: 27.786245316800958 kcal/mol , MM diff at (QM_high - QM_low) geo.: 73.10539138080105 kcal/mol , QM (high - low) in kcal/mol: 52.65000911303297 |
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TD record: 2703379 , LJ energy diff: 27.760419374408297 kcal/mol , MM diff at (QM_high - QM_low) geo.: 73.0216123335332 kcal/mol , QM (high - low) in kcal/mol: 52.647689794454834 |
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TD record: 2703384 , LJ energy diff: 26.2177724080478 kcal/mol , MM diff at (QM_high - QM_low) geo.: 63.777783496804346 kcal/mol , QM (high - low) in kcal/mol: 42.92368125466929 |
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TD record: 1762111 , LJ energy diff: 21.894760088223176 kcal/mol , MM diff at (QM_high - QM_low) geo.: 13.67092344214398 kcal/mol , QM (high - low) in kcal/mol: 5.968619020313509 |  | |
TD record: 21272410 , LJ energy diff: 21.827095529250762 kcal/mol , MM diff at (QM_high - QM_low) geo.: 13.59600999027424 kcal/mol , QM (high - low) in kcal/mol: 5.978408651946955 |
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TD record: 2703383 , LJ energy diff: 20.46516071836649 kcal/mol , MM diff at (QM_high - QM_low) geo.: 71.7002521462076 kcal/mol , QM (high - low) in kcal/mol: 41.6403045741134 |
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TD record: 21272392 , LJ energy diff: 19.903813918605003 kcal/mol , MM diff at (QM_high - QM_low) geo.: 15.672291225701144 kcal/mol , QM (high - low) in kcal/mol: 8.745653861973345 |
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TD record: 21272413 , LJ energy diff: 19.368012958913653 kcal/mol , MM diff at (QM_high - QM_low) geo.: 11.372351105461817 kcal/mol , QM (high - low) in kcal/mol: 6.596154019485118 |
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TD record: 2703389 , LJ energy diff: 19.110966749159992 kcal/mol , MM diff at (QM_high - QM_low) geo.: 44.59059113880667 kcal/mol , QM (high - low) in kcal/mol: 52.65363555684493 |
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TD record: 2703390 , LJ energy diff: 19.109719157239052 kcal/mol , MM diff at (QM_high - QM_low) geo.: 44.6239376470882 kcal/mol , QM (high - low) in kcal/mol: 52.65108810406099 |
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TD record: 1762227 , LJ energy diff: -17.93730206711862 kcal/mol , MM diff at (QM_high - QM_low) geo.: -5.2319130596672565 kcal/mol , QM (high - low) in kcal/mol: 6.91240264854326 |
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TD record: 21540657 , LJ energy diff: 17.514257851253085 kcal/mol , MM diff at (QM_high - QM_low) geo.: 24.48588512244173 kcal/mol , QM (high - low) in kcal/mol: 14.97568487655997 |
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TD record: 1762228 , LJ energy diff: -17.135636090993366 kcal/mol , MM diff at (QM_high - QM_low) geo.: -5.208631952414379 kcal/mol , QM (high - low) in kcal/mol: 2.802466627713657 |
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TD record: 2703482 , LJ energy diff: 16.476736682108122 kcal/mol , MM diff at (QM_high - QM_low) geo.: 58.06344776135018 kcal/mol , QM (high - low) in kcal/mol: 46.50217210352938 |
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TD record: 2703381 , LJ energy diff: 16.25011617670606 kcal/mol , MM diff at (QM_high - QM_low) geo.: 49.6100219400294 kcal/mol , QM (high - low) in kcal/mol: 35.13889824302058 |
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TD record: 1762266 , LJ energy diff: 16.09709176091058 kcal/mol , MM diff at (QM_high - QM_low) geo.: 16.251438372992524 kcal/mol , QM (high - low) in kcal/mol: 10.121104088363591 |
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TD record: 2703382 , LJ energy diff: 15.735310515948465 kcal/mol , MM diff at (QM_high - QM_low) geo.: 48.815483735494155 kcal/mol , QM (high - low) in kcal/mol: 34.609573696242016 |
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TD record: 1762107 , LJ energy diff: 14.911913818814849 kcal/mol , MM diff at (QM_high - QM_low) geo.: 13.798829876510823 kcal/mol , QM (high - low) in kcal/mol: 7.191145560226867 |
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TD record: 2703153 , LJ energy diff: 14.822339845472449 kcal/mol , MM diff at (QM_high - QM_low) geo.: 91.90603570385066 kcal/mol , QM (high - low) in kcal/mol: 47.67038140058971 |
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TD record: 2703215 , LJ energy diff: 14.819678395367855 kcal/mol , MM diff at (QM_high - QM_low) geo.: 91.36971570068292 kcal/mol , QM (high - low) in kcal/mol: 47.671229437289604 |
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TD record: 1762828 , LJ energy diff: 14.790701663945107 kcal/mol , MM diff at (QM_high - QM_low) geo.: 16.856556498726647 kcal/mol , QM (high - low) in kcal/mol: 16.652150277953186 |
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TD record: 21272384 , LJ energy diff: 14.266065490167477 kcal/mol , MM diff at (QM_high - QM_low) geo.: 18.581155997552273 kcal/mol , QM (high - low) in kcal/mol: 10.561268634004785 |
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TD record: 1762268 , LJ energy diff: 13.94154787421305 kcal/mol , MM diff at (QM_high - QM_low) geo.: 15.47784981156039 kcal/mol , QM (high - low) in kcal/mol: 6.459831860747179 |
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TD record: 2703377 , LJ energy diff: 13.355626779549517 kcal/mol , MM diff at (QM_high - QM_low) geo.: 42.8890469711139 kcal/mol , QM (high - low) in kcal/mol: 50.036641758798524 |
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TD record: 2703376 , LJ energy diff: 13.350257116312944 kcal/mol , MM diff at (QM_high - QM_low) geo.: 42.81040196968941 kcal/mol , QM (high - low) in kcal/mol: 50.03626163789865 |
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TD record: 1762528 , LJ energy diff: 13.267027939526498 kcal/mol , MM diff at (QM_high - QM_low) geo.: 8.769836832289059 kcal/mol , QM (high - low) in kcal/mol: 1.7039984459574813 |
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TD record: 2703207 , LJ energy diff: 13.073995604579546 kcal/mol , MM diff at (QM_high - QM_low) geo.: 94.50005847193881 kcal/mol , QM (high - low) in kcal/mol: 51.052348709717904 |
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TD record: 2703187 , LJ energy diff: 13.073564411029027 kcal/mol , MM diff at (QM_high - QM_low) geo.: 94.1386412231403 kcal/mol , QM (high - low) in kcal/mol: 51.05250488368475 |
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TD record: 2703393 , LJ energy diff: 12.960508526517213 kcal/mol , MM diff at (QM_high - QM_low) geo.: 46.73978059467623 kcal/mol , QM (high - low) in kcal/mol: 42.75017904218911 |
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TD record: 21540443 , LJ energy diff: -12.950039450699707 kcal/mol , MM diff at (QM_high - QM_low) geo.: -5.458065384451174 kcal/mol , QM (high - low) in kcal/mol: 3.5999656511641995 |
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TD record: 21540451 , LJ energy diff: -12.561825255164916 kcal/mol , MM diff at (QM_high - QM_low) geo.: -5.0233192267577635 kcal/mol , QM (high - low) in kcal/mol: 3.670161550304676 |
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TD record: 18536216 , LJ energy diff: 12.52396763725319 kcal/mol , MM diff at (QM_high - QM_low) geo.: 55.17871199346693 kcal/mol , QM (high - low) in kcal/mol: 40.63091727419283 |  |
TD record: 1762797 , LJ energy diff: -12.298190372660102 kcal/mol , MM diff at (QM_high - QM_low) geo.: -1.4694671054246626 kcal/mol , QM (high - low) in kcal/mol: 6.5431939536331605
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TD record: 2703472 , LJ energy diff: 8.045109945836233 kcal/mol , MM diff at (QM_high - QM_low) geo.: 59.51951590511209 kcal/mol , QM (high - low) in kcal/mol: 52.92677668840244
Molecules below have LJ energy difference less than 0.01 kcal/mol
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TD record: 18535822 , LJ energy diff: 0.009110961068785173 kcal/mol , MM diff at (QM_high - QM_low) geo.: 5.250257625162746 kcal/mol , QM (high - low) in kcal/mol: 5.712266550990404
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