# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:39:52 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: N-({(2S)-1-[(3R)-3-amino-4-(3-chlorophenyl)butanoyl]pyrrolidin-2-yl}methyl)-3-(methylsulfonyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(c1)C(=O)NC[C@@H]2CCCN2C(=O)C[C@H](N)Cc3cccc(Cl)c3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PS4  PS4  N-({(2S)-1-[(3R)-3-amino-4-(3-chlorophenyl)butanoyl]pyrrolidin-2-yl}methyl)-3-(methylsulfonyl)benzamide  ligand  60  32  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PS4
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PS4  C1    C   CH3   0  -0.789  -8.8849  -1.5775  -0.3838
 PS4  C7    C   CR16  0  -0.266   7.5362  -0.8576   0.5166
 PS4  C8    C   CR6   0   0.132   7.1165   0.3525  -0.0323
 PS4  C11   C   CR16  0  -0.234   9.2829   0.2741   1.7503
 PS4  C12   C   CR16  0  -0.245   8.8616   1.4779   1.2050
 PS4  C15   C   CH2   0  -0.576   3.4263   0.4082  -1.1491
 PS4  C16   C   C     0   0.567   2.1115   0.3043  -0.4062
 PS4  C18   C   CH1   0  -0.044  -0.0929   1.2169   0.1360
 PS4  C19   C   CH2   0  -0.300  -0.9954   0.1516  -0.4897
 PS4  C23   C   CH2   0  -0.458   0.5587   3.5083  -0.2400
 PS4  C24   C   CH2   0  -0.486  -0.6651   2.6326  -0.0064
 PS4  C27   C   CR16  0  -0.228  -5.8455   0.6629   2.4633
 PS4  C30   C   CR16  0  -0.255  -5.8881   0.3888  -0.3035
 PS4  C31   C   CR6   0  -0.186  -7.0612   0.3750   0.4309
 PS4  O32   O   O     0  -0.482  -3.4787   0.9272  -1.6424
 PS4  C28   C   CR6   0  -0.017  -4.6709   0.5177   0.3572
 PS4  C29   C   CR16  0  -0.230  -7.0592   0.5162   1.8125
 PS4  C26   C   CR16  0  -0.275  -4.6599   0.6623   1.7420
 PS4  S4    S   S     0   1.218  -8.6088   0.1778  -0.4203
 PS4  O2    O   OS    0  -0.665  -8.4225   0.5887  -1.8099
 PS4  O3    O   OS    0  -0.666  -9.6516   0.8265   0.3708
 PS4  N20   N   NH1   0  -0.650  -2.3022   0.1476   0.1288
 PS4  C22   C   CH2   0  -0.279   1.4448   2.6198  -1.0972
 PS4  N17   N   NT    0  -0.483   1.2067   1.2912  -0.5397
 PS4  O5    O   O     0  -0.517   1.8807  -0.6893   0.2767
 PS4  C14   C   CH1   0  -0.086   4.5987   0.4410  -0.1697
 PS4  N21   N   NH2   0  -0.786   4.4489   1.5895   0.7058
 PS4  C13   C   CH2   0  -0.524   5.9276   0.3861  -0.9470
 PS4  C10   C   CR16  0  -0.313   7.7888   1.5187   0.3249
 PS4  C9    C   CR6   0  -0.020   8.6076  -0.8832   1.3938
 PS4  CL6   CL  CL    0  -0.135   9.1212  -2.4034   2.0570
 PS4  H1    H   HCH3  0   0.297  -8.9507  -1.9109   0.6492
 PS4  H1A   H   HCH3  0   0.313  -9.8260  -1.7689  -0.8987
 PS4  H1B   H   HCH3  0   0.297  -8.0686  -2.0830  -0.8945
 PS4  H11   H   HCR6  0   0.278  10.1204   0.2379   2.4334
 PS4  H12   H   HCR6  0   0.266   9.3793   2.3908   1.4690
 PS4  H15   H   HCH2  0   0.274   3.5074  -0.4800  -1.7810
 PS4  H15A  H   HCH2  0   0.256   3.4820   1.2661  -1.8200
 PS4  H18   H   HCH1  0   0.251   0.0649   0.9752   1.1921
 PS4  H19   H   HCH2  0   0.252  -1.1114   0.3453  -1.5551
 PS4  H19A  H   HCH2  0   0.266  -0.5547  -0.8375  -0.3749
 PS4  H23   H   HCH2  0   0.251   0.3206   4.4526  -0.7282
 PS4  H23A  H   HCH2  0   0.238   1.0601   3.7328   0.7040
 PS4  H24   H   HCH2  0   0.239  -1.3285   2.6874  -0.8730
 PS4  H24A  H   HCH2  0   0.255  -1.2407   2.9295   0.8688
 PS4  H27   H   HCR6  0   0.283  -5.8224   0.7878   3.5368
 PS4  H30   H   HCR6  0   0.286  -5.9080   0.2978  -1.3811
 PS4  H29   H   HCR6  0   0.292  -7.9813   0.5215   2.3778
 PS4  H26   H   HCR6  0   0.273  -3.7301   0.8033   2.2782
 PS4  HN20  H   HNH1  0   0.411  -2.3621  -0.2537   1.0507
 PS4  H22   H   HCH2  0   0.240   1.1447   2.6647  -2.1484
 PS4  H22A  H   HCH2  0   0.252   2.4914   2.9041  -1.0342
 PS4  H14   H   HCH1  0   0.245   4.5402  -0.4536   0.4573
 PS4  HN21  H   HNH2  0   0.354   5.1463   1.5727   1.4396
 PS4  HN2A  H   HNH2  0   0.340   4.6053   2.4472   0.1885
 PS4  H13   H   HCH2  0   0.248   5.9923   1.2556  -1.6082
 PS4  H13A  H   HCH2  0   0.251   5.9293  -0.5011  -1.5858
 PS4  H10   H   HCR6  0   0.255   7.4782   2.4664  -0.0979
 PS4  C25   C   C     0   0.547  -3.4274   0.5539  -0.4790
 PS4  H7    H   HCR6  0   0.270   7.0282  -1.7771   0.2525

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PS4  C1   S4    single    1.777  0.020  1.777
 PS4  C7   C8    aromatic  1.394  0.020  1.394
 PS4  C7   C9    aromatic  1.385  0.020  1.385
 PS4  C8   C13   single    1.500  0.020  1.500
 PS4  C8   C10   aromatic  1.393  0.020  1.393
 PS4  C11  C12   aromatic  1.387  0.020  1.387
 PS4  C11  C9    aromatic  1.386  0.020  1.386
 PS4  C12  C10   aromatic  1.388  0.020  1.388
 PS4  C15  C16   single    1.514  0.020  1.514
 PS4  C15  C14   single    1.528  0.020  1.528
 PS4  C16  N17   single    1.346  0.020  1.346
 PS4  C16  O5    double    1.228  0.020  1.228
 PS4  C18  C19   single    1.530  0.020  1.530
 PS4  C18  C24   single    1.534  0.020  1.534
 PS4  C18  N17   single    1.467  0.020  1.467
 PS4  C19  N20   single    1.446  0.020  1.446
 PS4  C23  C24   single    1.523  0.020  1.523
 PS4  C23  C22   single    1.520  0.020  1.520
 PS4  C27  C29   aromatic  1.385  0.020  1.385
 PS4  C27  C26   aromatic  1.388  0.020  1.388
 PS4  C30  C31   aromatic  1.384  0.020  1.384
 PS4  C30  C28   aromatic  1.391  0.020  1.391
 PS4  C31  C29   aromatic  1.389  0.020  1.389
 PS4  C31  S4    single    1.777  0.020  1.777
 PS4  O32  C25   double    1.223  0.020  1.223
 PS4  C25  C28   single    1.499  0.020  1.499
 PS4  C25  N20   single    1.342  0.020  1.342
 PS4  C28  C26   aromatic  1.392  0.020  1.392
 PS4  S4   O2    double    1.461  0.020  1.461
 PS4  S4   O3    double    1.461  0.020  1.461
 PS4  C22  N17   single    1.460  0.020  1.460
 PS4  C14  N21   single    1.452  0.020  1.452
 PS4  C14  C13   single    1.541  0.020  1.541
 PS4  C9   CL6   single    1.736  0.020  1.736
 PS4  C1   H1    single    0.970  0.020  1.090
 PS4  C1   H1A   single    0.970  0.020  1.090
 PS4  C1   H1B   single    0.970  0.020  1.090
 PS4  C7   H7    single    0.930  0.020  1.080
 PS4  C11  H11   single    0.930  0.020  1.080
 PS4  C12  H12   single    0.930  0.020  1.080
 PS4  C15  H15   single    0.970  0.020  1.090
 PS4  C15  H15A  single    0.970  0.020  1.090
 PS4  C18  H18   single    0.970  0.020  1.090
 PS4  C19  H19   single    0.970  0.020  1.090
 PS4  C19  H19A  single    0.970  0.020  1.090
 PS4  C23  H23   single    0.970  0.020  1.090
 PS4  C23  H23A  single    0.970  0.020  1.090
 PS4  C24  H24   single    0.970  0.020  1.090
 PS4  C24  H24A  single    0.970  0.020  1.090
 PS4  C27  H27   single    0.930  0.020  1.080
 PS4  C30  H30   single    0.930  0.020  1.080
 PS4  C29  H29   single    0.930  0.020  1.080
 PS4  C26  H26   single    0.930  0.020  1.080
 PS4  N20  HN20  single    0.860  0.020  1.020
 PS4  C22  H22   single    0.970  0.020  1.090
 PS4  C22  H22A  single    0.970  0.020  1.090
 PS4  C14  H14   single    0.970  0.020  1.090
 PS4  N21  HN21  single    0.890  0.020  1.040
 PS4  N21  HN2A  single    0.890  0.020  1.040
 PS4  C13  H13   single    0.970  0.020  1.090
 PS4  C13  H13A  single    0.970  0.020  1.090
 PS4  C10  H10   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PS4  H1B   C1   H1A   110.17  3.000
 PS4  H1B   C1   H1    110.43  3.000
 PS4  H1A   C1   H1    110.04  3.000
 PS4  H1B   C1   S4    109.44  3.000
 PS4  H1A   C1   S4    107.33  3.000
 PS4  H1    C1   S4    109.37  3.000
 PS4  H7    C7   C9    120.11  3.000
 PS4  H7    C7   C8    119.99  3.000
 PS4  C9    C7   C8    119.90  3.000
 PS4  C10   C8   C13   121.34  3.000
 PS4  C10   C8   C7    118.73  3.000
 PS4  C13   C8   C7    119.89  3.000
 PS4  H11   C11  C9    120.78  3.000
 PS4  H11   C11  C12   120.83  3.000
 PS4  C9    C11  C12   118.38  3.000
 PS4  H12   C12  C10   119.97  3.000
 PS4  H12   C12  C11   119.40  3.000
 PS4  C10   C12  C11   120.63  3.000
 PS4  H15A  C15  H15   106.25  3.000
 PS4  H15A  C15  C14   109.77  3.000
 PS4  H15   C15  C14   109.33  3.000
 PS4  H15A  C15  C16   113.60  3.000
 PS4  H15   C15  C16   107.00  3.000
 PS4  C14   C15  C16   110.69  3.000
 PS4  O5    C16  N17   121.50  3.000
 PS4  O5    C16  C15   119.47  3.000
 PS4  N17   C16  C15   119.01  3.000
 PS4  H18   C18  N17   109.14  3.000
 PS4  H18   C18  C24   110.32  3.000
 PS4  N17   C18  C24   103.95  3.000
 PS4  H18   C18  C19   109.01  3.000
 PS4  N17   C18  C19   111.69  3.000
 PS4  C24   C18  C19   112.63  3.000
 PS4  H19A  C19  H19   107.93  3.000
 PS4  H19A  C19  N20   108.56  3.000
 PS4  H19   C19  N20   108.83  3.000
 PS4  H19A  C19  C18   110.53  3.000
 PS4  H19   C19  C18   109.82  3.000
 PS4  N20   C19  C18   111.11  3.000
 PS4  H23A  C23  H23   108.02  3.000
 PS4  H23A  C23  C22   109.88  3.000
 PS4  H23   C23  C22   112.43  3.000
 PS4  H23A  C23  C24   110.77  3.000
 PS4  H23   C23  C24   113.06  3.000
 PS4  C22   C23  C24   102.64  3.000
 PS4  H24A  C24  H24   107.63  3.000
 PS4  H24A  C24  C23   113.04  3.000
 PS4  H24   C24  C23   109.72  3.000
 PS4  H24A  C24  C18   111.98  3.000
 PS4  H24   C24  C18   110.27  3.000
 PS4  C23   C24  C18   104.20  3.000
 PS4  H27   C27  C26   119.87  3.000
 PS4  H27   C27  C29   119.84  3.000
 PS4  C26   C27  C29   120.29  3.000
 PS4  H30   C30  C28   119.81  3.000
 PS4  H30   C30  C31   120.81  3.000
 PS4  C28   C30  C31   119.38  3.000
 PS4  S4    C31  C29   119.27  3.000
 PS4  S4    C31  C30   119.02  3.000
 PS4  C29   C31  C30   121.71  3.000
 PS4  C26   C28  C25   123.08  3.000
 PS4  C26   C28  C30   119.27  3.000
 PS4  C25   C28  C30   117.60  3.000
 PS4  H29   C29  C31   121.28  3.000
 PS4  H29   C29  C27   120.07  3.000
 PS4  C31   C29  C27   118.65  3.000
 PS4  H26   C26  C28   120.86  3.000
 PS4  H26   C26  C27   118.44  3.000
 PS4  C28   C26  C27   120.68  3.000
 PS4  O3    S4   O2    118.76  3.000
 PS4  O3    S4   C31   108.24  3.000
 PS4  O2    S4   C31   108.26  3.000
 PS4  O3    S4   C1    108.46  3.000
 PS4  O2    S4   C1    108.49  3.000
 PS4  C31   S4   C1    103.59  3.000
 PS4  HN20  N20  C25   119.04  3.000
 PS4  HN20  N20  C19   116.51  3.000
 PS4  C25   N20  C19   124.28  3.000
 PS4  H22A  C22  H22   108.02  3.000
 PS4  H22A  C22  N17   111.90  3.000
 PS4  H22   C22  N17   111.07  3.000
 PS4  H22A  C22  C23   112.09  3.000
 PS4  H22   C22  C23   110.98  3.000
 PS4  N17   C22  C23   102.80  3.000
 PS4  C22   N17  C18   111.50  3.000
 PS4  C22   N17  C16   126.55  3.000
 PS4  C18   N17  C16   120.86  3.000
 PS4  H14   C14  C13   107.83  3.000
 PS4  H14   C14  N21   107.21  3.000
 PS4  C13   C14  N21   114.93  3.000
 PS4  H14   C14  C15   107.98  3.000
 PS4  C13   C14  C15   109.73  3.000
 PS4  N21   C14  C15   108.93  3.000
 PS4  HN2A  N21  HN21  106.12  3.000
 PS4  HN2A  N21  C14   110.22  3.000
 PS4  HN21  N21  C14   110.66  3.000
 PS4  H13A  C13  H13   106.96  3.000
 PS4  H13A  C13  C14   108.98  3.000
 PS4  H13   C13  C14   109.12  3.000
 PS4  H13A  C13  C8    109.68  3.000
 PS4  H13   C13  C8    109.83  3.000
 PS4  C14   C13  C8    112.13  3.000
 PS4  H10   C10  C12   119.65  3.000
 PS4  H10   C10  C8    119.61  3.000
 PS4  C12   C10  C8    120.74  3.000
 PS4  CL6   C9   C11   119.24  3.000
 PS4  CL6   C9   C7    119.14  3.000
 PS4  C11   C9   C7    121.62  3.000
 PS4  N20   C25  C28   115.83  3.000
 PS4  N20   C25  O32   123.96  3.000
 PS4  C28   C25  O32   120.22  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PS4  CONST_01  C12   C10  C8   C7     0.00   0.0  0
 PS4  CONST_02  C12   C11  C9   C7     0.00   0.0  0
 PS4  CONST_03  C11   C9   C7   C8     0.00   0.0  0
 PS4  CONST_04  C11   C12  C10  C8     0.00   0.0  0
 PS4  CONST_05  C30   C31  C29  C27    0.00   0.0  0
 PS4  CONST_06  C30   C28  C26  C27    0.00   0.0  0
 PS4  CONST_07  C26   C28  C30  C31    0.00   0.0  0
 PS4  CONST_08  C26   C27  C29  C31    0.00   0.0  0
 PS4  CONST_09  C29   C31  C30  C28    0.00   0.0  0
 PS4  CONST_10  C29   C27  C26  C28    0.00   0.0  0
 PS4  CONST_11  C9    C7   C8   C10    0.00   0.0  0
 PS4  CONST_12  C9    C11  C12  C10    0.00   0.0  0
 PS4  CONST_13  CL6   C9   C7   C8   180.00   0.0  0
 PS4  CONST_14  CL6   C9   C11  C12  180.00   0.0  0
 PS4  CONST_15  C13   C8   C10  C12  180.00   0.0  0
 PS4  CONST_16  S4    C31  C29  C27  180.00   0.0  0
 PS4  CONST_17  C25   C28  C26  C27  180.00   0.0  0
 PS4  CONST_18  C25   C28  C30  C31  180.00   0.0  0
 PS4  CONST_19  S4    C31  C30  C28  180.00   0.0  0
 PS4  CONST_20  C9    C7   C8   C13  180.00   0.0  0
 PS4  CONST_21  H10   C10  C8   C7   180.00   0.0  0
 PS4  CONST_22  H11   C11  C9   C7   180.00   0.0  0
 PS4  CONST_23  H12   C12  C10  C8   180.00   0.0  0
 PS4  CONST_24  H7    C7   C9   C11  180.00   0.0  0
 PS4  CONST_25  H29   C29  C31  C30  180.00   0.0  0
 PS4  CONST_26  H26   C26  C28  C30  180.00   0.0  0
 PS4  CONST_27  H27   C27  C29  C31  180.00   0.0  0
 PS4  CONST_28  H30   C30  C31  C29  180.00   0.0  0
 PS4  CONST_29  C18   N17  C16  C15  180.00   0.0  0
 PS4  CONST_30  C22   N17  C16  C15    0.00   0.0  0
 PS4  CONST_31  O5    C16  N17  C18    0.00   0.0  0
 PS4  CONST_32  O5    C16  N17  C22  180.00   0.0  0
 PS4  CONST_33  C28   C25  N20  C19  180.00   0.0  0
 PS4  CONST_34  HN20  N20  C25  C28    0.00   0.0  0
 PS4  CONST_35  O32   C25  N20  C19    0.00   0.0  0
 PS4  Var_01    C22   C23  C24  C18   36.69  30.0  1
 PS4  Var_02    C23   C22  N17  C18   24.12  30.0  1
 PS4  Var_03    N17   C22  C23  C24  -36.87  30.0  1
 PS4  Var_04    C30   C31  S4   C1    92.59  30.0  1
 PS4  Var_05    C14   C13  C8   C7    83.15  30.0  2
 PS4  Var_06    O32   C25  C28  C30   25.11  30.0  2
 PS4  Var_07    C25   N20  C19  C18  110.20  30.0  3
 PS4  Var_08    C14   C15  C16  N17  118.67  30.0  2
 PS4  Var_09    H1    C1   S4   C31   60.88  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PS4  chir_01  C18  C19  C24  N17  positiv
 PS4  chir_02  C14  N21  C15  C13  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PS4  plan-1  C7    0.020
 PS4  plan-1  C8    0.020
 PS4  plan-1  C11   0.020
 PS4  plan-1  C12   0.020
 PS4  plan-1  C13   0.020
 PS4  plan-1  C10   0.020
 PS4  plan-1  C9    0.020
 PS4  plan-1  CL6   0.020
 PS4  plan-1  H11   0.020
 PS4  plan-1  H12   0.020
 PS4  plan-1  H10   0.020
 PS4  plan-1  H7    0.020
 PS4  plan-2  C27   0.020
 PS4  plan-2  C30   0.020
 PS4  plan-2  C31   0.020
 PS4  plan-2  C28   0.020
 PS4  plan-2  C29   0.020
 PS4  plan-2  C26   0.020
 PS4  plan-2  S4    0.020
 PS4  plan-2  H27   0.020
 PS4  plan-2  H30   0.020
 PS4  plan-2  H29   0.020
 PS4  plan-2  H26   0.020
 PS4  plan-2  C25   0.020
 PS4  plan-3  C19   0.020
 PS4  plan-3  O32   0.020
 PS4  plan-3  C28   0.020
 PS4  plan-3  N20   0.020
 PS4  plan-3  HN20  0.020
 PS4  plan-3  C25   0.020
 PS4  plan-4  C15   0.020
 PS4  plan-4  C16   0.020
 PS4  plan-4  C18   0.020
 PS4  plan-4  C22   0.020
 PS4  plan-4  N17   0.020
 PS4  plan-4  O5    0.020

