# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 13 06:04:07 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-[4-[(3~{S})-3-[[(1~{R})-1-naphthalen-1-ylethyl]amino]pyrrolidin-1-yl]phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N[C@H]1CCN(C1)c2ccc(CC(O)=O)cc2)c3cccc4ccccc34
#
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
 H43  H43  '2-[4-[(3~{S})-3-[[(1~{R})-1-naphthalen-1-ylethyl]amino]pyrrolidin-1-yl]phenyl]ethanoic acid'  ligand  53  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H43
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
 H43  C10   C  CH2    0  -0.273  146.8948  164.4378  131.2294
 H43  N12   N  NH1    0  -0.587  146.2336  166.2106  129.6665
 H43  C13   C  CH1    0  -0.191  146.7178  165.7041  128.3868
 H43  C15   C  CR66   0   0.107  144.4297  165.0749  127.4394
 H43  C17   C  CR16   0  -0.272  143.1199  163.2908  128.4459
 H43  C20   C  CR66   0   0.107  143.3942  165.2619  126.4835
 H43  C21   C  CR16   0  -0.331  143.5312  166.2602  125.4898
 H43  C22   C  CR16   0  -0.239  144.6553  167.0314  125.4439
 H43  C24   C  CH3    0  -0.683  148.0609  166.2902  127.9538
 H43  C26   C  CH2    0  -0.259  145.1666  165.6803  132.3419
 H43  C28   C  CR16   0  -0.299  144.4236  160.9217  131.4651
 H43  C2    C  C      0   0.416  141.1627  159.7890  130.7018
 H43  C5    C  CR6    0   0.143  143.1085  160.9902  131.9131
 H43  C6    C  CR16   0  -0.285  142.6845  162.2216  132.4071
 H43  C7    C  CR16   0  -0.360  143.5086  163.3340  132.4313
 H43  C8    C  CR6    0   0.376  144.8287  163.2661  131.9502
 H43  C11   C  CH1    0  -0.129  147.0230  165.9124  130.8509
 H43  C14   C  CR6    0   0.130  145.6062  165.8867  127.3684
 H43  C16   C  CR16   0  -0.326  144.2458  164.0689  128.4205
 H43  C18   C  CR16   0  -0.270  142.1013  163.4795  127.4913
 H43  C19   C  CR16   0  -0.311  142.2383  164.4464  126.5340
 H43  C23   C  CR16   0  -0.352  145.6903  166.8363  126.3824
 H43  C25   C  CH2    0  -0.489  146.3621  166.5808  132.0541
 H43  C27   C  CR16   0  -0.350  145.2733  162.0180  131.4840
 H43  N9    N  NT     0  -0.519  145.6373  164.3682  131.9465
 H43  O1    O  O      0  -0.585  141.2650  160.6506  129.8085
 H43  O3    O  OC    -1  -0.617  140.3144  158.8772  130.7652
 H43  H102  H  HCH2   0   0.234  146.8996  163.7840  130.3541
 H43  H101  H  HCH2   0   0.234  147.7437  164.1312  131.8523
 H43  H1    H  HNH1   0   0.345  146.1078  167.2137  129.5914
 H43  H131  H  HCH1   0   0.237  146.8743  164.6267  128.4991
 H43  H171  H  HCR6   0   0.270  143.0015  162.5257  129.2028
 H43  H211  H  HCR6   0   0.250  142.7351  166.3997  124.7682
 H43  H221  H  HCR6   0   0.251  144.7652  167.7960  124.6857
 H43  H243  H  HCH3   0   0.244  148.8360  166.0220  128.6715
 H43  H241  H  HCH3   0   0.234  148.3702  165.9053  126.9816
 H43  H242  H  HCH3   0   0.223  148.0319  167.3797  127.8972
 H43  H261  H  HCH2   0   0.216  144.2912  165.9876  131.7570
 H43  H262  H  HCH2   0   0.230  144.8789  165.7068  133.3967
 H43  H281  H  HCR6   0   0.231  144.8083  159.9791  131.0904
 H43  H042  H  HCH2   0   0.237  142.7764  158.8881  131.8003
 H43  H041  H  HCH2   0   0.229  141.6305  159.7304  132.8044
 H43  H061  H  HCR6   0   0.230  141.6720  162.3224  132.7834
 H43  H071  H  HCR6   0   0.252  143.1169  164.2637  132.8225
 H43  H111  H  HCH1   0   0.233  148.0794  166.1971  130.7616
 H43  H161  H  HCR6   0   0.261  144.9983  163.9093  129.1770
 H43  H181  H  HCR6   0   0.248  141.2149  162.8591  127.5215
 H43  H191  H  HCR6   0   0.249  141.4614  164.6032  125.7948
 H43  H231  H  HCR6   0   0.250  146.5704  167.4608  126.3044
 H43  H252  H  HCH2   0   0.246  147.0542  166.5795  132.8985
 H43  H251  H  HCH2   0   0.252  146.0729  167.6160  131.8678
 H43  H271  H  HCR6   0   0.250  146.2917  161.8914  131.1404
 H43  C4    C  CH2    0  -0.690  142.1891  159.8104  131.8667

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
 H43  C19  C18   aromatic  1.367  0.020  1.367
 H43  C19  C20   aromatic  1.416  0.020  1.416
 H43  C18  C17   aromatic  1.409  0.020  1.409
 H43  C21  C20   aromatic  1.415  0.020  1.415
 H43  C21  C22   aromatic  1.364  0.020  1.364
 H43  C20  C15   aromatic  1.422  0.020  1.422
 H43  C22  C23   aromatic  1.411  0.020  1.411
 H43  C17  C16   aromatic  1.369  0.020  1.369
 H43  C15  C16   aromatic  1.417  0.020  1.417
 H43  C15  C14   aromatic  1.431  0.020  1.431
 H43  C23  C14   aromatic  1.371  0.020  1.371
 H43  C14  C13   single    1.519  0.020  1.519
 H43  C13  C24   single    1.528  0.020  1.528
 H43  C13  N12   single    1.459  0.020  1.459
 H43  N12  C11   single    1.454  0.020  1.454
 H43  C11  C10   single    1.528  0.020  1.528
 H43  C11  C25   single    1.527  0.020  1.527
 H43  C10  N9    single    1.449  0.020  1.449
 H43  N9   C26   single    1.449  0.020  1.449
 H43  N9   C8    single    1.367  0.020  1.367
 H43  C27  C8    aromatic  1.405  0.020  1.405
 H43  C27  C28   aromatic  1.387  0.020  1.387
 H43  C25  C26   single    1.524  0.020  1.524
 H43  C8   C7    aromatic  1.407  0.020  1.407
 H43  C28  C5    aromatic  1.391  0.020  1.391
 H43  O1   C2    deloc     1.245  0.020  1.245
 H43  C7   C6    aromatic  1.385  0.020  1.385
 H43  C5   C6    aromatic  1.393  0.020  1.393
 H43  C5   C4    single    1.496  0.020  1.496
 H43  C2   O3    deloc     1.247  0.020  1.247
 H43  C2   C4    single    1.553  0.020  1.553
 H43  C10  H102  single    0.970  0.020  1.090
 H43  C10  H101  single    0.970  0.020  1.090
 H43  N12  H1    single    0.890  0.020  1.040
 H43  C13  H131  single    0.970  0.020  1.090
 H43  C17  H171  single    0.930  0.020  1.080
 H43  C21  H211  single    0.930  0.020  1.080
 H43  C22  H221  single    0.930  0.020  1.080
 H43  C24  H243  single    0.970  0.020  1.090
 H43  C24  H241  single    0.970  0.020  1.090
 H43  C24  H242  single    0.970  0.020  1.090
 H43  C26  H261  single    0.970  0.020  1.090
 H43  C26  H262  single    0.970  0.020  1.090
 H43  C28  H281  single    0.930  0.020  1.080
 H43  C4   H042  single    0.970  0.020  1.090
 H43  C4   H041  single    0.970  0.020  1.090
 H43  C6   H061  single    0.930  0.020  1.080
 H43  C7   H071  single    0.930  0.020  1.080
 H43  C11  H111  single    0.970  0.020  1.090
 H43  C16  H161  single    0.930  0.020  1.080
 H43  C18  H181  single    0.930  0.020  1.080
 H43  C19  H191  single    0.930  0.020  1.080
 H43  C23  H231  single    0.930  0.020  1.080
 H43  C25  H252  single    0.970  0.020  1.090
 H43  C25  H251  single    0.970  0.020  1.090
 H43  C27  H271  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
 H43  H101  C10  H102  106.52  3.000
 H43  H101  C10  N9    112.16  3.000
 H43  H102  C10  N9    111.80  3.000
 H43  H101  C10  C11   110.22  3.000
 H43  H102  C10  C11   112.26  3.000
 H43  N9    C10  C11   103.99  3.000
 H43  H1    N12  C11   109.30  3.000
 H43  H1    N12  C13   108.64  3.000
 H43  C11   N12  C13   117.58  3.000
 H43  H131  C13  C14   106.97  3.000
 H43  H131  C13  C24   106.31  3.000
 H43  C14   C13  C24   114.03  3.000
 H43  H131  C13  N12   107.41  3.000
 H43  C24   C13  N12   114.03  3.000
 H43  C14   C13  N12   107.67  3.000
 H43  C16   C15  C14   122.94  3.000
 H43  C14   C15  C20   119.39  3.000
 H43  C16   C15  C20   117.67  3.000
 H43  H171  C17  C18   119.30  3.000
 H43  H171  C17  C16   120.30  3.000
 H43  C18   C17  C16   120.40  3.000
 H43  C19   C20  C21   120.70  3.000
 H43  C21   C20  C15   119.63  3.000
 H43  C19   C20  C15   119.67  3.000
 H43  H211  C21  C22   120.68  3.000
 H43  H211  C21  C20   119.16  3.000
 H43  C22   C21  C20   120.15  3.000
 H43  H221  C22  C23   119.29  3.000
 H43  H221  C22  C21   120.44  3.000
 H43  C23   C22  C21   120.27  3.000
 H43  H242  C24  H241  108.28  3.000
 H43  H242  C24  H243  107.38  3.000
 H43  H241  C24  H243  107.37  3.000
 H43  H242  C24  C13   111.98  3.000
 H43  H241  C24  C13   111.51  3.000
 H43  H243  C24  C13   110.13  3.000
 H43  H262  C26  H261  107.31  3.000
 H43  H262  C26  N9    111.75  3.000
 H43  H261  C26  N9    111.56  3.000
 H43  H262  C26  C25   111.97  3.000
 H43  H261  C26  C25   111.09  3.000
 H43  N9    C26  C25   103.22  3.000
 H43  H281  C28  C27   118.30  3.000
 H43  H281  C28  C5    119.30  3.000
 H43  C27   C28  C5    122.40  3.000
 H43  O3    C2   O1    126.74  3.000
 H43  O3    C2   C4    114.94  3.000
 H43  O1    C2   C4    118.32  3.000
 H43  C6    C5   C4    121.40  3.000
 H43  C4    C5   C28   122.14  3.000
 H43  C6    C5   C28   116.46  3.000
 H43  H061  C6   C7    118.34  3.000
 H43  H061  C6   C5    119.29  3.000
 H43  C7    C6   C5    122.36  3.000
 H43  H071  C7   C8    120.33  3.000
 H43  H071  C7   C6    118.75  3.000
 H43  C8    C7   C6    120.92  3.000
 H43  N9    C8   C27   121.89  3.000
 H43  C27   C8   C7    116.97  3.000
 H43  N9    C8   C7    121.14  3.000
 H43  H111  C11  C25   111.54  3.000
 H43  H111  C11  N12   113.76  3.000
 H43  C25   C11  N12   108.49  3.000
 H43  H111  C11  C10   110.56  3.000
 H43  C25   C11  C10   101.01  3.000
 H43  N12   C11  C10   110.74  3.000
 H43  C23   C14  C15   118.61  3.000
 H43  C23   C14  C13   121.36  3.000
 H43  C15   C14  C13   120.02  3.000
 H43  H161  C16  C17   118.46  3.000
 H43  H161  C16  C15   119.99  3.000
 H43  C17   C16  C15   121.54  3.000
 H43  H181  C18  C19   120.45  3.000
 H43  H181  C18  C17   119.77  3.000
 H43  C19   C18  C17   119.78  3.000
 H43  H191  C19  C18   120.53  3.000
 H43  H191  C19  C20   118.53  3.000
 H43  C18   C19  C20   120.94  3.000
 H43  H231  C23  C14   120.10  3.000
 H43  H231  C23  C22   117.97  3.000
 H43  C14   C23  C22   121.94  3.000
 H43  H251  C25  H252  107.53  3.000
 H43  H251  C25  C11   113.30  3.000
 H43  H252  C25  C11   109.54  3.000
 H43  H251  C25  C26   112.64  3.000
 H43  H252  C25  C26   110.52  3.000
 H43  C11   C25  C26   103.28  3.000
 H43  H271  C27  C8    120.47  3.000
 H43  H271  C27  C28   118.66  3.000
 H43  C8    C27  C28   120.86  3.000
 H43  C8    N9   C26   122.49  3.000
 H43  C8    N9   C10   123.60  3.000
 H43  C26   N9   C10   111.92  3.000
 H43  H041  C4   H042  105.31  3.000
 H43  H041  C4   C5    110.16  3.000
 H43  H042  C4   C5    109.65  3.000
 H43  H041  C4   C2    107.72  3.000
 H43  H042  C4   C2    107.30  3.000
 H43  C5    C4   C2    116.12  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
 H43  CONST_01  C18   C19  C20  C15     0.00   0.0  0
 H43  CONST_02  C22   C21  C20  C15     0.00   0.0  0
 H43  CONST_03  C18   C17  C16  C15     0.00   0.0  0
 H43  CONST_04  C22   C23  C14  C15     0.00   0.0  0
 H43  CONST_05  C20   C19  C18  C17     0.00   0.0  0
 H43  CONST_06  C20   C15  C16  C17     0.00   0.0  0
 H43  CONST_07  C14   C15  C16  C17   180.00   0.0  0
 H43  CONST_08  C23   C22  C21  C20     0.00   0.0  0
 H43  CONST_09  C23   C14  C15  C20     0.00   0.0  0
 H43  CONST_10  C18   C19  C20  C21   180.00   0.0  0
 H43  CONST_11  C16   C15  C20  C21   180.00   0.0  0
 H43  CONST_12  C14   C15  C20  C21     0.00   0.0  0
 H43  CONST_13  C14   C23  C22  C21     0.00   0.0  0
 H43  CONST_14  C19   C20  C21  C22   180.00   0.0  0
 H43  CONST_15  C7    C8   C27  C28     0.00   0.0  0
 H43  CONST_16  C7    C6   C5   C28     0.00   0.0  0
 H43  CONST_17  C8    C27  C28  C5      0.00   0.0  0
 H43  CONST_18  C8    C7   C6   C5      0.00   0.0  0
 H43  CONST_19  C27   C8   C7   C6      0.00   0.0  0
 H43  CONST_20  C27   C28  C5   C6      0.00   0.0  0
 H43  CONST_21  C19   C20  C15  C14   180.00   0.0  0
 H43  CONST_22  C19   C18  C17  C16     0.00   0.0  0
 H43  CONST_23  C19   C20  C15  C16     0.00   0.0  0
 H43  CONST_24  C23   C14  C15  C16   180.00   0.0  0
 H43  CONST_25  N9    C8   C27  C28   180.00   0.0  0
 H43  CONST_26  N9    C8   C7   C6    180.00   0.0  0
 H43  CONST_27  C20   C15  C14  C13   180.00   0.0  0
 H43  CONST_28  C16   C15  C14  C13     0.00   0.0  0
 H43  CONST_29  C22   C23  C14  C13   180.00   0.0  0
 H43  CONST_30  C27   C28  C5   C4    180.00   0.0  0
 H43  CONST_31  C7    C6   C5   C4    180.00   0.0  0
 H43  CONST_32  H191  C19  C20  C15   180.00   0.0  0
 H43  CONST_33  H211  C21  C20  C15   180.00   0.0  0
 H43  CONST_34  H171  C17  C16  C15   180.00   0.0  0
 H43  CONST_35  H231  C23  C14  C15   180.00   0.0  0
 H43  CONST_36  H181  C18  C19  C20   180.00   0.0  0
 H43  CONST_37  H221  C22  C21  C20   180.00   0.0  0
 H43  CONST_38  H161  C16  C15  C20   180.00   0.0  0
 H43  CONST_39  H061  C6   C5   C28   180.00   0.0  0
 H43  CONST_40  H271  C27  C28  C5    180.00   0.0  0
 H43  CONST_41  H071  C7   C6   C5    180.00   0.0  0
 H43  CONST_42  H281  C28  C5   C6    180.00   0.0  0
 H43  Var_01    C25   C26  N9   C10   -10.56  30.0  1
 H43  Var_02    C27   C8   N9   C10    13.20  30.0  2
 H43  Var_03    C11   C10  N9   C26   -15.02  30.0  1
 H43  Var_04    N9    C26  C25  C11    31.88  30.0  1
 H43  Var_05    C2    C4   C5   C28  -101.26  30.0  2
 H43  Var_06    O1    C2   C4   C5      8.12  30.0  2

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
 H43  chir_01  C13  C14  C24  N12  negativ
 H43  chir_02  C11  N12  C10  C25  positiv

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
 H43  plan-1  C28   0.020
 H43  plan-1  C5    0.020
 H43  plan-1  C6    0.020
 H43  plan-1  C7    0.020
 H43  plan-1  C8    0.020
 H43  plan-1  C27   0.020
 H43  plan-1  N9    0.020
 H43  plan-1  H281  0.020
 H43  plan-1  H061  0.020
 H43  plan-1  H071  0.020
 H43  plan-1  H271  0.020
 H43  plan-1  C4    0.020
 H43  plan-2  C13   0.020
 H43  plan-2  C15   0.020
 H43  plan-2  C17   0.020
 H43  plan-2  C20   0.020
 H43  plan-2  C21   0.020
 H43  plan-2  C22   0.020
 H43  plan-2  C14   0.020
 H43  plan-2  C16   0.020
 H43  plan-2  C18   0.020
 H43  plan-2  C19   0.020
 H43  plan-2  C23   0.020
 H43  plan-2  H171  0.020
 H43  plan-2  H211  0.020
 H43  plan-2  H221  0.020
 H43  plan-2  H161  0.020
 H43  plan-2  H181  0.020
 H43  plan-2  H191  0.020
 H43  plan-2  H231  0.020
 H43  plan-3  C2    0.020
 H43  plan-3  O1    0.020
 H43  plan-3  O3    0.020
 H43  plan-3  C4    0.020

