# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:59:34 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2-nitro-4-{[(3S)-1-{[4-(trifluoromethoxy)phenyl]methyl}pyrrolidin-3-yl]amino}phenyl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(N[C@H]2CCN(C2)Cc3ccc(OC(F)(F)F)cc3)cc1[N+]([O-])=O
#
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
 S73  S73  (2-nitro-4-{[(3S)-1-{[4-(trifluoromethoxy)phenyl]methyl}pyrrolidin-3-yl]amino}phenyl)methanol  ligand  49  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S73
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
 S73  N    N  N      1   0.326  -7.3023  -0.5060  -1.0862
 S73  O    O  OH1    0  -0.666  -7.5153   0.7164   3.0917
 S73  C1   C  CR6    0   0.013  -6.3441   0.2245   1.0839
 S73  C10  C  CH2    0  -0.468  -0.8733  -0.1528   0.4740
 S73  C12  C  CR6    0   0.097   3.2681   0.4692  -0.8980
 S73  C13  C  CR16   0  -0.281   3.5390   1.0644   0.3316
 S73  C14  C  CR16   0  -0.285   4.7245   0.8086   1.0019
 S73  C15  C  CR6    0   0.296   5.6464  -0.0542   0.4320
 S73  C16  C  CT     0   1.071   7.8952   0.3835   0.9008
 S73  C17  C  CR16   0  -0.283   5.4027  -0.6675  -0.7828
 S73  C18  C  CR16   0  -0.313   4.2075  -0.4015  -1.4382
 S73  C2   C  CR6    0   0.229  -6.1913  -0.0093  -0.2868
 S73  C3   C  CR16   0  -0.387  -5.0043   0.1942  -0.9690
 S73  C4   C  CR16   0  -0.291  -5.1972   0.6769   1.7304
 S73  C5   C  CR16   0  -0.306  -3.9892   0.8679   1.0822
 S73  C6   C  CR6    0   0.388  -3.8635   0.6348  -0.2927
 S73  C7   C  CR15   0  -0.116  -1.4385   1.0555  -0.3211
 S73  C8   C  CH2    0  -0.281  -0.3467   1.3622  -1.3522
 S73  C9   C  CH2    0  -0.273   0.4512  -0.4660  -0.2144
 S73  F    F  F      0  -0.300   7.6996   1.6796   1.1542
 S73  F1   F  F      0  -0.300   8.3195   0.3008  -0.3624
 S73  F2   F  F      0  -0.278   8.8618  -0.0541   1.6927
 S73  N1   N  NH1    0  -0.703  -2.7021   0.8446  -0.9835
 S73  N2   N  NR5    0  -0.429   0.8526   0.8218  -0.7520
 S73  O1   O  O     -1  -0.378  -7.3308  -0.2315  -2.2631
 S73  O2   O  O      0  -0.379  -8.1410  -1.1827  -0.5361
 S73  O3   O  O2     0  -0.523   6.8097  -0.3608   1.1343
 S73  H1   H  HCH2   0   0.231  -7.8087  -1.0257   2.0147
 S73  H2   H  HCH2   0   0.214  -8.4760   0.4273   1.2856
 S73  H3   H  HOH1   0   0.464  -8.2006   0.3771   3.6735
 S73  H4   H  HCH2   0   0.242  -0.7064   0.1227   1.5160
 S73  H5   H  HCH2   0   0.247  -1.5560  -1.0026   0.4652
 S73  H6   H  HCH2   0   0.259   2.0901   1.7598  -2.1120
 S73  H7   H  HCH2   0   0.216   1.8567   0.0510  -2.4526
 S73  H8   H  HCR6   0   0.257   2.8088   1.7274   0.7769
 S73  H9   H  HCR6   0   0.276   4.9195   1.2637   1.9641
 S73  H10  H  HCR6   0   0.277   6.1172  -1.3599  -1.2078
 S73  H11  H  HCR6   0   0.261   4.0062  -0.8866  -2.3856
 S73  H12  H  HCR6   0   0.291  -4.9486  -0.0010  -2.0318
 S73  H13  H  HCR6   0   0.271  -5.2405   0.8850   2.7893
 S73  H14  H  HCR6   0   0.276  -3.1417   1.2021   1.6659
 S73  H15  H  HCR5   0   0.261  -1.5459   1.9138   0.3460
 S73  H16  H  HCH2   0   0.200  -0.5907   0.8644  -2.3082
 S73  H17  H  HCH2   0   0.253  -0.2436   2.4290  -1.5578
 S73  H18  H  HCH2   0   0.241   1.2029  -0.8663   0.4673
 S73  H19  H  HCH2   0   0.200   0.3061  -1.2088  -1.0174
 S73  H20  H  HNH1   0   0.381  -2.6510   0.3926  -1.8836
 S73  C    C  CH2    0  -0.175  -7.6265   0.0435   1.8618
 S73  C11  C  CH2    0  -0.323   1.9907   0.7794  -1.6353

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
 S73  O1   N    single    1.209  0.020  1.209
 S73  O2   N    double    1.210  0.020  1.210
 S73  N    C2   single    1.456  0.020  1.456
 S73  C2   C3   aromatic  1.384  0.020  1.384
 S73  C2   C1   aromatic  1.399  0.020  1.399
 S73  C3   C6   aromatic  1.397  0.020  1.397
 S73  C    C1   single    1.511  0.020  1.511
 S73  C    O    single    1.406  0.020  1.406
 S73  C1   C4   aromatic  1.392  0.020  1.392
 S73  N1   C6   single    1.367  0.020  1.367
 S73  N1   C7   single    1.442  0.020  1.442
 S73  C6   C5   aromatic  1.400  0.020  1.400
 S73  C10  C7   single    1.553  0.020  1.553
 S73  C10  C9   single    1.525  0.020  1.525
 S73  C4   C5   aromatic  1.384  0.020  1.384
 S73  C7   C8   single    1.533  0.020  1.533
 S73  C9   N2   single    1.452  0.020  1.452
 S73  C8   N2   single    1.446  0.020  1.446
 S73  N2   C11  single    1.441  0.020  1.441
 S73  C11  C12  single    1.507  0.020  1.507
 S73  C13  C12  aromatic  1.393  0.020  1.393
 S73  C13  C14  aromatic  1.386  0.020  1.386
 S73  C12  C18  aromatic  1.390  0.020  1.390
 S73  C14  C15  aromatic  1.385  0.020  1.385
 S73  C18  C17  aromatic  1.389  0.020  1.389
 S73  C15  C17  aromatic  1.382  0.020  1.382
 S73  C15  O3   single    1.393  0.020  1.393
 S73  O3   C16  single    1.337  0.020  1.337
 S73  F2   C16  single    1.324  0.020  1.324
 S73  C16  F    single    1.335  0.020  1.335
 S73  C16  F1   single    1.335  0.020  1.335
 S73  C    H1   single    0.970  0.020  1.090
 S73  C    H2   single    0.970  0.020  1.090
 S73  O    H3   single    0.850  0.020  0.980
 S73  C10  H4   single    0.970  0.020  1.090
 S73  C10  H5   single    0.970  0.020  1.090
 S73  C11  H6   single    0.970  0.020  1.090
 S73  C11  H7   single    0.970  0.020  1.090
 S73  C13  H8   single    0.930  0.020  1.080
 S73  C14  H9   single    0.930  0.020  1.080
 S73  C17  H10  single    0.930  0.020  1.080
 S73  C18  H11  single    0.930  0.020  1.080
 S73  C3   H12  single    0.930  0.020  1.080
 S73  C4   H13  single    0.930  0.020  1.080
 S73  C5   H14  single    0.930  0.020  1.080
 S73  C7   H15  single    0.970  0.020  1.090
 S73  C8   H16  single    0.970  0.020  1.090
 S73  C8   H17  single    0.970  0.020  1.090
 S73  C9   H18  single    0.970  0.020  1.090
 S73  C9   H19  single    0.970  0.020  1.090
 S73  N1   H20  single    0.890  0.020  1.040

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
 S73  O2   N    O1   123.59  3.000
 S73  O2   N    C2   118.04  3.000
 S73  O1   N    C2   118.36  3.000
 S73  H3   O    C    107.71  3.000
 S73  C4   C1   C2   114.79  3.000
 S73  C4   C1   C    119.94  3.000
 S73  C2   C1   C    125.25  3.000
 S73  H5   C10  H4   107.48  3.000
 S73  H5   C10  C9   112.34  3.000
 S73  H4   C10  C9   110.50  3.000
 S73  H5   C10  C7   111.99  3.000
 S73  H4   C10  C7   110.39  3.000
 S73  C9   C10  C7   104.17  3.000
 S73  C18  C12  C13  118.64  3.000
 S73  C18  C12  C11  120.77  3.000
 S73  C13  C12  C11  120.59  3.000
 S73  H8   C13  C14  119.43  3.000
 S73  H8   C13  C12  119.60  3.000
 S73  C14  C13  C12  120.97  3.000
 S73  H9   C14  C15  120.52  3.000
 S73  H9   C14  C13  120.43  3.000
 S73  C15  C14  C13  119.04  3.000
 S73  O3   C15  C17  119.51  3.000
 S73  O3   C15  C14  119.04  3.000
 S73  C17  C15  C14  121.36  3.000
 S73  O3   C16  F2   107.72  3.000
 S73  F2   C16  F1   108.27  3.000
 S73  O3   C16  F1   112.88  3.000
 S73  F1   C16  F    106.64  3.000
 S73  F2   C16  F    108.32  3.000
 S73  O3   C16  F    112.86  3.000
 S73  H10  C17  C18  120.36  3.000
 S73  H10  C17  C15  120.84  3.000
 S73  C18  C17  C15  118.78  3.000
 S73  H11  C18  C17  119.14  3.000
 S73  H11  C18  C12  119.66  3.000
 S73  C17  C18  C12  121.21  3.000
 S73  C3   C2   C1   123.51  3.000
 S73  C1   C2   N    120.77  3.000
 S73  C3   C2   N    115.72  3.000
 S73  H12  C3   C6   119.36  3.000
 S73  H12  C3   C2   120.11  3.000
 S73  C6   C3   C2   120.52  3.000
 S73  H13  C4   C5   117.87  3.000
 S73  H13  C4   C1   119.00  3.000
 S73  C5   C4   C1   123.12  3.000
 S73  H14  C5   C6   120.72  3.000
 S73  H14  C5   C4   118.27  3.000
 S73  C6   C5   C4   121.01  3.000
 S73  N1   C6   C5   123.14  3.000
 S73  C5   C6   C3   117.03  3.000
 S73  N1   C6   C3   119.81  3.000
 S73  H15  C7   N1   108.01  3.000
 S73  H15  C7   C8   108.88  3.000
 S73  N1   C7   C8   110.15  3.000
 S73  H15  C7   C10  109.54  3.000
 S73  C8   C7   C10  103.94  3.000
 S73  N1   C7   C10  116.12  3.000
 S73  H17  C8   H16  107.35  3.000
 S73  H17  C8   N2   111.42  3.000
 S73  H16  C8   N2   111.95  3.000
 S73  H17  C8   C7   112.94  3.000
 S73  H16  C8   C7   109.54  3.000
 S73  N2   C8   C7   103.70  3.000
 S73  H19  C9   H18  107.36  3.000
 S73  H19  C9   N2   111.34  3.000
 S73  H18  C9   N2   111.49  3.000
 S73  H19  C9   C10  110.64  3.000
 S73  H18  C9   C10  113.06  3.000
 S73  N2   C9   C10  103.01  3.000
 S73  H20  N1   C7   115.53  3.000
 S73  H20  N1   C6   115.16  3.000
 S73  C7   N1   C6   122.31  3.000
 S73  C9   N2   C8   104.82  3.000
 S73  C8   N2   C11  114.31  3.000
 S73  C9   N2   C11  114.78  3.000
 S73  C16  O3   C15  117.88  3.000
 S73  H2   C    H1   106.64  3.000
 S73  H2   C    C1   110.20  3.000
 S73  H1   C    C1   109.27  3.000
 S73  H2   C    O    110.70  3.000
 S73  H1   C    O    110.99  3.000
 S73  C1   C    O    109.02  3.000
 S73  H7   C11  H6   106.24  3.000
 S73  H7   C11  N2   112.19  3.000
 S73  H6   C11  N2   108.20  3.000
 S73  H7   C11  C12  109.24  3.000
 S73  H6   C11  C12  108.68  3.000
 S73  N2   C11  C12  112.06  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
 S73  CONST_01  C6   C3   C2   C1      0.00   0.0  0
 S73  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 S73  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 S73  CONST_04  C15  C17  C18  C12     0.00   0.0  0
 S73  CONST_05  C17  C18  C12  C13     0.00   0.0  0
 S73  CONST_06  C17  C15  C14  C13     0.00   0.0  0
 S73  CONST_07  C18  C12  C13  C14     0.00   0.0  0
 S73  CONST_08  C18  C17  C15  C14     0.00   0.0  0
 S73  CONST_09  C5   C6   C3   C2      0.00   0.0  0
 S73  CONST_10  C5   C4   C1   C2      0.00   0.0  0
 S73  CONST_11  C4   C1   C2   C3      0.00   0.0  0
 S73  CONST_12  C4   C5   C6   C3      0.00   0.0  0
 S73  CONST_13  C6   C3   C2   N     180.00   0.0  0
 S73  CONST_14  C4   C1   C2   N     180.00   0.0  0
 S73  CONST_15  C3   C2   C1   C     180.00   0.0  0
 S73  CONST_16  C5   C4   C1   C     180.00   0.0  0
 S73  CONST_17  C14  C13  C12  C11   180.00   0.0  0
 S73  CONST_18  C17  C18  C12  C11   180.00   0.0  0
 S73  CONST_19  O3   C15  C14  C13   180.00   0.0  0
 S73  CONST_20  O3   C15  C17  C18   180.00   0.0  0
 S73  CONST_21  N1   C6   C3   C2    180.00   0.0  0
 S73  CONST_22  N1   C6   C5   C4    180.00   0.0  0
 S73  CONST_23  C7   N1   C6   C3    180.00   0.0  0
 S73  CONST_24  C7   N1   C6   C5      0.00   0.0  0
 S73  CONST_25  H12  C3   C2   C1    180.00   0.0  0
 S73  CONST_26  H14  C5   C4   C1    180.00   0.0  0
 S73  CONST_27  H9   C14  C13  C12   180.00   0.0  0
 S73  CONST_28  H10  C17  C18  C12   180.00   0.0  0
 S73  CONST_29  H11  C18  C12  C13   180.00   0.0  0
 S73  CONST_30  H8   C13  C14  C15   180.00   0.0  0
 S73  CONST_31  H13  C4   C1   C2    180.00   0.0  0
 S73  Var_01    C8   N2   C9   C10   -44.89  30.0  1
 S73  Var_02    N2   C9   C10  C7     28.01  30.0  1
 S73  Var_03    C9   N2   C8   C7     43.25  30.0  1
 S73  Var_04    N2   C11  C12  C13   -42.19  30.0  3
 S73  Var_05    C2   C1   C    O    -163.49  30.0  2
 S73  Var_06    C17  C15  O3   C16    90.47  30.0  2
 S73  Var_07    F2   C16  O3   C15   178.33  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
 S73  chir_01  C7  N1  C10  C8  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
 S73  plan-1  C12  0.020
 S73  plan-1  C13  0.020
 S73  plan-1  C14  0.020
 S73  plan-1  C15  0.020
 S73  plan-1  C17  0.020
 S73  plan-1  C18  0.020
 S73  plan-1  O3   0.020
 S73  plan-1  H8   0.020
 S73  plan-1  H9   0.020
 S73  plan-1  H10  0.020
 S73  plan-1  H11  0.020
 S73  plan-1  C11  0.020
 S73  plan-2  N    0.020
 S73  plan-2  C1   0.020
 S73  plan-2  C2   0.020
 S73  plan-2  C3   0.020
 S73  plan-2  C4   0.020
 S73  plan-2  C5   0.020
 S73  plan-2  C6   0.020
 S73  plan-2  N1   0.020
 S73  plan-2  H12  0.020
 S73  plan-2  H13  0.020
 S73  plan-2  H14  0.020
 S73  plan-2  C    0.020
 S73  plan-3  N    0.020
 S73  plan-3  C2   0.020
 S73  plan-3  O1   0.020
 S73  plan-3  O2   0.020
 S73  plan-4  C6   0.020
 S73  plan-4  C7   0.020
 S73  plan-4  N1   0.020
 S73  plan-4  H20  0.020

