# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 18:36:26 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (3R,4R)-3-{[(4-hydroxyphenyl)carbonyl]amino}azepan-4-yl 4-hydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C(=O)N[C@@H]2CNCCC[C@H]2OC(=O)c3ccc(O)cc3
#
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
 B1L  B1L  '(3R,4R)-3-{[(4-hydroxyphenyl)carbonyl]amino}azepan-4-yl 4-hydroxybenzoate'  ligand  49  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B1L
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
 B1L  O1    O  OH1   0  -0.625   5.3772  -1.3566  -1.0182
 B1L  C1    C  CR6   0   0.358   4.2661  -0.8786  -0.4335
 B1L  C2    C  CR16  0  -0.374   4.2360   0.3419   0.2396
 B1L  C3    C  CR16  0  -0.257   3.0583   0.7836   0.8136
 B1L  C4    C  CR6   0  -0.041   1.8965   0.0175   0.7568
 B1L  C5    C  CR16  0  -0.266   1.9407  -1.1997   0.0776
 B1L  C6    C  CR16  0  -0.319   3.1061  -1.6462  -0.5157
 B1L  C7    C  C     0   0.529   0.6546   0.5687   1.3653
 B1L  O7    O  O     0  -0.485   0.5061   1.7733   1.5197
 B1L  N8    N  NH1   0  -0.668  -0.2785  -0.3328   1.7409
 B1L  C8    C  CH1   0  -0.088  -1.5864   0.0370   2.2301
 B1L  C9    C  CH1   0   0.039  -2.6349   0.0357   1.0886
 B1L  C10   C  CH2   0  -0.459  -3.7699   1.0278   1.2887
 B1L  C11   C  CH2   0  -0.446  -4.4430   0.9852   2.6682
 B1L  C12   C  CH2   0  -0.312  -4.3803  -0.3398   3.4226
 B1L  N13   N  NH1   0  -0.596  -3.1141  -0.5065   4.1200
 B1L  C14   C  CH2   0  -0.301  -1.9874  -0.9489   3.3302
 B1L  O9    O  O2    0  -0.475  -2.0027   0.3905  -0.1426
 B1L  C15   C  C     0   0.595  -1.4968  -0.5674  -0.9137
 B1L  O15   O  O     0  -0.454  -1.7324  -1.7458  -0.7668
 B1L  C16   C  CR6   0  -0.118  -0.6118  -0.0372  -1.9674
 B1L  C17   C  CR16  0  -0.244  -0.2025   1.2970  -2.0069
 B1L  C18   C  CR16  0  -0.321   0.6716   1.7393  -2.9795
 B1L  C19   C  CR6   0   0.369   1.1564   0.8492  -3.9381
 B1L  C20   C  CR16  0  -0.370   0.7530  -0.4859  -3.9081
 B1L  C21   C  CR16  0  -0.234  -0.1173  -0.9181  -2.9278
 B1L  O19   O  OH1   0  -0.620   2.0049   1.3245  -4.8609
 B1L  HO1   H  HOH1  0   0.477   6.1125  -0.7448  -0.8981
 B1L  H2    H  HCR6  0   0.274   5.1319   0.9481   0.3116
 B1L  H3    H  HCR6  0   0.259   3.0483   1.7379   1.3233
 B1L  H5    H  HCR6  0   0.248   1.0557  -1.8134  -0.0289
 B1L  H6    H  HCR6  0   0.266   3.1187  -2.5862  -1.0526
 B1L  HN8   H  HNH1  0   0.403  -0.0576  -1.3149   1.6964
 B1L  H8    H  HCH1  0   0.259  -1.5088   1.0396   2.6553
 B1L  H9    H  HCH1  0   0.241  -3.0413  -0.9749   0.9992
 B1L  H101  H  HCH2  0   0.243  -4.5136   0.8335   0.5125
 B1L  H102  H  HCH2  0   0.242  -3.3911   2.0372   1.1095
 B1L  H111  H  HCH2  0   0.240  -5.4903   1.2623   2.5354
 B1L  H112  H  HCH2  0   0.229  -4.0091   1.7451   3.3214
 B1L  H121  H  HCH2  0   0.201  -4.6246  -1.1813   2.7541
 B1L  H122  H  HCH2  0   0.242  -5.1582  -0.3275   4.1873
 B1L  H13   H  HNH1  0   0.360  -3.2395  -1.1653   4.8760
 B1L  H141  H  HCH2  0   0.201  -2.1480  -1.9353   2.8604
 B1L  H142  H  HCH2  0   0.249  -1.1387  -1.0581   4.0089
 B1L  H17   H  HCR6  0   0.262  -0.5530   2.0014  -1.2661
 B1L  H18   H  HCR6  0   0.268   0.9891   2.7739  -2.9991
 B1L  H20   H  HCR6  0   0.276   1.1246  -1.1860  -4.6472
 B1L  H21   H  HCR6  0   0.263  -0.4132  -1.9584  -2.9106
 B1L  H19   H  HOH1  0   0.479   2.2705   0.6258  -5.4699

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
 B1L  O1   C1    single    1.343  0.020  1.343
 B1L  O1   HO1   single    0.850  0.020  0.980
 B1L  C1   C2    aromatic  1.394  0.020  1.394
 B1L  C1   C6    aromatic  1.393  0.020  1.393
 B1L  C2   C3    aromatic  1.383  0.020  1.383
 B1L  C2   H2    single    0.930  0.020  1.080
 B1L  C3   C4    aromatic  1.393  0.020  1.393
 B1L  C3   H3    single    0.930  0.020  1.080
 B1L  C4   C5    aromatic  1.395  0.020  1.395
 B1L  C4   C7    single    1.489  0.020  1.489
 B1L  C5   C6    aromatic  1.382  0.020  1.382
 B1L  C5   H5    single    0.930  0.020  1.080
 B1L  C6   H6    single    0.930  0.020  1.080
 B1L  C7   O7    double    1.224  0.020  1.224
 B1L  C7   N8    single    1.351  0.020  1.351
 B1L  N8   C8    single    1.445  0.020  1.445
 B1L  N8   HN8   single    0.860  0.020  1.020
 B1L  C8   C9    single    1.550  0.020  1.550
 B1L  C8   C14   single    1.531  0.020  1.531
 B1L  C8   H8    single    0.970  0.020  1.090
 B1L  C9   C10   single    1.521  0.020  1.521
 B1L  C9   O9    single    1.429  0.020  1.429
 B1L  C9   H9    single    0.970  0.020  1.090
 B1L  C10  C11   single    1.536  0.020  1.536
 B1L  C10  H101  single    0.970  0.020  1.090
 B1L  C10  H102  single    0.970  0.020  1.090
 B1L  C11  C12   single    1.526  0.020  1.526
 B1L  C11  H111  single    0.970  0.020  1.090
 B1L  C11  H112  single    0.970  0.020  1.090
 B1L  C12  N13   single    1.455  0.020  1.455
 B1L  C12  H121  single    0.970  0.020  1.090
 B1L  C12  H122  single    0.970  0.020  1.090
 B1L  N13  C14   single    1.445  0.020  1.445
 B1L  N13  H13   single    0.890  0.020  1.040
 B1L  C14  H141  single    0.970  0.020  1.090
 B1L  C14  H142  single    0.970  0.020  1.090
 B1L  O9   C15   single    1.330  0.020  1.330
 B1L  C15  O15   double    1.211  0.020  1.211
 B1L  C15  C16   single    1.475  0.020  1.475
 B1L  C16  C17   aromatic  1.396  0.020  1.396
 B1L  C16  C21   aromatic  1.394  0.020  1.394
 B1L  C17  C18   aromatic  1.380  0.020  1.380
 B1L  C17  H17   single    0.930  0.020  1.080
 B1L  C18  C19   aromatic  1.395  0.020  1.395
 B1L  C18  H18   single    0.930  0.020  1.080
 B1L  C19  C20   aromatic  1.395  0.020  1.395
 B1L  C19  O19   single    1.341  0.020  1.341
 B1L  C20  C21   aromatic  1.380  0.020  1.380
 B1L  C20  H20   single    0.930  0.020  1.080
 B1L  C21  H21   single    0.930  0.020  1.080
 B1L  O19  H19   single    0.850  0.020  0.980

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
 B1L  HO1   O1   C1    110.54  3.000
 B1L  C6    C1   C2    119.52  3.000
 B1L  C6    C1   O1    117.83  3.000
 B1L  C2    C1   O1    122.65  3.000
 B1L  H2    C2   C3    119.85  3.000
 B1L  H2    C2   C1    120.25  3.000
 B1L  C3    C2   C1    119.90  3.000
 B1L  H3    C3   C4    119.78  3.000
 B1L  H3    C3   C2    119.03  3.000
 B1L  C4    C3   C2    121.19  3.000
 B1L  C7    C4   C5    123.27  3.000
 B1L  C7    C4   C3    118.39  3.000
 B1L  C5    C4   C3    118.26  3.000
 B1L  H5    C5   C6    117.66  3.000
 B1L  H5    C5   C4    121.13  3.000
 B1L  C6    C5   C4    121.19  3.000
 B1L  H6    C6   C5    120.22  3.000
 B1L  H6    C6   C1    119.86  3.000
 B1L  C5    C6   C1    119.92  3.000
 B1L  N8    C7   O7    122.56  3.000
 B1L  N8    C7   C4    116.29  3.000
 B1L  O7    C7   C4    121.16  3.000
 B1L  HN8   N8   C8    117.58  3.000
 B1L  HN8   N8   C7    119.13  3.000
 B1L  C8    N8   C7    123.29  3.000
 B1L  H8    C8   C14   109.28  3.000
 B1L  H8    C8   C9    109.62  3.000
 B1L  C14   C8   C9    110.58  3.000
 B1L  H8    C8   N8    107.61  3.000
 B1L  C14   C8   N8    108.40  3.000
 B1L  C9    C8   N8    111.28  3.000
 B1L  H9    C9   O9    108.89  3.000
 B1L  H9    C9   C10   109.66  3.000
 B1L  O9    C9   C10   106.36  3.000
 B1L  H9    C9   C8    108.21  3.000
 B1L  O9    C9   C8    109.58  3.000
 B1L  C10   C9   C8    114.04  3.000
 B1L  H102  C10  H101  106.49  3.000
 B1L  H102  C10  C11   108.95  3.000
 B1L  H101  C10  C11   109.57  3.000
 B1L  H102  C10  C9    108.80  3.000
 B1L  H101  C10  C9    107.37  3.000
 B1L  C11   C10  C9    115.29  3.000
 B1L  H112  C11  H111  106.11  3.000
 B1L  H112  C11  C12   106.99  3.000
 B1L  H111  C11  C12   108.66  3.000
 B1L  H112  C11  C10   110.12  3.000
 B1L  H111  C11  C10   107.72  3.000
 B1L  C12   C11  C10   116.75  3.000
 B1L  H122  C12  H121  106.01  3.000
 B1L  H122  C12  N13   106.61  3.000
 B1L  H121  C12  N13   113.34  3.000
 B1L  H122  C12  C11   107.90  3.000
 B1L  H121  C12  C11   110.73  3.000
 B1L  N13   C12  C11   111.85  3.000
 B1L  H13   N13  C14   107.82  3.000
 B1L  H13   N13  C12   108.98  3.000
 B1L  C14   N13  C12   116.84  3.000
 B1L  H142  C14  H141  106.75  3.000
 B1L  H142  C14  N13   107.26  3.000
 B1L  H141  C14  N13   113.11  3.000
 B1L  H142  C14  C8    107.91  3.000
 B1L  H141  C14  C8    107.92  3.000
 B1L  N13   C14  C8    113.56  3.000
 B1L  C15   O9   C9    119.29  3.000
 B1L  C16   C15  O15   123.61  3.000
 B1L  C16   C15  O9    112.56  3.000
 B1L  O15   C15  O9    123.83  3.000
 B1L  C21   C16  C17   118.71  3.000
 B1L  C21   C16  C15   118.56  3.000
 B1L  C17   C16  C15   122.67  3.000
 B1L  H17   C17  C18   118.66  3.000
 B1L  H17   C17  C16   120.56  3.000
 B1L  C18   C17  C16   120.78  3.000
 B1L  H18   C18  C19   119.70  3.000
 B1L  H18   C18  C17   120.31  3.000
 B1L  C19   C18  C17   119.99  3.000
 B1L  O19   C19  C20   122.49  3.000
 B1L  O19   C19  C18   117.82  3.000
 B1L  C20   C19  C18   119.69  3.000
 B1L  H20   C20  C21   119.88  3.000
 B1L  H20   C20  C19   120.29  3.000
 B1L  C21   C20  C19   119.82  3.000
 B1L  H21   C21  C20   119.01  3.000
 B1L  H21   C21  C16   119.98  3.000
 B1L  C20   C21  C16   121.00  3.000
 B1L  H19   O19  C19   110.62  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
 B1L  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 B1L  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 B1L  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 B1L  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 B1L  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 B1L  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 B1L  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 B1L  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 B1L  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 B1L  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 B1L  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 B1L  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 B1L  CONST_13  C3   C2   C1   O1    180.00   0.0  0
 B1L  CONST_14  C5   C6   C1   O1    180.00   0.0  0
 B1L  CONST_15  C7   C4   C3   C2    180.00   0.0  0
 B1L  CONST_16  C7   C4   C5   C6    180.00   0.0  0
 B1L  CONST_17  C18  C17  C16  C15   180.00   0.0  0
 B1L  CONST_18  C20  C21  C16  C15   180.00   0.0  0
 B1L  CONST_19  O19  C19  C18  C17   180.00   0.0  0
 B1L  CONST_20  O19  C19  C20  C21   180.00   0.0  0
 B1L  CONST_21  H3   C3   C2   C1    180.00   0.0  0
 B1L  CONST_22  H5   C5   C6   C1    180.00   0.0  0
 B1L  CONST_23  H6   C6   C1   C2    180.00   0.0  0
 B1L  CONST_24  H2   C2   C3   C4    180.00   0.0  0
 B1L  CONST_25  H18  C18  C17  C16   180.00   0.0  0
 B1L  CONST_26  H20  C20  C21  C16   180.00   0.0  0
 B1L  CONST_27  H21  C21  C16  C17   180.00   0.0  0
 B1L  CONST_28  H17  C17  C18  C19   180.00   0.0  0
 B1L  CONST_29  C8   N8   C7   C4    180.00   0.0  0
 B1L  CONST_30  C8   N8   C7   O7      0.00   0.0  0
 B1L  CONST_31  HN8  N8   C7   C4      0.00   0.0  0
 B1L  Var_01    O7   C7   C4   C3     23.30  30.0  2
 B1L  Var_02    C16  C15  O9   C9   -166.41  30.0  3
 B1L  Var_03    C17  C16  C15  O9      9.11  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
 B1L  chir_01  C8  N8  C9   C14  negativ
 B1L  chir_02  C9  O9  C10  C8   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
 B1L  plan-1  O1   0.020
 B1L  plan-1  C1   0.020
 B1L  plan-1  C2   0.020
 B1L  plan-1  C3   0.020
 B1L  plan-1  C4   0.020
 B1L  plan-1  C5   0.020
 B1L  plan-1  C6   0.020
 B1L  plan-1  C7   0.020
 B1L  plan-1  H2   0.020
 B1L  plan-1  H3   0.020
 B1L  plan-1  H5   0.020
 B1L  plan-1  H6   0.020
 B1L  plan-2  C15  0.020
 B1L  plan-2  C16  0.020
 B1L  plan-2  C17  0.020
 B1L  plan-2  C18  0.020
 B1L  plan-2  C19  0.020
 B1L  plan-2  C20  0.020
 B1L  plan-2  C21  0.020
 B1L  plan-2  O19  0.020
 B1L  plan-2  H17  0.020
 B1L  plan-2  H18  0.020
 B1L  plan-2  H20  0.020
 B1L  plan-2  H21  0.020
 B1L  plan-3  C4   0.020
 B1L  plan-3  C7   0.020
 B1L  plan-3  O7   0.020
 B1L  plan-3  N8   0.020
 B1L  plan-3  C8   0.020
 B1L  plan-3  HN8  0.020
 B1L  plan-4  O9   0.020
 B1L  plan-4  C15  0.020
 B1L  plan-4  O15  0.020
 B1L  plan-4  C16  0.020

