# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:32:49 2022
#   Inital geometry file: a 156 line input string
#   Ligand name: (3R,4R)-3-{[(4-hydroxyphenyl)carbonyl]amino}azepan-4-yl 4-[(2-hydroxyphenyl)carbonyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C(=O)N[C@@H]2CNCCC[C@H]2OC(=O)c3ccc(cc3)C(=O)c4ccccc4O
#
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
 BD2  BD2  '(3R,4R)-3-{[(4-hydroxyphenyl)carbonyl]amino}azepan-4-yl 4-[(2-hydroxyphenyl)carbonyl]benzoate'  ligand  61  35  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BD2
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
 BD2  O1    O  OH1   0  -0.646   4.0452  -1.6962  -1.3625
 BD2  C1    C  CR6   0   0.359   3.2684  -1.2467  -0.3530
 BD2  C2    C  CR16  0  -0.358   3.6199  -0.1519   0.4317
 BD2  C3    C  CR16  0  -0.258   2.7484   0.3010   1.4051
 BD2  C4    C  CR6   0  -0.041   1.5321  -0.3366   1.6362
 BD2  C5    C  CR16  0  -0.273   1.2076  -1.4461   0.8562
 BD2  C6    C  CR16  0  -0.301   2.0605  -1.8997  -0.1315
 BD2  C7    C  C     0   0.527   0.5991   0.2600   2.6323
 BD2  O7    O  O     0  -0.481   0.6715   1.4438   2.9313
 BD2  N8    N  NH1   0  -0.668  -0.3187  -0.5725   3.1694
 BD2  C8    C  CH1   0  -0.092  -1.3967  -0.1191   4.0177
 BD2  C9    C  CH1   0   0.036  -2.7018   0.0720   3.2038
 BD2  C10   C  CH2   0  -0.458  -3.6476   1.1248   3.7628
 BD2  C11   C  CH2   0  -0.448  -3.8755   1.0752   5.2784
 BD2  C12   C  CH2   0  -0.310  -3.7667  -0.2927   5.9468
 BD2  N13   N  NH1   0  -0.595  -2.3859  -0.6394   6.2439
 BD2  C14   C  CH2   0  -0.299  -1.5970  -1.1405   5.1422
 BD2  O9    O  O2    0  -0.469  -2.3727   0.4993   1.8766
 BD2  C15   C  C     0   0.606  -2.2162  -0.4022   0.9199
 BD2  O15   O  O     0  -0.439  -2.5196  -1.5671   1.0221
 BD2  C16   C  CR6   0  -0.094  -1.6077   0.1731  -0.3082
 BD2  C17   C  CR16  0  -0.252  -1.1327   1.4822  -0.3608
 BD2  C18   C  CR16  0  -0.257  -0.5417   1.9561  -1.5182
 BD2  C19   C  CR6   0   0.006  -0.3896   1.1245  -2.6251
 BD2  C20   C  CR16  0  -0.247  -0.8561  -0.1857  -2.5655
 BD2  C21   C  CR16  0  -0.238  -1.4711  -0.6540  -1.4196
 BD2  C22   C  C     0   0.370   0.1983   1.6723  -3.8784
 BD2  O22   O  O     0  -0.379   0.1055   2.8554  -4.1334
 BD2  C23   C  CR6   0  -0.158   0.8347   0.7387  -4.8453
 BD2  C24   C  CR16  0  -0.262   0.4773   0.8155  -6.1902
 BD2  C25   C  CR16  0  -0.277   1.0404  -0.0335  -7.1273
 BD2  C26   C  CR16  0  -0.238   1.9992  -0.9530  -6.7178
 BD2  C27   C  CR16  0  -0.373   2.3955  -1.0209  -5.3923
 BD2  C28   C  CR6   0   0.354   1.8199  -0.1736  -4.4478
 BD2  O28   O  OH1   0  -0.614   2.1924  -0.1599  -3.1622
 BD2  HO1   H  HOH1  0   0.482   4.8680  -1.1944  -1.4077
 BD2  H2    H  HCR6  0   0.277   4.5633   0.3576   0.2721
 BD2  H3    H  HCR6  0   0.261   3.0212   1.1700   1.9889
 BD2  H5    H  HCR6  0   0.249   0.2605  -1.9563   0.9746
 BD2  H6    H  HCR6  0   0.270   1.7807  -2.7455  -0.7460
 BD2  HN8   H  HNH1  0   0.404  -0.2623  -1.5589   2.9704
 BD2  H8    H  HCH1  0   0.262  -1.0931   0.8343   4.4537
 BD2  H9    H  HCH1  0   0.245  -3.2160  -0.8909   3.1476
 BD2  H101  H  HCH2  0   0.244  -4.6025   1.0114   3.2450
 BD2  H102  H  HCH2  0   0.244  -3.2680   2.1150   3.4986
 BD2  H111  H  HCH2  0   0.242  -4.8681   1.4840   5.4749
 BD2  H112  H  HCH2  0   0.230  -3.1695   1.7370   5.7846
 BD2  H121  H  HCH2  0   0.200  -4.2862  -1.0596   5.3502
 BD2  H122  H  HCH2  0   0.242  -4.2924  -0.2449   6.9014
 BD2  H13   H  HNH1  0   0.360  -2.3712  -1.3350   6.9770
 BD2  H141  H  HCH2  0   0.201  -2.0099  -2.0639   4.6994
 BD2  H142  H  HCH2  0   0.251  -0.6115  -1.3964   5.5360
 BD2  H17   H  HCR6  0   0.266  -1.2122   2.1347   0.4969
 BD2  H18   H  HCR6  0   0.267  -0.1803   2.9752  -1.5528
 BD2  H20   H  HCR6  0   0.263  -0.7611  -0.8423  -3.4205
 BD2  H21   H  HCR6  0   0.267  -1.8360  -1.6713  -1.3872
 BD2  H24   H  HCR6  0   0.266  -0.2733   1.5339  -6.4956
 BD2  H25   H  HCR6  0   0.260   0.7371   0.0193  -8.1638
 BD2  H26   H  HCR6  0   0.268   2.4512  -1.6230  -7.4375
 BD2  H27   H  HCR6  0   0.275   3.1616  -1.7268  -5.0921
 BD2  H28   H  HOH1  0   0.474   2.8441  -0.8473  -2.9696

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
 BD2  O1   C1    single    1.351  0.020  1.351
 BD2  O1   HO1   single    0.850  0.020  0.980
 BD2  C1   C2    aromatic  1.392  0.020  1.392
 BD2  C1   C6    aromatic  1.391  0.020  1.391
 BD2  C2   C3    aromatic  1.383  0.020  1.383
 BD2  C2   H2    single    0.930  0.020  1.080
 BD2  C3   C4    aromatic  1.393  0.020  1.393
 BD2  C3   H3    single    0.930  0.020  1.080
 BD2  C4   C5    aromatic  1.395  0.020  1.395
 BD2  C4   C7    single    1.489  0.020  1.489
 BD2  C5   C6    aromatic  1.382  0.020  1.382
 BD2  C5   H5    single    0.930  0.020  1.080
 BD2  C6   H6    single    0.930  0.020  1.080
 BD2  C7   O7    double    1.223  0.020  1.223
 BD2  C7   N8    single    1.351  0.020  1.351
 BD2  N8   C8    single    1.445  0.020  1.445
 BD2  N8   HN8   single    0.860  0.020  1.020
 BD2  C8   C9    single    1.550  0.020  1.550
 BD2  C8   C14   single    1.532  0.020  1.532
 BD2  C8   H8    single    0.970  0.020  1.090
 BD2  C9   C10   single    1.522  0.020  1.522
 BD2  C9   O9    single    1.433  0.020  1.433
 BD2  C9   H9    single    0.970  0.020  1.090
 BD2  C10  C11   single    1.533  0.020  1.533
 BD2  C10  H101  single    0.970  0.020  1.090
 BD2  C10  H102  single    0.970  0.020  1.090
 BD2  C11  C12   single    1.526  0.020  1.526
 BD2  C11  H111  single    0.970  0.020  1.090
 BD2  C11  H112  single    0.970  0.020  1.090
 BD2  C12  N13   single    1.454  0.020  1.454
 BD2  C12  H121  single    0.970  0.020  1.090
 BD2  C12  H122  single    0.970  0.020  1.090
 BD2  N13  C14   single    1.445  0.020  1.445
 BD2  N13  H13   single    0.890  0.020  1.040
 BD2  C14  H141  single    0.970  0.020  1.090
 BD2  C14  H142  single    0.970  0.020  1.090
 BD2  O9   C15   single    1.324  0.020  1.324
 BD2  C15  O15   double    1.208  0.020  1.208
 BD2  C15  C16   single    1.486  0.020  1.486
 BD2  C16  C17   aromatic  1.394  0.020  1.394
 BD2  C16  C21   aromatic  1.392  0.020  1.392
 BD2  C17  C18   aromatic  1.383  0.020  1.383
 BD2  C17  H17   single    0.930  0.020  1.080
 BD2  C18  C19   aromatic  1.393  0.020  1.393
 BD2  C18  H18   single    0.930  0.020  1.080
 BD2  C19  C20   aromatic  1.392  0.020  1.392
 BD2  C19  C22   single    1.489  0.020  1.489
 BD2  C20  C21   aromatic  1.382  0.020  1.382
 BD2  C20  H20   single    0.930  0.020  1.080
 BD2  C21  H21   single    0.930  0.020  1.080
 BD2  C22  O22   double    1.214  0.020  1.214
 BD2  C22  C23   single    1.487  0.020  1.487
 BD2  C23  C24   aromatic  1.394  0.020  1.394
 BD2  C23  C28   aromatic  1.400  0.020  1.400
 BD2  C24  C25   aromatic  1.384  0.020  1.384
 BD2  C24  H24   single    0.930  0.020  1.080
 BD2  C25  C26   aromatic  1.390  0.020  1.390
 BD2  C25  H25   single    0.930  0.020  1.080
 BD2  C26  C27   aromatic  1.385  0.020  1.385
 BD2  C26  H26   single    0.930  0.020  1.080
 BD2  C27  C28   aromatic  1.393  0.020  1.393
 BD2  C27  H27   single    0.930  0.020  1.080
 BD2  C28  O28   single    1.339  0.020  1.339
 BD2  O28  H28   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
 BD2  HO1   O1   C1    110.64  3.000
 BD2  C6    C1   C2    119.92  3.000
 BD2  C6    C1   O1    117.53  3.000
 BD2  C2    C1   O1    122.53  3.000
 BD2  H2    C2   C3    119.88  3.000
 BD2  H2    C2   C1    120.42  3.000
 BD2  C3    C2   C1    119.69  3.000
 BD2  H3    C3   C4    119.89  3.000
 BD2  H3    C3   C2    118.95  3.000
 BD2  C4    C3   C2    121.16  3.000
 BD2  C7    C4   C5    123.16  3.000
 BD2  C7    C4   C3    118.34  3.000
 BD2  C5    C4   C3    118.34  3.000
 BD2  H5    C5   C6    117.63  3.000
 BD2  H5    C5   C4    121.16  3.000
 BD2  C6    C5   C4    121.16  3.000
 BD2  H6    C6   C5    120.19  3.000
 BD2  H6    C6   C1    120.07  3.000
 BD2  C5    C6   C1    119.73  3.000
 BD2  N8    C7   O7    122.66  3.000
 BD2  N8    C7   C4    116.41  3.000
 BD2  O7    C7   C4    120.93  3.000
 BD2  HN8   N8   C8    117.70  3.000
 BD2  HN8   N8   C7    119.12  3.000
 BD2  C8    N8   C7    123.17  3.000
 BD2  H8    C8   C14   109.00  3.000
 BD2  H8    C8   C9    109.65  3.000
 BD2  C14   C8   C9    110.95  3.000
 BD2  H8    C8   N8    107.53  3.000
 BD2  C14   C8   N8    108.62  3.000
 BD2  C9    C8   N8    111.01  3.000
 BD2  H9    C9   O9    108.86  3.000
 BD2  H9    C9   C10   109.64  3.000
 BD2  O9    C9   C10   106.07  3.000
 BD2  H9    C9   C8    108.33  3.000
 BD2  O9    C9   C8    109.26  3.000
 BD2  C10   C9   C8    114.56  3.000
 BD2  H102  C10  H101  106.45  3.000
 BD2  H102  C10  C11   108.66  3.000
 BD2  H101  C10  C11   109.59  3.000
 BD2  H102  C10  C9    108.79  3.000
 BD2  H101  C10  C9    107.30  3.000
 BD2  C11   C10  C9    115.66  3.000
 BD2  H112  C11  H111  106.11  3.000
 BD2  H112  C11  C12   107.10  3.000
 BD2  H111  C11  C12   108.77  3.000
 BD2  H112  C11  C10   110.02  3.000
 BD2  H111  C11  C10   107.52  3.000
 BD2  C12   C11  C10   116.82  3.000
 BD2  H122  C12  H121  106.08  3.000
 BD2  H122  C12  N13   106.81  3.000
 BD2  H121  C12  N13   113.10  3.000
 BD2  H122  C12  C11   108.04  3.000
 BD2  H121  C12  C11   110.68  3.000
 BD2  N13   C12  C11   111.77  3.000
 BD2  H13   N13  C14   107.85  3.000
 BD2  H13   N13  C12   109.04  3.000
 BD2  C14   N13  C12   116.45  3.000
 BD2  H142  C14  H141  106.63  3.000
 BD2  H142  C14  N13   107.41  3.000
 BD2  H141  C14  N13   113.06  3.000
 BD2  H142  C14  C8    107.63  3.000
 BD2  H141  C14  C8    108.18  3.000
 BD2  N13   C14  C8    113.57  3.000
 BD2  C15   O9   C9    119.58  3.000
 BD2  C16   C15  O15   123.09  3.000
 BD2  C16   C15  O9    112.46  3.000
 BD2  O15   C15  O9    124.46  3.000
 BD2  C21   C16  C17   119.64  3.000
 BD2  C21   C16  C15   118.02  3.000
 BD2  C17   C16  C15   122.29  3.000
 BD2  H17   C17  C18   119.26  3.000
 BD2  H17   C17  C16   120.81  3.000
 BD2  C18   C17  C16   119.94  3.000
 BD2  H18   C18  C19   120.04  3.000
 BD2  H18   C18  C17   119.49  3.000
 BD2  C19   C18  C17   120.47  3.000
 BD2  C22   C19  C20   120.98  3.000
 BD2  C22   C19  C18   119.50  3.000
 BD2  C20   C19  C18   119.43  3.000
 BD2  H20   C20  C21   119.23  3.000
 BD2  H20   C20  C19   120.52  3.000
 BD2  C21   C20  C19   120.23  3.000
 BD2  H21   C21  C20   119.59  3.000
 BD2  H21   C21  C16   120.13  3.000
 BD2  C20   C21  C16   120.28  3.000
 BD2  C23   C22  O22   120.53  3.000
 BD2  C23   C22  C19   119.03  3.000
 BD2  O22   C22  C19   120.36  3.000
 BD2  C28   C23  C24   119.36  3.000
 BD2  C28   C23  C22   121.70  3.000
 BD2  C24   C23  C22   118.89  3.000
 BD2  H24   C24  C25   119.86  3.000
 BD2  H24   C24  C23   119.11  3.000
 BD2  C25   C24  C23   121.01  3.000
 BD2  H25   C25  C26   120.54  3.000
 BD2  H25   C25  C24   120.33  3.000
 BD2  C26   C25  C24   119.13  3.000
 BD2  H26   C26  C27   119.11  3.000
 BD2  H26   C26  C25   120.11  3.000
 BD2  C27   C26  C25   120.78  3.000
 BD2  H27   C27  C28   120.01  3.000
 BD2  H27   C27  C26   119.94  3.000
 BD2  C28   C27  C26   120.04  3.000
 BD2  O28   C28  C27   122.84  3.000
 BD2  O28   C28  C23   117.51  3.000
 BD2  C27   C28  C23   119.63  3.000
 BD2  H28   O28  C28   111.82  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
 BD2  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 BD2  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 BD2  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 BD2  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 BD2  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 BD2  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 BD2  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 BD2  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 BD2  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 BD2  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 BD2  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 BD2  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 BD2  CONST_13  C26  C25  C24  C23     0.00   0.0  0
 BD2  CONST_14  C26  C27  C28  C23     0.00   0.0  0
 BD2  CONST_15  C27  C28  C23  C24     0.00   0.0  0
 BD2  CONST_16  C27  C26  C25  C24     0.00   0.0  0
 BD2  CONST_17  C28  C23  C24  C25     0.00   0.0  0
 BD2  CONST_18  C28  C27  C26  C25     0.00   0.0  0
 BD2  CONST_19  C3   C2   C1   O1    180.00   0.0  0
 BD2  CONST_20  C5   C6   C1   O1    180.00   0.0  0
 BD2  CONST_21  C7   C4   C3   C2    180.00   0.0  0
 BD2  CONST_22  C7   C4   C5   C6    180.00   0.0  0
 BD2  CONST_23  C18  C17  C16  C15   180.00   0.0  0
 BD2  CONST_24  C20  C21  C16  C15   180.00   0.0  0
 BD2  CONST_25  C22  C19  C18  C17   180.00   0.0  0
 BD2  CONST_26  C22  C19  C20  C21   180.00   0.0  0
 BD2  CONST_27  C25  C24  C23  C22   180.00   0.0  0
 BD2  CONST_28  C27  C28  C23  C22   180.00   0.0  0
 BD2  CONST_29  O28  C28  C23  C24   180.00   0.0  0
 BD2  CONST_30  O28  C28  C27  C26   180.00   0.0  0
 BD2  CONST_31  H3   C3   C2   C1    180.00   0.0  0
 BD2  CONST_32  H5   C5   C6   C1    180.00   0.0  0
 BD2  CONST_33  H6   C6   C1   C2    180.00   0.0  0
 BD2  CONST_34  H2   C2   C3   C4    180.00   0.0  0
 BD2  CONST_35  H18  C18  C17  C16   180.00   0.0  0
 BD2  CONST_36  H20  C20  C21  C16   180.00   0.0  0
 BD2  CONST_37  H21  C21  C16  C17   180.00   0.0  0
 BD2  CONST_38  H17  C17  C18  C19   180.00   0.0  0
 BD2  CONST_39  H25  C25  C24  C23   180.00   0.0  0
 BD2  CONST_40  H27  C27  C28  C23   180.00   0.0  0
 BD2  CONST_41  H26  C26  C25  C24   180.00   0.0  0
 BD2  CONST_42  H24  C24  C25  C26   180.00   0.0  0
 BD2  CONST_43  C8   N8   C7   C4    180.00   0.0  0
 BD2  CONST_44  C8   N8   C7   O7      0.00   0.0  0
 BD2  CONST_45  HN8  N8   C7   C4      0.00   0.0  0
 BD2  Var_01    C23  C22  C19  C18   156.77  30.0  2
 BD2  Var_02    C24  C23  C22  C19   130.47  30.0  2
 BD2  Var_03    O7   C7   C4   C3     22.34  30.0  2
 BD2  Var_04    C16  C15  O9   C9   -168.06  30.0  3
 BD2  Var_05    C17  C16  C15  O9      6.52  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
 BD2  chir_01  C8  N8  C9   C14  negativ
 BD2  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
 BD2  plan-1  O1   0.020
 BD2  plan-1  C1   0.020
 BD2  plan-1  C2   0.020
 BD2  plan-1  C3   0.020
 BD2  plan-1  C4   0.020
 BD2  plan-1  C5   0.020
 BD2  plan-1  C6   0.020
 BD2  plan-1  C7   0.020
 BD2  plan-1  H2   0.020
 BD2  plan-1  H3   0.020
 BD2  plan-1  H5   0.020
 BD2  plan-1  H6   0.020
 BD2  plan-2  C15  0.020
 BD2  plan-2  C16  0.020
 BD2  plan-2  C17  0.020
 BD2  plan-2  C18  0.020
 BD2  plan-2  C19  0.020
 BD2  plan-2  C20  0.020
 BD2  plan-2  C21  0.020
 BD2  plan-2  C22  0.020
 BD2  plan-2  H17  0.020
 BD2  plan-2  H18  0.020
 BD2  plan-2  H20  0.020
 BD2  plan-2  H21  0.020
 BD2  plan-3  C22  0.020
 BD2  plan-3  C23  0.020
 BD2  plan-3  C24  0.020
 BD2  plan-3  C25  0.020
 BD2  plan-3  C26  0.020
 BD2  plan-3  C27  0.020
 BD2  plan-3  C28  0.020
 BD2  plan-3  O28  0.020
 BD2  plan-3  H24  0.020
 BD2  plan-3  H25  0.020
 BD2  plan-3  H26  0.020
 BD2  plan-3  H27  0.020
 BD2  plan-4  C4   0.020
 BD2  plan-4  C7   0.020
 BD2  plan-4  O7   0.020
 BD2  plan-4  N8   0.020
 BD2  plan-4  C8   0.020
 BD2  plan-4  HN8  0.020
 BD2  plan-5  C19  0.020
 BD2  plan-5  C22  0.020
 BD2  plan-5  O22  0.020
 BD2  plan-5  C23  0.020
 BD2  plan-6  O9   0.020
 BD2  plan-6  C15  0.020
 BD2  plan-6  O15  0.020
 BD2  plan-6  C16  0.020

