# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:43:30 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (1S,5S,7R)-N~7~-(biphenyl-4-ylmethyl)-N~3~-hydroxy-6,8-dioxa-3-azabicyclo[3.2.1]octane-3,7-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)N1C[C@H]2O[C@@H](C1)[C@@H](O2)C(=O)NCc3ccc(cc3)c4ccccc4
#
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
 37A  37A  (1S,5S,7R)-N~7~-(biphenyl-4-ylmethyl)-N~3~-hydroxy-6,8-dioxa-3-azabicyclo[3.2.1]octane-3,7-dicarboxamide  ligand  49  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_37A
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
 37A  O6    O  O     0  -0.474  0.0352  -1.0320   0.2449
 37A  C9    C  C     0   0.529  0.8227  -0.2420  -0.2442
 37A  C6    C  CH1   0  -0.077  1.3162  -0.3782  -1.6804
 37A  O2    O  O2    0  -0.490  0.3879  -1.1099  -2.4404
 37A  C5    C  CH1   0  -0.127  2.5807  -1.2600  -1.7335
 37A  C7    C  CH2   0  -0.265  3.4406  -0.9569  -2.9456
 37A  N1    N  NT    0  -0.519  2.6418  -1.0649  -4.1560
 37A  C21   C  C     0   0.709  3.0465  -0.3703  -5.2566
 37A  O1    O  O     0  -0.513  3.9077   0.4905  -5.2192
 37A  N2    N  NH1   0  -0.439  2.3485  -0.6652  -6.4149
 37A  O4    O  OH1   0  -0.548  2.8969  -0.1370  -7.5590
 37A  C3    C  CH2   0  -0.319  1.6604  -2.1353  -4.2054
 37A  O3    O  O2    0  -0.468  2.0016  -2.5454  -1.8704
 37A  C1    C  CH1   0   0.223  1.0209  -2.3076  -2.8345
 37A  N3    N  NH1   0  -0.619  1.3689   0.7910   0.4150
 37A  C12   C  CH2   0  -0.400  1.1939   1.0176   1.8362
 37A  C13   C  CR6   0   0.118  2.2387   0.3111   2.6620
 37A  C15   C  CR16  0  -0.284  3.3988   0.9704   3.0547
 37A  C19   C  CR16  0  -0.297  4.3780   0.3156   3.7861
 37A  C17   C  CR6   0   0.077  4.2256  -1.0230   4.1483
 37A  C16   C  CR16  0  -0.298  3.0594  -1.6813   3.7536
 37A  C14   C  CR16  0  -0.277  2.0827  -1.0252   3.0220
 37A  C18   C  CR6   0   0.088  5.2663  -1.7201   4.9305
 37A  C11   C  CR16  0  -0.310  6.6203  -1.4733   4.6955
 37A  C2    C  CR16  0  -0.240  7.6000  -2.1247   5.4304
 37A  C20   C  CR16  0  -0.311  4.9216  -2.6401   5.9226
 37A  C10   C  CR16  0  -0.240  5.9008  -3.2919   6.6580
 37A  C4    C  CR16  0  -0.266  7.2443  -3.0369   6.4154
 37A  H6    H  HCH1  0   0.283  1.4928   0.6068  -2.1261
 37A  H5    H  HCH1  0   0.290  3.1861  -1.2273  -0.8271
 37A  H71   H  HCH2  0   0.274  3.8452   0.0495  -2.8628
 37A  H72   H  HCH2  0   0.261  4.2851  -1.6553  -2.9635
 37A  HN2   H  HNH1  0   0.411  2.0767  -1.6256  -6.5747
 37A  HO4   H  HOH1  0   0.474  2.2914   0.5631  -7.8277
 37A  H31   H  HCH2  0   0.257  2.1043  -3.0899  -4.5116
 37A  H32   H  HCH2  0   0.271  0.8688  -1.8918  -4.9142
 37A  H1    H  HCH1  0   0.274  0.3005  -3.1270  -2.8429
 37A  HN3   H  HNH1  0   0.406  2.0271   1.3821  -0.0679
 37A  H121  H  HCH2  0   0.269  0.1944   0.6904   2.1193
 37A  H122  H  HCH2  0   0.275  1.2414   2.0928   2.0069
 37A  H15   H  HCR6  0   0.254  3.5393   2.0132   2.7950
 37A  H19   H  HCR6  0   0.254  5.2599   0.8619   4.0976
 37A  H16   H  HCR6  0   0.253  2.9159  -2.7246   4.0064
 37A  H14   H  HCR6  0   0.253  1.1913  -1.5610   2.7207
 37A  H11   H  HCR6  0   0.254  6.9132  -0.7794   3.9170
 37A  H2    H  HCR6  0   0.258  8.6440  -1.9238   5.2272
 37A  H20   H  HCR6  0   0.254  3.8782  -2.8342   6.1388
 37A  H10   H  HCR6  0   0.258  5.6127  -3.9945   7.4294
 37A  H4    H  HCR6  0   0.258  8.0073  -3.5447   6.9906

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
 37A  O6   C9    double    1.218  0.020  1.218
 37A  C9   C6    single    1.525  0.020  1.525
 37A  C9   N3    single    1.342  0.020  1.342
 37A  C6   C5    single    1.543  0.020  1.543
 37A  C6   O2    single    1.405  0.020  1.405
 37A  C6   H6    single    0.970  0.020  1.090
 37A  O2   C1    single    1.411  0.020  1.411
 37A  C5   C7    single    1.517  0.020  1.517
 37A  C5   O3    single    1.416  0.020  1.416
 37A  C5   H5    single    0.970  0.020  1.090
 37A  C7   N1    single    1.454  0.020  1.454
 37A  C7   H71   single    0.970  0.020  1.090
 37A  C7   H72   single    0.970  0.020  1.090
 37A  N1   C3    single    1.453  0.020  1.453
 37A  N1   C21   single    1.363  0.020  1.363
 37A  C21  O1    double    1.218  0.020  1.218
 37A  C21  N2    single    1.384  0.020  1.384
 37A  N2   O4    single    1.374  0.020  1.374
 37A  N2   HN2   single    0.890  0.020  1.040
 37A  O4   HO4   single    0.850  0.020  0.980
 37A  C3   C1    single    1.523  0.020  1.523
 37A  C3   H31   single    0.970  0.020  1.090
 37A  C3   H32   single    0.970  0.020  1.090
 37A  O3   C1    single    1.396  0.020  1.396
 37A  C1   H1    single    0.970  0.020  1.090
 37A  N3   C12   single    1.450  0.020  1.450
 37A  N3   HN3   single    0.860  0.020  1.020
 37A  C12  C13   single    1.508  0.020  1.508
 37A  C12  H121  single    0.970  0.020  1.090
 37A  C12  H122  single    0.970  0.020  1.090
 37A  C13  C14   aromatic  1.393  0.020  1.393
 37A  C13  C15   aromatic  1.391  0.020  1.391
 37A  C15  C19   aromatic  1.387  0.020  1.387
 37A  C15  H15   single    0.930  0.020  1.080
 37A  C19  C17   aromatic  1.395  0.020  1.395
 37A  C19  H19   single    0.930  0.020  1.080
 37A  C17  C16   aromatic  1.396  0.020  1.396
 37A  C17  C18   single    1.477  0.020  1.477
 37A  C16  C14   aromatic  1.386  0.020  1.386
 37A  C16  H16   single    0.930  0.020  1.080
 37A  C14  H14   single    0.930  0.020  1.080
 37A  C18  C11   aromatic  1.396  0.020  1.396
 37A  C18  C20   aromatic  1.396  0.020  1.396
 37A  C11  C2    aromatic  1.387  0.020  1.387
 37A  C11  H11   single    0.930  0.020  1.080
 37A  C2   C4    aromatic  1.389  0.020  1.389
 37A  C2   H2    single    0.930  0.020  1.080
 37A  C20  C10   aromatic  1.387  0.020  1.387
 37A  C20  H20   single    0.930  0.020  1.080
 37A  C10  C4    aromatic  1.389  0.020  1.389
 37A  C10  H10   single    0.930  0.020  1.080
 37A  C4   H4    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
 37A  N3    C9   C6    113.57  3.000
 37A  N3    C9   O6    124.42  3.000
 37A  C6    C9   O6    121.98  3.000
 37A  H6    C6   C5    111.58  3.000
 37A  H6    C6   O2    110.77  3.000
 37A  C5    C6   O2    103.02  3.000
 37A  H6    C6   C9    110.80  3.000
 37A  O2    C6   C9    110.01  3.000
 37A  C5    C6   C9    110.42  3.000
 37A  C1    O2   C6    107.26  3.000
 37A  H5    C5   O3    109.54  3.000
 37A  H5    C5   C7    110.09  3.000
 37A  O3    C5   C7    109.63  3.000
 37A  H5    C5   C6    114.16  3.000
 37A  O3    C5   C6    100.78  3.000
 37A  C7    C5   C6    112.22  3.000
 37A  H72   C7   H71   107.71  3.000
 37A  H72   C7   N1    111.25  3.000
 37A  H71   C7   N1    109.65  3.000
 37A  H72   C7   C5    108.82  3.000
 37A  H71   C7   C5    109.56  3.000
 37A  N1    C7   C5    109.81  3.000
 37A  C3    N1   C21   123.26  3.000
 37A  C21   N1   C7    118.11  3.000
 37A  C3    N1   C7    117.00  3.000
 37A  N2    C21  O1    122.19  3.000
 37A  N2    C21  N1    114.68  3.000
 37A  O1    C21  N1    123.04  3.000
 37A  HN2   N2   O4    109.93  3.000
 37A  HN2   N2   C21   118.06  3.000
 37A  O4    N2   C21   114.43  3.000
 37A  HO4   O4   N2    105.11  3.000
 37A  H32   C3   H31   107.87  3.000
 37A  H32   C3   C1    107.80  3.000
 37A  H31   C3   C1    108.84  3.000
 37A  H32   C3   N1    110.37  3.000
 37A  H31   C3   N1    112.18  3.000
 37A  C1    C3   N1    109.66  3.000
 37A  C1    O3   C5    101.50  3.000
 37A  H1    C1   O3    109.96  3.000
 37A  H1    C1   C3    110.82  3.000
 37A  O3    C1   C3    110.25  3.000
 37A  H1    C1   O2    110.09  3.000
 37A  O3    C1   O2    105.49  3.000
 37A  C3    C1   O2    110.11  3.000
 37A  HN3   N3   C12   117.18  3.000
 37A  HN3   N3   C9    118.82  3.000
 37A  C12   N3   C9    123.57  3.000
 37A  H122  C12  H121  107.20  3.000
 37A  H122  C12  C13   110.27  3.000
 37A  H121  C12  C13   110.66  3.000
 37A  H122  C12  N3    107.61  3.000
 37A  H121  C12  N3    108.58  3.000
 37A  C13   C12  N3    112.34  3.000
 37A  C14   C13  C15   118.38  3.000
 37A  C15   C13  C12   120.70  3.000
 37A  C14   C13  C12   120.90  3.000
 37A  H15   C15  C19   119.28  3.000
 37A  H15   C15  C13   119.78  3.000
 37A  C19   C15  C13   120.94  3.000
 37A  H19   C19  C17   119.88  3.000
 37A  H19   C19  C15   119.24  3.000
 37A  C17   C19  C15   120.86  3.000
 37A  C18   C17  C16   121.05  3.000
 37A  C18   C17  C19   120.90  3.000
 37A  C16   C17  C19   118.05  3.000
 37A  H16   C16  C14   119.08  3.000
 37A  H16   C16  C17   119.93  3.000
 37A  C14   C16  C17   120.99  3.000
 37A  H14   C14  C16   119.53  3.000
 37A  H14   C14  C13   119.68  3.000
 37A  C16   C14  C13   120.79  3.000
 37A  C20   C18  C11   118.39  3.000
 37A  C20   C18  C17   120.89  3.000
 37A  C11   C18  C17   120.71  3.000
 37A  H11   C11  C2    119.38  3.000
 37A  H11   C11  C18   119.77  3.000
 37A  C2    C11  C18   120.84  3.000
 37A  H2    C2   C4    120.14  3.000
 37A  H2    C2   C11   119.64  3.000
 37A  C4    C2   C11   120.21  3.000
 37A  H20   C20  C10   119.34  3.000
 37A  H20   C20  C18   119.85  3.000
 37A  C10   C20  C18   120.80  3.000
 37A  H10   C10  C4    120.07  3.000
 37A  H10   C10  C20   119.66  3.000
 37A  C4    C10  C20   120.26  3.000
 37A  H4    C4   C10   120.20  3.000
 37A  H4    C4   C2    120.31  3.000
 37A  C10   C4   C2    119.49  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
 37A  CONST_01  C17  C16  C14  C13    0.00   0.0  0
 37A  CONST_02  C17  C19  C15  C13    0.00   0.0  0
 37A  CONST_03  C16  C14  C13  C15    0.00   0.0  0
 37A  CONST_04  C16  C17  C19  C15    0.00   0.0  0
 37A  CONST_05  C18  C17  C19  C15  180.00   0.0  0
 37A  CONST_06  C14  C13  C15  C19    0.00   0.0  0
 37A  CONST_07  C14  C16  C17  C19    0.00   0.0  0
 37A  CONST_10  C2   C11  C18  C17  180.00   0.0  0
 37A  CONST_11  C10  C20  C18  C17  180.00   0.0  0
 37A  CONST_14  C18  C17  C16  C14  180.00   0.0  0
 37A  CONST_15  C4   C2   C11  C18    0.00   0.0  0
 37A  CONST_16  C4   C10  C20  C18    0.00   0.0  0
 37A  CONST_17  C10  C20  C18  C11    0.00   0.0  0
 37A  CONST_18  C10  C4   C2   C11    0.00   0.0  0
 37A  CONST_19  C20  C18  C11  C2     0.00   0.0  0
 37A  CONST_20  C20  C10  C4   C2     0.00   0.0  0
 37A  CONST_21  C16  C14  C13  C12  180.00   0.0  0
 37A  CONST_22  C19  C15  C13  C12  180.00   0.0  0
 37A  CONST_23  H16  C16  C14  C13  180.00   0.0  0
 37A  CONST_24  H19  C19  C15  C13  180.00   0.0  0
 37A  CONST_25  H14  C14  C13  C15  180.00   0.0  0
 37A  CONST_26  H15  C15  C19  C17  180.00   0.0  0
 37A  CONST_27  H11  C11  C18  C17    0.00   0.0  0
 37A  CONST_28  H20  C20  C18  C17    0.00   0.0  0
 37A  CONST_29  H2   C2   C11  C18  180.00   0.0  0
 37A  CONST_30  H10  C10  C20  C18  180.00   0.0  0
 37A  CONST_31  H4   C4   C2   C11  180.00   0.0  0
 37A  CONST_32  O1   C21  N1   C7     0.00   0.0  0
 37A  CONST_33  C3   N1   C21  O1   180.00   0.0  0
 37A  CONST_34  N2   C21  N1   C7   180.00   0.0  0
 37A  CONST_35  C3   N1   C21  N2     0.00   0.0  0
 37A  CONST_36  C12  N3   C9   C6   180.00   0.0  0
 37A  CONST_37  O4   N2   C21  N1   180.00   0.0  0
 37A  CONST_38  HN3  N3   C9   C6     0.00   0.0  0
 37A  CONST_40  C12  N3   C9   O6     0.00   0.0  0
 37A  CONST_41  O4   N2   C21  O1     0.00   0.0  0
 37A  Var_01    C3   N1   C7   C5   -38.42  30.0  1
 37A  Var_02    C1   C3   N1   C7    37.79  30.0  1
 37A  Var_03    C14  C13  C12  N3   -84.33  30.0  2
 37A  Var_04    C13  C12  N3   C9    88.53  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
 37A  chir_01  C6  C9  C5  O2  negativ
 37A  chir_02  C5  O3  C7  C6  negativ
 37A  chir_03  C1  O3  O2  C3  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
 37A  plan-1  C12  0.020
 37A  plan-1  C13  0.020
 37A  plan-1  C15  0.020
 37A  plan-1  C19  0.020
 37A  plan-1  C17  0.020
 37A  plan-1  C16  0.020
 37A  plan-1  C14  0.020
 37A  plan-1  C18  0.020
 37A  plan-1  H15  0.020
 37A  plan-1  H19  0.020
 37A  plan-1  H16  0.020
 37A  plan-1  H14  0.020
 37A  plan-2  C17  0.020
 37A  plan-2  C18  0.020
 37A  plan-2  C11  0.020
 37A  plan-2  C2   0.020
 37A  plan-2  C20  0.020
 37A  plan-2  C10  0.020
 37A  plan-2  C4   0.020
 37A  plan-2  H11  0.020
 37A  plan-2  H2   0.020
 37A  plan-2  H20  0.020
 37A  plan-2  H10  0.020
 37A  plan-2  H4   0.020
 37A  plan-3  O6   0.020
 37A  plan-3  C9   0.020
 37A  plan-3  C6   0.020
 37A  plan-3  N3   0.020
 37A  plan-3  C12  0.020
 37A  plan-3  HN3  0.020
 37A  plan-4  C7   0.020
 37A  plan-4  N1   0.020
 37A  plan-4  C21  0.020
 37A  plan-4  O1   0.020
 37A  plan-4  N2   0.020
 37A  plan-4  O4   0.020
 37A  plan-4  C3   0.020
 37A  plan-4  HN2  0.020

