# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 03:50:24 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 6-[2-(3'-methoxybiphenyl-3-yl)ethyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(CCc3cccc(N)n3)c2
#
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
 7IP  7IP  6-[2-(3'-methoxybiphenyl-3-yl)ethyl]pyridin-2-amine  ligand  43  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7IP
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
 7IP  C1    C  CH3   0  -0.441   5.5916  -5.8696   1.1816
 7IP  O2    O  O2    0  -0.472   6.1851  -5.1652   0.1102
 7IP  C3    C  CR6   0   0.401   5.6614  -3.9757  -0.2427
 7IP  C4    C  CR16  0  -0.351   6.2810  -3.3236  -1.3113
 7IP  C5    C  CR16  0  -0.226   5.7925  -2.1054  -1.7458
 7IP  C6    C  CR16  0  -0.340   4.6911  -1.5193  -1.1335
 7IP  C7    C  CR6   0   0.099   4.0713  -2.1603  -0.0652
 7IP  C8    C  CR16  0  -0.448   4.5612  -3.3921   0.3784
 7IP  C9    C  CR6   0   0.100   2.8965  -1.5584   0.5993
 7IP  C10   C  CR16  0  -0.327   1.8819  -0.9653  -0.1525
 7IP  C11   C  CR16  0  -0.226   0.7742  -0.4201   0.4783
 7IP  C12   C  CR16  0  -0.331   0.6687  -0.4560   1.8617
 7IP  C13   C  CR6   0   0.162   1.6742  -1.0315   2.6340
 7IP  C14   C  CH2   0  -0.517   1.5533  -1.0802   4.1306
 7IP  C15   C  CH2   0  -0.496   0.9112  -2.3805   4.6425
 7IP  C16   C  CR6   0   0.256   1.7538  -3.5945   4.3740
 7IP  C17   C  CR16  0  -0.370   2.8446  -3.8791   5.1853
 7IP  C18   C  CR16  0  -0.148   3.6004  -5.0095   4.8967
 7IP  C19   C  CR16  0  -0.394   3.2623  -5.8025   3.8213
 7IP  C20   C  CR6   0   0.436   2.1549  -5.4259   3.0452
 7IP  N21   N  NH2   0  -0.836   1.8099  -6.1321   1.9270
 7IP  N22   N  N     0  -0.465   1.4200  -4.3532   3.3319
 7IP  C23   C  CR16  0  -0.350   2.7783  -1.5780   1.9882
 7IP  H11A  H  HCH3  0   0.223   4.5438  -6.1096   0.9806
 7IP  H12A  H  HCH3  0   0.225   5.6494  -5.3099   2.1187
 7IP  H13   H  HCH3  0   0.262   6.1497  -6.7961   1.2926
 7IP  H4    H  HCR6  0   0.262   7.1367  -3.7804  -1.7931
 7IP  H5    H  HCR6  0   0.258   6.2803  -1.6005  -2.5696
 7IP  H6    H  HCR6  0   0.250   4.3327  -0.5563  -1.4737
 7IP  H8    H  HCR6  0   0.279   4.0476  -3.8919   1.1905
 7IP  H10   H  HCR6  0   0.250   1.9488  -0.9476  -1.2333
 7IP  H11   H  HCR6  0   0.253  -0.0134   0.0315  -0.1113
 7IP  H12   H  HCR6  0   0.247  -0.1999  -0.0269   2.3474
 7IP  H141  H  HCH2  0   0.249   2.5373  -0.9580   4.5903
 7IP  H142  H  HCH2  0   0.252   0.9447  -0.2417   4.4756
 7IP  H151  H  HCH2  0   0.246  -0.0696  -2.5093   4.1814
 7IP  H152  H  HCH2  0   0.250   0.7534  -2.2796   5.7187
 7IP  H17   H  HCR6  0   0.249   3.0877  -3.2432   6.0265
 7IP  H18   H  HCR6  0   0.262   4.4481  -5.2749   5.5159
 7IP  H19   H  HCR6  0   0.264   3.8261  -6.6948   3.5816
 7IP  H211  H  HNH2  0   0.379   0.8793  -5.9732   1.5761
 7IP  H212  H  HNH2  0   0.387   2.1049  -7.0929   1.8770
 7IP  H23   H  HCR6  0   0.240   3.5752  -2.0108   2.5832

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
 7IP  C1   O2    single    1.413  0.020  1.413
 7IP  C1   H11A  single    0.970  0.020  1.090
 7IP  C1   H12A  single    0.970  0.020  1.090
 7IP  C1   H13   single    0.970  0.020  1.090
 7IP  O2   C3    single    1.347  0.020  1.347
 7IP  C3   C4    aromatic  1.397  0.020  1.397
 7IP  C3   C8    aromatic  1.392  0.020  1.392
 7IP  C4   C5    aromatic  1.383  0.020  1.383
 7IP  C4   H4    single    0.930  0.020  1.080
 7IP  C5   C6    aromatic  1.390  0.020  1.390
 7IP  C5   H5    single    0.930  0.020  1.080
 7IP  C6   C7    aromatic  1.392  0.020  1.392
 7IP  C6   H6    single    0.930  0.020  1.080
 7IP  C7   C8    aromatic  1.398  0.020  1.398
 7IP  C7   C9    single    1.478  0.020  1.478
 7IP  C8   H8    single    0.930  0.020  1.080
 7IP  C9   C23   aromatic  1.394  0.020  1.394
 7IP  C9   C10   aromatic  1.395  0.020  1.395
 7IP  C10  C11   aromatic  1.386  0.020  1.386
 7IP  C10  H10   single    0.930  0.020  1.080
 7IP  C11  C12   aromatic  1.388  0.020  1.388
 7IP  C11  H11   single    0.930  0.020  1.080
 7IP  C12  C13   aromatic  1.392  0.020  1.392
 7IP  C12  H12   single    0.930  0.020  1.080
 7IP  C13  C23   aromatic  1.391  0.020  1.391
 7IP  C13  C14   single    1.502  0.020  1.502
 7IP  C14  C15   single    1.538  0.020  1.538
 7IP  C14  H141  single    0.970  0.020  1.090
 7IP  C14  H142  single    0.970  0.020  1.090
 7IP  C15  C16   single    1.502  0.020  1.502
 7IP  C15  H151  single    0.970  0.020  1.090
 7IP  C15  H152  single    0.970  0.020  1.090
 7IP  C16  N22   aromatic  1.331  0.020  1.331
 7IP  C16  C17   aromatic  1.389  0.020  1.389
 7IP  C17  C18   aromatic  1.390  0.020  1.390
 7IP  C17  H17   single    0.930  0.020  1.080
 7IP  C18  C19   aromatic  1.378  0.020  1.378
 7IP  C18  H18   single    0.930  0.020  1.080
 7IP  C19  C20   aromatic  1.404  0.020  1.404
 7IP  C19  H19   single    0.930  0.020  1.080
 7IP  C20  N21   single    1.367  0.020  1.367
 7IP  C20  N22   aromatic  1.332  0.020  1.332
 7IP  N21  H211  single    0.890  0.020  1.040
 7IP  N21  H212  single    0.890  0.020  1.040
 7IP  C23  H23   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
 7IP  H13   C1   H12A  108.76  3.000
 7IP  H13   C1   H11A  108.88  3.000
 7IP  H12A  C1   H11A  108.70  3.000
 7IP  H13   C1   O2    106.65  3.000
 7IP  H12A  C1   O2    111.88  3.000
 7IP  H11A  C1   O2    111.87  3.000
 7IP  C3    O2   C1    118.40  3.000
 7IP  C8    C3   C4    119.76  3.000
 7IP  C8    C3   O2    124.12  3.000
 7IP  C4    C3   O2    116.12  3.000
 7IP  H4    C4   C5    120.73  3.000
 7IP  H4    C4   C3    119.60  3.000
 7IP  C5    C4   C3    119.67  3.000
 7IP  H5    C5   C6    119.72  3.000
 7IP  H5    C5   C4    119.40  3.000
 7IP  C6    C5   C4    120.88  3.000
 7IP  H6    C6   C7    120.24  3.000
 7IP  H6    C6   C5    119.95  3.000
 7IP  C7    C6   C5    119.80  3.000
 7IP  C9    C7   C8    119.66  3.000
 7IP  C9    C7   C6    120.78  3.000
 7IP  C8    C7   C6    119.57  3.000
 7IP  H8    C8   C7    118.58  3.000
 7IP  H8    C8   C3    121.06  3.000
 7IP  C7    C8   C3    120.33  3.000
 7IP  C23   C9   C10   118.76  3.000
 7IP  C10   C9   C7    120.60  3.000
 7IP  C23   C9   C7    120.64  3.000
 7IP  H10   C10  C11   119.80  3.000
 7IP  H10   C10  C9    119.98  3.000
 7IP  C11   C10  C9    120.20  3.000
 7IP  H11   C11  C12   119.90  3.000
 7IP  H11   C11  C10   119.84  3.000
 7IP  C12   C11  C10   120.27  3.000
 7IP  H12   C12  C13   119.59  3.000
 7IP  H12   C12  C11   119.82  3.000
 7IP  C13   C12  C11   120.58  3.000
 7IP  C23   C13  C14   120.91  3.000
 7IP  C14   C13  C12   120.52  3.000
 7IP  C23   C13  C12   118.56  3.000
 7IP  H142  C14  H141  106.44  3.000
 7IP  H142  C14  C15   108.14  3.000
 7IP  H141  C14  C15   109.30  3.000
 7IP  H142  C14  C13   109.56  3.000
 7IP  H141  C14  C13   110.06  3.000
 7IP  C15   C14  C13   113.12  3.000
 7IP  H152  C15  H151  107.30  3.000
 7IP  H152  C15  C16   109.38  3.000
 7IP  H151  C15  C16   109.46  3.000
 7IP  H152  C15  C14   108.07  3.000
 7IP  H151  C15  C14   109.54  3.000
 7IP  C16   C15  C14   112.94  3.000
 7IP  N22   C16  C17   122.51  3.000
 7IP  C17   C16  C15   120.11  3.000
 7IP  N22   C16  C15   117.37  3.000
 7IP  H17   C17  C18   121.14  3.000
 7IP  H17   C17  C16   120.67  3.000
 7IP  C18   C17  C16   118.18  3.000
 7IP  H18   C18  C19   119.82  3.000
 7IP  H18   C18  C17   120.41  3.000
 7IP  C19   C18  C17   119.77  3.000
 7IP  H19   C19  C20   120.64  3.000
 7IP  H19   C19  C18   121.29  3.000
 7IP  C20   C19  C18   118.07  3.000
 7IP  N22   C20  N21   116.95  3.000
 7IP  N22   C20  C19   122.17  3.000
 7IP  N21   C20  C19   120.85  3.000
 7IP  H212  N21  H211  113.84  3.000
 7IP  H212  N21  C20   117.39  3.000
 7IP  H211  N21  C20   115.89  3.000
 7IP  C20   N22  C16   119.29  3.000
 7IP  H23   C23  C13   119.03  3.000
 7IP  H23   C23  C9    119.33  3.000
 7IP  C13   C23  C9    121.63  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
 7IP  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 7IP  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 7IP  CONST_03  C9    C7   C8   C3    180.00   0.0  0
 7IP  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 7IP  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 7IP  CONST_06  C8    C3   C4   C5      0.00   0.0  0
 7IP  CONST_07  C8    C7   C6   C5      0.00   0.0  0
 7IP  CONST_08  C9    C7   C6   C5    180.00   0.0  0
 7IP  CONST_11  C13   C23  C9   C7    180.00   0.0  0
 7IP  CONST_12  C11   C10  C9   C7    180.00   0.0  0
 7IP  CONST_15  C12   C13  C23  C9      0.00   0.0  0
 7IP  CONST_16  C12   C11  C10  C9      0.00   0.0  0
 7IP  CONST_17  C13   C23  C9   C10     0.00   0.0  0
 7IP  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 7IP  CONST_19  C23   C9   C10  C11     0.00   0.0  0
 7IP  CONST_20  C23   C13  C12  C11     0.00   0.0  0
 7IP  CONST_21  C19   C20  N22  C16     0.00   0.0  0
 7IP  CONST_22  C19   C18  C17  C16     0.00   0.0  0
 7IP  CONST_23  C20   N22  C16  C17     0.00   0.0  0
 7IP  CONST_24  C20   C19  C18  C17     0.00   0.0  0
 7IP  CONST_25  N22   C16  C17  C18     0.00   0.0  0
 7IP  CONST_26  N22   C20  C19  C18     0.00   0.0  0
 7IP  CONST_27  C5    C4   C3   O2    180.00   0.0  0
 7IP  CONST_28  C7    C8   C3   O2    180.00   0.0  0
 7IP  CONST_29  C14   C13  C23  C9    180.00   0.0  0
 7IP  CONST_30  C14   C13  C12  C11   180.00   0.0  0
 7IP  CONST_31  C20   N22  C16  C15   180.00   0.0  0
 7IP  CONST_32  C18   C17  C16  C15   180.00   0.0  0
 7IP  CONST_33  N21   C20  N22  C16   180.00   0.0  0
 7IP  CONST_34  N21   C20  C19  C18   180.00   0.0  0
 7IP  CONST_35  H5    C5   C4   C3    180.00   0.0  0
 7IP  CONST_36  H8    C8   C3   C4    180.00   0.0  0
 7IP  CONST_37  H6    C6   C5   C4    180.00   0.0  0
 7IP  CONST_38  H4    C4   C5   C6    180.00   0.0  0
 7IP  CONST_39  H23   C23  C9   C7      0.00   0.0  0
 7IP  CONST_40  H10   C10  C9   C7      0.00   0.0  0
 7IP  CONST_41  H11   C11  C10  C9    180.00   0.0  0
 7IP  CONST_42  H12   C12  C11  C10   180.00   0.0  0
 7IP  CONST_43  H18   C18  C17  C16   180.00   0.0  0
 7IP  CONST_44  H19   C19  C18  C17   180.00   0.0  0
 7IP  CONST_45  H17   C17  C18  C19   180.00   0.0  0
 7IP  Var_01    C4    C3   O2   C1   -179.71  30.0  2
 7IP  Var_02    C15   C14  C13  C12    92.40  30.0  2
 7IP  Var_03    C16   C15  C14  C13    65.59  30.0  3
 7IP  Var_04    N22   C16  C15  C14  -100.34  30.0  2
 7IP  Var_05    H11A  C1   O2   C3     60.33  30.0  3

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
 7IP  plan-1  O2    0.020
 7IP  plan-1  C3    0.020
 7IP  plan-1  C4    0.020
 7IP  plan-1  C5    0.020
 7IP  plan-1  C6    0.020
 7IP  plan-1  C7    0.020
 7IP  plan-1  C8    0.020
 7IP  plan-1  C9    0.020
 7IP  plan-1  H4    0.020
 7IP  plan-1  H5    0.020
 7IP  plan-1  H6    0.020
 7IP  plan-1  H8    0.020
 7IP  plan-2  C7    0.020
 7IP  plan-2  C9    0.020
 7IP  plan-2  C10   0.020
 7IP  plan-2  C11   0.020
 7IP  plan-2  C12   0.020
 7IP  plan-2  C13   0.020
 7IP  plan-2  C14   0.020
 7IP  plan-2  C23   0.020
 7IP  plan-2  H10   0.020
 7IP  plan-2  H11   0.020
 7IP  plan-2  H12   0.020
 7IP  plan-2  H23   0.020
 7IP  plan-3  C15   0.020
 7IP  plan-3  C16   0.020
 7IP  plan-3  C17   0.020
 7IP  plan-3  C18   0.020
 7IP  plan-3  C19   0.020
 7IP  plan-3  C20   0.020
 7IP  plan-3  N21   0.020
 7IP  plan-3  N22   0.020
 7IP  plan-3  H17   0.020
 7IP  plan-3  H18   0.020
 7IP  plan-3  H19   0.020
 7IP  plan-4  C20   0.020
 7IP  plan-4  N21   0.020
 7IP  plan-4  H211  0.020
 7IP  plan-4  H212  0.020

