# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:55:27 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-biphenyl-2-ylmethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccccc1c2ccccc2
#
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
 B2Y  B2Y  1-biphenyl-2-ylmethanamine  ligand  27  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B2Y
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
 B2Y  N1    N  NH2   0  -0.776   0.3423  -2.3947  -1.3117
 B2Y  C4    C  CR16  0  -0.293   2.7871  -0.6661   0.1595
 B2Y  C5    C  CR16  0  -0.254   3.4250   0.5673   0.1487
 B2Y  C6    C  CR16  0  -0.255   2.6675   1.7276   0.1123
 B2Y  C7    C  CR16  0  -0.285   1.2819   1.6408   0.0956
 B2Y  C8    C  CR6   0   0.039   0.6361   0.4062   0.1132
 B2Y  C10   C  CR16  0  -0.289  -1.5606   0.8278  -0.9958
 B2Y  C13   C  CR16  0  -0.245  -2.9416  -0.0296   1.2493
 B2Y  C2    C  CH2   0  -0.379   0.7690  -2.1345   0.0567
 B2Y  C3    C  CR6   0   0.077   1.3992  -0.7688   0.1427
 B2Y  C9    C  CR6   0   0.070  -0.8470   0.3795   0.1130
 B2Y  C11   C  CR16  0  -0.245  -2.9487   0.8469  -0.9850
 B2Y  C12   C  CR16  0  -0.267  -3.6442   0.4167   0.1374
 B2Y  C14   C  CR16  0  -0.299  -1.5535  -0.0451   1.2368
 B2Y  HN1   H  HNH2  0   0.338   1.1586  -2.4353  -1.9097
 B2Y  HN1A  H  HNH2  0   0.347  -0.0783  -3.3147  -1.3577
 B2Y  H5    H  HCR6  0   0.254   4.5059   0.6190   0.1641
 B2Y  H6    H  HCR6  0   0.254   3.1485   2.6975   0.1027
 B2Y  H7    H  HCR6  0   0.248   0.6879   2.5467   0.0788
 B2Y  H10   H  HCR6  0   0.246  -1.0261   1.1619  -1.8763
 B2Y  H13   H  HCR6  0   0.255  -3.4732  -0.3632   2.1312
 B2Y  H2    H  HCH2  0   0.237  -0.1094  -2.1928   0.7002
 B2Y  H2A   H  HCH2  0   0.212   1.4843  -2.8719   0.4444
 B2Y  H11   H  HCR6  0   0.254  -3.4874   1.1975  -1.8561
 B2Y  H12   H  HCR6  0   0.254  -4.7264   0.4329   0.1473
 B2Y  H14   H  HCR6  0   0.252  -1.0140  -0.3821   2.1140
 B2Y  H4    H  HCR6  0   0.249   3.3814  -1.5725   0.1774

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
 B2Y  N1   C2    single    1.457  0.020  1.457
 B2Y  C4   C5    aromatic  1.389  0.020  1.389
 B2Y  C4   C3    aromatic  1.392  0.020  1.392
 B2Y  C5   C6    aromatic  1.386  0.020  1.386
 B2Y  C6   C7    aromatic  1.388  0.020  1.388
 B2Y  C7   C8    aromatic  1.393  0.020  1.393
 B2Y  C8   C3    aromatic  1.401  0.020  1.401
 B2Y  C8   C9    single    1.483  0.020  1.483
 B2Y  C10  C9    aromatic  1.393  0.020  1.393
 B2Y  C10  C11   aromatic  1.388  0.020  1.388
 B2Y  C13  C12   aromatic  1.389  0.020  1.389
 B2Y  C13  C14   aromatic  1.388  0.020  1.388
 B2Y  C2   C3    single    1.506  0.020  1.506
 B2Y  C9   C14   aromatic  1.394  0.020  1.394
 B2Y  C11  C12   aromatic  1.389  0.020  1.389
 B2Y  N1   HN1   single    0.890  0.020  1.040
 B2Y  N1   HN1A  single    0.890  0.020  1.040
 B2Y  C4   H4    single    0.930  0.020  1.080
 B2Y  C5   H5    single    0.930  0.020  1.080
 B2Y  C6   H6    single    0.930  0.020  1.080
 B2Y  C7   H7    single    0.930  0.020  1.080
 B2Y  C10  H10   single    0.930  0.020  1.080
 B2Y  C13  H13   single    0.930  0.020  1.080
 B2Y  C2   H2    single    0.970  0.020  1.090
 B2Y  C2   H2A   single    0.970  0.020  1.090
 B2Y  C11  H11   single    0.930  0.020  1.080
 B2Y  C12  H12   single    0.930  0.020  1.080
 B2Y  C14  H14   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
 B2Y  HN1A  N1   HN1  105.75  3.000
 B2Y  HN1A  N1   C2   109.06  3.000
 B2Y  HN1   N1   C2   109.01  3.000
 B2Y  H4    C4   C3   119.02  3.000
 B2Y  H4    C4   C5   119.41  3.000
 B2Y  C3    C4   C5   121.57  3.000
 B2Y  H5    C5   C6   120.41  3.000
 B2Y  H5    C5   C4   120.07  3.000
 B2Y  C6    C5   C4   119.52  3.000
 B2Y  H6    C6   C7   119.95  3.000
 B2Y  H6    C6   C5   120.49  3.000
 B2Y  C7    C6   C5   119.56  3.000
 B2Y  H7    C7   C8   119.13  3.000
 B2Y  H7    C7   C6   119.68  3.000
 B2Y  C8    C7   C6   121.19  3.000
 B2Y  C9    C8   C3   121.96  3.000
 B2Y  C9    C8   C7   118.65  3.000
 B2Y  C3    C8   C7   119.39  3.000
 B2Y  H10   C10  C11  119.71  3.000
 B2Y  H10   C10  C9   119.59  3.000
 B2Y  C11   C10  C9   120.70  3.000
 B2Y  H13   C13  C14  119.67  3.000
 B2Y  H13   C13  C12  120.18  3.000
 B2Y  C14   C13  C12  120.15  3.000
 B2Y  H2A   C2   H2   106.29  3.000
 B2Y  H2A   C2   C3   108.42  3.000
 B2Y  H2    C2   C3   110.60  3.000
 B2Y  H2A   C2   N1   113.73  3.000
 B2Y  H2    C2   N1   107.99  3.000
 B2Y  C3    C2   N1   109.76  3.000
 B2Y  C2    C3   C8   122.08  3.000
 B2Y  C2    C3   C4   119.00  3.000
 B2Y  C8    C3   C4   118.77  3.000
 B2Y  C14   C9   C10  118.71  3.000
 B2Y  C14   C9   C8   120.81  3.000
 B2Y  C10   C9   C8   120.44  3.000
 B2Y  H11   C11  C12  120.10  3.000
 B2Y  H11   C11  C10  119.72  3.000
 B2Y  C12   C11  C10  120.18  3.000
 B2Y  H12   C12  C11  120.23  3.000
 B2Y  H12   C12  C13  120.22  3.000
 B2Y  C11   C12  C13  119.55  3.000
 B2Y  H14   C14  C9   119.68  3.000
 B2Y  H14   C14  C13  119.60  3.000
 B2Y  C9    C14  C13  120.71  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
 B2Y  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 B2Y  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 B2Y  CONST_03  C9   C8   C3   C4    180.00   0.0  0
 B2Y  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 B2Y  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 B2Y  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 B2Y  CONST_07  C3   C8   C7   C6      0.00   0.0  0
 B2Y  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 B2Y  CONST_11  C11  C10  C9   C8    180.00   0.0  0
 B2Y  CONST_12  C13  C14  C9   C8    180.00   0.0  0
 B2Y  CONST_14  C13  C14  C9   C10     0.00   0.0  0
 B2Y  CONST_15  C13  C12  C11  C10     0.00   0.0  0
 B2Y  CONST_17  C12  C11  C10  C9      0.00   0.0  0
 B2Y  CONST_18  C12  C13  C14  C9      0.00   0.0  0
 B2Y  CONST_19  C14  C9   C10  C11     0.00   0.0  0
 B2Y  CONST_20  C14  C13  C12  C11     0.00   0.0  0
 B2Y  CONST_21  C2   C3   C4   C5    180.00   0.0  0
 B2Y  CONST_22  C2   C3   C8   C7    180.00   0.0  0
 B2Y  CONST_23  C9   C8   C3   C2      0.00   0.0  0
 B2Y  CONST_24  H6   C6   C5   C4    180.00   0.0  0
 B2Y  CONST_25  H7   C7   C6   C5    180.00   0.0  0
 B2Y  CONST_26  H4   C4   C5   C6    180.00   0.0  0
 B2Y  CONST_27  H5   C5   C6   C7    180.00   0.0  0
 B2Y  CONST_28  H10  C10  C9   C8      0.00   0.0  0
 B2Y  CONST_29  H14  C14  C9   C8      0.00   0.0  0
 B2Y  CONST_30  H12  C12  C11  C10   180.00   0.0  0
 B2Y  CONST_31  H11  C11  C12  C13   180.00   0.0  0
 B2Y  CONST_32  H13  C13  C14  C9    180.00   0.0  0
 B2Y  Var_01    C4   C3   C2   N1   -100.69  30.0  2
 B2Y  Var_02    HN1  N1   C2   C3     64.92  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
 B2Y  plan-1  C4   0.020
 B2Y  plan-1  C5   0.020
 B2Y  plan-1  C6   0.020
 B2Y  plan-1  C7   0.020
 B2Y  plan-1  C8   0.020
 B2Y  plan-1  C2   0.020
 B2Y  plan-1  C3   0.020
 B2Y  plan-1  C9   0.020
 B2Y  plan-1  H5   0.020
 B2Y  plan-1  H6   0.020
 B2Y  plan-1  H7   0.020
 B2Y  plan-1  H4   0.020
 B2Y  plan-2  C8   0.020
 B2Y  plan-2  C10  0.020
 B2Y  plan-2  C13  0.020
 B2Y  plan-2  C9   0.020
 B2Y  plan-2  C11  0.020
 B2Y  plan-2  C12  0.020
 B2Y  plan-2  C14  0.020
 B2Y  plan-2  H10  0.020
 B2Y  plan-2  H13  0.020
 B2Y  plan-2  H11  0.020
 B2Y  plan-2  H12  0.020
 B2Y  plan-2  H14  0.020

