# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:19:44 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: phenanthren-9-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc2ccccc2c3ccccc13
#
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
 9AP  9AP  'phenanthren-9-amine      '  ligand  26  15  .  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_9AP
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
 9AP  C1    C  CR16  0  -0.259  -1.0350  -0.0725  -3.3225
 9AP  C2    C  CR16  0  -0.296   0.2259  -0.0835  -2.7764
 9AP  C3    C  CR16  0  -0.353  -1.9850   0.0270  -1.1195
 9AP  C4    C  CR66  0   0.031   0.4204  -0.0251  -1.3834
 9AP  C5    C  CR16  0  -0.240  -2.1515  -0.0092  -2.4833
 9AP  C6    C  CR66  0   0.114  -0.7070   0.0117  -0.5294
 9AP  C7    C  CR6   0   0.260   1.7536  -0.0151  -0.8187
 9AP  C8    C  CR16  0  -0.440   1.9029  -0.0152   0.5357
 9AP  N1    N  NH2   0  -0.860   2.8411  -0.0690  -1.6675
 9AP  C9    C  CR66  0   0.100   0.7882  -0.0140   1.4210
 9AP  C10   C  CR16  0  -0.326   0.9855  -0.0202   2.8170
 9AP  C11   C  CR66  0   0.085  -0.5273   0.0160   0.9087
 9AP  C12   C  CR16  0  -0.262  -0.0804   0.0033   3.6819
 9AP  C13   C  CR16  0  -0.258  -1.3871   0.0343   3.1771
 9AP  C14   C  CR16  0  -0.345  -1.6004   0.0403   1.8181
 9AP  H1    H  HCR6  0   0.260  -1.1602  -0.1182  -4.3961
 9AP  H2    H  HCR6  0   0.250   1.0747  -0.1525  -3.4431
 9AP  H3    H  HCR6  0   0.255  -2.8676   0.0647  -0.4958
 9AP  H5    H  HCR6  0   0.260  -3.1485   0.0032  -2.9042
 9AP  H8    H  HCR6  0   0.250   2.8996  -0.0048   0.9633
 9AP  HN11  H  HNH2  0   0.382   3.7267   0.0897  -1.2117
 9AP  HN12  H  HNH2  0   0.383   2.7753   0.4877  -2.5056
 9AP  H10   H  HCR6  0   0.250   1.9983  -0.0429   3.2020
 9AP  H12   H  HCR6  0   0.254   0.0863  -0.0021   4.7514
 9AP  H13   H  HCR6  0   0.255  -2.2298   0.0536   3.8554
 9AP  H14   H  HCR6  0   0.249  -2.6204   0.0638   1.4597

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
 9AP  C1   C2    aromatic  1.374  0.020  1.374
 9AP  C1   C5    aromatic  1.398  0.020  1.398
 9AP  C1   H1    single    0.930  0.020  1.080
 9AP  C2   C4    aromatic  1.408  0.020  1.408
 9AP  C2   H2    single    0.930  0.020  1.080
 9AP  C3   C5    aromatic  1.374  0.020  1.374
 9AP  C3   C6    aromatic  1.408  0.020  1.408
 9AP  C3   H3    single    0.930  0.020  1.080
 9AP  C4   C6    aromatic  1.415  0.020  1.415
 9AP  C4   C7    aromatic  1.448  0.020  1.448
 9AP  C5   H5    single    0.930  0.020  1.080
 9AP  C6   C11   aromatic  1.449  0.020  1.449
 9AP  C7   C8    aromatic  1.363  0.020  1.363
 9AP  C7   N1    single    1.381  0.020  1.381
 9AP  C8   C9    aromatic  1.423  0.020  1.423
 9AP  C8   H8    single    0.930  0.020  1.080
 9AP  N1   HN11  single    0.890  0.020  1.040
 9AP  N1   HN12  single    0.890  0.020  1.040
 9AP  C9   C10   aromatic  1.410  0.020  1.410
 9AP  C9   C11   aromatic  1.412  0.020  1.412
 9AP  C10  C12   aromatic  1.373  0.020  1.373
 9AP  C10  H10   single    0.930  0.020  1.080
 9AP  C11  C14   aromatic  1.407  0.020  1.407
 9AP  C12  C13   aromatic  1.401  0.020  1.401
 9AP  C12  H12   single    0.930  0.020  1.080
 9AP  C13  C14   aromatic  1.376  0.020  1.376
 9AP  C13  H13   single    0.930  0.020  1.080
 9AP  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
 9AP  H1    C1   C5    120.34  3.000
 9AP  H1    C1   C2    120.01  3.000
 9AP  C5    C1   C2    119.64  3.000
 9AP  H2    C2   C4    120.28  3.000
 9AP  H2    C2   C1    118.41  3.000
 9AP  C4    C2   C1    121.31  3.000
 9AP  H3    C3   C6    119.97  3.000
 9AP  H3    C3   C5    118.32  3.000
 9AP  C6    C3   C5    121.71  3.000
 9AP  C7    C4   C6    119.87  3.000
 9AP  C7    C4   C2    120.89  3.000
 9AP  C6    C4   C2    119.23  3.000
 9AP  H5    C5   C3    119.81  3.000
 9AP  H5    C5   C1    120.18  3.000
 9AP  C3    C5   C1    120.00  3.000
 9AP  C11   C6   C4    120.02  3.000
 9AP  C11   C6   C3    121.90  3.000
 9AP  C4    C6   C3    118.08  3.000
 9AP  N1    C7   C8    121.65  3.000
 9AP  N1    C7   C4    119.03  3.000
 9AP  C8    C7   C4    119.25  3.000
 9AP  H8    C8   C9    118.32  3.000
 9AP  H8    C8   C7    119.51  3.000
 9AP  C9    C8   C7    122.17  3.000
 9AP  HN12  N1   HN11  110.24  3.000
 9AP  HN12  N1   C7    115.98  3.000
 9AP  HN11  N1   C7    114.06  3.000
 9AP  C11   C9   C10   119.32  3.000
 9AP  C11   C9   C8    120.26  3.000
 9AP  C10   C9   C8    120.41  3.000
 9AP  H10   C10  C12   120.14  3.000
 9AP  H10   C10  C9    118.86  3.000
 9AP  C12   C10  C9    121.00  3.000
 9AP  C14   C11  C9    118.46  3.000
 9AP  C14   C11  C6    123.16  3.000
 9AP  C9    C11  C6    118.39  3.000
 9AP  H12   C12  C13   119.99  3.000
 9AP  H12   C12  C10   120.18  3.000
 9AP  C13   C12  C10   119.83  3.000
 9AP  H13   C13  C14   119.90  3.000
 9AP  H13   C13  C12   120.06  3.000
 9AP  C14   C13  C12   120.04  3.000
 9AP  H14   C14  C13   118.28  3.000
 9AP  H14   C14  C11   120.37  3.000
 9AP  C13   C14  C11   121.35  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
 9AP  CONST_01  C6    C4   C2   C1     0.00  0.0  0
 9AP  CONST_02  C7    C4   C2   C1   180.00  0.0  0
 9AP  CONST_03  C6    C3   C5   C1     0.00  0.0  0
 9AP  CONST_04  C3    C5   C1   C2     0.00  0.0  0
 9AP  CONST_05  C3    C6   C4   C2     0.00  0.0  0
 9AP  CONST_06  C11   C6   C4   C2   180.00  0.0  0
 9AP  CONST_07  C8    C7   C4   C2   180.00  0.0  0
 9AP  CONST_08  C7    C4   C6   C3   180.00  0.0  0
 9AP  CONST_09  C9    C11  C6   C3   180.00  0.0  0
 9AP  CONST_10  C14   C11  C6   C3     0.00  0.0  0
 9AP  CONST_11  C5    C1   C2   C4     0.00  0.0  0
 9AP  CONST_12  C5    C3   C6   C4     0.00  0.0  0
 9AP  CONST_13  C9    C11  C6   C4     0.00  0.0  0
 9AP  CONST_14  C14   C11  C6   C4   180.00  0.0  0
 9AP  CONST_15  C9    C8   C7   C4     0.00  0.0  0
 9AP  CONST_16  C11   C6   C3   C5   180.00  0.0  0
 9AP  CONST_17  C8    C7   C4   C6     0.00  0.0  0
 9AP  CONST_18  C8    C9   C11  C6     0.00  0.0  0
 9AP  CONST_19  C10   C9   C11  C6   180.00  0.0  0
 9AP  CONST_20  C13   C14  C11  C6   180.00  0.0  0
 9AP  CONST_21  C11   C6   C4   C7     0.00  0.0  0
 9AP  CONST_22  C10   C9   C8   C7   180.00  0.0  0
 9AP  CONST_23  C11   C9   C8   C7     0.00  0.0  0
 9AP  CONST_24  C12   C10  C9   C8   180.00  0.0  0
 9AP  CONST_25  C14   C11  C9   C8   180.00  0.0  0
 9AP  CONST_26  C13   C12  C10  C9     0.00  0.0  0
 9AP  CONST_27  C13   C14  C11  C9     0.00  0.0  0
 9AP  CONST_28  C14   C11  C9   C10    0.00  0.0  0
 9AP  CONST_29  C14   C13  C12  C10    0.00  0.0  0
 9AP  CONST_30  C12   C10  C9   C11    0.00  0.0  0
 9AP  CONST_31  C12   C13  C14  C11    0.00  0.0  0
 9AP  CONST_32  N1    C7   C4   C2     0.00  0.0  0
 9AP  CONST_33  N1    C7   C4   C6   180.00  0.0  0
 9AP  CONST_34  C9    C8   C7   N1   180.00  0.0  0
 9AP  CONST_35  H3    C3   C5   C1   180.00  0.0  0
 9AP  CONST_36  H5    C5   C1   C2   180.00  0.0  0
 9AP  CONST_37  H1    C1   C5   C3   180.00  0.0  0
 9AP  CONST_38  H8    C8   C7   C4   180.00  0.0  0
 9AP  CONST_39  H2    C2   C1   C5   180.00  0.0  0
 9AP  CONST_40  H14   C14  C11  C6     0.00  0.0  0
 9AP  CONST_41  H10   C10  C9   C8     0.00  0.0  0
 9AP  CONST_42  H12   C12  C10  C9   180.00  0.0  0
 9AP  CONST_43  H13   C13  C12  C10  180.00  0.0  0
 9AP  CONST_44  HN11  N1   C7   C4   180.00  0.0  0

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
 9AP  plan-1  C1    0.020
 9AP  plan-1  C2    0.020
 9AP  plan-1  C3    0.020
 9AP  plan-1  C4    0.020
 9AP  plan-1  C5    0.020
 9AP  plan-1  C6    0.020
 9AP  plan-1  C7    0.020
 9AP  plan-1  C8    0.020
 9AP  plan-1  N1    0.020
 9AP  plan-1  C9    0.020
 9AP  plan-1  C10   0.020
 9AP  plan-1  C11   0.020
 9AP  plan-1  C12   0.020
 9AP  plan-1  C13   0.020
 9AP  plan-1  C14   0.020
 9AP  plan-1  H1    0.020
 9AP  plan-1  H2    0.020
 9AP  plan-1  H3    0.020
 9AP  plan-1  H5    0.020
 9AP  plan-1  H8    0.020
 9AP  plan-1  H10   0.020
 9AP  plan-1  H12   0.020
 9AP  plan-1  H13   0.020
 9AP  plan-1  H14   0.020
 9AP  plan-2  C7    0.020
 9AP  plan-2  N1    0.020
 9AP  plan-2  HN11  0.020
 9AP  plan-2  HN12  0.020

