# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:12:23 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: N~3~-benzylpyridine-2,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1NCc2ccccc2
#
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
 8AP  8AP  N~3~-benzylpyridine-2,3-diamine  ligand  28  15  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8AP
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
 8AP  N1    N  NH2   0  -0.832  -0.5875  -4.2770   5.5265
 8AP  C2    C  CR6   0   0.361  -0.0736  -3.4044   6.4582
 8AP  N3    N  N     0  -0.441  -0.3085  -3.6390   7.7342
 8AP  C4    C  CR16  0  -0.102   0.1595  -2.7848   8.6498
 8AP  C5    C  CR16  0  -0.341   0.8917  -1.6674   8.3236
 8AP  C6    C  CR16  0  -0.248   1.1286  -1.4005   6.9721
 8AP  C7    C  CR6   0   0.222   0.6424  -2.2618   6.0065
 8AP  N8    N  NH1   0  -0.686   0.8332  -2.1087   4.6402
 8AP  C9    C  CH2   0  -0.343   1.5398  -0.9448   4.1523
 8AP  C10   C  CR6   0   0.089   1.6798  -1.0030   2.6552
 8AP  C11   C  CR16  0  -0.285   2.2609  -2.1117   2.0412
 8AP  C12   C  CR16  0  -0.241   2.4007  -2.1616   0.6622
 8AP  C13   C  CR16  0  -0.268   1.9607  -1.1030  -0.1247
 8AP  C14   C  CR16  0  -0.240   1.3800   0.0035   0.4779
 8AP  C15   C  CR16  0  -0.313   1.2390   0.0491   1.8602
 8AP  HN11  H  HNH2  0   0.379  -0.9137  -5.1468   5.9190
 8AP  HN12  H  HNH2  0   0.379  -0.0150  -4.4239   4.7082
 8AP  H4    H  HCR6  0   0.247  -0.0592  -3.0252   9.6840
 8AP  H5    H  HCR6  0   0.255   1.2633  -1.0032   9.0916
 8AP  H6    H  HCR6  0   0.277   1.6784  -0.5118   6.6913
 8AP  HN8   H  HNH1  0   0.374  -0.0027  -2.3019   4.1035
 8AP  H91   H  HCH2  0   0.253   2.5344  -0.9301   4.6081
 8AP  H92   H  HCH2  0   0.236   1.0535  -0.0026   4.4400
 8AP  H11   H  HCR6  0   0.250   2.6077  -2.9414   2.6454
 8AP  H12   H  HCR6  0   0.255   2.8557  -3.0279   0.1997
 8AP  H13   H  HCR6  0   0.256   2.0705  -1.1426  -1.2007
 8AP  H14   H  HCR6  0   0.256   1.0308   0.8318  -0.1253
 8AP  H15   H  HCR6  0   0.253   0.7805   0.9141   2.3245

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
 8AP  N1   C2    single    1.376  0.020  1.376
 8AP  N1   HN11  single    0.890  0.020  1.040
 8AP  N1   HN12  single    0.890  0.020  1.040
 8AP  C2   N3    aromatic  1.319  0.020  1.319
 8AP  C2   C7    aromatic  1.422  0.020  1.422
 8AP  N3   C4    aromatic  1.337  0.020  1.337
 8AP  C4   C5    aromatic  1.375  0.020  1.375
 8AP  C4   H4    single    0.930  0.020  1.080
 8AP  C5   C6    aromatic  1.398  0.020  1.398
 8AP  C5   H5    single    0.930  0.020  1.080
 8AP  C6   C7    aromatic  1.382  0.020  1.382
 8AP  C6   H6    single    0.930  0.020  1.080
 8AP  C7   N8    single    1.388  0.020  1.388
 8AP  N8   C9    single    1.446  0.020  1.446
 8AP  N8   HN8   single    0.890  0.020  1.040
 8AP  C9   C10   single    1.505  0.020  1.505
 8AP  C9   H91   single    0.970  0.020  1.090
 8AP  C9   H92   single    0.970  0.020  1.090
 8AP  C10  C11   aromatic  1.394  0.020  1.394
 8AP  C10  C15   aromatic  1.390  0.020  1.390
 8AP  C11  C12   aromatic  1.387  0.020  1.387
 8AP  C11  H11   single    0.930  0.020  1.080
 8AP  C12  C13   aromatic  1.391  0.020  1.391
 8AP  C12  H12   single    0.930  0.020  1.080
 8AP  C13  C14   aromatic  1.387  0.020  1.387
 8AP  C13  H13   single    0.930  0.020  1.080
 8AP  C14  C15   aromatic  1.390  0.020  1.390
 8AP  C14  H14   single    0.930  0.020  1.080
 8AP  C15  H15   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
 8AP  HN12  N1   HN11  111.92  3.000
 8AP  HN12  N1   C2    115.42  3.000
 8AP  HN11  N1   C2    113.85  3.000
 8AP  C7    C2   N3    122.69  3.000
 8AP  C7    C2   N1    118.85  3.000
 8AP  N3    C2   N1    118.41  3.000
 8AP  C4    N3   C2    119.12  3.000
 8AP  H4    C4   C5    120.92  3.000
 8AP  H4    C4   N3    116.17  3.000
 8AP  C5    C4   N3    122.90  3.000
 8AP  H5    C5   C6    120.75  3.000
 8AP  H5    C5   C4    120.91  3.000
 8AP  C6    C5   C4    118.34  3.000
 8AP  H6    C6   C7    120.60  3.000
 8AP  H6    C6   C5    119.59  3.000
 8AP  C7    C6   C5    119.80  3.000
 8AP  N8    C7   C6    124.79  3.000
 8AP  N8    C7   C2    118.06  3.000
 8AP  C6    C7   C2    117.12  3.000
 8AP  HN8   N8   C9    112.22  3.000
 8AP  HN8   N8   C7    112.80  3.000
 8AP  C9    N8   C7    119.21  3.000
 8AP  H92   C9   H91   106.36  3.000
 8AP  H92   C9   C10   109.57  3.000
 8AP  H91   C9   C10   109.30  3.000
 8AP  H92   C9   N8    112.68  3.000
 8AP  H91   C9   N8    108.32  3.000
 8AP  C10   C9   N8    110.48  3.000
 8AP  C15   C10  C11   118.82  3.000
 8AP  C15   C10  C9    120.67  3.000
 8AP  C11   C10  C9    120.51  3.000
 8AP  H11   C11  C12   119.65  3.000
 8AP  H11   C11  C10   119.78  3.000
 8AP  C12   C11  C10   120.56  3.000
 8AP  H12   C12  C13   120.04  3.000
 8AP  H12   C12  C11   119.74  3.000
 8AP  C13   C12  C11   120.22  3.000
 8AP  H13   C13  C14   120.23  3.000
 8AP  H13   C13  C12   120.17  3.000
 8AP  C14   C13  C12   119.60  3.000
 8AP  H14   C14  C15   119.75  3.000
 8AP  H14   C14  C13   120.22  3.000
 8AP  C15   C14  C13   120.03  3.000
 8AP  H15   C15  C14   119.68  3.000
 8AP  H15   C15  C10   119.55  3.000
 8AP  C14   C15  C10   120.77  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
 8AP  CONST_01  C5    C4   N3   C2     0.00   0.0  0
 8AP  CONST_02  C5    C6   C7   C2     0.00   0.0  0
 8AP  CONST_03  C6    C7   C2   N3     0.00   0.0  0
 8AP  CONST_04  C6    C5   C4   N3     0.00   0.0  0
 8AP  CONST_05  C7    C2   N3   C4     0.00   0.0  0
 8AP  CONST_06  C7    C6   C5   C4     0.00   0.0  0
 8AP  CONST_07  C13   C12  C11  C10    0.00   0.0  0
 8AP  CONST_08  C13   C14  C15  C10    0.00   0.0  0
 8AP  CONST_09  C14   C15  C10  C11    0.00   0.0  0
 8AP  CONST_10  C14   C13  C12  C11    0.00   0.0  0
 8AP  CONST_11  C15   C10  C11  C12    0.00   0.0  0
 8AP  CONST_12  C15   C14  C13  C12    0.00   0.0  0
 8AP  CONST_13  C4    N3   C2   N1   180.00   0.0  0
 8AP  CONST_14  C6    C7   C2   N1   180.00   0.0  0
 8AP  CONST_15  N8    C7   C2   N3   180.00   0.0  0
 8AP  CONST_16  N8    C7   C6   C5   180.00   0.0  0
 8AP  CONST_17  C12   C11  C10  C9   180.00   0.0  0
 8AP  CONST_18  C14   C15  C10  C9   180.00   0.0  0
 8AP  CONST_19  H4    C4   N3   C2   180.00   0.0  0
 8AP  CONST_20  H6    C6   C7   C2   180.00   0.0  0
 8AP  CONST_21  H5    C5   C4   N3   180.00   0.0  0
 8AP  CONST_22  H12   C12  C11  C10  180.00   0.0  0
 8AP  CONST_23  H14   C14  C15  C10  180.00   0.0  0
 8AP  CONST_24  H15   C15  C10  C11  180.00   0.0  0
 8AP  CONST_25  H13   C13  C12  C11  180.00   0.0  0
 8AP  CONST_26  H11   C11  C12  C13  180.00   0.0  0
 8AP  CONST_27  C9    N8   C7   C2   180.00   0.0  0
 8AP  CONST_28  C9    N8   C7   C6     0.00   0.0  0
 8AP  CONST_30  HN11  N1   C2   N3     0.00   0.0  0
 8AP  Var_01    C10   C9   N8   C7   177.86  30.0  3
 8AP  Var_02    C11   C10  C9   N8   -54.79  30.0  2

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
 8AP  plan-1  N1    0.020
 8AP  plan-1  C2    0.020
 8AP  plan-1  N3    0.020
 8AP  plan-1  C4    0.020
 8AP  plan-1  C5    0.020
 8AP  plan-1  C6    0.020
 8AP  plan-1  C7    0.020
 8AP  plan-1  N8    0.020
 8AP  plan-1  H4    0.020
 8AP  plan-1  H5    0.020
 8AP  plan-1  H6    0.020
 8AP  plan-2  C9    0.020
 8AP  plan-2  C10   0.020
 8AP  plan-2  C11   0.020
 8AP  plan-2  C12   0.020
 8AP  plan-2  C13   0.020
 8AP  plan-2  C14   0.020
 8AP  plan-2  C15   0.020
 8AP  plan-2  H11   0.020
 8AP  plan-2  H12   0.020
 8AP  plan-2  H13   0.020
 8AP  plan-2  H14   0.020
 8AP  plan-2  H15   0.020
 8AP  plan-3  N1    0.020
 8AP  plan-3  C2    0.020
 8AP  plan-3  HN11  0.020
 8AP  plan-3  HN12  0.020
 8AP  plan-4  C7    0.020
 8AP  plan-4  N8    0.020
 8AP  plan-4  C9    0.020
 8AP  plan-4  HN8   0.020

