# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:13:31 2021
#   Inital geometry file: a 44 line input string
#   Ligand name: 1-(5-bromopyridin-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cncc(Br)c1
#
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
 WPV  WPV  1-(5-bromopyridin-3-yl)methanamine  ligand  16  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WPV
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
 WPV  N1  N   N     0  -0.391  -7.3405  15.3699  -0.0778
 WPV  C4  C   CR16  0  -0.052  -6.0554  15.0503  -0.0366
 WPV  C5  C   CR16  0  -0.092  -8.0536  15.2835   1.0363
 WPV  C3  C   CR6   0  -0.172  -5.4489  14.6284   1.1382
 WPV  C2  C   CR16  0  -0.150  -6.1882  14.5391   2.3053
 WPV  C1  C   CR6   0  -0.001  -7.5338  14.8817   2.2627
 WPV  C   C   CH2   0  -0.335  -8.4026  14.8431   3.4921
 WPV  N   N   NH2   0  -0.795  -7.9302  13.8717   4.4589
 WPV  H1  H   HCR6  0   0.280  -5.4964  15.1260  -0.9626
 WPV  H2  H   HCR6  0   0.265  -9.1043  15.5444   0.9552
 WPV  H3  H   HCR6  0   0.285  -5.7482  14.2050   3.2357
 WPV  H4  H   HCH2  0   0.255  -8.3714  15.8303   3.9619
 WPV  H5  H   HCH2  0   0.225  -9.4436  14.6956   3.1758
 WPV  H6  H   HNH2  0   0.361  -8.4410  13.9862   5.3240
 WPV  H7  H   HNH2  0   0.349  -8.1361  12.9361   4.1318
 WPV  BR  BR  BR    0  -0.031  -3.6202  14.1763   1.1304

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
 WPV  C4  N1  aromatic  1.325  0.020  1.325
 WPV  C4  C3  aromatic  1.388  0.020  1.388
 WPV  N1  C5  aromatic  1.326  0.020  1.326
 WPV  BR  C3  single    1.884  0.020  1.884
 WPV  C3  C2  aromatic  1.384  0.020  1.384
 WPV  C5  C1  aromatic  1.391  0.020  1.391
 WPV  C2  C1  aromatic  1.389  0.020  1.389
 WPV  C1  C   single    1.506  0.020  1.506
 WPV  C   N   single    1.450  0.020  1.450
 WPV  C4  H1  single    0.930  0.020  1.080
 WPV  C5  H2  single    0.930  0.020  1.080
 WPV  C2  H3  single    0.930  0.020  1.080
 WPV  C   H4  single    0.970  0.020  1.090
 WPV  C   H5  single    0.970  0.020  1.090
 WPV  N   H6  single    0.890  0.020  1.040
 WPV  N   H7  single    0.890  0.020  1.040

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
 WPV  C5  N1  C4  118.68  3.000
 WPV  H1  C4  C3  121.26  3.000
 WPV  H1  C4  N1  117.17  3.000
 WPV  C3  C4  N1  121.57  3.000
 WPV  H2  C5  C1  119.79  3.000
 WPV  H2  C5  N1  116.25  3.000
 WPV  C1  C5  N1  123.97  3.000
 WPV  C2  C3  BR  120.42  3.000
 WPV  C2  C3  C4  119.99  3.000
 WPV  BR  C3  C4  119.58  3.000
 WPV  H3  C2  C1  119.76  3.000
 WPV  H3  C2  C3  121.84  3.000
 WPV  C1  C2  C3  118.39  3.000
 WPV  C   C1  C2  121.84  3.000
 WPV  C   C1  C5  120.76  3.000
 WPV  C2  C1  C5  117.39  3.000
 WPV  H5  C   H4  105.79  3.000
 WPV  H5  C   N   114.27  3.000
 WPV  H4  C   N   108.00  3.000
 WPV  H5  C   C1  108.38  3.000
 WPV  H4  C   C1  108.12  3.000
 WPV  N   C   C1  111.94  3.000
 WPV  H7  N   H6  106.16  3.000
 WPV  H7  N   C   109.73  3.000
 WPV  H6  N   C   109.28  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
 WPV  CONST_01  C2  C3  C4  N1    0.00   0.0  0
 WPV  CONST_02  C2  C1  C5  N1    0.00   0.0  0
 WPV  CONST_03  C1  C5  N1  C4    0.00   0.0  0
 WPV  CONST_04  C1  C2  C3  C4    0.00   0.0  0
 WPV  CONST_05  C3  C4  N1  C5    0.00   0.0  0
 WPV  CONST_06  C3  C2  C1  C5    0.00   0.0  0
 WPV  CONST_07  BR  C3  C4  N1  180.00   0.0  0
 WPV  CONST_08  C   C1  C5  N1  180.00   0.0  0
 WPV  CONST_09  C1  C2  C3  BR  180.00   0.0  0
 WPV  CONST_10  C   C1  C2  C3  180.00   0.0  0
 WPV  CONST_11  H2  C5  N1  C4  180.00   0.0  0
 WPV  CONST_12  H3  C2  C3  C4  180.00   0.0  0
 WPV  CONST_13  H1  C4  N1  C5  180.00   0.0  0
 WPV  Var_01    N   C   C1  C5  153.29  30.0  2
 WPV  Var_02    H6  N   C   C1  170.54  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
 WPV  plan-1  N1  0.020
 WPV  plan-1  C4  0.020
 WPV  plan-1  C5  0.020
 WPV  plan-1  C3  0.020
 WPV  plan-1  C2  0.020
 WPV  plan-1  C1  0.020
 WPV  plan-1  C   0.020
 WPV  plan-1  H1  0.020
 WPV  plan-1  H2  0.020
 WPV  plan-1  H3  0.020
 WPV  plan-1  BR  0.020

