# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 08:16:02 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-[4-(aminomethyl)phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(CC(O)=O)cc1
#
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
 BVK  BVK  '2-[4-(aminomethyl)phenyl]ethanoic acid'  ligand  23  12  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BVK
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
 BVK  N1   N  NH2   0  -0.792   4.3477   0.6522   0.1863
 BVK  C2   C  CR16  0  -0.283   0.1246   0.9865   0.5586
 BVK  C3   C  CR16  0  -0.275   1.4640   0.9716   0.2005
 BVK  C4   C  CR6   0   0.079   2.0823  -0.2108  -0.2008
 BVK  C5   C  CR16  0  -0.297   1.3216  -1.3753  -0.2200
 BVK  C6   C  CR16  0  -0.284  -0.0200  -1.3596   0.1378
 BVK  C    C  C     0   0.556  -2.9904   0.1994  -0.2401
 BVK  O    O  O     0  -0.435  -2.6216   0.4909  -1.3486
 BVK  C1   C  CR6   0   0.132  -0.6370  -0.1781   0.5308
 BVK  C7   C  CH2   0  -0.339   3.5291  -0.2320  -0.6250
 BVK  H1   H  HNH2  0   0.343   4.4403   0.2676   1.1181
 BVK  H2   H  HNH2  0   0.353   5.2835   0.6871  -0.1962
 BVK  H4   H  HCR6  0   0.248  -0.3321   1.9187   0.8707
 BVK  H5   H  HCR6  0   0.245   2.0424   1.8857   0.2404
 BVK  H6   H  HCR6  0   0.246   1.7823  -2.3122  -0.5119
 BVK  H7   H  HCR6  0   0.249  -0.5881  -2.2827   0.1222
 BVK  H8   H  HCH2  0   0.303  -2.2697   0.5592   1.7182
 BVK  H9   H  HCH2  0   0.302  -2.4004  -1.1310   1.3042
 BVK  H11  H  HCH2  0   0.239   3.5946   0.1126  -1.6615
 BVK  H12  H  HCH2  0   0.213   3.8734  -1.2748  -0.6370
 BVK  O1   O  OH1   0  -0.594  -4.2694   0.1600   0.1182
 BVK  H3   H  HOH1  0   0.481  -4.8319   0.3997  -0.6333
 BVK  CA   C  CH2   0  -0.689  -2.0862  -0.1592   0.9137

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
 BVK  C   CA   single    1.509  0.020  1.509
 BVK  C   O    double    1.204  0.020  1.204
 BVK  CA  C1   single    1.499  0.020  1.499
 BVK  C1  C2   aromatic  1.392  0.020  1.392
 BVK  C1  C6   aromatic  1.390  0.020  1.390
 BVK  C2  C3   aromatic  1.387  0.020  1.387
 BVK  C6  C5   aromatic  1.389  0.020  1.389
 BVK  C3  C4   aromatic  1.393  0.020  1.393
 BVK  C5  C4   aromatic  1.391  0.020  1.391
 BVK  C4  C7   single    1.508  0.020  1.508
 BVK  C7  N1   single    1.453  0.020  1.453
 BVK  N1  H1   single    0.890  0.020  1.040
 BVK  N1  H2   single    0.890  0.020  1.040
 BVK  C2  H4   single    0.930  0.020  1.080
 BVK  C3  H5   single    0.930  0.020  1.080
 BVK  C5  H6   single    0.930  0.020  1.080
 BVK  C6  H7   single    0.930  0.020  1.080
 BVK  CA  H8   single    0.970  0.020  1.090
 BVK  CA  H9   single    0.970  0.020  1.090
 BVK  C7  H11  single    0.970  0.020  1.090
 BVK  C7  H12  single    0.970  0.020  1.090
 BVK  C   O1   single    1.329  0.020  1.329
 BVK  O1  H3   single    0.850  0.020  0.980

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
 BVK  H2   N1  H1   106.05  3.000
 BVK  H2   N1  C7   109.34  3.000
 BVK  H1   N1  C7   109.54  3.000
 BVK  H4   C2  C1   119.66  3.000
 BVK  H4   C2  C3   119.38  3.000
 BVK  C1   C2  C3   120.96  3.000
 BVK  H5   C3  C4   119.35  3.000
 BVK  H5   C3  C2   119.84  3.000
 BVK  C4   C3  C2   120.81  3.000
 BVK  C7   C4  C5   120.60  3.000
 BVK  C7   C4  C3   121.25  3.000
 BVK  C5   C4  C3   118.15  3.000
 BVK  H6   C5  C6   119.32  3.000
 BVK  H6   C5  C4   119.66  3.000
 BVK  C6   C5  C4   121.02  3.000
 BVK  H7   C6  C1   119.70  3.000
 BVK  H7   C6  C5   119.54  3.000
 BVK  C1   C6  C5   120.76  3.000
 BVK  O1   C   O    123.39  3.000
 BVK  O1   C   CA   111.31  3.000
 BVK  O    C   CA   125.30  3.000
 BVK  CA   C1  C6   120.81  3.000
 BVK  C6   C1  C2   118.31  3.000
 BVK  CA   C1  C2   120.89  3.000
 BVK  H12  C7  H11  105.66  3.000
 BVK  H12  C7  C4   108.49  3.000
 BVK  H11  C7  C4   108.63  3.000
 BVK  H12  C7  N1   114.05  3.000
 BVK  H11  C7  N1   107.68  3.000
 BVK  C4   C7  N1   112.03  3.000
 BVK  H3   O1  C    110.02  3.000
 BVK  H9   CA  H8   105.82  3.000
 BVK  H9   CA  C1   110.96  3.000
 BVK  H8   CA  C1   110.99  3.000
 BVK  H9   CA  C    108.19  3.000
 BVK  H8   CA  C    107.80  3.000
 BVK  C1   CA  C    112.77  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
 BVK  CONST_01  C5  C6  C1  C2    0.00   0.0  0
 BVK  CONST_02  C5  C4  C3  C2    0.00   0.0  0
 BVK  CONST_03  C6  C1  C2  C3    0.00   0.0  0
 BVK  CONST_04  C6  C5  C4  C3    0.00   0.0  0
 BVK  CONST_05  C1  C2  C3  C4    0.00   0.0  0
 BVK  CONST_06  C1  C6  C5  C4    0.00   0.0  0
 BVK  CONST_07  C7  C4  C3  C2  180.00   0.0  0
 BVK  CONST_08  CA  C1  C2  C3  180.00   0.0  0
 BVK  CONST_09  CA  C1  C6  C5  180.00   0.0  0
 BVK  CONST_10  C7  C4  C5  C6  180.00   0.0  0
 BVK  CONST_11  H7  C6  C1  C2  180.00   0.0  0
 BVK  CONST_12  H6  C5  C4  C3  180.00   0.0  0
 BVK  CONST_13  H4  C2  C3  C4  180.00   0.0  0
 BVK  CONST_14  H5  C3  C4  C5  180.00   0.0  0
 BVK  CONST_15  H3  O1  C   CA  180.00   0.0  0
 BVK  Var_01    C3  C4  C7  N1   38.31  30.0  2
 BVK  Var_02    C   CA  C1  C2   86.05  30.0  2
 BVK  Var_03    C1  CA  C   O    -2.51  30.0  3
 BVK  Var_04    H1  N1  C7  C4   70.53  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
 BVK  plan-1  C2  0.020
 BVK  plan-1  C3  0.020
 BVK  plan-1  C4  0.020
 BVK  plan-1  C5  0.020
 BVK  plan-1  C6  0.020
 BVK  plan-1  C1  0.020
 BVK  plan-1  C7  0.020
 BVK  plan-1  H4  0.020
 BVK  plan-1  H5  0.020
 BVK  plan-1  H6  0.020
 BVK  plan-1  H7  0.020
 BVK  plan-1  CA  0.020
 BVK  plan-2  C   0.020
 BVK  plan-2  O   0.020
 BVK  plan-2  O1  0.020
 BVK  plan-2  H3  0.020
 BVK  plan-2  CA  0.020

