# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:33:13 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 6-chloropyrazine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cncc(Cl)n1
#
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
 NMJ  NMJ  '6-chloropyrazine-2-carboxylic acid'  ligand  12  10  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NMJ
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
 NMJ  C01   C   CR16   0  -0.081   0.8231   1.5492   0.0140
 NMJ  C02   C   CR6    0   0.011   0.9308   0.1615   0.0400
 NMJ  N03   N   N      0  -0.336  -0.1696  -0.5881   0.0445
 NMJ  C04   C   CR6    0   0.105  -1.3192   0.0308   0.0253
 NMJ  C05   C   CR16   0  -0.052  -1.4391   1.4153   0.0039
 NMJ  N06   N   N      0  -0.348  -0.3528   2.1664  -0.0030
 NMJ  CL07  CL  CL     0  -0.104  -2.7559  -0.9381   0.0272
 NMJ  C08   C   C      0   0.395   2.2935  -0.5335   0.0638
 NMJ  O09   O   O      0  -0.581   3.2738   0.2319   0.0452
 NMJ  O10   O   OC    -1  -0.578   2.2792  -1.7710   0.0983
 NMJ  H1    H   HCR6   0   0.276   1.7076   2.1710   0.0081
 NMJ  H2    H   HCR6   0   0.293  -2.4066   1.9020  -0.0083

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
 NMJ  C05   N06  aromatic  1.321  0.020  1.321
 NMJ  C05   C04  aromatic  1.390  0.020  1.390
 NMJ  N06   C01  aromatic  1.328  0.020  1.328
 NMJ  O09   C08  deloc     1.244  0.020  1.244
 NMJ  CL07  C04  single    1.733  0.020  1.733
 NMJ  C04   N03  aromatic  1.306  0.020  1.306
 NMJ  C01   C02  aromatic  1.392  0.020  1.392
 NMJ  N03   C02  aromatic  1.331  0.020  1.331
 NMJ  C02   C08  single    1.530  0.020  1.530
 NMJ  C08   O10  deloc     1.238  0.020  1.238
 NMJ  C01   H1   single    0.930  0.020  1.080
 NMJ  C05   H2   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
 NMJ  H1    C01  N06  117.20  3.000
 NMJ  H1    C01  C02  120.66  3.000
 NMJ  N06   C01  C02  122.14  3.000
 NMJ  C08   C02  N03  118.71  3.000
 NMJ  C08   C02  C01  121.47  3.000
 NMJ  N03   C02  C01  119.82  3.000
 NMJ  C04   N03  C02  117.43  3.000
 NMJ  CL07  C04  C05  119.04  3.000
 NMJ  CL07  C04  N03  117.70  3.000
 NMJ  C05   C04  N03  123.26  3.000
 NMJ  H2    C05  N06  118.63  3.000
 NMJ  H2    C05  C04  121.66  3.000
 NMJ  N06   C05  C04  119.71  3.000
 NMJ  C05   N06  C01  117.64  3.000
 NMJ  O10   C08  O09  128.65  3.000
 NMJ  O10   C08  C02  116.38  3.000
 NMJ  O09   C08  C02  114.98  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
 NMJ  CONST_01  C04   C05  N06  C01    0.00   0.0  0
 NMJ  CONST_02  C04   N03  C02  C01    0.00   0.0  0
 NMJ  CONST_03  C05   N06  C01  C02    0.00   0.0  0
 NMJ  CONST_04  C05   C04  N03  C02    0.00   0.0  0
 NMJ  CONST_05  N06   C05  C04  N03    0.00   0.0  0
 NMJ  CONST_06  N06   C01  C02  N03    0.00   0.0  0
 NMJ  CONST_07  CL07  C04  N03  C02  180.00   0.0  0
 NMJ  CONST_08  C08   C02  N03  C04  180.00   0.0  0
 NMJ  CONST_09  CL07  C04  C05  N06  180.00   0.0  0
 NMJ  CONST_10  C08   C02  C01  N06  180.00   0.0  0
 NMJ  CONST_11  H2    C05  N06  C01  180.00   0.0  0
 NMJ  CONST_12  H1    C01  C02  N03  180.00   0.0  0
 NMJ  Var_01    O09   C08  C02  C01   -0.65  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
 NMJ  plan-1  C01   0.020
 NMJ  plan-1  C02   0.020
 NMJ  plan-1  N03   0.020
 NMJ  plan-1  C04   0.020
 NMJ  plan-1  C05   0.020
 NMJ  plan-1  N06   0.020
 NMJ  plan-1  CL07  0.020
 NMJ  plan-1  C08   0.020
 NMJ  plan-1  H1    0.020
 NMJ  plan-1  H2    0.020
 NMJ  plan-2  C02   0.020
 NMJ  plan-2  C08   0.020
 NMJ  plan-2  O09   0.020
 NMJ  plan-2  O10   0.020

