# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:34:18 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-azanyl-5-chloranyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(Cl)ccc1N
#
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
 5MK  5MK  2-azanyl-5-chloranyl-benzamide  ligand  18  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5MK
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
 5MK  NAB  N   NH2   0  -0.859   2.1749  -1.8498  -0.1725
 5MK  CAI  C   CR6   0   0.320   0.9648  -1.2392  -0.0338
 5MK  CAE  C   CR16  0  -0.334  -0.2077  -2.0114  -0.1179
 5MK  CAF  C   CR16  0  -0.207  -1.4605  -1.4474  -0.0243
 5MK  CAJ  C   CR6   0  -0.059  -1.5823  -0.0751   0.1559
 5MK  CLA  CL  CL    0  -0.143  -3.1558   0.6441   0.3035
 5MK  CAG  C   CR16  0  -0.245  -0.4547   0.7142   0.2258
 5MK  CAK  C   CR6   0  -0.119   0.8221   0.1583   0.1216
 5MK  CAH  C   C     0   0.508   2.0197   1.0402   0.2209
 5MK  OAC  O   O     0  -0.495   3.0842   0.6379   0.6833
 5MK  NAA  N   NH2   0  -0.802   1.8644   2.3023  -0.2078
 5MK  H1   H   HNH2  0   0.395   2.9743  -1.3721   0.2084
 5MK  H2   H   HNH2  0   0.387   2.1912  -2.8503  -0.0678
 5MK  H3   H   HCR6  0   0.273  -0.1204  -3.0830  -0.2491
 5MK  H4   H   HCR6  0   0.282  -2.3383  -2.0767  -0.0837
 5MK  H5   H   HCR6  0   0.280  -0.5680   1.7777   0.3898
 5MK  H6   H   HNH2  0   0.413   1.0704   2.5942  -0.7502
 5MK  H7   H   HNH2  0   0.406   2.6484   2.9335  -0.1738

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
 5MK  CAE  CAF  aromatic  1.377  0.020  1.377
 5MK  CAE  CAI  aromatic  1.406  0.020  1.406
 5MK  NAB  CAI  single    1.362  0.020  1.362
 5MK  CAF  CAJ  aromatic  1.389  0.020  1.389
 5MK  CAI  CAK  aromatic  1.413  0.020  1.413
 5MK  CAJ  CAG  aromatic  1.378  0.020  1.378
 5MK  CAJ  CLA  single    1.736  0.020  1.736
 5MK  CAK  CAG  aromatic  1.396  0.020  1.396
 5MK  CAK  CAH  single    1.491  0.020  1.491
 5MK  CAH  OAC  double    1.228  0.020  1.228
 5MK  CAH  NAA  single    1.342  0.020  1.342
 5MK  NAB  H1   single    0.890  0.020  1.040
 5MK  NAB  H2   single    0.890  0.020  1.040
 5MK  CAE  H3   single    0.930  0.020  1.080
 5MK  CAF  H4   single    0.930  0.020  1.080
 5MK  CAG  H5   single    0.930  0.020  1.080
 5MK  NAA  H6   single    0.860  0.020  1.020
 5MK  NAA  H7   single    0.860  0.020  1.020

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
 5MK  H2   NAB  H1   114.83  3.000
 5MK  H2   NAB  CAI  116.71  3.000
 5MK  H1   NAB  CAI  117.03  3.000
 5MK  CAK  CAI  CAE  117.73  3.000
 5MK  CAK  CAI  NAB  122.96  3.000
 5MK  CAE  CAI  NAB  119.23  3.000
 5MK  H3   CAE  CAF  119.13  3.000
 5MK  H3   CAE  CAI  118.90  3.000
 5MK  CAF  CAE  CAI  121.97  3.000
 5MK  H4   CAF  CAJ  120.70  3.000
 5MK  H4   CAF  CAE  119.75  3.000
 5MK  CAJ  CAF  CAE  119.55  3.000
 5MK  CAG  CAJ  CLA  120.00  3.000
 5MK  CLA  CAJ  CAF  119.97  3.000
 5MK  CAG  CAJ  CAF  120.03  3.000
 5MK  H5   CAG  CAK  119.89  3.000
 5MK  H5   CAG  CAJ  119.01  3.000
 5MK  CAK  CAG  CAJ  121.09  3.000
 5MK  CAH  CAK  CAG  119.61  3.000
 5MK  CAH  CAK  CAI  120.74  3.000
 5MK  CAG  CAK  CAI  119.62  3.000
 5MK  NAA  CAH  OAC  121.91  3.000
 5MK  NAA  CAH  CAK  116.24  3.000
 5MK  OAC  CAH  CAK  121.85  3.000
 5MK  H7   NAA  H6   116.83  3.000
 5MK  H7   NAA  CAH  119.25  3.000
 5MK  H6   NAA  CAH  122.48  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
 5MK  CONST_01  CAJ  CAF  CAE  CAI    0.00   0.0  0
 5MK  CONST_02  CAJ  CAG  CAK  CAI    0.00   0.0  0
 5MK  CONST_03  CAG  CAJ  CAF  CAE    0.00   0.0  0
 5MK  CONST_04  CAG  CAK  CAI  CAE    0.00   0.0  0
 5MK  CONST_05  CAK  CAI  CAE  CAF    0.00   0.0  0
 5MK  CONST_06  CAK  CAG  CAJ  CAF    0.00   0.0  0
 5MK  CONST_07  CAF  CAE  CAI  NAB  180.00   0.0  0
 5MK  CONST_08  CAG  CAK  CAI  NAB  180.00   0.0  0
 5MK  CONST_09  CLA  CAJ  CAF  CAE  180.00   0.0  0
 5MK  CONST_10  CAH  CAK  CAI  CAE  180.00   0.0  0
 5MK  CONST_11  CAH  CAK  CAG  CAJ  180.00   0.0  0
 5MK  CONST_12  CAK  CAG  CAJ  CLA  180.00   0.0  0
 5MK  CONST_13  H4   CAF  CAE  CAI  180.00   0.0  0
 5MK  CONST_14  H5   CAG  CAK  CAI  180.00   0.0  0
 5MK  CONST_15  H3   CAE  CAF  CAJ  180.00   0.0  0
 5MK  CONST_18  H6   NAA  CAH  CAK    0.00   0.0  0
 5MK  CONST_19  H7   NAA  CAH  CAK  180.00   0.0  0
 5MK  Var_01    OAC  CAH  CAK  CAI  -28.82  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
 5MK  plan-1  NAB  0.020
 5MK  plan-1  CAI  0.020
 5MK  plan-1  CAE  0.020
 5MK  plan-1  CAF  0.020
 5MK  plan-1  CAJ  0.020
 5MK  plan-1  CLA  0.020
 5MK  plan-1  CAG  0.020
 5MK  plan-1  CAK  0.020
 5MK  plan-1  CAH  0.020
 5MK  plan-1  H3   0.020
 5MK  plan-1  H4   0.020
 5MK  plan-1  H5   0.020
 5MK  plan-2  CAK  0.020
 5MK  plan-2  CAH  0.020
 5MK  plan-2  OAC  0.020
 5MK  plan-2  NAA  0.020
 5MK  plan-2  H6   0.020
 5MK  plan-2  H7   0.020
 5MK  plan-3  NAB  0.020
 5MK  plan-3  CAI  0.020
 5MK  plan-3  H1   0.020
 5MK  plan-3  H2   0.020

