# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:41:18 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (3-nitrophenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cccc(c1)[N+]([O-])=O
#
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
 MNP  MNP  '(3-nitrophenyl)acetic acid'  ligand  19  13  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNP
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
 MNP  C1   C  C      0   0.427  -0.5355   0.2078   2.9836
 MNP  C2   C  CH2    0  -0.698   0.0440  -0.9652   2.1479
 MNP  C1'  C  CR6    0   0.185   0.5324  -0.5595   0.7962
 MNP  C2'  C  CR16   0  -0.324  -0.3564  -0.4348  -0.2655
 MNP  C3'  C  CR6    0   0.261   0.1079  -0.0429  -1.5116
 MNP  N3'  N  N      1   0.328  -0.8385   0.0727  -2.6112
 MNP  O3'  O  O     -1  -0.382  -0.4138   0.3861  -3.6991
 MNP  O4'  O  O      0  -0.382  -2.0059  -0.1491  -2.3872
 MNP  C4'  C  CR16   0  -0.291   1.4466   0.2423  -1.7445
 MNP  C5'  C  CR16   0  -0.237   2.3286   0.1208  -0.6852
 MNP  C6'  C  CR16   0  -0.290   1.8761  -0.2762   0.5665
 MNP  O1   O  O      0  -0.593  -0.6535   1.3090   2.4208
 MNP  O2   O  OC    -1  -0.619  -0.8432  -0.0815   4.1553
 MNP  H21  H  HCH2   0   0.251   0.8500  -1.4378   2.7151
 MNP  H22  H  HCH2   0   0.255  -0.7386  -1.7237   2.0502
 MNP  H2'  H  HCR6   0   0.283  -1.4039  -0.6543  -0.1120
 MNP  H4'  H  HCR6   0   0.291   1.7997   0.5472  -2.7181
 MNP  H5'  H  HCR6   0   0.271   3.3777   0.3335  -0.8394
 MNP  H6'  H  HCR6   0   0.263   2.5848  -0.3690   1.3805

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
 MNP  C1   C2   single    1.552  0.020  1.552
 MNP  C1   O1   deloc     1.242  0.020  1.242
 MNP  C1   O2   deloc     1.245  0.020  1.245
 MNP  C2   C1'  single    1.493  0.020  1.493
 MNP  C2   H21  single    0.970  0.020  1.090
 MNP  C2   H22  single    0.970  0.020  1.090
 MNP  C1'  C2'  aromatic  1.390  0.020  1.390
 MNP  C1'  C6'  aromatic  1.392  0.020  1.392
 MNP  C2'  C3'  aromatic  1.386  0.020  1.386
 MNP  C2'  H2'  single    0.930  0.020  1.080
 MNP  C3'  N3'  single    1.455  0.020  1.455
 MNP  C3'  C4'  aromatic  1.388  0.020  1.388
 MNP  N3'  O3'  single    1.209  0.020  1.209
 MNP  N3'  O4'  double    1.209  0.020  1.209
 MNP  C4'  C5'  aromatic  1.384  0.020  1.384
 MNP  C4'  H4'  single    0.930  0.020  1.080
 MNP  C5'  C6'  aromatic  1.389  0.020  1.389
 MNP  C5'  H5'  single    0.930  0.020  1.080
 MNP  C6'  H6'  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
 MNP  O2   C1   O1   127.49  3.000
 MNP  O2   C1   C2   115.04  3.000
 MNP  O1   C1   C2   117.47  3.000
 MNP  H22  C2   H21  105.90  3.000
 MNP  H22  C2   C1'  109.96  3.000
 MNP  H21  C2   C1'  110.25  3.000
 MNP  H22  C2   C1   107.74  3.000
 MNP  H21  C2   C1   108.82  3.000
 MNP  C1'  C2   C1   113.83  3.000
 MNP  C6'  C1'  C2'  118.21  3.000
 MNP  C6'  C1'  C2   121.35  3.000
 MNP  C2'  C1'  C2   120.43  3.000
 MNP  H2'  C2'  C3'  120.63  3.000
 MNP  H2'  C2'  C1'  119.52  3.000
 MNP  C3'  C2'  C1'  119.85  3.000
 MNP  C4'  C3'  N3'  118.94  3.000
 MNP  C4'  C3'  C2'  122.13  3.000
 MNP  N3'  C3'  C2'  118.93  3.000
 MNP  O4'  N3'  O3'  123.59  3.000
 MNP  O4'  N3'  C3'  118.25  3.000
 MNP  O3'  N3'  C3'  118.16  3.000
 MNP  H4'  C4'  C5'  120.44  3.000
 MNP  H4'  C4'  C3'  121.64  3.000
 MNP  C5'  C4'  C3'  117.91  3.000
 MNP  H5'  C5'  C6'  120.05  3.000
 MNP  H5'  C5'  C4'  119.47  3.000
 MNP  C6'  C5'  C4'  120.48  3.000
 MNP  H6'  C6'  C5'  119.25  3.000
 MNP  H6'  C6'  C1'  119.34  3.000
 MNP  C5'  C6'  C1'  121.42  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
 MNP  CONST_01  C4'  C3'  C2'  C1'    0.00   0.0  0
 MNP  CONST_02  C4'  C5'  C6'  C1'    0.00   0.0  0
 MNP  CONST_03  C5'  C6'  C1'  C2'    0.00   0.0  0
 MNP  CONST_04  C5'  C4'  C3'  C2'    0.00   0.0  0
 MNP  CONST_05  C6'  C1'  C2'  C3'    0.00   0.0  0
 MNP  CONST_06  C6'  C5'  C4'  C3'    0.00   0.0  0
 MNP  CONST_07  C3'  C2'  C1'  C2   180.00   0.0  0
 MNP  CONST_08  C5'  C6'  C1'  C2   180.00   0.0  0
 MNP  CONST_09  N3'  C3'  C2'  C1'  180.00   0.0  0
 MNP  CONST_10  C5'  C4'  C3'  N3'  180.00   0.0  0
 MNP  CONST_11  H5'  C5'  C6'  C1'  180.00   0.0  0
 MNP  CONST_12  H6'  C6'  C1'  C2'  180.00   0.0  0
 MNP  CONST_13  H4'  C4'  C3'  C2'  180.00   0.0  0
 MNP  CONST_14  H2'  C2'  C3'  C4'  180.00   0.0  0
 MNP  CONST_15  O3'  N3'  C3'  C2'  180.00   0.0  0
 MNP  CONST_16  O4'  N3'  C3'  C2'    0.00   0.0  0
 MNP  CONST_17  C4'  C3'  N3'  O3'    0.00   0.0  0
 MNP  CONST_18  C4'  C3'  N3'  O4'  180.00   0.0  0
 MNP  Var_01    C2'  C1'  C2   C1   -82.71  30.0  2
 MNP  Var_02    O1   C1   C2   C1'    6.60  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
 MNP  plan-1  C2   0.020
 MNP  plan-1  C1'  0.020
 MNP  plan-1  C2'  0.020
 MNP  plan-1  C3'  0.020
 MNP  plan-1  N3'  0.020
 MNP  plan-1  C4'  0.020
 MNP  plan-1  C5'  0.020
 MNP  plan-1  C6'  0.020
 MNP  plan-1  H2'  0.020
 MNP  plan-1  H4'  0.020
 MNP  plan-1  H5'  0.020
 MNP  plan-1  H6'  0.020
 MNP  plan-2  C3'  0.020
 MNP  plan-2  N3'  0.020
 MNP  plan-2  O3'  0.020
 MNP  plan-2  O4'  0.020
 MNP  plan-3  C1   0.020
 MNP  plan-3  C2   0.020
 MNP  plan-3  O1   0.020
 MNP  plan-3  O2   0.020

