# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:05:37 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 3-nitropropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[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
 3NP  3NP  '3-nitropropanoic acid    '  ligand  13  8  .  2021-08-04  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3NP
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
 3NP  O1   O  OH1    0  -0.590   2.8369  -0.8280  -0.2010
 3NP  O2   O  O      0  -0.438   2.1117   1.2293   0.2711
 3NP  O4   O  O      0  -0.385  -2.8299   0.7390   0.2601
 3NP  O3   O  O     -1  -0.381  -2.0899  -1.1910  -0.2681
 3NP  C1   C  C      0   0.561   1.8897   0.0717   0.0204
 3NP  C2   C  CH2    0  -0.620   0.5177  -0.5402  -0.0805
 3NP  C3   C  CH2    0  -0.314  -0.5470   0.5162   0.1063
 3NP  N1   N  N      1   0.443  -1.9319  -0.0327   0.0269
 3NP  HO1  H  HOH1   0   0.484   3.7114  -0.4157  -0.1325
 3NP  H21  H  HCH2   0   0.307   0.4287  -1.0316  -1.0514
 3NP  H22  H  HCH2   0   0.309   0.4363  -1.3244   0.6760
 3NP  H31  H  HCH2   0   0.310  -0.4842   1.0052   1.0773
 3NP  H32  H  HCH2   0   0.314  -0.5024   1.2893  -0.6608

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
 3NP  O1  C1   single  1.325  0.020  1.325
 3NP  O1  HO1  single  0.850  0.020  0.980
 3NP  O2  C1   double  1.205  0.020  1.205
 3NP  O4  N1   double  1.207  0.020  1.207
 3NP  O3  N1   single  1.206  0.020  1.206
 3NP  C1  C2   single  1.506  0.020  1.506
 3NP  C2  C3   single  1.511  0.020  1.511
 3NP  C2  H21  single  0.970  0.020  1.090
 3NP  C2  H22  single  0.970  0.020  1.090
 3NP  C3  N1   single  1.492  0.020  1.492
 3NP  C3  H31  single  0.970  0.020  1.090
 3NP  C3  H32  single  0.970  0.020  1.090

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
 3NP  HO1  O1  C1   110.14  3.000
 3NP  C2   C1  O2   124.90  3.000
 3NP  C2   C1  O1   111.36  3.000
 3NP  O2   C1  O1   123.73  3.000
 3NP  H22  C2  H21  106.65  3.000
 3NP  H22  C2  C3   111.32  3.000
 3NP  H21  C2  C3   111.53  3.000
 3NP  H22  C2  C1   108.26  3.000
 3NP  H21  C2  C1   108.47  3.000
 3NP  C3   C2  C1   110.46  3.000
 3NP  H32  C3  H31  107.86  3.000
 3NP  H32  C3  N1   105.16  3.000
 3NP  H31  C3  N1   105.44  3.000
 3NP  H32  C3  C2   112.33  3.000
 3NP  H31  C3  C2   112.54  3.000
 3NP  N1   C3  C2   112.97  3.000
 3NP  C3   N1  O3   119.22  3.000
 3NP  C3   N1  O4   116.44  3.000
 3NP  O3   N1  O4   124.34  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
 3NP  CONST_01  HO1  O1  C1  O2     0.00   0.0  0
 3NP  Var_01    C3   C2  C1  O1  -177.16  30.0  3
 3NP  Var_02    N1   C3  C2  C1  -179.57  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
 3NP  plan-1  O1   0.020
 3NP  plan-1  O2   0.020
 3NP  plan-1  C1   0.020
 3NP  plan-1  C2   0.020
 3NP  plan-1  HO1  0.020
 3NP  plan-2  O4   0.020
 3NP  plan-2  O3   0.020
 3NP  plan-2  C3   0.020
 3NP  plan-2  N1   0.020

