# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:24:27 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R)-2-hydroxy-2-(nitromethyl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@](O)(C[N+]([O-])=O)C(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
 NTC  NTC  '(2R)-2-hydroxy-2-(nitromethyl)butanedioic acid'  ligand  18  13  .  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_NTC
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
 NTC  N1   N  N      1   0.427  -2.4806   0.5256  -0.1595
 NTC  O1   O  O     -1  -0.396  -2.9301   1.3553   0.5964
 NTC  O2   O  O      0  -0.386  -2.9966  -0.5484  -0.3630
 NTC  C2   C  CH2    0  -0.321  -1.2142   0.8346  -0.8597
 NTC  C3   C  CT     0   0.036  -0.0024   0.3387  -0.0345
 NTC  O7   O  OH1    0  -0.576  -0.0477   0.9026   1.2500
 NTC  C4   C  CH2    0  -0.585   1.2320   0.7948  -0.8050
 NTC  C5   C  C      0   0.435   2.5879   0.3935  -0.1978
 NTC  O3   O  O      0  -0.582   2.6165  -0.5705   0.5868
 NTC  O4   O  OC    -1  -0.683   3.5723   1.0341  -0.6235
 NTC  C6   C  C      0   0.395  -0.0935  -1.2095   0.0750
 NTC  O5   O  O      0  -0.480  -0.3933  -1.6898   1.1771
 NTC  O6   O  OC    -1  -0.830   0.0751  -1.8183  -0.9990
 NTC  H21  H  HCH2   0   0.253  -1.2473   0.3501  -1.8313
 NTC  H22  H  HCH2   0   0.313  -1.1808   1.9162  -0.9881
 NTC  HO7  H  HOH1   0   0.446   0.0779   1.8543   1.1636
 NTC  H41  H  HCH2   0   0.268   1.1877   0.4041  -1.8244
 NTC  H42  H  HCH2   0   0.264   1.2081   1.8859  -0.9129

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
 NTC  N1  O1   single  1.209  0.020  1.209
 NTC  N1  O2   double  1.209  0.020  1.209
 NTC  N1  C2   single  1.480  0.020  1.480
 NTC  C2  C3   single  1.548  0.020  1.548
 NTC  C2  H21  single  0.970  0.020  1.090
 NTC  C2  H22  single  0.970  0.020  1.090
 NTC  C3  O7   single  1.404  0.020  1.404
 NTC  C3  C4   single  1.525  0.020  1.525
 NTC  C3  C6   single  1.555  0.020  1.555
 NTC  O7  HO7  single  0.850  0.020  0.980
 NTC  C4  C5   single  1.539  0.020  1.539
 NTC  C4  H41  single  0.970  0.020  1.090
 NTC  C4  H42  single  0.970  0.020  1.090
 NTC  C5  O3   deloc   1.243  0.020  1.243
 NTC  C5  O4   deloc   1.249  0.020  1.249
 NTC  C6  O5   deloc   1.239  0.020  1.239
 NTC  C6  O6   deloc   1.246  0.020  1.246

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
 NTC  C2   N1  O2   118.11  3.000
 NTC  C2   N1  O1   118.08  3.000
 NTC  O2   N1  O1   123.80  3.000
 NTC  H22  C2  H21  109.77  3.000
 NTC  H22  C2  C3   110.91  3.000
 NTC  H21  C2  C3   110.98  3.000
 NTC  H22  C2  N1   106.81  3.000
 NTC  H21  C2  N1   107.70  3.000
 NTC  C3   C2  N1   110.54  3.000
 NTC  C6   C3  C4   112.39  3.000
 NTC  C6   C3  O7   109.49  3.000
 NTC  C4   C3  O7   111.61  3.000
 NTC  C6   C3  C2   108.10  3.000
 NTC  C4   C3  C2   105.58  3.000
 NTC  O7   C3  C2   109.52  3.000
 NTC  HO7  O7  C3   108.08  3.000
 NTC  H42  C4  H41  105.26  3.000
 NTC  H42  C4  C5   108.51  3.000
 NTC  H41  C4  C5   108.10  3.000
 NTC  H42  C4  C3   109.25  3.000
 NTC  H41  C4  C3   109.37  3.000
 NTC  C5   C4  C3   115.84  3.000
 NTC  O4   C5  O3   126.48  3.000
 NTC  O4   C5  C4   115.22  3.000
 NTC  O3   C5  C4   118.13  3.000
 NTC  O6   C6  O5   127.60  3.000
 NTC  O6   C6  C3   114.70  3.000
 NTC  O5   C6  C3   117.57  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
 NTC  Var_01  C3  C2  N1  O1  90.86  30.0  3
 NTC  Var_02  O3  C5  C4  C3  21.66  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NTC  chir_01  C3  O7  C4  C6  negativ

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
 NTC  plan-1  C4  0.020
 NTC  plan-1  C5  0.020
 NTC  plan-1  O3  0.020
 NTC  plan-1  O4  0.020
 NTC  plan-2  C3  0.020
 NTC  plan-2  C6  0.020
 NTC  plan-2  O5  0.020
 NTC  plan-2  O6  0.020
 NTC  plan-3  N1  0.020
 NTC  plan-3  O1  0.020
 NTC  plan-3  O2  0.020
 NTC  plan-3  C2  0.020

