# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 13:56:11 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  20  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   0.445  -2.4685   0.6010  -0.1432
 NTC  O1   O  O     -1  -0.372  -3.0663   1.5559   0.2824
 NTC  O2   O  O      0  -0.378  -2.8242  -0.5464  -0.0148
 NTC  C2   C  CH2    0  -0.338  -1.1925   0.8318  -0.8661
 NTC  C3   C  CT     0   0.068  -0.0023   0.3307  -0.0240
 NTC  O7   O  OH1    0  -0.642  -0.0393   0.8762   1.2562
 NTC  C4   C  CH2    0  -0.609   1.2574   0.7375  -0.7945
 NTC  C5   C  C      0   0.573   2.5258   0.2244  -0.1676
 NTC  O3   O  O      0  -0.428   2.5836  -0.7131   0.5866
 NTC  O4   O  OH1    0  -0.587   3.5805   0.9132  -0.5719
 NTC  C6   C  C      0   0.560  -0.0844  -1.1901   0.1658
 NTC  O5   O  O      0  -0.417  -0.2901  -1.7306   1.2149
 NTC  O6   O  OH1    0  -0.592   0.0729  -1.8127  -0.9906
 NTC  H21  H  HCH2   0   0.324  -1.2672   0.3208  -1.8243
 NTC  H22  H  HCH2   0   0.317  -1.1052   1.9027  -1.0392
 NTC  HO7  H  HOH1   0   0.466   0.0888   1.8303   1.1990
 NTC  H41  H  HCH2   0   0.322   1.2220   0.3793  -1.8270
 NTC  H42  H  HCH2   0   0.311   1.2992   1.8274  -0.8651
 NTC  HO4  H  HOH1   0   0.486   4.3911   0.5420  -0.1901
 NTC  HO6  H  HOH1   0   0.492  -0.0012  -2.7717  -0.8719

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  1.204  0.020  1.204
 NTC  N1  O2   double  1.208  0.020  1.208
 NTC  N1  C2   single  1.485  0.020  1.485
 NTC  C2  C3   single  1.542  0.020  1.542
 NTC  C2  H21  single  0.970  0.020  1.090
 NTC  C2  H22  single  0.970  0.020  1.090
 NTC  C3  O7   single  1.392  0.020  1.392
 NTC  C3  C4   single  1.532  0.020  1.532
 NTC  C3  C6   single  1.535  0.020  1.535
 NTC  O7  HO7  single  0.850  0.020  0.980
 NTC  C4  C5   single  1.505  0.020  1.505
 NTC  C4  H41  single  0.970  0.020  1.090
 NTC  C4  H42  single  0.970  0.020  1.090
 NTC  C5  O3   double  1.205  0.020  1.205
 NTC  C5  O4   single  1.323  0.020  1.323
 NTC  O4  HO4  single  0.850  0.020  0.980
 NTC  C6  O5   double  1.198  0.020  1.198
 NTC  C6  O6   single  1.323  0.020  1.323
 NTC  O6  HO6  single  0.850  0.020  0.980

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   116.90  3.000
 NTC  C2   N1  O1   118.39  3.000
 NTC  O2   N1  O1   124.70  3.000
 NTC  H22  C2  H21  109.11  3.000
 NTC  H22  C2  C3   110.17  3.000
 NTC  H21  C2  C3   112.41  3.000
 NTC  H22  C2  N1   107.42  3.000
 NTC  H21  C2  N1   107.26  3.000
 NTC  C3   C2  N1   110.31  3.000
 NTC  C6   C3  C4   111.68  3.000
 NTC  C6   C3  O7   105.85  3.000
 NTC  C4   C3  O7   112.36  3.000
 NTC  C6   C3  C2   110.39  3.000
 NTC  C4   C3  C2   105.89  3.000
 NTC  O7   C3  C2   110.76  3.000
 NTC  HO7  O7  C3   109.25  3.000
 NTC  H42  C4  H41  105.48  3.000
 NTC  H42  C4  C5   109.55  3.000
 NTC  H41  C4  C5   107.99  3.000
 NTC  H42  C4  C3   109.20  3.000
 NTC  H41  C4  C3   111.18  3.000
 NTC  C5   C4  C3   113.14  3.000
 NTC  O4   C5  O3   123.94  3.000
 NTC  O4   C5  C4   111.53  3.000
 NTC  O3   C5  C4   124.51  3.000
 NTC  HO4  O4  C5   110.29  3.000
 NTC  O6   C6  O5   125.00  3.000
 NTC  O6   C6  C3   110.61  3.000
 NTC  O5   C6  C3   124.38  3.000
 NTC  HO6  O6  C6   110.46  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  CONST_01  HO6  O6  C6  C3  180.00   0.0  0
 NTC  CONST_02  HO4  O4  C5  C4  180.00   0.0  0
 NTC  Var_01    C3   C2  N1  O1  110.05  30.0  3
 NTC  Var_02    O3   C5  C4  C3   21.51  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-1  HO4  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-2  HO6  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

