# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 23:43:13 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2,3-dideoxy-3-nitro-L-threo-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@H](CC(O)=O)[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
 NIC  NIC  '2,3-dideoxy-3-nitro-L-threo-pentaric 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 GRAND
;

data_comp_NIC
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
 NIC  C1   C  C      0   0.523  -2.3968  -0.0768  -0.4675
 NIC  O1   O  O      0  -0.432  -3.3355  -0.1054   0.2863
 NIC  O2   O  OH1    0  -0.577  -2.3560   0.5754  -1.6091
 NIC  C2   C  CH1    0  -0.062  -1.1357  -0.8930  -0.2178
 NIC  C3   C  CH1    0  -0.182   0.1552  -0.0716  -0.2941
 NIC  O7   O  OH1    0  -0.658  -1.2048  -1.5457   1.0087
 NIC  C4   C  CH2    0  -0.598   1.3873  -0.9484  -0.2583
 NIC  C5   C  C      0   0.560   2.6581  -0.1750  -0.4986
 NIC  O3   O  O      0  -0.439   2.7120   0.8791  -1.0803
 NIC  O4   O  OH1    0  -0.586   3.7176  -0.8174  -0.0348
 NIC  N6   N  N      1   0.463   0.1555   0.9092   0.8466
 NIC  O5   O  O     -1  -0.363   1.1082   0.9481   1.5802
 NIC  O6   O  O      0  -0.371  -0.8196   1.6126   0.9517
 NIC  HO2  H  HOH1   0   0.497  -3.1797   1.0661  -1.7541
 NIC  H2   H  HCH1   0   0.302  -1.0775  -1.6142  -1.0461
 NIC  H3   H  HCH1   0   0.346   0.1558   0.5429  -1.1967
 NIC  HO7  H  HOH1   0   0.461  -2.0720  -1.3741   1.3996
 NIC  H41  H  HCH2   0   0.324   1.2970  -1.6688  -1.0778
 NIC  H42  H  HCH2   0   0.307   1.4497  -1.5332   0.6590
 NIC  HO4  H  HOH1   0   0.485   4.5248  -0.3210  -0.2392

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
 NIC  C1  O1   double  1.204  0.020  1.204
 NIC  C1  O2   single  1.315  0.020  1.315
 NIC  C1  C2   single  1.523  0.020  1.523
 NIC  O2  HO2  single  0.850  0.020  0.980
 NIC  C2  C3   single  1.532  0.020  1.532
 NIC  C2  O7   single  1.391  0.020  1.391
 NIC  C2  H2   single  0.970  0.020  1.090
 NIC  C3  C4   single  1.513  0.020  1.513
 NIC  C3  N6   single  1.504  0.020  1.504
 NIC  C3  H3   single  0.970  0.020  1.090
 NIC  O7  HO7  single  0.850  0.020  0.980
 NIC  C4  C5   single  1.507  0.020  1.507
 NIC  C4  H41  single  0.970  0.020  1.090
 NIC  C4  H42  single  0.970  0.020  1.090
 NIC  C5  O3   double  1.205  0.020  1.205
 NIC  C5  O4   single  1.323  0.020  1.323
 NIC  O4  HO4  single  0.850  0.020  0.980
 NIC  N6  O5   single  1.203  0.020  1.203
 NIC  N6  O6   double  1.207  0.020  1.207

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
 NIC  C2   C1  O2   112.48  3.000
 NIC  C2   C1  O1   122.02  3.000
 NIC  O2   C1  O1   125.40  3.000
 NIC  HO2  O2  C1   110.75  3.000
 NIC  H2   C2  O7   111.03  3.000
 NIC  H2   C2  C3   105.64  3.000
 NIC  O7   C2  C3   109.71  3.000
 NIC  H2   C2  C1   105.78  3.000
 NIC  O7   C2  C1   110.79  3.000
 NIC  C3   C2  C1   113.72  3.000
 NIC  H3   C3  N6   105.07  3.000
 NIC  H3   C3  C4   110.20  3.000
 NIC  N6   C3  C4   111.09  3.000
 NIC  H3   C3  C2   110.08  3.000
 NIC  N6   C3  C2   108.18  3.000
 NIC  C4   C3  C2   111.99  3.000
 NIC  HO7  O7  C2   108.53  3.000
 NIC  H42  C4  H41  106.36  3.000
 NIC  H42  C4  C5   111.19  3.000
 NIC  H41  C4  C5   106.74  3.000
 NIC  H42  C4  C3   112.19  3.000
 NIC  H41  C4  C3   107.24  3.000
 NIC  C5   C4  C3   112.68  3.000
 NIC  O4   C5  O3   123.93  3.000
 NIC  O4   C5  C4   111.73  3.000
 NIC  O3   C5  C4   124.30  3.000
 NIC  HO4  O4  C5   110.14  3.000
 NIC  O6   N6  O5   124.60  3.000
 NIC  O6   N6  C3   116.48  3.000
 NIC  O5   N6  C3   118.93  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
 NIC  CONST_01  HO2  O2  C1  O1    0.00   0.0  0
 NIC  CONST_02  HO4  O4  C5  C4  180.00   0.0  0
 NIC  Var_01    O3   C5  C4  C3  -23.44  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
 NIC  chir_01  C2  C1  C3  O7  negativ
 NIC  chir_02  C3  N6  C4  C2  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
 NIC  plan-1  C1   0.020
 NIC  plan-1  O1   0.020
 NIC  plan-1  O2   0.020
 NIC  plan-1  C2   0.020
 NIC  plan-1  HO2  0.020
 NIC  plan-2  C4   0.020
 NIC  plan-2  C5   0.020
 NIC  plan-2  O3   0.020
 NIC  plan-2  O4   0.020
 NIC  plan-2  HO4  0.020
 NIC  plan-3  C3   0.020
 NIC  plan-3  N6   0.020
 NIC  plan-3  O5   0.020
 NIC  plan-3  O6   0.020

