# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:08:53 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  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_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   0.405  -2.3855  -0.1167  -0.5096
 NIC  O1   O  O      0  -0.601  -3.1947  -0.0828   0.4430
 NIC  O2   O  OC    -1  -0.586  -2.4803   0.4283  -1.6168
 NIC  C2   C  CH1    0  -0.099  -1.1261  -0.9818  -0.2427
 NIC  C3   C  CH1    0  -0.146   0.1739  -0.1685  -0.3587
 NIC  O7   O  OH1    0  -0.681  -1.2357  -1.6120   0.9975
 NIC  C4   C  CH2    0  -0.608   1.4242  -1.0112  -0.2647
 NIC  C5   C  C      0   0.429   2.7331  -0.2036  -0.3500
 NIC  O3   O  O      0  -0.604   2.6320   1.0110  -0.6122
 NIC  O4   O  OC    -1  -0.618   3.7838  -0.8458  -0.1639
 NIC  N6   N  N      1   0.452   0.1567   0.8775   0.7092
 NIC  O5   O  O     -1  -0.395   0.6749   0.6295   1.7697
 NIC  O6   O  O      0  -0.401  -0.4370   1.9066   0.4791
 NIC  H2   H  HCH1   0   0.233  -1.0594  -1.7255  -1.0495
 NIC  H3   H  HCH1   0   0.282   0.1495   0.3775  -1.3001
 NIC  HO7  H  HOH1   0   0.433  -2.0610  -1.2292   1.3530
 NIC  H41  H  HCH2   0   0.254   1.3966  -1.7094  -1.1080
 NIC  H42  H  HCH2   0   0.249   1.4195  -1.6322   0.6329

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   deloc   1.250  0.020  1.250
 NIC  C1  O2   deloc   1.238  0.020  1.238
 NIC  C1  C2   single  1.551  0.020  1.551
 NIC  C2  C3   single  1.538  0.020  1.538
 NIC  C2  O7   single  1.395  0.020  1.395
 NIC  C2  H2   single  0.970  0.020  1.090
 NIC  C3  C4   single  1.511  0.020  1.511
 NIC  C3  N6   single  1.495  0.020  1.495
 NIC  C3  H3   single  0.970  0.020  1.090
 NIC  O7  HO7  single  0.850  0.020  0.980
 NIC  C4  C5   single  1.540  0.020  1.540
 NIC  C4  H41  single  0.970  0.020  1.090
 NIC  C4  H42  single  0.970  0.020  1.090
 NIC  C5  O3   deloc   1.247  0.020  1.247
 NIC  C5  O4   deloc   1.245  0.020  1.245
 NIC  N6  O5   single  1.206  0.020  1.206
 NIC  N6  O6   double  1.210  0.020  1.210

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   117.50  3.000
 NIC  C2   C1  O1   114.18  3.000
 NIC  O2   C1  O1   128.31  3.000
 NIC  H2   C2  O7   110.58  3.000
 NIC  H2   C2  C3   104.55  3.000
 NIC  O7   C2  C3   111.86  3.000
 NIC  H2   C2  C1   107.48  3.000
 NIC  O7   C2  C1   109.94  3.000
 NIC  C3   C2  C1   112.24  3.000
 NIC  H3   C3  N6   105.46  3.000
 NIC  H3   C3  C4   110.62  3.000
 NIC  N6   C3  C4   110.82  3.000
 NIC  H3   C3  C2   108.15  3.000
 NIC  N6   C3  C2   107.84  3.000
 NIC  C4   C3  C2   113.57  3.000
 NIC  HO7  O7  C2   102.29  3.000
 NIC  H42  C4  H41  105.69  3.000
 NIC  H42  C4  C5   110.33  3.000
 NIC  H41  C4  C5   108.24  3.000
 NIC  H42  C4  C3   111.41  3.000
 NIC  H41  C4  C3   106.67  3.000
 NIC  C5   C4  C3   114.04  3.000
 NIC  O4   C5  O3   127.03  3.000
 NIC  O4   C5  C4   115.99  3.000
 NIC  O3   C5  C4   116.98  3.000
 NIC  O6   N6  O5   123.56  3.000
 NIC  O6   N6  C3   117.70  3.000
 NIC  O5   N6  C3   118.64  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  Var_01  O3  C5  C4  C3  -6.68  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-2  C4  0.020
 NIC  plan-2  C5  0.020
 NIC  plan-2  O3  0.020
 NIC  plan-2  O4  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

