# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:45:33 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (2S)-2-nitrobutane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[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
 NBT  NBT  '(2S)-2-nitrobutane       '  ligand  16  7  .  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_NBT
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
 NBT  C1    C  CH3    0  -0.658   0.1965  -2.0608  -0.1613
 NBT  C2    C  CH1    0  -0.157  -0.2433  -0.6407  -0.4658
 NBT  C3    C  CH2    0  -0.431  -1.5250  -0.2459   0.2605
 NBT  C4    C  CH3    0  -0.675  -1.9880   1.1791  -0.0066
 NBT  NCG   N  N      1   0.451   0.8486   0.3164  -0.0804
 NBT  H1C1  H  HCH3   0   0.245   0.3126  -2.2265   0.9084
 NBT  H1C2  H  HCH3   0   0.255  -0.5716  -2.7402  -0.5280
 NBT  H1C3  H  HCH3   0   0.257   1.1296  -2.3133  -0.6643
 NBT  H2    H  HCH1   0   0.285  -0.3683  -0.5034  -1.5396
 NBT  H3C1  H  HCH2   0   0.245  -1.4054  -0.4195   1.3323
 NBT  H3C2  H  HCH2   0   0.255  -2.2868  -0.9493  -0.0815
 NBT  H4C1  H  HCH3   0   0.231  -2.0629   1.3808  -1.0760
 NBT  H4C2  H  HCH3   0   0.247  -2.9731   1.3422   0.4290
 NBT  H4C3  H  HCH3   0   0.229  -1.3197   1.9217   0.4309
 NBT  O15   O  O     -1  -0.394   1.2401   0.2887   1.0621
 NBT  O16   O  O      0  -0.385   1.2666   1.0751  -0.9214

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
 NBT  C1   C2    single  1.518  0.020  1.518
 NBT  C1   H1C1  single  0.970  0.020  1.090
 NBT  C1   H1C2  single  0.970  0.020  1.090
 NBT  C1   H1C3  single  0.970  0.020  1.090
 NBT  C2   C3    single  1.525  0.020  1.525
 NBT  C2   NCG   single  1.502  0.020  1.502
 NBT  C2   H2    single  0.970  0.020  1.090
 NBT  C3   C4    single  1.522  0.020  1.522
 NBT  C3   H3C1  single  0.970  0.020  1.090
 NBT  C3   H3C2  single  0.970  0.020  1.090
 NBT  C4   H4C1  single  0.970  0.020  1.090
 NBT  C4   H4C2  single  0.970  0.020  1.090
 NBT  C4   H4C3  single  0.970  0.020  1.090
 NBT  O15  NCG   single  1.208  0.020  1.208
 NBT  O16  NCG   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
 NBT  H1C3  C1   H1C2  107.70  3.000
 NBT  H1C3  C1   H1C1  109.08  3.000
 NBT  H1C2  C1   H1C1  108.13  3.000
 NBT  H1C3  C1   C2    111.86  3.000
 NBT  H1C2  C1   C2    108.17  3.000
 NBT  H1C1  C1   C2    111.75  3.000
 NBT  H2    C2   NCG   104.83  3.000
 NBT  H2    C2   C3    109.89  3.000
 NBT  NCG   C2   C3    108.89  3.000
 NBT  H2    C2   C1    110.41  3.000
 NBT  NCG   C2   C1    109.52  3.000
 NBT  C3    C2   C1    112.97  3.000
 NBT  H3C2  C3   H3C1  106.34  3.000
 NBT  H3C2  C3   C4    109.63  3.000
 NBT  H3C1  C3   C4    110.75  3.000
 NBT  H3C2  C3   C2    105.69  3.000
 NBT  H3C1  C3   C2    109.52  3.000
 NBT  C4    C3   C2    114.48  3.000
 NBT  H4C3  C4   H4C2  106.97  3.000
 NBT  H4C3  C4   H4C1  108.02  3.000
 NBT  H4C2  C4   H4C1  107.59  3.000
 NBT  H4C3  C4   C3    112.38  3.000
 NBT  H4C2  C4   C3    110.19  3.000
 NBT  H4C1  C4   C3    111.47  3.000
 NBT  O16   NCG  O15   124.13  3.000
 NBT  O16   NCG  C2    118.25  3.000
 NBT  O15   NCG  C2    117.61  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
 NBT  Var_01  H4C1  C4  C3  C2  52.72  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
 NBT  chir_01  C2  C1  C3  NCG  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
 NBT  plan-1  C2   0.020
 NBT  plan-1  NCG  0.020
 NBT  plan-1  O15  0.020
 NBT  plan-1  O16  0.020

