# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:59:33 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (1R)-2-azido-1-(4-nitrophenyl)ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CN=[N+]=[N-])c1ccc(cc1)[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
 RPN  RPN  (1R)-2-azido-1-(4-nitrophenyl)ethanol  ligand  23  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RPN
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
 RPN  C1    C  CH2    0  -0.344  -2.3468  -0.6644  -0.7099
 RPN  C2    C  CH1    0  -0.027  -1.6672  -0.3647   0.6313
 RPN  O3    O  OH1    0  -0.648  -2.2815   0.7139   1.2795
 RPN  C4    C  CR6    0   0.096  -0.1793  -0.1949   0.4193
 RPN  N5    N  N      0  -0.355  -3.7468  -1.0353  -0.5267
 RPN  N6    N  N      1   0.359  -4.5409  -0.1311  -0.3401
 RPN  N7    N  N     -1  -0.221  -5.3638   0.6170  -0.1777
 RPN  C8    C  CR16   0  -0.282   0.5821  -1.3062   0.0578
 RPN  C9    C  CR16   0  -0.251   1.9401  -1.1997  -0.1703
 RPN  C10   C  CR6    0   0.239   2.5437   0.0433  -0.0332
 RPN  C11   C  CR16   0  -0.245   1.8148   1.1629   0.3337
 RPN  C12   C  CR16   0  -0.319   0.4545   1.0345   0.5623
 RPN  N13   N  N      1   0.330   3.9716   0.1715  -0.2716
 RPN  O14   O  O     -1  -0.379   4.5911  -0.8247  -0.5628
 RPN  O15   O  O      0  -0.379   4.4699   1.2678  -0.1677
 RPN  HC11  H  HCH2   0   0.271  -2.2411   0.1918  -1.3856
 RPN  HC12  H  HCH2   0   0.279  -1.8727  -1.5182  -1.1895
 RPN  HC2   H  HCH1   0   0.278  -1.8175  -1.2288   1.2855
 RPN  H03   H  HOH1   0   0.456  -2.2362   1.4997   0.7224
 RPN  HC8   H  HCR6   0   0.277   0.1121  -2.2773  -0.0380
 RPN  HC9   H  HCR6   0   0.299   2.5089  -2.0757  -0.4456
 RPN  H11   H  HCR6   0   0.299   2.2872   2.1275   0.4490
 RPN  H12   H  HCR6   0   0.267  -0.0959   1.9154   0.8619

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
 RPN  C1   C2    single    1.533  0.020  1.533
 RPN  C1   N5    single    1.460  0.020  1.460
 RPN  C1   HC11  single    0.970  0.020  1.090
 RPN  C1   HC12  single    0.970  0.020  1.090
 RPN  C2   O3    single    1.400  0.020  1.400
 RPN  C2   C4    single    1.513  0.020  1.513
 RPN  C2   HC2   single    0.970  0.020  1.090
 RPN  O3   H03   single    0.850  0.020  0.980
 RPN  C4   C8    aromatic  1.395  0.020  1.395
 RPN  C4   C12   aromatic  1.390  0.020  1.390
 RPN  N5   N6    double    1.218  0.020  1.218
 RPN  N6   N7    double    1.124  0.020  1.124
 RPN  C8   C9    aromatic  1.381  0.020  1.381
 RPN  C8   HC8   single    0.930  0.020  1.080
 RPN  C9   C10   aromatic  1.389  0.020  1.389
 RPN  C9   HC9   single    0.930  0.020  1.080
 RPN  C10  C11   aromatic  1.385  0.020  1.385
 RPN  C10  N13   single    1.453  0.020  1.453
 RPN  C11  C12   aromatic  1.385  0.020  1.385
 RPN  C11  H11   single    0.930  0.020  1.080
 RPN  C12  H12   single    0.930  0.020  1.080
 RPN  N13  O14   single    1.209  0.020  1.209
 RPN  N13  O15   double    1.209  0.020  1.209

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
 RPN  HC12  C1   HC11  107.42  3.000
 RPN  HC12  C1   N5    105.89  3.000
 RPN  HC11  C1   N5    111.62  3.000
 RPN  HC12  C1   C2    110.23  3.000
 RPN  HC11  C1   C2    110.12  3.000
 RPN  N5    C1   C2    111.40  3.000
 RPN  HC2   C2   C4    107.91  3.000
 RPN  HC2   C2   O3    105.75  3.000
 RPN  C4    C2   O3    114.20  3.000
 RPN  HC2   C2   C1    107.92  3.000
 RPN  C4    C2   C1    109.60  3.000
 RPN  O3    C2   C1    111.16  3.000
 RPN  H03   O3   C2    109.86  3.000
 RPN  C12   C4   C8    118.84  3.000
 RPN  C12   C4   C2    122.22  3.000
 RPN  C8    C4   C2    118.94  3.000
 RPN  N6    N5   C1    117.12  3.000
 RPN  N7    N6   N5    173.62  3.000
 RPN  HC8   C8   C9    118.77  3.000
 RPN  HC8   C8   C4    120.03  3.000
 RPN  C9    C8   C4    121.20  3.000
 RPN  HC9   C9   C10   121.49  3.000
 RPN  HC9   C9   C8    119.82  3.000
 RPN  C10   C9   C8    118.70  3.000
 RPN  N13   C10  C11   119.28  3.000
 RPN  N13   C10  C9    119.33  3.000
 RPN  C11   C10  C9    121.39  3.000
 RPN  H11   C11  C12   119.64  3.000
 RPN  H11   C11  C10   121.32  3.000
 RPN  C12   C11  C10   119.04  3.000
 RPN  H12   C12  C11   118.04  3.000
 RPN  H12   C12  C4    121.12  3.000
 RPN  C11   C12  C4    120.83  3.000
 RPN  O15   N13  O14   123.84  3.000
 RPN  O15   N13  C10   118.09  3.000
 RPN  O14   N13  C10   118.06  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
 RPN  CONST_01  C10   C9   C8   C4     0.00   0.0  0
 RPN  CONST_02  C10   C11  C12  C4     0.00   0.0  0
 RPN  CONST_03  C11   C12  C4   C8     0.00   0.0  0
 RPN  CONST_04  C11   C10  C9   C8     0.00   0.0  0
 RPN  CONST_05  C12   C4   C8   C9     0.00   0.0  0
 RPN  CONST_06  C12   C11  C10  C9     0.00   0.0  0
 RPN  CONST_07  C9    C8   C4   C2   180.00   0.0  0
 RPN  CONST_08  C11   C12  C4   C2   180.00   0.0  0
 RPN  CONST_09  N13   C10  C9   C8   180.00   0.0  0
 RPN  CONST_10  N13   C10  C11  C12  180.00   0.0  0
 RPN  CONST_11  HC9   C9   C8   C4   180.00   0.0  0
 RPN  CONST_12  H11   C11  C12  C4   180.00   0.0  0
 RPN  CONST_13  H12   C12  C4   C8   180.00   0.0  0
 RPN  CONST_14  HC8   C8   C9   C10  180.00   0.0  0
 RPN  CONST_15  O14   N13  C10  C9     0.00   0.0  0
 RPN  CONST_16  O15   N13  C10  C9   180.00   0.0  0
 RPN  CONST_17  O14   N13  C10  C11  180.00   0.0  0
 RPN  CONST_18  O15   N13  C10  C11    0.00   0.0  0
 RPN  Var_01    HC11  C1   N5   N6   -44.44  30.0  1

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
 RPN  chir_01  C2  C1  O3  C4  positiv

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
 RPN  plan-1  C2   0.020
 RPN  plan-1  C4   0.020
 RPN  plan-1  C8   0.020
 RPN  plan-1  C9   0.020
 RPN  plan-1  C10  0.020
 RPN  plan-1  C11  0.020
 RPN  plan-1  C12  0.020
 RPN  plan-1  N13  0.020
 RPN  plan-1  HC8  0.020
 RPN  plan-1  HC9  0.020
 RPN  plan-1  H11  0.020
 RPN  plan-1  H12  0.020
 RPN  plan-2  C10  0.020
 RPN  plan-2  N13  0.020
 RPN  plan-2  O14  0.020
 RPN  plan-2  O15  0.020
 RPN  plan-3  C1   0.020
 RPN  plan-3  N5   0.020
 RPN  plan-3  N6   0.020
 RPN  plan-3  N7   0.020

