# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:02:36 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2R)-2-(4-nitrophenyl)oxirane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(cc1)[C@@H]2CO2
#
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
 RNO  RNO  (2R)-2-(4-nitrophenyl)oxirane  ligand  19  12  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RNO
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
 RNO  C1   C  CR6    0   0.241   1.3797  -0.0062   0.0589
 RNO  C2   C  CR16   0  -0.253   0.8532  -1.2755   0.2512
 RNO  C3   C  CR16   0  -0.296  -0.5197  -1.4211   0.3302
 RNO  C4   C  CR6    0   0.134  -1.3628  -0.3191   0.2119
 RNO  C5   C  CR16   0  -0.306  -0.8094   0.9461   0.0289
 RNO  C6   C  CR16   0  -0.250   0.5613   1.1093  -0.0509
 RNO  C7   C  CH1    0  -0.065  -2.8303  -0.5208   0.2725
 RNO  C8   C  CH2    0  -0.243  -3.7003  -0.0329  -0.8023
 RNO  N1   N  N      1   0.330   2.8207   0.1602  -0.0228
 RNO  O1   O  O     -1  -0.380   3.5138  -0.8261   0.0679
 RNO  O2   O  O      0  -0.380   3.2568   1.2770  -0.1782
 RNO  O3   O  O2     0  -0.469  -3.6334   0.6262   0.4488
 RNO  H2   H  HCR6   0   0.299   1.4921  -2.1412   0.3442
 RNO  H3   H  HCR6   0   0.275  -0.9365  -2.4076   0.4893
 RNO  H5   H  HCR6   0   0.277  -1.4467   1.8166  -0.0469
 RNO  H6   H  HCR6   0   0.298   0.9755   2.0966  -0.1940
 RNO  H7   H  HCH1   0   0.276  -3.1517  -1.4029   0.8234
 RNO  H81  H  HCH2   0   0.252  -3.2595   0.4965  -1.6426
 RNO  H82  H  HCH2   0   0.259  -4.6263  -0.5587  -1.0164

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
 RNO  C1  C2   aromatic  1.388  0.020  1.388
 RNO  C1  C6   aromatic  1.388  0.020  1.388
 RNO  C1  N1   single    1.453  0.020  1.453
 RNO  C2  C3   aromatic  1.383  0.020  1.383
 RNO  C2  H2   single    0.930  0.020  1.080
 RNO  C3  C4   aromatic  1.393  0.020  1.393
 RNO  C3  H3   single    0.930  0.020  1.080
 RNO  C4  C5   aromatic  1.393  0.020  1.393
 RNO  C4  C7   single    1.482  0.020  1.482
 RNO  C5  C6   aromatic  1.383  0.020  1.383
 RNO  C5  H5   single    0.930  0.020  1.080
 RNO  C6  H6   single    0.930  0.020  1.080
 RNO  C7  C8   single    1.466  0.020  1.466
 RNO  C7  O3   single    1.411  0.020  1.411
 RNO  C7  H7   single    0.970  0.020  1.090
 RNO  C8  O3   single    1.416  0.020  1.416
 RNO  C8  H81  single    0.970  0.020  1.090
 RNO  C8  H82  single    0.970  0.020  1.090
 RNO  N1  O1   single    1.209  0.020  1.209
 RNO  N1  O2   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
 RNO  N1   C1  C6   119.23  3.000
 RNO  N1   C1  C2   119.27  3.000
 RNO  C6   C1  C2   121.50  3.000
 RNO  H2   C2  C3   119.87  3.000
 RNO  H2   C2  C1   121.38  3.000
 RNO  C3   C2  C1   118.75  3.000
 RNO  H3   C3  C4   120.03  3.000
 RNO  H3   C3  C2   119.11  3.000
 RNO  C4   C3  C2   120.86  3.000
 RNO  C7   C4  C5   121.48  3.000
 RNO  C7   C4  C3   119.22  3.000
 RNO  C5   C4  C3   119.30  3.000
 RNO  H5   C5  C6   119.02  3.000
 RNO  H5   C5  C4   120.40  3.000
 RNO  C6   C5  C4   120.57  3.000
 RNO  H6   C6  C5   119.72  3.000
 RNO  H6   C6  C1   121.26  3.000
 RNO  C5   C6  C1   119.02  3.000
 RNO  H7   C7  O3   115.30  3.000
 RNO  H7   C7  C8   117.73  3.000
 RNO  O3   C7  C8    58.90  3.000
 RNO  H7   C7  C4   115.04  3.000
 RNO  O3   C7  C4   117.25  3.000
 RNO  C8   C7  C4   120.80  3.000
 RNO  H82  C8  H81  115.42  3.000
 RNO  H82  C8  O3   116.10  3.000
 RNO  H81  C8  O3   115.93  3.000
 RNO  H82  C8  C7   119.29  3.000
 RNO  H81  C8  C7   119.22  3.000
 RNO  O3   C8  C7    58.61  3.000
 RNO  O2   N1  O1   123.82  3.000
 RNO  O2   N1  C1   118.09  3.000
 RNO  O1   N1  C1   118.09  3.000
 RNO  C8   O3  C7    62.49  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
 RNO  CONST_01  C4  C3  C2  C1     0.00   0.0  0
 RNO  CONST_02  C4  C5  C6  C1     0.00   0.0  0
 RNO  CONST_03  C5  C6  C1  C2     0.00   0.0  0
 RNO  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 RNO  CONST_05  C6  C1  C2  C3     0.00   0.0  0
 RNO  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 RNO  CONST_07  C7  C4  C3  C2   180.00   0.0  0
 RNO  CONST_08  C7  C4  C5  C6   180.00   0.0  0
 RNO  CONST_09  N1  C1  C2  C3   180.00   0.0  0
 RNO  CONST_10  N1  C1  C6  C5   180.00   0.0  0
 RNO  CONST_11  H3  C3  C2  C1   180.00   0.0  0
 RNO  CONST_12  H5  C5  C6  C1   180.00   0.0  0
 RNO  CONST_13  H6  C6  C1  C2   180.00   0.0  0
 RNO  CONST_14  H2  C2  C3  C4   180.00   0.0  0
 RNO  CONST_15  O1  N1  C1  C2     0.00   0.0  0
 RNO  CONST_16  O2  N1  C1  C2   180.00   0.0  0
 RNO  CONST_17  O1  N1  C1  C6   180.00   0.0  0
 RNO  CONST_18  O2  N1  C1  C6     0.00   0.0  0
 RNO  Var_01    C8  C7  C4  C3  -125.46  30.0  2
 RNO  Var_02    O3  C8  C7  C4  -105.24  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
 RNO  chir_01  C7  C4  C8  O3  both

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
 RNO  plan-1  C1  0.020
 RNO  plan-1  C2  0.020
 RNO  plan-1  C3  0.020
 RNO  plan-1  C4  0.020
 RNO  plan-1  C5  0.020
 RNO  plan-1  C6  0.020
 RNO  plan-1  C7  0.020
 RNO  plan-1  N1  0.020
 RNO  plan-1  H2  0.020
 RNO  plan-1  H3  0.020
 RNO  plan-1  H5  0.020
 RNO  plan-1  H6  0.020
 RNO  plan-2  C1  0.020
 RNO  plan-2  N1  0.020
 RNO  plan-2  O1  0.020
 RNO  plan-2  O2  0.020

