# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:14:55 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (2S)-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
 SNO  SNO  (2S)-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_SNO
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
 SNO  C1   C  CR6    0   0.241   1.3841  -0.0116  -0.0153
 SNO  C2   C  CR16   0  -0.253   0.8495  -1.2828  -0.1693
 SNO  C3   C  CR16   0  -0.295  -0.5238  -1.4210  -0.2532
 SNO  C4   C  CR6    0   0.132  -1.3593  -0.3095  -0.1767
 SNO  C5   C  CR16   0  -0.306  -0.7978   0.9571  -0.0327
 SNO  C6   C  CR16   0  -0.250   0.5735   1.1130   0.0513
 SNO  C7   C  CH1    0  -0.064  -2.8280  -0.5033  -0.2363
 SNO  C8   C  CH2    0  -0.242  -3.6955   0.0150   0.8263
 SNO  N1   N  N      1   0.330   2.8258   0.1473   0.0714
 SNO  O1   O  O     -1  -0.380   3.5120  -0.8468   0.0224
 SNO  O2   O  O      0  -0.380   3.2692   1.2657   0.1881
 SNO  O3   O  O2     0  -0.469  -3.6235   0.6444  -0.4396
 SNO  H22  H  HCR6   0   0.299   1.4832  -2.1554  -0.2285
 SNO  H33  H  HCR6   0   0.275  -0.9474  -2.4090  -0.3820
 SNO  H55  H  HCR6   0   0.277  -1.4300   1.8337   0.0106
 SNO  H66  H  HCR6   0   0.298   0.9944   2.1013   0.1638
 SNO  H77  H  HCH1   0   0.276  -3.1541  -1.3957  -0.7672
 SNO  H81  H  HCH2   0   0.259  -4.6251  -0.4999   1.0513
 SNO  H82  H  HCH2   0   0.252  -3.2514   0.5599   1.6547

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
 SNO  C1  C2   aromatic  1.388  0.020  1.388
 SNO  C1  C6   aromatic  1.388  0.020  1.388
 SNO  C1  N1   single    1.453  0.020  1.453
 SNO  C2  C3   aromatic  1.383  0.020  1.383
 SNO  C2  H22  single    0.930  0.020  1.080
 SNO  C3  C4   aromatic  1.393  0.020  1.393
 SNO  C3  H33  single    0.930  0.020  1.080
 SNO  C4  C5   aromatic  1.393  0.020  1.393
 SNO  C4  C7   single    1.483  0.020  1.483
 SNO  C5  C6   aromatic  1.383  0.020  1.383
 SNO  C5  H55  single    0.930  0.020  1.080
 SNO  C6  H66  single    0.930  0.020  1.080
 SNO  C7  C8   single    1.466  0.020  1.466
 SNO  C7  O3   single    1.411  0.020  1.411
 SNO  C7  H77  single    0.970  0.020  1.090
 SNO  C8  O3   single    1.416  0.020  1.416
 SNO  C8  H81  single    0.970  0.020  1.090
 SNO  C8  H82  single    0.970  0.020  1.090
 SNO  N1  O1   single    1.209  0.020  1.209
 SNO  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
 SNO  N1   C1  C6   119.21  3.000
 SNO  N1   C1  C2   119.28  3.000
 SNO  C6   C1  C2   121.51  3.000
 SNO  H22  C2  C3   119.91  3.000
 SNO  H22  C2  C1   121.34  3.000
 SNO  C3   C2  C1   118.75  3.000
 SNO  H33  C3  C4   120.01  3.000
 SNO  H33  C3  C2   119.15  3.000
 SNO  C4   C3  C2   120.85  3.000
 SNO  C7   C4  C5   121.49  3.000
 SNO  C7   C4  C3   119.20  3.000
 SNO  C5   C4  C3   119.31  3.000
 SNO  H55  C5  C6   119.07  3.000
 SNO  H55  C5  C4   120.36  3.000
 SNO  C6   C5  C4   120.57  3.000
 SNO  H66  C6  C5   119.74  3.000
 SNO  H66  C6  C1   121.25  3.000
 SNO  C5   C6  C1   119.01  3.000
 SNO  H77  C7  O3   115.32  3.000
 SNO  H77  C7  C8   117.77  3.000
 SNO  O3   C7  C8    58.90  3.000
 SNO  H77  C7  C4   115.06  3.000
 SNO  O3   C7  C4   117.26  3.000
 SNO  C8   C7  C4   120.71  3.000
 SNO  H82  C8  H81  115.44  3.000
 SNO  H82  C8  O3   115.98  3.000
 SNO  H81  C8  O3   116.08  3.000
 SNO  H82  C8  C7   119.20  3.000
 SNO  H81  C8  C7   119.27  3.000
 SNO  O3   C8  C7    58.60  3.000
 SNO  O2   N1  O1   123.82  3.000
 SNO  O2   N1  C1   118.09  3.000
 SNO  O1   N1  C1   118.09  3.000
 SNO  C8   O3  C7    62.50  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
 SNO  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 SNO  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 SNO  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 SNO  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 SNO  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 SNO  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 SNO  CONST_07  C7   C4  C3  C2  180.00   0.0  0
 SNO  CONST_08  C7   C4  C5  C6  180.00   0.0  0
 SNO  CONST_09  N1   C1  C2  C3  180.00   0.0  0
 SNO  CONST_10  N1   C1  C6  C5  180.00   0.0  0
 SNO  CONST_11  H33  C3  C2  C1  180.00   0.0  0
 SNO  CONST_12  H55  C5  C6  C1  180.00   0.0  0
 SNO  CONST_13  H66  C6  C1  C2  180.00   0.0  0
 SNO  CONST_14  H22  C2  C3  C4  180.00   0.0  0
 SNO  CONST_15  O1   N1  C1  C2    0.00   0.0  0
 SNO  CONST_16  O2   N1  C1  C2  180.00   0.0  0
 SNO  CONST_17  O1   N1  C1  C6  180.00   0.0  0
 SNO  CONST_18  O2   N1  C1  C6    0.00   0.0  0
 SNO  Var_01    C8   C7  C4  C3  124.74  30.0  2
 SNO  Var_02    O3   C8  C7  C4  105.29  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
 SNO  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
 SNO  plan-1  C1   0.020
 SNO  plan-1  C2   0.020
 SNO  plan-1  C3   0.020
 SNO  plan-1  C4   0.020
 SNO  plan-1  C5   0.020
 SNO  plan-1  C6   0.020
 SNO  plan-1  C7   0.020
 SNO  plan-1  N1   0.020
 SNO  plan-1  H22  0.020
 SNO  plan-1  H33  0.020
 SNO  plan-1  H55  0.020
 SNO  plan-1  H66  0.020
 SNO  plan-2  C1   0.020
 SNO  plan-2  N1   0.020
 SNO  plan-2  O1   0.020
 SNO  plan-2  O2   0.020

