# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:57:03 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-naphthalen-1-yl-~{N}-oxidanyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CCc1cccc2ccccc12
#
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
 8SQ  8SQ  3-naphthalen-1-yl-~{N}-oxidanyl-propanamide  ligand  29  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SQ
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
 8SQ  C10  C  CR16  0  -0.339  -1.1788   1.4982  -0.4990
 8SQ  C13  C  C     0   0.531   3.0910   0.3281   0.0175
 8SQ  C01  C  CR66  0   0.117  -2.8143  -0.1466   0.2405
 8SQ  C02  C  CR66  0   0.086  -1.4933   0.1508  -0.1937
 8SQ  C03  C  CR6   0   0.118  -0.5413  -0.9059  -0.3084
 8SQ  C04  C  CR16  0  -0.336  -0.9315  -2.1864  -0.0071
 8SQ  C05  C  CR16  0  -0.242  -2.2425  -2.4823   0.4167
 8SQ  C06  C  CR16  0  -0.335  -3.1653  -1.4834   0.5421
 8SQ  C07  C  CR16  0  -0.311  -3.7590   0.9001   0.3605
 8SQ  C08  C  CR16  0  -0.260  -3.4192   2.1912   0.0643
 8SQ  C09  C  CR16  0  -0.251  -2.1136   2.4903  -0.3729
 8SQ  C11  C  CH2   0  -0.545   0.8801  -0.6307  -0.7122
 8SQ  C12  C  CH2   0  -0.579   1.7074  -0.0917   0.4587
 8SQ  N01  N  NH1   0  -0.375   4.0700  -0.1081   0.8291
 8SQ  O01  O  O     0  -0.481   3.2904   1.0255  -0.9625
 8SQ  O02  O  OH1   0  -0.544   5.3758   0.0951   0.5026
 8SQ  H1   H  HCR6  0   0.249  -0.1856   1.7577  -0.8412
 8SQ  H2   H  HCR6  0   0.250  -0.2132  -2.9931  -0.0937
 8SQ  H3   H  HCR6  0   0.257  -2.5115  -3.5060   0.6420
 8SQ  H4   H  HCR6  0   0.254  -4.1746  -1.7026   0.8688
 8SQ  H5   H  HCR6  0   0.255  -4.7624   0.6598   0.6916
 8SQ  H6   H  HCR6  0   0.258  -4.1491   2.9840   0.1611
 8SQ  H7   H  HCR6  0   0.259  -1.8480   3.5121  -0.6104
 8SQ  H8   H  HCH2  0   0.268   1.3360  -1.5564  -1.0687
 8SQ  H9   H  HCH2  0   0.258   0.9182   0.0715  -1.5466
 8SQ  H10  H  HCH2  0   0.267   1.7497  -0.8400   1.2526
 8SQ  H11  H  HCH2  0   0.281   1.2249   0.7863   0.8949
 8SQ  H12  H  HNH1  0   0.415   3.9133  -0.7932   1.5538
 8SQ  H13  H  HOH1  0   0.478   5.6559   0.8843   0.9840

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
 8SQ  C08  C07  aromatic  1.368  0.020  1.368
 8SQ  C08  C09  aromatic  1.409  0.020  1.409
 8SQ  C07  C01  aromatic  1.415  0.020  1.415
 8SQ  C09  C10  aromatic  1.369  0.020  1.369
 8SQ  C01  C06  aromatic  1.415  0.020  1.415
 8SQ  C01  C02  aromatic  1.422  0.020  1.422
 8SQ  C10  C02  aromatic  1.417  0.020  1.417
 8SQ  C06  C05  aromatic  1.366  0.020  1.366
 8SQ  C02  C03  aromatic  1.427  0.020  1.427
 8SQ  C05  C04  aromatic  1.409  0.020  1.409
 8SQ  C03  C04  aromatic  1.372  0.020  1.372
 8SQ  C03  C11  single    1.503  0.020  1.503
 8SQ  C11  C12  single    1.532  0.020  1.532
 8SQ  C12  C13  single    1.512  0.020  1.512
 8SQ  N01  O02  single    1.361  0.020  1.361
 8SQ  N01  C13  single    1.344  0.020  1.344
 8SQ  C13  O01  double    1.219  0.020  1.219
 8SQ  C10  H1   single    0.930  0.020  1.080
 8SQ  C04  H2   single    0.930  0.020  1.080
 8SQ  C05  H3   single    0.930  0.020  1.080
 8SQ  C06  H4   single    0.930  0.020  1.080
 8SQ  C07  H5   single    0.930  0.020  1.080
 8SQ  C08  H6   single    0.930  0.020  1.080
 8SQ  C09  H7   single    0.930  0.020  1.080
 8SQ  C11  H8   single    0.970  0.020  1.090
 8SQ  C11  H9   single    0.970  0.020  1.090
 8SQ  C12  H10  single    0.970  0.020  1.090
 8SQ  C12  H11  single    0.970  0.020  1.090
 8SQ  N01  H12  single    0.860  0.020  1.020
 8SQ  O02  H13  single    0.850  0.020  0.980

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
 8SQ  H1   C10  C09  118.82  3.000
 8SQ  H1   C10  C02  120.00  3.000
 8SQ  C09  C10  C02  121.18  3.000
 8SQ  O01  C13  N01  123.48  3.000
 8SQ  O01  C13  C12  122.90  3.000
 8SQ  N01  C13  C12  113.59  3.000
 8SQ  C07  C01  C06  121.01  3.000
 8SQ  C06  C01  C02  119.56  3.000
 8SQ  C07  C01  C02  119.43  3.000
 8SQ  C03  C02  C01  119.31  3.000
 8SQ  C03  C02  C10  122.60  3.000
 8SQ  C01  C02  C10  118.09  3.000
 8SQ  C11  C03  C04  119.92  3.000
 8SQ  C11  C03  C02  121.13  3.000
 8SQ  C04  C03  C02  118.93  3.000
 8SQ  H2   C04  C05  118.97  3.000
 8SQ  H2   C04  C03  119.25  3.000
 8SQ  C05  C04  C03  121.77  3.000
 8SQ  H3   C05  C06  120.32  3.000
 8SQ  H3   C05  C04  119.51  3.000
 8SQ  C06  C05  C04  120.17  3.000
 8SQ  H4   C06  C05  120.62  3.000
 8SQ  H4   C06  C01  119.12  3.000
 8SQ  C05  C06  C01  120.26  3.000
 8SQ  H5   C07  C08  120.37  3.000
 8SQ  H5   C07  C01  118.69  3.000
 8SQ  C08  C07  C01  120.94  3.000
 8SQ  H6   C08  C09  119.82  3.000
 8SQ  H6   C08  C07  120.32  3.000
 8SQ  C09  C08  C07  119.86  3.000
 8SQ  H7   C09  C08  119.74  3.000
 8SQ  H7   C09  C10  119.77  3.000
 8SQ  C08  C09  C10  120.50  3.000
 8SQ  H9   C11  H8   106.34  3.000
 8SQ  H9   C11  C12  109.83  3.000
 8SQ  H8   C11  C12  108.82  3.000
 8SQ  H9   C11  C03  110.87  3.000
 8SQ  H8   C11  C03  109.11  3.000
 8SQ  C12  C11  C03  111.71  3.000
 8SQ  H11  C12  H10  106.12  3.000
 8SQ  H11  C12  C11  110.45  3.000
 8SQ  H10  C12  C11  109.61  3.000
 8SQ  H11  C12  C13  107.31  3.000
 8SQ  H10  C12  C13  111.53  3.000
 8SQ  C11  C12  C13  111.65  3.000
 8SQ  H12  N01  O02  114.99  3.000
 8SQ  H12  N01  C13  122.72  3.000
 8SQ  O02  N01  C13  120.35  3.000
 8SQ  H13  O02  N01  106.29  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
 8SQ  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 8SQ  CONST_02  C07  C01  C02  C10     0.00   0.0  0
 8SQ  CONST_03  C06  C01  C02  C10   180.00   0.0  0
 8SQ  CONST_04  C04  C03  C02  C10   180.00   0.0  0
 8SQ  CONST_05  C09  C08  C07  C01     0.00   0.0  0
 8SQ  CONST_06  C04  C05  C06  C01     0.00   0.0  0
 8SQ  CONST_07  C09  C10  C02  C01     0.00   0.0  0
 8SQ  CONST_08  C04  C03  C02  C01     0.00   0.0  0
 8SQ  CONST_09  C08  C07  C01  C02     0.00   0.0  0
 8SQ  CONST_10  C05  C06  C01  C02     0.00   0.0  0
 8SQ  CONST_11  C08  C09  C10  C02     0.00   0.0  0
 8SQ  CONST_12  C05  C04  C03  C02     0.00   0.0  0
 8SQ  CONST_13  C07  C01  C02  C03   180.00   0.0  0
 8SQ  CONST_14  C06  C01  C02  C03     0.00   0.0  0
 8SQ  CONST_15  C09  C10  C02  C03   180.00   0.0  0
 8SQ  CONST_16  C06  C05  C04  C03     0.00   0.0  0
 8SQ  CONST_17  C07  C01  C06  C05   180.00   0.0  0
 8SQ  CONST_18  C08  C07  C01  C06   180.00   0.0  0
 8SQ  CONST_19  C11  C03  C02  C10     0.00   0.0  0
 8SQ  CONST_20  C11  C03  C02  C01   180.00   0.0  0
 8SQ  CONST_21  C11  C03  C04  C05   180.00   0.0  0
 8SQ  CONST_22  H6   C08  C09  C10   180.00   0.0  0
 8SQ  CONST_23  H3   C05  C06  C01   180.00   0.0  0
 8SQ  CONST_24  H1   C10  C02  C01   180.00   0.0  0
 8SQ  CONST_25  H5   C07  C01  C02   180.00   0.0  0
 8SQ  CONST_26  H4   C06  C01  C02   180.00   0.0  0
 8SQ  CONST_27  H7   C09  C10  C02   180.00   0.0  0
 8SQ  CONST_28  H2   C04  C03  C02   180.00   0.0  0
 8SQ  CONST_29  O02  N01  C13  C12   180.00   0.0  0
 8SQ  CONST_30  O02  N01  C13  O01     0.00   0.0  0
 8SQ  CONST_31  H12  N01  C13  C12     0.00   0.0  0
 8SQ  Var_01    C12  C11  C03  C02    78.91  30.0  2
 8SQ  Var_02    C03  C11  C12  C13  -173.71  30.0  2
 8SQ  Var_03    N01  C13  C12  C11  -134.13  30.0  3

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
 8SQ  plan-1  C10  0.020
 8SQ  plan-1  C01  0.020
 8SQ  plan-1  C02  0.020
 8SQ  plan-1  C03  0.020
 8SQ  plan-1  C04  0.020
 8SQ  plan-1  C05  0.020
 8SQ  plan-1  C06  0.020
 8SQ  plan-1  C07  0.020
 8SQ  plan-1  C08  0.020
 8SQ  plan-1  C09  0.020
 8SQ  plan-1  C11  0.020
 8SQ  plan-1  H1   0.020
 8SQ  plan-1  H2   0.020
 8SQ  plan-1  H3   0.020
 8SQ  plan-1  H4   0.020
 8SQ  plan-1  H5   0.020
 8SQ  plan-1  H6   0.020
 8SQ  plan-1  H7   0.020
 8SQ  plan-2  C13  0.020
 8SQ  plan-2  C12  0.020
 8SQ  plan-2  N01  0.020
 8SQ  plan-2  O01  0.020
 8SQ  plan-2  O02  0.020
 8SQ  plan-2  H12  0.020

