# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:06:41 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(c2ccccc12)[S](=O)(=O)NCc3ccccn3
#
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
 PYV  PYV  4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide  ligand  35  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PYV
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
 PYV  S     S   S     0   1.366  -1.2450  -2.0229   0.4093
 PYV  C1    C   CR6   0  -0.193   2.7017   0.0016  -0.6273
 PYV  N1    N   NC1   0  -0.724  -2.3715  -0.8261   0.4157
 PYV  O1    O   OS    0  -0.648  -1.2444  -2.5975   1.7438
 PYV  C2    C   CR66  0   0.193   2.1240   0.3357   0.6294
 PYV  N2    N   N     0  -0.405  -4.9462  -0.1022  -0.8257
 PYV  O2    O   OS    0  -0.639  -1.5331  -2.8734  -0.7320
 PYV  C3    C   CR66  0   0.195   0.9075  -0.3118   1.0073
 PYV  C4    C   CR6   0  -0.266   0.3233  -1.2359   0.0916
 PYV  C5    C   CR16  0  -0.251   0.9156  -1.5170  -1.1078
 PYV  C6    C   CR16  0  -0.229   2.1231  -0.9014  -1.4711
 PYV  C7    C   CR16  0  -0.348   0.3443   0.0076   2.2663
 PYV  C8    C   CR16  0  -0.231   0.9308   0.9249   3.0939
 PYV  C9    C   CR16  0  -0.242   2.1183   1.5690   2.7140
 PYV  C10   C   CR16  0  -0.313   2.7021   1.2753   1.5137
 PYV  C11   C   CH2   0  -0.356  -2.5337   0.0035  -0.7744
 PYV  C12   C   CR6   0   0.239  -3.8764   0.6819  -0.7254
 PYV  C13   C   CR16  0  -0.077  -6.1438   0.4623  -0.7796
 PYV  C14   C   CR16  0  -0.323  -6.3414   1.8297  -0.6337
 PYV  C15   C   CR16  0  -0.147  -5.2264   2.6438  -0.5319
 PYV  C16   C   CR16  0  -0.333  -3.9683   2.0585  -0.5761
 PYV  HN1   H   HNC1  0   0.418  -2.4003  -0.3127   1.2902
 PYV  H5    H   HCR6  0   0.301   0.4671  -2.2135  -1.8009
 PYV  H6    H   HCR6  0   0.297   2.5692  -1.1497  -2.4238
 PYV  H7    H   HCR6  0   0.260  -0.5453  -0.4919   2.6171
 PYV  H8    H   HCR6  0   0.276   0.4779   1.1477   4.0506
 PYV  H9    H   HCR6  0   0.274   2.5775   2.2929   3.3730
 PYV  H10   H   HCR6  0   0.269   3.6217   1.7751   1.2466
 PYV  H11   H   HCH2  0   0.265  -1.7381   0.7487  -0.8650
 PYV  H11A  H   HCH2  0   0.286  -2.4912  -0.6387  -1.6542
 PYV  H13   H   HCR6  0   0.266  -6.9948  -0.2039  -0.8677
 PYV  H14   H   HCR6  0   0.273  -7.3429   2.2360  -0.6035
 PYV  H15   H   HCR6  0   0.277  -5.3296   3.7148  -0.4191
 PYV  H16   H   HCR6  0   0.274  -3.0733   2.6607  -0.4955
 PYV  BR    BR  BR    0  -0.005   4.3120   0.8046  -1.1878

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
 PYV  S    N1    single    1.644  0.020  1.644
 PYV  S    O1    double    1.453  0.020  1.453
 PYV  S    O2    double    1.452  0.020  1.452
 PYV  S    C4    single    1.783  0.020  1.783
 PYV  BR   C1    single    1.885  0.020  1.885
 PYV  C1   C2    aromatic  1.423  0.020  1.423
 PYV  C1   C6    aromatic  1.365  0.020  1.365
 PYV  N1   C11   single    1.460  0.020  1.460
 PYV  C2   C3    aromatic  1.429  0.020  1.429
 PYV  C2   C10   aromatic  1.414  0.020  1.414
 PYV  N2   C12   aromatic  1.330  0.020  1.330
 PYV  N2   C13   aromatic  1.325  0.020  1.325
 PYV  C3   C4    aromatic  1.426  0.020  1.426
 PYV  C3   C7    aromatic  1.416  0.020  1.416
 PYV  C4   C5    aromatic  1.367  0.020  1.367
 PYV  C5   C6    aromatic  1.403  0.020  1.403
 PYV  C7   C8    aromatic  1.368  0.020  1.368
 PYV  C8   C9    aromatic  1.403  0.020  1.403
 PYV  C9   C10   aromatic  1.367  0.020  1.367
 PYV  C11  C12   single    1.505  0.020  1.505
 PYV  C12  C16   aromatic  1.388  0.020  1.388
 PYV  C13  C14   aromatic  1.389  0.020  1.389
 PYV  C14  C15   aromatic  1.384  0.020  1.384
 PYV  C15  C16   aromatic  1.388  0.020  1.388
 PYV  N1   HN1   single    0.890  0.020  1.040
 PYV  C5   H5    single    0.930  0.020  1.080
 PYV  C6   H6    single    0.930  0.020  1.080
 PYV  C7   H7    single    0.930  0.020  1.080
 PYV  C8   H8    single    0.930  0.020  1.080
 PYV  C9   H9    single    0.930  0.020  1.080
 PYV  C10  H10   single    0.930  0.020  1.080
 PYV  C11  H11   single    0.970  0.020  1.090
 PYV  C11  H11A  single    0.970  0.020  1.090
 PYV  C13  H13   single    0.930  0.020  1.080
 PYV  C14  H14   single    0.930  0.020  1.080
 PYV  C15  H15   single    0.930  0.020  1.080
 PYV  C16  H16   single    0.930  0.020  1.080

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
 PYV  C4    S    O2   107.04  3.000
 PYV  C4    S    O1   109.75  3.000
 PYV  O2    S    O1   119.36  3.000
 PYV  C4    S    N1   106.38  3.000
 PYV  O2    S    N1   107.07  3.000
 PYV  O1    S    N1   106.54  3.000
 PYV  C6    C1   C2   121.96  3.000
 PYV  C6    C1   BR   117.41  3.000
 PYV  C2    C1   BR   120.63  3.000
 PYV  HN1   N1   C11  114.33  3.000
 PYV  HN1   N1   S    113.04  3.000
 PYV  C11   N1   S    119.13  3.000
 PYV  C10   C2   C3   118.93  3.000
 PYV  C10   C2   C1   122.85  3.000
 PYV  C3    C2   C1   118.22  3.000
 PYV  C13   N2   C12  118.25  3.000
 PYV  C7    C3   C4   123.66  3.000
 PYV  C7    C3   C2   118.14  3.000
 PYV  C4    C3   C2   118.20  3.000
 PYV  C5    C4   C3   121.28  3.000
 PYV  C5    C4   S    116.53  3.000
 PYV  C3    C4   S    122.13  3.000
 PYV  H5    C5   C6   118.29  3.000
 PYV  H5    C5   C4   121.05  3.000
 PYV  C6    C5   C4   120.66  3.000
 PYV  H6    C6   C5   118.86  3.000
 PYV  H6    C6   C1   121.47  3.000
 PYV  C5    C6   C1   119.67  3.000
 PYV  H7    C7   C8   117.87  3.000
 PYV  H7    C7   C3   120.85  3.000
 PYV  C8    C7   C3   121.26  3.000
 PYV  H8    C8   C9   119.95  3.000
 PYV  H8    C8   C7   119.59  3.000
 PYV  C9    C8   C7   120.46  3.000
 PYV  H9    C9   C10  119.85  3.000
 PYV  H9    C9   C8   120.11  3.000
 PYV  C10   C9   C8   120.04  3.000
 PYV  H10   C10  C9   118.78  3.000
 PYV  H10   C10  C2   120.06  3.000
 PYV  C9    C10  C2   121.16  3.000
 PYV  H11A  C11  H11  107.83  3.000
 PYV  H11A  C11  C12  109.05  3.000
 PYV  H11   C11  C12  110.14  3.000
 PYV  H11A  C11  N1   108.59  3.000
 PYV  H11   C11  N1   111.96  3.000
 PYV  C12   C11  N1   109.19  3.000
 PYV  C16   C12  C11  120.64  3.000
 PYV  C16   C12  N2   122.65  3.000
 PYV  C11   C12  N2   116.70  3.000
 PYV  H13   C13  C14  120.11  3.000
 PYV  H13   C13  N2   116.41  3.000
 PYV  C14   C13  N2   123.48  3.000
 PYV  H14   C14  C15  121.53  3.000
 PYV  H14   C14  C13  120.30  3.000
 PYV  C15   C14  C13  118.17  3.000
 PYV  H15   C15  C16  120.47  3.000
 PYV  H15   C15  C14  120.87  3.000
 PYV  C16   C15  C14  118.66  3.000
 PYV  H16   C16  C15  120.85  3.000
 PYV  H16   C16  C12  120.36  3.000
 PYV  C15   C16  C12  118.80  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
 PYV  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 PYV  CONST_02  C7   C3   C2   C1   180.00   0.0  0
 PYV  CONST_03  C9   C10  C2   C1   180.00   0.0  0
 PYV  CONST_04  C4   C5   C6   C1     0.00   0.0  0
 PYV  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 PYV  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 PYV  CONST_07  C8   C7   C3   C2     0.00   0.0  0
 PYV  CONST_08  C8   C9   C10  C2     0.00   0.0  0
 PYV  CONST_09  C15  C16  C12  N2     0.00   0.0  0
 PYV  CONST_10  C15  C14  C13  N2     0.00   0.0  0
 PYV  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 PYV  CONST_12  C9   C10  C2   C3     0.00   0.0  0
 PYV  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 PYV  CONST_14  C9   C8   C7   C3     0.00   0.0  0
 PYV  CONST_15  C10  C2   C3   C4   180.00   0.0  0
 PYV  CONST_16  C8   C7   C3   C4   180.00   0.0  0
 PYV  CONST_17  C7   C3   C4   C5   180.00   0.0  0
 PYV  CONST_18  C10  C2   C1   C6   180.00   0.0  0
 PYV  CONST_19  C10  C2   C3   C7     0.00   0.0  0
 PYV  CONST_20  C10  C9   C8   C7     0.00   0.0  0
 PYV  CONST_21  C14  C13  N2   C12    0.00   0.0  0
 PYV  CONST_22  C14  C15  C16  C12    0.00   0.0  0
 PYV  CONST_23  C16  C12  N2   C13    0.00   0.0  0
 PYV  CONST_24  C16  C15  C14  C13    0.00   0.0  0
 PYV  CONST_25  C2   C3   C4   S    180.00   0.0  0
 PYV  CONST_26  C7   C3   C4   S      0.00   0.0  0
 PYV  CONST_27  C6   C5   C4   S    180.00   0.0  0
 PYV  CONST_28  C3   C2   C1   BR   180.00   0.0  0
 PYV  CONST_29  C10  C2   C1   BR     0.00   0.0  0
 PYV  CONST_30  C5   C6   C1   BR   180.00   0.0  0
 PYV  CONST_31  C13  N2   C12  C11  180.00   0.0  0
 PYV  CONST_32  C15  C16  C12  C11  180.00   0.0  0
 PYV  CONST_33  H10  C10  C2   C1     0.00   0.0  0
 PYV  CONST_34  H5   C5   C6   C1   180.00   0.0  0
 PYV  CONST_35  H6   C6   C1   C2   180.00   0.0  0
 PYV  CONST_36  H7   C7   C3   C2   180.00   0.0  0
 PYV  CONST_37  H9   C9   C10  C2   180.00   0.0  0
 PYV  CONST_38  H16  C16  C12  N2   180.00   0.0  0
 PYV  CONST_39  H14  C14  C13  N2   180.00   0.0  0
 PYV  CONST_40  H8   C8   C7   C3   180.00   0.0  0
 PYV  CONST_41  H13  C13  N2   C12  180.00   0.0  0
 PYV  CONST_42  H15  C15  C16  C12  180.00   0.0  0
 PYV  Var_01    C3   C4   S    N1    64.98  30.0  2
 PYV  Var_02    N2   C12  C11  N1   -66.83  30.0  2
 PYV  Var_03    C12  C11  N1   S    160.93  30.0  3
 PYV  Var_04    C11  N1   S    C4    58.68  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
 PYV  plan-1  N2   0.020
 PYV  plan-1  C11  0.020
 PYV  plan-1  C12  0.020
 PYV  plan-1  C13  0.020
 PYV  plan-1  C14  0.020
 PYV  plan-1  C15  0.020
 PYV  plan-1  C16  0.020
 PYV  plan-1  H13  0.020
 PYV  plan-1  H14  0.020
 PYV  plan-1  H15  0.020
 PYV  plan-1  H16  0.020
 PYV  plan-2  S    0.020
 PYV  plan-2  C1   0.020
 PYV  plan-2  C2   0.020
 PYV  plan-2  C3   0.020
 PYV  plan-2  C4   0.020
 PYV  plan-2  C5   0.020
 PYV  plan-2  C6   0.020
 PYV  plan-2  C7   0.020
 PYV  plan-2  C8   0.020
 PYV  plan-2  C9   0.020
 PYV  plan-2  C10  0.020
 PYV  plan-2  H5   0.020
 PYV  plan-2  H6   0.020
 PYV  plan-2  H7   0.020
 PYV  plan-2  H8   0.020
 PYV  plan-2  H9   0.020
 PYV  plan-2  H10  0.020
 PYV  plan-2  BR   0.020

