# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:07:44 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=[S](=O)(NCc1ccccn1)c2cccc3ccccc23
#
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
 P2M  P2M  N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide  ligand  35  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P2M
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
 P2M  S     S  S     0   1.375   0.4716  -2.0386   0.8301
 P2M  C1    C  CR16  0  -0.291   3.1373   0.4820  -1.8725
 P2M  N1    N  NC1   0  -0.738  -1.0083  -1.3276   0.7572
 P2M  O1    O  OS    0  -0.651   0.8934  -1.9943   2.2202
 P2M  C2    C  CR66  0   0.098   2.6049   1.0945  -0.7139
 P2M  N2    N  N     0  -0.407  -3.9199  -0.3890  -0.3094
 P2M  O2    O  OS    0  -0.645   0.3483  -3.3215   0.1595
 P2M  C3    C  CR66  0   0.202   1.8100   0.3369   0.1906
 P2M  C4    C  CR6   0  -0.278   1.5524  -1.0232  -0.1550
 P2M  C5    C  CR16  0  -0.241   2.0744  -1.5865  -1.2896
 P2M  C6    C  CR16  0  -0.252   2.8890  -0.8302  -2.1515
 P2M  C7    C  CR16  0  -0.353   1.3227   0.9881   1.3497
 P2M  C8    C  CR16  0  -0.231   1.5821   2.3143   1.5722
 P2M  C9    C  CR16  0  -0.255   2.3526   3.0643   0.6656
 P2M  C10   C  CR16  0  -0.300   2.8604   2.4593  -0.4495
 P2M  C11   C  CH2   0  -0.340  -1.6495  -1.1858  -0.5547
 P2M  C12   C  CR6   0   0.202  -2.6462  -0.0615  -0.4946
 P2M  C13   C  CR16  0  -0.072  -4.8147   0.5886  -0.2275
 P2M  C14   C  CR16  0  -0.321  -4.4870   1.9330  -0.3184
 P2M  C15   C  CR16  0  -0.147  -3.1568   2.2730  -0.5116
 P2M  C16   C  CR16  0  -0.315  -2.2186   1.2578  -0.6035
 P2M  HN1   H  HNC1  0   0.419  -1.1059  -0.5342   1.3799
 P2M  H5    H  HCR6  0   0.292   1.8616  -2.6160  -1.5394
 P2M  H6    H  HCR6  0   0.276   3.2989  -1.2949  -3.0373
 P2M  H7    H  HCR6  0   0.256   0.7679   0.4492   2.1025
 P2M  H8    H  HCR6  0   0.271   1.1948   2.7864   2.4651
 P2M  H9    H  HCR6  0   0.267   2.5487   4.1102   0.8593
 P2M  H10   H  HCR6  0   0.267   3.4683   3.0182  -1.1501
 P2M  H11   H  HCH2  0   0.266  -0.9124  -0.9743  -1.3367
 P2M  H11A  H  HCH2  0   0.283  -2.1575  -2.1136  -0.8128
 P2M  H13   H  HCR6  0   0.268  -5.8457   0.2868  -0.0819
 P2M  H14   H  HCR6  0   0.276  -5.2566   2.6883  -0.2437
 P2M  H15   H  HCR6  0   0.279  -2.8559   3.3087  -0.5957
 P2M  H16   H  HCR6  0   0.267  -1.1721   1.4829  -0.7667
 P2M  H1    H  HCR6  0   0.273   3.7482   1.0765  -2.5405

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
 P2M  S    N1    single    1.644  0.020  1.644
 P2M  S    O1    double    1.453  0.020  1.453
 P2M  S    O2    double    1.453  0.020  1.453
 P2M  S    C4    single    1.780  0.020  1.780
 P2M  C1   C2    aromatic  1.415  0.020  1.415
 P2M  C1   C6    aromatic  1.364  0.020  1.364
 P2M  N1   C11   single    1.467  0.020  1.467
 P2M  C2   C3    aromatic  1.423  0.020  1.423
 P2M  C2   C10   aromatic  1.413  0.020  1.413
 P2M  N2   C12   aromatic  1.328  0.020  1.328
 P2M  N2   C13   aromatic  1.328  0.020  1.328
 P2M  C3   C4    aromatic  1.427  0.020  1.427
 P2M  C3   C7    aromatic  1.416  0.020  1.416
 P2M  C4   C5    aromatic  1.370  0.020  1.370
 P2M  C5   C6    aromatic  1.407  0.020  1.407
 P2M  C7   C8    aromatic  1.369  0.020  1.369
 P2M  C8   C9    aromatic  1.406  0.020  1.406
 P2M  C9   C10   aromatic  1.366  0.020  1.366
 P2M  C11  C12   single    1.504  0.020  1.504
 P2M  C12  C16   aromatic  1.391  0.020  1.391
 P2M  C13  C14   aromatic  1.387  0.020  1.387
 P2M  C14  C15   aromatic  1.387  0.020  1.387
 P2M  C15  C16   aromatic  1.385  0.020  1.385
 P2M  C1   H1    single    0.930  0.020  1.080
 P2M  N1   HN1   single    0.890  0.020  1.040
 P2M  C5   H5    single    0.930  0.020  1.080
 P2M  C6   H6    single    0.930  0.020  1.080
 P2M  C7   H7    single    0.930  0.020  1.080
 P2M  C8   H8    single    0.930  0.020  1.080
 P2M  C9   H9    single    0.930  0.020  1.080
 P2M  C10  H10   single    0.930  0.020  1.080
 P2M  C11  H11   single    0.970  0.020  1.090
 P2M  C11  H11A  single    0.970  0.020  1.090
 P2M  C13  H13   single    0.930  0.020  1.080
 P2M  C14  H14   single    0.930  0.020  1.080
 P2M  C15  H15   single    0.930  0.020  1.080
 P2M  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
 P2M  C4    S    O2   107.44  3.000
 P2M  C4    S    O1   109.61  3.000
 P2M  O2    S    O1   119.54  3.000
 P2M  C4    S    N1   105.98  3.000
 P2M  O2    S    N1   106.57  3.000
 P2M  O1    S    N1   106.89  3.000
 P2M  H1    C1   C6   120.30  3.000
 P2M  H1    C1   C2   118.67  3.000
 P2M  C6    C1   C2   121.03  3.000
 P2M  HN1   N1   C11  115.58  3.000
 P2M  HN1   N1   S    113.47  3.000
 P2M  C11   N1   S    118.36  3.000
 P2M  C10   C2   C3   119.75  3.000
 P2M  C10   C2   C1   120.22  3.000
 P2M  C3    C2   C1   120.03  3.000
 P2M  C13   N2   C12  118.25  3.000
 P2M  C7    C3   C4   125.07  3.000
 P2M  C7    C3   C2   117.89  3.000
 P2M  C4    C3   C2   117.04  3.000
 P2M  C5    C4   C3   121.58  3.000
 P2M  C5    C4   S    117.07  3.000
 P2M  C3    C4   S    121.28  3.000
 P2M  H5    C5   C6   118.99  3.000
 P2M  H5    C5   C4   120.54  3.000
 P2M  C6    C5   C4   120.47  3.000
 P2M  H6    C6   C5   119.38  3.000
 P2M  H6    C6   C1   120.79  3.000
 P2M  C5    C6   C1   119.82  3.000
 P2M  H7    C7   C8   117.88  3.000
 P2M  H7    C7   C3   121.21  3.000
 P2M  C8    C7   C3   120.87  3.000
 P2M  H8    C8   C9   119.70  3.000
 P2M  H8    C8   C7   119.27  3.000
 P2M  C9    C8   C7   121.03  3.000
 P2M  H9    C9   C10  120.46  3.000
 P2M  H9    C9   C8   119.97  3.000
 P2M  C10   C9   C8   119.56  3.000
 P2M  H10   C10  C9   120.53  3.000
 P2M  H10   C10  C2   118.61  3.000
 P2M  C9    C10  C2   120.87  3.000
 P2M  H11A  C11  H11  108.02  3.000
 P2M  H11A  C11  C12  109.71  3.000
 P2M  H11   C11  C12  109.29  3.000
 P2M  H11A  C11  N1   109.48  3.000
 P2M  H11   C11  N1   111.28  3.000
 P2M  C12   C11  N1   109.03  3.000
 P2M  C16   C12  C11  120.15  3.000
 P2M  C16   C12  N2   122.65  3.000
 P2M  C11   C12  N2   117.19  3.000
 P2M  H13   C13  C14  120.22  3.000
 P2M  H13   C13  N2   116.38  3.000
 P2M  C14   C13  N2   123.40  3.000
 P2M  H14   C14  C15  121.42  3.000
 P2M  H14   C14  C13  120.31  3.000
 P2M  C15   C14  C13  118.27  3.000
 P2M  H15   C15  C16  120.53  3.000
 P2M  H15   C15  C14  120.83  3.000
 P2M  C16   C15  C14  118.64  3.000
 P2M  H16   C16  C15  120.81  3.000
 P2M  H16   C16  C12  120.40  3.000
 P2M  C15   C16  C12  118.79  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
 P2M  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 P2M  CONST_02  C7   C3   C2   C1    180.00   0.0  0
 P2M  CONST_03  C9   C10  C2   C1    180.00   0.0  0
 P2M  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 P2M  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 P2M  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 P2M  CONST_07  C8   C7   C3   C2      0.00   0.0  0
 P2M  CONST_08  C8   C9   C10  C2      0.00   0.0  0
 P2M  CONST_09  C15  C16  C12  N2      0.00   0.0  0
 P2M  CONST_10  C15  C14  C13  N2      0.00   0.0  0
 P2M  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 P2M  CONST_12  C9   C10  C2   C3      0.00   0.0  0
 P2M  CONST_13  C6   C5   C4   C3      0.00   0.0  0
 P2M  CONST_14  C9   C8   C7   C3      0.00   0.0  0
 P2M  CONST_15  C10  C2   C3   C4    180.00   0.0  0
 P2M  CONST_16  C8   C7   C3   C4    180.00   0.0  0
 P2M  CONST_17  C7   C3   C4   C5    180.00   0.0  0
 P2M  CONST_18  C10  C2   C1   C6    180.00   0.0  0
 P2M  CONST_19  C10  C2   C3   C7      0.00   0.0  0
 P2M  CONST_20  C10  C9   C8   C7      0.00   0.0  0
 P2M  CONST_21  C14  C13  N2   C12     0.00   0.0  0
 P2M  CONST_22  C14  C15  C16  C12     0.00   0.0  0
 P2M  CONST_23  C16  C12  N2   C13     0.00   0.0  0
 P2M  CONST_24  C16  C15  C14  C13     0.00   0.0  0
 P2M  CONST_25  C2   C3   C4   S     180.00   0.0  0
 P2M  CONST_26  C7   C3   C4   S       0.00   0.0  0
 P2M  CONST_27  C6   C5   C4   S     180.00   0.0  0
 P2M  CONST_28  C13  N2   C12  C11   180.00   0.0  0
 P2M  CONST_29  C15  C16  C12  C11   180.00   0.0  0
 P2M  CONST_30  H10  C10  C2   C1      0.00   0.0  0
 P2M  CONST_31  H5   C5   C6   C1    180.00   0.0  0
 P2M  CONST_32  H6   C6   C1   C2    180.00   0.0  0
 P2M  CONST_33  H7   C7   C3   C2    180.00   0.0  0
 P2M  CONST_34  H9   C9   C10  C2    180.00   0.0  0
 P2M  CONST_35  H16  C16  C12  N2    180.00   0.0  0
 P2M  CONST_36  H14  C14  C13  N2    180.00   0.0  0
 P2M  CONST_37  H1   C1   C2   C3    180.00   0.0  0
 P2M  CONST_38  H8   C8   C7   C3    180.00   0.0  0
 P2M  CONST_39  H13  C13  N2   C12   180.00   0.0  0
 P2M  CONST_40  H15  C15  C16  C12   180.00   0.0  0
 P2M  Var_01    C3   C4   S    N1     62.29  30.0  2
 P2M  Var_02    N2   C12  C11  N1    -98.32  30.0  2
 P2M  Var_03    C12  C11  N1   S    -156.64  30.0  3
 P2M  Var_04    C11  N1   S    C4     60.59  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
 P2M  plan-1  N2   0.020
 P2M  plan-1  C11  0.020
 P2M  plan-1  C12  0.020
 P2M  plan-1  C13  0.020
 P2M  plan-1  C14  0.020
 P2M  plan-1  C15  0.020
 P2M  plan-1  C16  0.020
 P2M  plan-1  H13  0.020
 P2M  plan-1  H14  0.020
 P2M  plan-1  H15  0.020
 P2M  plan-1  H16  0.020
 P2M  plan-2  S    0.020
 P2M  plan-2  C1   0.020
 P2M  plan-2  C2   0.020
 P2M  plan-2  C3   0.020
 P2M  plan-2  C4   0.020
 P2M  plan-2  C5   0.020
 P2M  plan-2  C6   0.020
 P2M  plan-2  C7   0.020
 P2M  plan-2  C8   0.020
 P2M  plan-2  C9   0.020
 P2M  plan-2  C10  0.020
 P2M  plan-2  H5   0.020
 P2M  plan-2  H6   0.020
 P2M  plan-2  H7   0.020
 P2M  plan-2  H8   0.020
 P2M  plan-2  H9   0.020
 P2M  plan-2  H10  0.020
 P2M  plan-2  H1   0.020

