# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:11:05 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCC(=O)NCCCCCn1ccc2cc(Cl)c(Cl)cc12
#
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
 W45  W45  N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide  ligand  39  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W45
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
 W45  C02  C   C     0   0.570   6.3780   0.3129   0.0239
 W45  C03  C   CH2   0  -0.687   7.2442   0.9039   1.1195
 W45  C06  C   CH2   0  -0.230   4.1311  -0.4796  -0.5359
 W45  C07  C   CH2   0  -0.477   2.7855  -0.6346   0.1533
 W45  C08  C   CH2   0  -0.427   1.7287  -1.1942  -0.7897
 W45  C09  C   CH2   0  -0.435   0.3712  -1.3411  -0.1157
 W45  C10  C   CH2   0  -0.315  -0.6723  -1.9104  -1.0693
 W45  C12  C   CR15  0  -0.018  -2.4764  -3.2085   0.0871
 W45  C13  C   CR15  0  -0.421  -3.6898  -2.9772   0.6666
 W45  C14  C   CR56  0   0.059  -3.9634  -1.5896   0.4831
 W45  C15  C   CR16  0  -0.317  -5.0242  -0.7540   0.8374
 W45  C16  C   CR6   0  -0.020  -4.9674   0.5803   0.4933
 W45  C18  C   CR6   0  -0.028  -3.8630   1.1003  -0.2067
 W45  C20  C   CR16  0  -0.267  -2.8008   0.2974  -0.5684
 W45  C21  C   CR56  0   0.382  -2.8634  -1.0477  -0.2188
 W45  N05  N   NH1   0  -0.639   5.1133   0.0654   0.3811
 W45  N11  N   NR5   0  -0.527  -1.9752  -2.0564  -0.4553
 W45  O01  O   O     0  -0.491   6.8187   0.0869  -1.0930
 W45  S04  S   S2    0  -0.224   8.9041   1.1717   0.4402
 W45  CL1  CL  CL    0  -0.109  -3.8205   2.7744  -0.6297
 W45  H1   H   HCH2  0   0.304   6.8140   1.8449   1.4659
 W45  H2   H   HCH2  0   0.305   7.2831   0.2241   1.9720
 W45  H3   H   HCH2  0   0.234   4.4713  -1.4495  -0.9091
 W45  H4   H   HCH2  0   0.234   4.0307   0.1785  -1.4034
 W45  H5   H   HCH2  0   0.235   2.8902  -1.2965   1.0186
 W45  H6   H   HCH2  0   0.234   2.4563   0.3372   0.5349
 W45  H7   H   HCH2  0   0.226   1.6360  -0.5385  -1.6614
 W45  H8   H   HCH2  0   0.227   2.0567  -2.1673  -1.1691
 W45  H9   H   HCH2  0   0.236   0.4544  -1.9989   0.7538
 W45  H10  H   HCH2  0   0.234   0.0394  -0.3676   0.2577
 W45  H11  H   HCH2  0   0.258  -0.7700  -1.2775  -1.9546
 W45  H12  H   HCH2  0   0.269  -0.3627  -2.8944  -1.4232
 W45  H13  H   HCR5  0   0.289  -1.9183  -4.1287   0.0093
 W45  H14  H   HCR5  0   0.254  -4.3130  -3.7076   1.1566
 W45  H15  H   HCR6  0   0.276  -5.8811  -1.1400   1.3735
 W45  H16  H   HCR6  0   0.288  -1.9582   0.7160  -1.1021
 W45  H17  H   HNH1  0   0.404   4.8169   0.2928   1.3171
 W45  H18  H   HSH1  0   0.217   9.4324   1.6656   1.5658
 W45  CL2  CL  CL    0  -0.101  -6.2744   1.6209   0.9327

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
 W45  CL1  C18  single    1.727  0.020  1.727
 W45  CL2  C16  single    1.727  0.020  1.727
 W45  C18  C16  aromatic  1.407  0.020  1.407
 W45  C18  C20  aromatic  1.380  0.020  1.380
 W45  C16  C15  aromatic  1.379  0.020  1.379
 W45  C03  S04  single    1.813  0.020  1.813
 W45  C03  C02  single    1.517  0.020  1.517
 W45  C20  C21  aromatic  1.391  0.020  1.391
 W45  O01  C02  double    1.222  0.020  1.222
 W45  C15  C14  aromatic  1.396  0.020  1.396
 W45  C02  N05  single    1.337  0.020  1.337
 W45  C21  C14  aromatic  1.413  0.020  1.413
 W45  C21  N11  aromatic  1.365  0.020  1.365
 W45  C14  C13  aromatic  1.426  0.020  1.426
 W45  N05  C06  single    1.450  0.020  1.450
 W45  C07  C08  single    1.523  0.020  1.523
 W45  C07  C06  single    1.520  0.020  1.520
 W45  C08  C09  single    1.523  0.020  1.523
 W45  C09  C10  single    1.524  0.020  1.524
 W45  N11  C10  single    1.448  0.020  1.448
 W45  N11  C12  aromatic  1.369  0.020  1.369
 W45  C13  C12  aromatic  1.364  0.020  1.364
 W45  C03  H1   single    0.970  0.020  1.090
 W45  C03  H2   single    0.970  0.020  1.090
 W45  C06  H3   single    0.970  0.020  1.090
 W45  C06  H4   single    0.970  0.020  1.090
 W45  C07  H5   single    0.970  0.020  1.090
 W45  C07  H6   single    0.970  0.020  1.090
 W45  C08  H7   single    0.970  0.020  1.090
 W45  C08  H8   single    0.970  0.020  1.090
 W45  C09  H9   single    0.970  0.020  1.090
 W45  C09  H10  single    0.970  0.020  1.090
 W45  C10  H11  single    0.970  0.020  1.090
 W45  C10  H12  single    0.970  0.020  1.090
 W45  C12  H13  single    0.930  0.020  1.080
 W45  C13  H14  single    0.930  0.020  1.080
 W45  C15  H15  single    0.930  0.020  1.080
 W45  C20  H16  single    0.930  0.020  1.080
 W45  N05  H17  single    0.860  0.020  1.020
 W45  S04  H18  single    1.200  0.020  1.300

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
 W45  O01  C02  N05  123.44  3.000
 W45  N05  C02  C03  114.79  3.000
 W45  O01  C02  C03  121.77  3.000
 W45  H2   C03  H1   107.66  3.000
 W45  H2   C03  S04  110.61  3.000
 W45  H1   C03  S04  110.63  3.000
 W45  H2   C03  C02  110.00  3.000
 W45  H1   C03  C02  109.89  3.000
 W45  S04  C03  C02  108.04  3.000
 W45  H4   C06  H3   106.95  3.000
 W45  H4   C06  N05  109.74  3.000
 W45  H3   C06  N05  109.78  3.000
 W45  H4   C06  C07  109.87  3.000
 W45  H3   C06  C07  109.87  3.000
 W45  N05  C06  C07  110.57  3.000
 W45  H6   C07  H5   106.86  3.000
 W45  H6   C07  C08  109.48  3.000
 W45  H5   C07  C08  109.49  3.000
 W45  H6   C07  C06  109.50  3.000
 W45  H5   C07  C06  109.60  3.000
 W45  C08  C07  C06  111.78  3.000
 W45  H8   C08  H7   106.37  3.000
 W45  H8   C08  C09  109.56  3.000
 W45  H7   C08  C09  109.56  3.000
 W45  H8   C08  C07  109.47  3.000
 W45  H7   C08  C07  109.37  3.000
 W45  C09  C08  C07  112.33  3.000
 W45  H10  C09  H9   106.68  3.000
 W45  H10  C09  C10  109.78  3.000
 W45  H9   C09  C10  108.96  3.000
 W45  H10  C09  C08  109.60  3.000
 W45  H9   C09  C08  110.01  3.000
 W45  C10  C09  C08  111.68  3.000
 W45  H12  C10  H11  106.57  3.000
 W45  H12  C10  N11  107.59  3.000
 W45  H11  C10  N11  108.76  3.000
 W45  H12  C10  C09  110.23  3.000
 W45  H11  C10  C09  110.60  3.000
 W45  N11  C10  C09  112.86  3.000
 W45  H13  C12  N11  120.00  3.000
 W45  H13  C12  C13  129.43  3.000
 W45  N11  C12  C13  110.57  3.000
 W45  H14  C13  C14  127.36  3.000
 W45  H14  C13  C12  126.32  3.000
 W45  C14  C13  C12  106.32  3.000
 W45  C21  C14  C15  119.21  3.000
 W45  C21  C14  C13  106.72  3.000
 W45  C15  C14  C13  134.07  3.000
 W45  H15  C15  C16  120.09  3.000
 W45  H15  C15  C14  120.93  3.000
 W45  C16  C15  C14  118.98  3.000
 W45  CL2  C16  C18  119.85  3.000
 W45  C18  C16  C15  120.93  3.000
 W45  CL2  C16  C15  119.22  3.000
 W45  CL1  C18  C20  118.74  3.000
 W45  C20  C18  C16  121.31  3.000
 W45  CL1  C18  C16  119.95  3.000
 W45  H16  C20  C21  122.22  3.000
 W45  H16  C20  C18  120.25  3.000
 W45  C21  C20  C18  117.52  3.000
 W45  N11  C21  C20  129.93  3.000
 W45  N11  C21  C14  108.02  3.000
 W45  C20  C21  C14  122.05  3.000
 W45  H17  N05  C06  118.22  3.000
 W45  H17  N05  C02  118.98  3.000
 W45  C06  N05  C02  122.77  3.000
 W45  C21  N11  C12  108.37  3.000
 W45  C12  N11  C10  125.63  3.000
 W45  C21  N11  C10  125.79  3.000
 W45  H18  S04  C03   95.78  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
 W45  CONST_01  C20  C21  N11  C12   180.00   0.0  0
 W45  CONST_02  C14  C21  N11  C12     0.00   0.0  0
 W45  CONST_03  C15  C14  C13  C12   180.00   0.0  0
 W45  CONST_04  C21  C14  C13  C12     0.00   0.0  0
 W45  CONST_05  C16  C15  C14  C13   180.00   0.0  0
 W45  CONST_06  C20  C21  C14  C13   180.00   0.0  0
 W45  CONST_07  N11  C21  C14  C13     0.00   0.0  0
 W45  CONST_08  C21  N11  C12  C13     0.00   0.0  0
 W45  CONST_09  C18  C16  C15  C14     0.00   0.0  0
 W45  CONST_10  C18  C20  C21  C14     0.00   0.0  0
 W45  CONST_11  N11  C12  C13  C14     0.00   0.0  0
 W45  CONST_12  C20  C18  C16  C15     0.00   0.0  0
 W45  CONST_13  C20  C21  C14  C15     0.00   0.0  0
 W45  CONST_14  N11  C21  C14  C15   180.00   0.0  0
 W45  CONST_15  C21  C20  C18  C16     0.00   0.0  0
 W45  CONST_16  C21  C14  C15  C16     0.00   0.0  0
 W45  CONST_17  N11  C21  C20  C18   180.00   0.0  0
 W45  CONST_18  C20  C21  N11  C10     0.00   0.0  0
 W45  CONST_19  C14  C21  N11  C10   180.00   0.0  0
 W45  CONST_20  C13  C12  N11  C10   180.00   0.0  0
 W45  CONST_21  CL2  C16  C15  C14   180.00   0.0  0
 W45  CONST_22  CL1  C18  C16  C15   180.00   0.0  0
 W45  CONST_23  CL2  C16  C18  C20   180.00   0.0  0
 W45  CONST_24  CL1  C18  C20  C21   180.00   0.0  0
 W45  CONST_25  H15  C15  C14  C13     0.00   0.0  0
 W45  CONST_26  H16  C20  C21  C14   180.00   0.0  0
 W45  CONST_27  H13  C12  C13  C14   180.00   0.0  0
 W45  CONST_28  H14  C13  C14  C15     0.00   0.0  0
 W45  CONST_29  C06  N05  C02  C03   180.00   0.0  0
 W45  CONST_30  O01  C02  N05  C06     0.00   0.0  0
 W45  CONST_31  H17  N05  C02  C03     0.00   0.0  0
 W45  Var_01    C21  N11  C10  C09    77.16  30.0  2
 W45  Var_02    N11  C10  C09  C08  -179.79  30.0  3
 W45  Var_03    C07  C06  N05  C02  -179.36  30.0  3
 W45  Var_04    C09  C08  C07  C06  -179.41  30.0  3
 W45  Var_05    C10  C09  C08  C07  -179.63  30.0  3
 W45  Var_06    N05  C06  C07  C08   179.49  30.0  3
 W45  Var_07    S04  C03  C02  N05  -179.72  30.0  2

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
 W45  plan-1  C10  0.020
 W45  plan-1  C12  0.020
 W45  plan-1  C13  0.020
 W45  plan-1  C14  0.020
 W45  plan-1  C15  0.020
 W45  plan-1  C16  0.020
 W45  plan-1  C18  0.020
 W45  plan-1  C20  0.020
 W45  plan-1  C21  0.020
 W45  plan-1  N11  0.020
 W45  plan-1  CL1  0.020
 W45  plan-1  H13  0.020
 W45  plan-1  H14  0.020
 W45  plan-1  H15  0.020
 W45  plan-1  H16  0.020
 W45  plan-1  CL2  0.020
 W45  plan-2  C02  0.020
 W45  plan-2  C03  0.020
 W45  plan-2  C06  0.020
 W45  plan-2  N05  0.020
 W45  plan-2  O01  0.020
 W45  plan-2  H17  0.020

