# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:09:35 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(2-{[(4-chlorophenyl)methyl]disulfanyl}ethyl)decan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCNCCSSCc1ccc(Cl)cc1
#
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
 8EA  8EA  N-(2-{[(4-chlorophenyl)methyl]disulfanyl}ethyl)decan-1-amine  ligand  55  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8EA
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
 8EA  C10  C   CH2   0  -0.442   -3.4193  -0.2136   0.2078
 8EA  C13  C   CH2   0  -0.419  -12.3541   0.1102  -0.1197
 8EA  C15  C   CH3   0  -0.663  -13.5715   0.0181   0.7901
 8EA  C17  C   CH2   0  -0.667    4.2884   1.4900   0.8091
 8EA  C20  C   CR16  0  -0.292    6.6940   1.3701   0.1071
 8EA  C21  C   CR16  0  -0.201    6.8995  -1.2444   1.0166
 8EA  C22  C   CR16  0  -0.200    7.8936   0.6918  -0.0289
 8EA  CL   CL  CL    0  -0.131    9.4811  -1.4743   0.2592
 8EA  S02  S   S2    0  -0.041    2.9572  -0.4646  -1.0813
 8EA  S03  S   S2    0  -0.034    3.3538   1.5204  -0.7670
 8EA  N04  N   NH1   0  -0.601   -0.9717  -0.3433   0.0098
 8EA  C05  C   CH2   0  -0.411   -7.2705   0.0357  -0.3937
 8EA  C06  C   CH2   0  -0.411   -5.9576  -0.1326   0.3605
 8EA  C07  C   CH2   0  -0.411   -8.4986  -0.0744   0.5013
 8EA  C08  C   CH2   0  -0.415   -4.7325  -0.0092  -0.5368
 8EA  C09  C   CH2   0  -0.411   -9.8112   0.0761  -0.2573
 8EA  C11  C   CH2   0  -0.406  -11.0393  -0.0244   0.6386
 8EA  C12  C   CH2   0  -0.248   -2.2075  -0.0539  -0.6960
 8EA  C14  C   CH2   0  -0.238    0.2075  -0.1307  -0.8059
 8EA  C16  C   CH2   0  -0.580    1.4303  -0.7221  -0.1276
 8EA  C18  C   CR6   0   0.165    5.5865   0.7624   0.6951
 8EA  C19  C   CR16  0  -0.289    5.7051  -0.5481   1.1457
 8EA  C23  C   CR6   0  -0.053    7.9833  -0.6160   0.4272
 8EA  H1   H   HCH2  0   0.213   -3.3542   0.5024   1.0349
 8EA  H2   H   HCH2  0   0.215   -3.4021  -1.2107   0.6588
 8EA  H3   H   HCH2  0   0.210  -12.4104  -0.6679  -0.8874
 8EA  H4   H   HCH2  0   0.210  -12.3669   1.0649  -0.6554
 8EA  H5   H   HCH3  0   0.215  -13.5929  -0.9352   1.3222
 8EA  H6   H   HCH3  0   0.216  -13.5642   0.8117   1.5395
 8EA  H7   H   HCH3  0   0.225  -14.5027   0.1021   0.2284
 8EA  H8   H   HCH2  0   0.308    4.4363   2.5457   1.0457
 8EA  H9   H   HCH2  0   0.298    3.6515   1.0637   1.5839
 8EA  H10  H   HCR6  0   0.265    6.6224   2.3901  -0.2510
 8EA  H11  H   HCR6  0   0.279    6.9795  -2.2622   1.3733
 8EA  H12  H   HCR6  0   0.279    8.7476   1.1758  -0.4827
 8EA  H13  H   HNH1  0   0.339   -0.9155   0.2540   0.8271
 8EA  H15  H   HCH2  0   0.206   -7.2767   1.0077  -0.8999
 8EA  H16  H   HCH2  0   0.206   -7.3308  -0.7183  -1.1864
 8EA  H17  H   HCH2  0   0.208   -5.8988   0.6142   1.1600
 8EA  H18  H   HCH2  0   0.207   -5.9478  -1.1093   0.8571
 8EA  H19  H   HCH2  0   0.206   -8.4870  -1.0416   1.0166
 8EA  H20  H   HCH2  0   0.206   -8.4441   0.6872   1.2873
 8EA  H21  H   HCH2  0   0.209   -4.7332   0.9760  -1.0163
 8EA  H22  H   HCH2  0   0.210   -4.8034  -0.7415  -1.3485
 8EA  H23  H   HCH2  0   0.206   -9.8206   1.0399  -0.7790
 8EA  H24  H   HCH2  0   0.206   -9.8680  -0.6906  -1.0382
 8EA  H25  H   HCH2  0   0.205  -10.9879   0.7490   1.4134
 8EA  H26  H   HCH2  0   0.205  -11.0250  -0.9837   1.1689
 8EA  H27  H   HCH2  0   0.213   -2.2878  -0.7534  -1.5346
 8EA  H28  H   HCH2  0   0.185   -2.2163   0.9558  -1.1380
 8EA  H29  H   HCH2  0   0.229    0.0609  -0.6360  -1.7641
 8EA  H30  H   HCH2  0   0.203    0.3874   0.9299  -1.0360
 8EA  H31  H   HCH2  0   0.284    1.3316  -1.8061  -0.0369
 8EA  H32  H   HCH2  0   0.273    1.5747  -0.3232   0.8783
 8EA  H33  H   HCR6  0   0.262    4.8589  -1.0375   1.6107

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
 8EA  CL   C23  single    1.734  0.020  1.734
 8EA  C23  C22  aromatic  1.388  0.020  1.388
 8EA  C23  C21  aromatic  1.384  0.020  1.384
 8EA  C22  C20  aromatic  1.385  0.020  1.385
 8EA  C21  C19  aromatic  1.389  0.020  1.389
 8EA  C20  C18  aromatic  1.393  0.020  1.393
 8EA  C19  C18  aromatic  1.391  0.020  1.391
 8EA  C18  C17  single    1.492  0.020  1.492
 8EA  C17  S03  single    1.833  0.020  1.833
 8EA  N04  C12  single    1.452  0.020  1.452
 8EA  N04  C14  single    1.449  0.020  1.449
 8EA  C16  C14  single    1.518  0.020  1.518
 8EA  C16  S02  single    1.819  0.020  1.819
 8EA  S03  S02  single    2.049  0.020  2.049
 8EA  C12  C10  single    1.520  0.020  1.520
 8EA  C10  C08  single    1.523  0.020  1.523
 8EA  C08  C06  single    1.524  0.020  1.524
 8EA  C06  C05  single    1.523  0.020  1.523
 8EA  C05  C07  single    1.524  0.020  1.524
 8EA  C07  C09  single    1.524  0.020  1.524
 8EA  C09  C11  single    1.524  0.020  1.524
 8EA  C11  C13  single    1.524  0.020  1.524
 8EA  C13  C15  single    1.523  0.020  1.523
 8EA  C10  H1   single    0.970  0.020  1.090
 8EA  C10  H2   single    0.970  0.020  1.090
 8EA  C13  H3   single    0.970  0.020  1.090
 8EA  C13  H4   single    0.970  0.020  1.090
 8EA  C15  H5   single    0.970  0.020  1.090
 8EA  C15  H6   single    0.970  0.020  1.090
 8EA  C15  H7   single    0.970  0.020  1.090
 8EA  C17  H8   single    0.970  0.020  1.090
 8EA  C17  H9   single    0.970  0.020  1.090
 8EA  C20  H10  single    0.930  0.020  1.080
 8EA  C21  H11  single    0.930  0.020  1.080
 8EA  C22  H12  single    0.930  0.020  1.080
 8EA  N04  H13  single    0.890  0.020  1.040
 8EA  C05  H15  single    0.970  0.020  1.090
 8EA  C05  H16  single    0.970  0.020  1.090
 8EA  C06  H17  single    0.970  0.020  1.090
 8EA  C06  H18  single    0.970  0.020  1.090
 8EA  C07  H19  single    0.970  0.020  1.090
 8EA  C07  H20  single    0.970  0.020  1.090
 8EA  C08  H21  single    0.970  0.020  1.090
 8EA  C08  H22  single    0.970  0.020  1.090
 8EA  C09  H23  single    0.970  0.020  1.090
 8EA  C09  H24  single    0.970  0.020  1.090
 8EA  C11  H25  single    0.970  0.020  1.090
 8EA  C11  H26  single    0.970  0.020  1.090
 8EA  C12  H27  single    0.970  0.020  1.090
 8EA  C12  H28  single    0.970  0.020  1.090
 8EA  C14  H29  single    0.970  0.020  1.090
 8EA  C14  H30  single    0.970  0.020  1.090
 8EA  C16  H31  single    0.970  0.020  1.090
 8EA  C16  H32  single    0.970  0.020  1.090
 8EA  C19  H33  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
 8EA  H2   C10  H1   106.45  3.000
 8EA  H2   C10  C12  109.15  3.000
 8EA  H1   C10  C12  109.44  3.000
 8EA  H2   C10  C08  109.70  3.000
 8EA  H1   C10  C08  109.42  3.000
 8EA  C12  C10  C08  112.49  3.000
 8EA  H4   C13  H3   106.03  3.000
 8EA  H4   C13  C11  109.31  3.000
 8EA  H3   C13  C11  109.30  3.000
 8EA  H4   C13  C15  109.63  3.000
 8EA  H3   C13  C15  109.57  3.000
 8EA  C11  C13  C15  112.78  3.000
 8EA  H7   C15  H6   107.65  3.000
 8EA  H7   C15  H5   107.54  3.000
 8EA  H6   C15  H5   107.48  3.000
 8EA  H7   C15  C13  111.73  3.000
 8EA  H6   C15  C13  111.15  3.000
 8EA  H5   C15  C13  111.08  3.000
 8EA  H9   C17  H8   107.66  3.000
 8EA  H9   C17  C18  111.83  3.000
 8EA  H8   C17  C18  111.72  3.000
 8EA  H9   C17  S03  108.66  3.000
 8EA  H8   C17  S03  103.85  3.000
 8EA  C18  C17  S03  112.70  3.000
 8EA  H10  C20  C18  119.84  3.000
 8EA  H10  C20  C22  119.07  3.000
 8EA  C18  C20  C22  121.09  3.000
 8EA  H11  C21  C23  120.65  3.000
 8EA  H11  C21  C19  120.32  3.000
 8EA  C23  C21  C19  119.03  3.000
 8EA  H12  C22  C23  120.57  3.000
 8EA  H12  C22  C20  120.40  3.000
 8EA  C23  C22  C20  119.03  3.000
 8EA  C16  S02  S03  102.67  3.000
 8EA  S02  S03  C17  102.39  3.000
 8EA  H13  N04  C14  108.79  3.000
 8EA  H13  N04  C12  108.76  3.000
 8EA  C14  N04  C12  112.92  3.000
 8EA  H16  C05  H15  106.01  3.000
 8EA  H16  C05  C07  109.32  3.000
 8EA  H15  C05  C07  109.32  3.000
 8EA  H16  C05  C06  109.24  3.000
 8EA  H15  C05  C06  109.36  3.000
 8EA  C07  C05  C06  113.32  3.000
 8EA  H18  C06  H17  106.04  3.000
 8EA  H18  C06  C08  109.39  3.000
 8EA  H17  C06  C08  109.36  3.000
 8EA  H18  C06  C05  109.30  3.000
 8EA  H17  C06  C05  109.40  3.000
 8EA  C08  C06  C05  113.11  3.000
 8EA  H20  C07  H19  105.99  3.000
 8EA  H20  C07  C09  109.35  3.000
 8EA  H19  C07  C09  109.30  3.000
 8EA  H20  C07  C05  109.33  3.000
 8EA  H19  C07  C05  109.36  3.000
 8EA  C09  C07  C05  113.25  3.000
 8EA  H22  C08  H21  106.07  3.000
 8EA  H22  C08  C06  109.28  3.000
 8EA  H21  C08  C06  109.27  3.000
 8EA  H22  C08  C10  109.17  3.000
 8EA  H21  C08  C10  109.57  3.000
 8EA  C06  C08  C10  113.23  3.000
 8EA  H24  C09  H23  106.00  3.000
 8EA  H24  C09  C11  109.33  3.000
 8EA  H23  C09  C11  109.33  3.000
 8EA  H24  C09  C07  109.29  3.000
 8EA  H23  C09  C07  109.35  3.000
 8EA  C11  C09  C07  113.28  3.000
 8EA  H26  C11  H25  105.96  3.000
 8EA  H26  C11  C09  109.37  3.000
 8EA  H25  C11  C09  109.35  3.000
 8EA  H26  C11  C13  109.23  3.000
 8EA  H25  C11  C13  109.27  3.000
 8EA  C09  C11  C13  113.40  3.000
 8EA  H28  C12  H27  106.11  3.000
 8EA  H28  C12  N04  112.59  3.000
 8EA  H27  C12  N04  107.90  3.000
 8EA  H28  C12  C10  109.16  3.000
 8EA  H27  C12  C10  109.26  3.000
 8EA  N04  C12  C10  111.62  3.000
 8EA  H30  C14  H29  106.52  3.000
 8EA  H30  C14  C16  109.71  3.000
 8EA  H29  C14  C16  108.64  3.000
 8EA  H30  C14  N04  113.09  3.000
 8EA  H29  C14  N04  108.44  3.000
 8EA  C16  C14  N04  110.28  3.000
 8EA  H32  C16  H31  107.35  3.000
 8EA  H32  C16  C14  112.08  3.000
 8EA  H31  C16  C14  110.54  3.000
 8EA  H32  C16  S02  108.68  3.000
 8EA  H31  C16  S02  105.06  3.000
 8EA  C14  C16  S02  112.75  3.000
 8EA  C19  C18  C20  118.67  3.000
 8EA  C19  C18  C17  120.59  3.000
 8EA  C20  C18  C17  120.72  3.000
 8EA  H33  C19  C18  119.90  3.000
 8EA  H33  C19  C21  119.06  3.000
 8EA  C18  C19  C21  121.05  3.000
 8EA  CL   C23  C22  119.35  3.000
 8EA  C22  C23  C21  121.13  3.000
 8EA  CL   C23  C21  119.51  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
 8EA  CONST_01  C21  C23  C22  C20     0.00   0.0  0
 8EA  CONST_02  C21  C19  C18  C20     0.00   0.0  0
 8EA  CONST_03  C19  C21  C23  C22     0.00   0.0  0
 8EA  CONST_04  C19  C18  C20  C22     0.00   0.0  0
 8EA  CONST_05  C23  C22  C20  C18     0.00   0.0  0
 8EA  CONST_06  C23  C21  C19  C18     0.00   0.0  0
 8EA  CONST_07  C22  C20  C18  C17   180.00   0.0  0
 8EA  CONST_08  C21  C19  C18  C17   180.00   0.0  0
 8EA  CONST_09  CL   C23  C22  C20   180.00   0.0  0
 8EA  CONST_10  C19  C21  C23  CL    180.00   0.0  0
 8EA  CONST_11  H33  C19  C18  C20   180.00   0.0  0
 8EA  CONST_12  H12  C22  C23  C21   180.00   0.0  0
 8EA  CONST_13  H11  C21  C23  C22   180.00   0.0  0
 8EA  CONST_14  H10  C20  C18  C19   180.00   0.0  0
 8EA  Var_01    S03  C17  C18  C20    78.21  30.0  2
 8EA  Var_02    C18  C17  S03  S02    63.75  30.0  1
 8EA  Var_03    C14  N04  C12  C10  -176.90  30.0  1
 8EA  Var_04    C05  C06  C08  C10  -178.48  30.0  3
 8EA  Var_05    C07  C09  C11  C13  -179.36  30.0  1
 8EA  Var_06    C09  C11  C13  C15  -179.57  30.0  1
 8EA  Var_07    N04  C14  C16  S02  -178.91  30.0  3
 8EA  Var_08    C14  C16  S02  S03    74.67  30.0  2
 8EA  Var_09    C08  C10  C12  N04  -176.02  30.0  3
 8EA  Var_10    C11  C09  C07  C05  -179.61  30.0  3
 8EA  Var_11    C12  C10  C08  C06  -178.62  30.0  1
 8EA  Var_12    C09  C07  C05  C06  -179.25  30.0  3
 8EA  Var_13    C08  C06  C05  C07  -179.49  30.0  1
 8EA  Var_14    C16  C14  N04  C12  -168.01  30.0  3
 8EA  Var_15    H5   C15  C13  C11   -59.09  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
 8EA  plan-1  C17  0.020
 8EA  plan-1  C20  0.020
 8EA  plan-1  C21  0.020
 8EA  plan-1  C22  0.020
 8EA  plan-1  CL   0.020
 8EA  plan-1  C18  0.020
 8EA  plan-1  C19  0.020
 8EA  plan-1  C23  0.020
 8EA  plan-1  H10  0.020
 8EA  plan-1  H11  0.020
 8EA  plan-1  H12  0.020
 8EA  plan-1  H33  0.020

