# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:11:57 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: tridecanethial
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC=S
#
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
 3LX  3LX  'tridecanethial           '  ligand  40  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3LX
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
 3LX  C1   C  C1    0  -0.242  -6.3499   0.1781   0.5717
 3LX  S1   S  S1    0  -0.158  -7.5565   0.4896  -0.4549
 3LX  C2   C  CH2   0  -0.463  -5.1315  -0.6149   0.2759
 3LX  C3   C  CH2   0  -0.427  -3.8711   0.2544   0.3828
 3LX  C4   C  CH2   0  -0.413  -2.5985  -0.5535   0.1641
 3LX  C5   C  CH2   0  -0.414  -1.3370   0.2949   0.2617
 3LX  C6   C  CH2   0  -0.412  -0.0599  -0.5084   0.0507
 3LX  C7   C  CH2   0  -0.412   1.2049   0.3347   0.1552
 3LX  C8   C  CH2   0  -0.411   2.4818  -0.4688  -0.0549
 3LX  C9   C  CH2   0  -0.411   3.7484   0.3692   0.0650
 3LX  C10  C  CH2   0  -0.411   5.0253  -0.4361  -0.1395
 3LX  C11  C  CH2   0  -0.406   6.2918   0.3998  -0.0085
 3LX  C12  C  CH2   0  -0.418   7.5712  -0.4049  -0.2020
 3LX  C13  C  CH3   0  -0.662   8.8286   0.4418  -0.0630
 3LX  H1   H  H     0   0.290  -6.3877   0.5891   1.5819
 3LX  H2   H  HCH2  0   0.261  -5.0661  -1.4162   1.0212
 3LX  H3   H  HCH2  0   0.250  -5.2006  -1.0750  -0.7108
 3LX  H4   H  HCH2  0   0.231  -3.9283   1.0607  -0.3543
 3LX  H5   H  HCH2  0   0.229  -3.8395   0.7335   1.3661
 3LX  H6   H  HCH2  0   0.216  -2.5525  -1.3626   0.9008
 3LX  H7   H  HCH2  0   0.216  -2.6376  -1.0361  -0.8183
 3LX  H8   H  HCH2  0   0.210  -1.3840   1.1030  -0.4764
 3LX  H9   H  HCH2  0   0.210  -1.3029   0.7817   1.2428
 3LX  H10  H  HCH2  0   0.208  -0.0166  -1.3192   0.7864
 3LX  H11  H  HCH2  0   0.208  -0.0927  -0.9928  -0.9317
 3LX  H12  H  HCH2  0   0.207   1.1621   1.1471  -0.5788
 3LX  H13  H  HCH2  0   0.206   1.2370   0.8174   1.1386
 3LX  H14  H  HCH2  0   0.206   2.5184  -1.2866   0.6736
 3LX  H15  H  HCH2  0   0.206   2.4539  -0.9449  -1.0416
 3LX  H16  H  HCH2  0   0.206   3.7142   1.1864  -0.6644
 3LX  H17  H  HCH2  0   0.206   3.7743   0.8462   1.0513
 3LX  H18  H  HCH2  0   0.205   5.0556  -1.2565   0.5866
 3LX  H19  H  HCH2  0   0.206   5.0028  -0.9088  -1.1280
 3LX  H20  H  HCH2  0   0.205   6.2656   1.2178  -0.7374
 3LX  H21  H  HCH2  0   0.205   6.3108   0.8766   0.9782
 3LX  H22  H  HCH2  0   0.209   7.5981  -1.2216   0.5263
 3LX  H23  H  HCH2  0   0.209   7.5549  -0.8801  -1.1880
 3LX  H24  H  HCH3  0   0.215   8.8520   1.2403  -0.8072
 3LX  H25  H  HCH3  0   0.215   8.8793   0.9108   0.9216
 3LX  H26  H  HCH3  0   0.225   9.7325  -0.1551  -0.1905

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
 3LX  C13  C12  single  1.522  0.020  1.522
 3LX  C12  C11  single  1.524  0.020  1.524
 3LX  C11  C10  single  1.523  0.020  1.523
 3LX  C10  C9   single  1.523  0.020  1.523
 3LX  C9   C8   single  1.523  0.020  1.523
 3LX  C8   C7   single  1.523  0.020  1.523
 3LX  C6   C7   single  1.524  0.020  1.524
 3LX  C6   C5   single  1.523  0.020  1.523
 3LX  C2   C3   single  1.535  0.020  1.535
 3LX  C2   C1   single  1.483  0.020  1.483
 3LX  C4   C5   single  1.523  0.020  1.523
 3LX  C4   C3   single  1.523  0.020  1.523
 3LX  C1   S1   double  1.615  0.020  1.615
 3LX  C1   H1   single  0.930  0.020  1.080
 3LX  C2   H2   single  0.970  0.020  1.090
 3LX  C2   H3   single  0.970  0.020  1.090
 3LX  C3   H4   single  0.970  0.020  1.090
 3LX  C3   H5   single  0.970  0.020  1.090
 3LX  C4   H6   single  0.970  0.020  1.090
 3LX  C4   H7   single  0.970  0.020  1.090
 3LX  C5   H8   single  0.970  0.020  1.090
 3LX  C5   H9   single  0.970  0.020  1.090
 3LX  C6   H10  single  0.970  0.020  1.090
 3LX  C6   H11  single  0.970  0.020  1.090
 3LX  C7   H12  single  0.970  0.020  1.090
 3LX  C7   H13  single  0.970  0.020  1.090
 3LX  C8   H14  single  0.970  0.020  1.090
 3LX  C8   H15  single  0.970  0.020  1.090
 3LX  C9   H16  single  0.970  0.020  1.090
 3LX  C9   H17  single  0.970  0.020  1.090
 3LX  C10  H18  single  0.970  0.020  1.090
 3LX  C10  H19  single  0.970  0.020  1.090
 3LX  C11  H20  single  0.970  0.020  1.090
 3LX  C11  H21  single  0.970  0.020  1.090
 3LX  C12  H22  single  0.970  0.020  1.090
 3LX  C12  H23  single  0.970  0.020  1.090
 3LX  C13  H24  single  0.970  0.020  1.090
 3LX  C13  H25  single  0.970  0.020  1.090
 3LX  C13  H26  single  0.970  0.020  1.090

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
 3LX  H1   C1   C2   114.48  3.000
 3LX  H1   C1   S1   119.34  3.000
 3LX  C2   C1   S1   126.16  3.000
 3LX  H3   C2   H2   108.08  3.000
 3LX  H3   C2   C3   110.72  3.000
 3LX  H2   C2   C3   108.52  3.000
 3LX  H3   C2   C1   110.72  3.000
 3LX  H2   C2   C1   107.70  3.000
 3LX  C3   C2   C1   110.97  3.000
 3LX  H5   C3   H4   106.52  3.000
 3LX  H5   C3   C4   109.70  3.000
 3LX  H4   C3   C4   109.75  3.000
 3LX  H5   C3   C2   109.53  3.000
 3LX  H4   C3   C2   109.12  3.000
 3LX  C4   C3   C2   112.07  3.000
 3LX  H7   C4   H6   106.21  3.000
 3LX  H7   C4   C5   109.42  3.000
 3LX  H6   C4   C5   109.48  3.000
 3LX  H7   C4   C3   109.43  3.000
 3LX  H6   C4   C3   109.29  3.000
 3LX  C5   C4   C3   112.79  3.000
 3LX  H9   C5   H8   106.08  3.000
 3LX  H9   C5   C6   109.41  3.000
 3LX  H8   C5   C6   109.37  3.000
 3LX  H9   C5   C4   109.30  3.000
 3LX  H8   C5   C4   109.39  3.000
 3LX  C6   C5   C4   113.06  3.000
 3LX  H11  C6   H10  106.02  3.000
 3LX  H11  C6   C7   109.33  3.000
 3LX  H10  C6   C7   109.30  3.000
 3LX  H11  C6   C5   109.40  3.000
 3LX  H10  C6   C5   109.29  3.000
 3LX  C7   C6   C5   113.24  3.000
 3LX  H13  C7   H12  106.00  3.000
 3LX  H13  C7   C8   109.36  3.000
 3LX  H12  C7   C8   109.35  3.000
 3LX  H13  C7   C6   109.25  3.000
 3LX  H12  C7   C6   109.38  3.000
 3LX  C8   C7   C6   113.24  3.000
 3LX  H15  C8   H14  105.97  3.000
 3LX  H15  C8   C9   109.33  3.000
 3LX  H14  C8   C9   109.29  3.000
 3LX  H15  C8   C7   109.39  3.000
 3LX  H14  C8   C7   109.26  3.000
 3LX  C9   C8   C7   113.32  3.000
 3LX  H17  C9   H16  105.97  3.000
 3LX  H17  C9   C10  109.34  3.000
 3LX  H16  C9   C10  109.33  3.000
 3LX  H17  C9   C8   109.27  3.000
 3LX  H16  C9   C8   109.38  3.000
 3LX  C10  C9   C8   113.30  3.000
 3LX  H19  C10  H18  105.98  3.000
 3LX  H19  C10  C11  109.35  3.000
 3LX  H18  C10  C11  109.32  3.000
 3LX  H19  C10  C9   109.38  3.000
 3LX  H18  C10  C9   109.26  3.000
 3LX  C11  C10  C9   113.29  3.000
 3LX  H21  C11  H20  105.93  3.000
 3LX  H21  C11  C12  109.24  3.000
 3LX  H20  C11  C12  109.25  3.000
 3LX  H21  C11  C10  109.30  3.000
 3LX  H20  C11  C10  109.42  3.000
 3LX  C12  C11  C10  113.42  3.000
 3LX  H23  C12  H22  106.01  3.000
 3LX  H23  C12  C13  109.63  3.000
 3LX  H22  C12  C13  109.51  3.000
 3LX  H23  C12  C11  109.34  3.000
 3LX  H22  C12  C11  109.28  3.000
 3LX  C13  C12  C11  112.84  3.000
 3LX  H26  C13  H25  107.58  3.000
 3LX  H26  C13  H24  107.63  3.000
 3LX  H25  C13  H24  107.44  3.000
 3LX  H26  C13  C12  111.68  3.000
 3LX  H25  C13  C12  111.08  3.000
 3LX  H24  C13  C12  111.24  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
 3LX  Var_01  C4   C3   C2   C1    176.64  30.0  3
 3LX  Var_02  C3   C2   C1   S1    116.60  30.0  2
 3LX  Var_03  C5   C4   C3   C2    179.79  30.0  1
 3LX  Var_04  C6   C5   C4   C3    179.72  30.0  3
 3LX  Var_05  C7   C6   C5   C4   -179.68  30.0  1
 3LX  Var_06  C8   C7   C6   C5    179.96  30.0  3
 3LX  Var_07  C9   C8   C7   C6   -179.34  30.0  1
 3LX  Var_08  C10  C9   C8   C7    179.76  30.0  1
 3LX  Var_09  C11  C10  C9   C8   -179.54  30.0  1
 3LX  Var_10  C12  C11  C10  C9    179.56  30.0  1
 3LX  Var_11  C13  C12  C11  C10  -179.78  30.0  1
 3LX  Var_12  H24  C13  C12  C11   -60.56  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
 3LX  plan-1  C1  0.020
 3LX  plan-1  S1  0.020
 3LX  plan-1  C2  0.020
 3LX  plan-1  H1  0.020

