# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:08:04 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: tridecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC
#
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
 TRD  TRD  'tridecane                '  ligand  41  13  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TRD
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
 TRD  C1    C  CH3   0  -0.662  -0.3861   0.0120   7.6322
 TRD  C2    C  CH2   0  -0.419   0.4755   0.0122   6.3768
 TRD  C3    C  CH2   0  -0.406  -0.3510   0.0105   5.0963
 TRD  C4    C  CH2   0  -0.412   0.4946   0.0102   3.8288
 TRD  C5    C  CH2   0  -0.411  -0.3382   0.0065   2.5528
 TRD  C6    C  CH2   0  -0.412   0.5023   0.0103   1.2819
 TRD  C7    C  CH2   0  -0.412  -0.3355   0.0053   0.0091
 TRD  C8    C  CH2   0  -0.412   0.5002   0.0098  -1.2649
 TRD  C9    C  CH2   0  -0.411  -0.3422   0.0044  -2.5346
 TRD  C10   C  CH2   0  -0.412   0.4888   0.0093  -3.8118
 TRD  C11   C  CH2   0  -0.406  -0.3585   0.0039  -5.0781
 TRD  C12   C  CH2   0  -0.419   0.4660   0.0086  -6.3598
 TRD  C13   C  CH3   0  -0.662  -0.3976   0.0066  -7.6139
 TRD  H11   H  HCH3  0   0.215  -1.0300  -0.8691   7.6658
 TRD  H12   H  HCH3  0   0.225   0.2198   0.0123   8.5391
 TRD  H13   H  HCH3  0   0.215  -1.0312   0.8921   7.6656
 TRD  H21   H  HCH2  0   0.210   1.1328   0.8874   6.3816
 TRD  H22   H  HCH2  0   0.210   1.1348  -0.8616   6.3829
 TRD  H31   H  HCH2  0   0.205  -1.0098  -0.8655   5.0930
 TRD  H32   H  HCH2  0   0.205  -1.0121   0.8848   5.0918
 TRD  H41   H  HCH2  0   0.206   1.1526   0.8867   3.8309
 TRD  H42   H  HCH2  0   0.206   1.1555  -0.8641   3.8338
 TRD  H51   H  HCH2  0   0.206  -0.9935  -0.8720   2.5509
 TRD  H52   H  HCH2  0   0.206  -1.0023   0.8784   2.5509
 TRD  H61   H  HCH2  0   0.206   1.1569   0.8892   1.2820
 TRD  H62   H  HCH2  0   0.206   1.1665  -0.8615   1.2828
 TRD  H71   H  HCH2  0   0.206  -0.9902  -0.8737   0.0100
 TRD  H72   H  HCH2  0   0.206  -1.0003   0.8766   0.0096
 TRD  H81   H  HCH2  0   0.206   1.1541   0.8893  -1.2669
 TRD  H82   H  HCH2  0   0.206   1.1651  -0.8614  -1.2663
 TRD  H91   H  HCH2  0   0.206  -0.9966  -0.8749  -2.5315
 TRD  H92   H  HCH2  0   0.206  -1.0073   0.8756  -2.5318
 TRD  H101  H  HCH2  0   0.206   1.1425   0.8890  -3.8161
 TRD  H102  H  HCH2  0   0.206   1.1539  -0.8617  -3.8157
 TRD  H111  H  HCH2  0   0.205  -1.0132  -0.8752  -5.0728
 TRD  H112  H  HCH2  0   0.205  -1.0237   0.8751  -5.0733
 TRD  H121  H  HCH2  0   0.210   1.1206   0.8858  -6.3653
 TRD  H122  H  HCH2  0   0.210   1.1280  -0.8631  -6.3674
 TRD  H131  H  HCH3  0   0.225   0.2070   0.0034  -8.5218
 TRD  H132  H  HCH3  0   0.215  -1.0434  -0.8732  -7.6441
 TRD  H133  H  HCH3  0   0.215  -1.0409   0.8880  -7.6488

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
 TRD  C1   C2    single  1.523  0.020  1.523
 TRD  C1   H11   single  0.970  0.020  1.090
 TRD  C1   H12   single  0.970  0.020  1.090
 TRD  C1   H13   single  0.970  0.020  1.090
 TRD  C2   C3    single  1.524  0.020  1.524
 TRD  C2   H21   single  0.970  0.020  1.090
 TRD  C2   H22   single  0.970  0.020  1.090
 TRD  C3   C4    single  1.524  0.020  1.524
 TRD  C3   H31   single  0.970  0.020  1.090
 TRD  C3   H32   single  0.970  0.020  1.090
 TRD  C4   C5    single  1.524  0.020  1.524
 TRD  C4   H41   single  0.970  0.020  1.090
 TRD  C4   H42   single  0.970  0.020  1.090
 TRD  C5   C6    single  1.524  0.020  1.524
 TRD  C5   H51   single  0.970  0.020  1.090
 TRD  C5   H52   single  0.970  0.020  1.090
 TRD  C6   C7    single  1.524  0.020  1.524
 TRD  C6   H61   single  0.970  0.020  1.090
 TRD  C6   H62   single  0.970  0.020  1.090
 TRD  C7   C8    single  1.524  0.020  1.524
 TRD  C7   H71   single  0.970  0.020  1.090
 TRD  C7   H72   single  0.970  0.020  1.090
 TRD  C8   C9    single  1.524  0.020  1.524
 TRD  C8   H81   single  0.970  0.020  1.090
 TRD  C8   H82   single  0.970  0.020  1.090
 TRD  C9   C10   single  1.524  0.020  1.524
 TRD  C9   H91   single  0.970  0.020  1.090
 TRD  C9   H92   single  0.970  0.020  1.090
 TRD  C10  C11   single  1.524  0.020  1.524
 TRD  C10  H101  single  0.970  0.020  1.090
 TRD  C10  H102  single  0.970  0.020  1.090
 TRD  C11  C12   single  1.524  0.020  1.524
 TRD  C11  H111  single  0.970  0.020  1.090
 TRD  C11  H112  single  0.970  0.020  1.090
 TRD  C12  C13   single  1.523  0.020  1.523
 TRD  C12  H121  single  0.970  0.020  1.090
 TRD  C12  H122  single  0.970  0.020  1.090
 TRD  C13  H131  single  0.970  0.020  1.090
 TRD  C13  H132  single  0.970  0.020  1.090
 TRD  C13  H133  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
 TRD  H13   C1   H12   107.61  3.000
 TRD  H13   C1   H11   107.52  3.000
 TRD  H12   C1   H11   107.59  3.000
 TRD  H13   C1   C2    111.07  3.000
 TRD  H12   C1   C2    111.79  3.000
 TRD  H11   C1   C2    111.05  3.000
 TRD  H22   C2   H21   106.06  3.000
 TRD  H22   C2   C3    109.30  3.000
 TRD  H21   C2   C3    109.29  3.000
 TRD  H22   C2   C1    109.64  3.000
 TRD  H21   C2   C1    109.65  3.000
 TRD  C3    C2   C1    112.70  3.000
 TRD  H32   C3   H31   105.96  3.000
 TRD  H32   C3   C4    109.35  3.000
 TRD  H31   C3   C4    109.32  3.000
 TRD  H32   C3   C2    109.25  3.000
 TRD  H31   C3   C2    109.23  3.000
 TRD  C4    C3   C2    113.45  3.000
 TRD  H42   C4   H41   106.02  3.000
 TRD  H42   C4   C5    109.35  3.000
 TRD  H41   C4   C5    109.37  3.000
 TRD  H42   C4   C3    109.33  3.000
 TRD  H41   C4   C3    109.36  3.000
 TRD  C5    C4   C3    113.16  3.000
 TRD  H52   C5   H51   105.98  3.000
 TRD  H52   C5   C6    109.31  3.000
 TRD  H51   C5   C6    109.29  3.000
 TRD  H52   C5   C4    109.31  3.000
 TRD  H51   C5   C4    109.28  3.000
 TRD  C6    C5   C4    113.39  3.000
 TRD  H62   C6   H61   106.01  3.000
 TRD  H62   C6   C7    109.35  3.000
 TRD  H61   C6   C7    109.33  3.000
 TRD  H62   C6   C5    109.37  3.000
 TRD  H61   C6   C5    109.36  3.000
 TRD  C7    C6   C5    113.17  3.000
 TRD  H72   C7   H71   105.98  3.000
 TRD  H72   C7   C8    109.31  3.000
 TRD  H71   C7   C8    109.31  3.000
 TRD  H72   C7   C6    109.30  3.000
 TRD  H71   C7   C6    109.29  3.000
 TRD  C8    C7   C6    113.38  3.000
 TRD  H82   C8   H81   106.02  3.000
 TRD  H82   C8   C9    109.36  3.000
 TRD  H81   C8   C9    109.34  3.000
 TRD  H82   C8   C7    109.35  3.000
 TRD  H81   C8   C7    109.34  3.000
 TRD  C9    C8   C7    113.17  3.000
 TRD  H92   C9   H91   105.98  3.000
 TRD  H92   C9   C10   109.30  3.000
 TRD  H91   C9   C10   109.30  3.000
 TRD  H92   C9   C8    109.30  3.000
 TRD  H91   C9   C8    109.31  3.000
 TRD  C10   C9   C8    113.39  3.000
 TRD  H102  C10  H101  106.01  3.000
 TRD  H102  C10  C11   109.37  3.000
 TRD  H101  C10  C11   109.35  3.000
 TRD  H102  C10  C9    109.35  3.000
 TRD  H101  C10  C9    109.34  3.000
 TRD  C11   C10  C9    113.16  3.000
 TRD  H112  C11  H111  105.96  3.000
 TRD  H112  C11  C12   109.24  3.000
 TRD  H111  C11  C12   109.25  3.000
 TRD  H112  C11  C10   109.33  3.000
 TRD  H111  C11  C10   109.33  3.000
 TRD  C12   C11  C10   113.46  3.000
 TRD  H122  C12  H121  106.05  3.000
 TRD  H122  C12  C13   109.65  3.000
 TRD  H121  C12  C13   109.64  3.000
 TRD  H122  C12  C11   109.30  3.000
 TRD  H121  C12  C11   109.28  3.000
 TRD  C13   C12  C11   112.69  3.000
 TRD  H133  C13  H132  107.52  3.000
 TRD  H133  C13  H131  107.60  3.000
 TRD  H132  C13  H131  107.61  3.000
 TRD  H133  C13  C12   111.07  3.000
 TRD  H132  C13  C12   111.06  3.000
 TRD  H131  C13  C12   111.79  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
 TRD  Var_01  C4    C3   C2   C1   -179.98  30.0  3
 TRD  Var_02  C5    C4   C3   C2    179.92  30.0  3
 TRD  Var_03  C6    C5   C4   C3    179.83  30.0  3
 TRD  Var_04  C7    C6   C5   C4    179.95  30.0  3
 TRD  Var_05  C8    C7   C6   C5    179.97  30.0  3
 TRD  Var_06  C9    C8   C7   C6    179.98  30.0  3
 TRD  Var_07  C10   C9   C8   C7    179.98  30.0  3
 TRD  Var_08  C11   C10  C9   C8   -180.00  30.0  3
 TRD  Var_09  C12   C11  C10  C9   -179.99  30.0  3
 TRD  Var_10  C13   C12  C11  C10  -179.86  30.0  3
 TRD  Var_11  H11   C1   C2   C3     59.77  30.0  3
 TRD  Var_12  H131  C13  C12  C11  -179.63  30.0  3

