# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:14:46 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: pentadecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCC
#
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
 MYS  MYS  'pentadecane              '  ligand  47  15  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MYS
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
 MYS  C1    C  CH3   0  -0.662  -0.4224  -0.0241   8.9077
 MYS  C2    C  CH2   0  -0.419   0.4390  -0.0182   7.6521
 MYS  C3    C  CH2   0  -0.406  -0.3873  -0.0251   6.3717
 MYS  C4    C  CH2   0  -0.412   0.4583  -0.0161   5.1041
 MYS  C5    C  CH2   0  -0.411  -0.3741  -0.0249   3.8281
 MYS  C6    C  CH2   0  -0.412   0.4661  -0.0094   2.5569
 MYS  C7    C  CH2   0  -0.412  -0.3721  -0.0197   1.2844
 MYS  C8    C  CH2   0  -0.412   0.4634  -0.0052   0.0103
 MYS  C9    C  CH2   0  -0.412  -0.3788  -0.0146  -1.2595
 MYS  C10   C  CH2   0  -0.412   0.4518  -0.0022  -2.5365
 MYS  C11   C  CH2   0  -0.411  -0.3951  -0.0102  -3.8033
 MYS  C12   C  CH2   0  -0.412   0.4313   0.0016  -5.0833
 MYS  C13   C  CH2   0  -0.406  -0.4200  -0.0200  -6.3468
 MYS  C14   C  CH2   0  -0.419   0.4005  -0.0078  -7.6309
 MYS  C15   C  CH3   0  -0.662  -0.4664  -0.0287  -8.8826
 MYS  H11   H  HCH3  0   0.215  -1.0606  -0.9093   8.9417
 MYS  H12   H  HCH3  0   0.225   0.1837  -0.0195   9.8144
 MYS  H13   H  HCH3  0   0.215  -1.0732   0.8519   8.9411
 MYS  H21   H  HCH2  0   0.210   1.0912   0.8610   7.6573
 MYS  H22   H  HCH2  0   0.210   1.1037  -0.8877   7.6583
 MYS  H31   H  HCH2  0   0.205  -1.0388  -0.9066   6.3672
 MYS  H32   H  HCH2  0   0.205  -1.0556   0.8437   6.3682
 MYS  H41   H  HCH2  0   0.206   1.1089   0.8660   5.1079
 MYS  H42   H  HCH2  0   0.206   1.1269  -0.8845   5.1073
 MYS  H51   H  HCH2  0   0.206  -1.0209  -0.9097   3.8237
 MYS  H52   H  HCH2  0   0.206  -1.0467   0.8404   3.8282
 MYS  H61   H  HCH2  0   0.206   1.1119   0.8762   2.5592
 MYS  H62   H  HCH2  0   0.206   1.1387  -0.8745   2.5557
 MYS  H71   H  HCH2  0   0.206  -1.0194  -0.9042   1.2838
 MYS  H72   H  HCH2  0   0.206  -1.0444   0.8459   1.2866
 MYS  H81   H  HCH2  0   0.206   1.1109   0.8792   0.0108
 MYS  H82   H  HCH2  0   0.206   1.1349  -0.8713   0.0068
 MYS  H91   H  HCH2  0   0.206  -1.0270  -0.8986  -1.2574
 MYS  H92   H  HCH2  0   0.206  -1.0500   0.8518  -1.2550
 MYS  H101  H  HCH2  0   0.206   1.1013   0.8808  -2.5393
 MYS  H102  H  HCH2  0   0.206   1.1214  -0.8698  -2.5425
 MYS  H111  H  HCH2  0   0.206  -1.0449  -0.8928  -3.7989
 MYS  H112  H  HCH2  0   0.206  -1.0648   0.8573  -3.7961
 MYS  H121  H  HCH2  0   0.206   1.0731   0.8899  -5.0932
 MYS  H122  H  HCH2  0   0.206   1.1080  -0.8604  -5.0868
 MYS  H131  H  HCH2  0   0.205  -1.0625  -0.9081  -6.3368
 MYS  H132  H  HCH2  0   0.205  -1.0974   0.8417  -6.3427
 MYS  H141  H  HCH2  0   0.210   1.0418   0.8793  -7.6420
 MYS  H142  H  HCH2  0   0.210   1.0757  -0.8692  -7.6370
 MYS  H151  H  HCH3  0   0.225   0.1358  -0.0207  -9.7919
 MYS  H152  H  HCH3  0   0.215  -1.0940  -0.9215  -8.9102
 MYS  H153  H  HCH3  0   0.215  -1.1274   0.8395  -8.9168

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
 MYS  C1   C2    single  1.523  0.020  1.523
 MYS  C1   H11   single  0.970  0.020  1.090
 MYS  C1   H12   single  0.970  0.020  1.090
 MYS  C1   H13   single  0.970  0.020  1.090
 MYS  C2   C3    single  1.524  0.020  1.524
 MYS  C2   H21   single  0.970  0.020  1.090
 MYS  C2   H22   single  0.970  0.020  1.090
 MYS  C3   C4    single  1.524  0.020  1.524
 MYS  C3   H31   single  0.970  0.020  1.090
 MYS  C3   H32   single  0.970  0.020  1.090
 MYS  C4   C5    single  1.524  0.020  1.524
 MYS  C4   H41   single  0.970  0.020  1.090
 MYS  C4   H42   single  0.970  0.020  1.090
 MYS  C5   C6    single  1.524  0.020  1.524
 MYS  C5   H51   single  0.970  0.020  1.090
 MYS  C5   H52   single  0.970  0.020  1.090
 MYS  C6   C7    single  1.524  0.020  1.524
 MYS  C6   H61   single  0.970  0.020  1.090
 MYS  C6   H62   single  0.970  0.020  1.090
 MYS  C7   C8    single  1.524  0.020  1.524
 MYS  C7   H71   single  0.970  0.020  1.090
 MYS  C7   H72   single  0.970  0.020  1.090
 MYS  C8   C9    single  1.524  0.020  1.524
 MYS  C8   H81   single  0.970  0.020  1.090
 MYS  C8   H82   single  0.970  0.020  1.090
 MYS  C9   C10   single  1.523  0.020  1.523
 MYS  C9   H91   single  0.970  0.020  1.090
 MYS  C9   H92   single  0.970  0.020  1.090
 MYS  C10  C11   single  1.524  0.020  1.524
 MYS  C10  H101  single  0.970  0.020  1.090
 MYS  C10  H102  single  0.970  0.020  1.090
 MYS  C11  C12   single  1.524  0.020  1.524
 MYS  C11  H111  single  0.970  0.020  1.090
 MYS  C11  H112  single  0.970  0.020  1.090
 MYS  C12  C13   single  1.524  0.020  1.524
 MYS  C12  H121  single  0.970  0.020  1.090
 MYS  C12  H122  single  0.970  0.020  1.090
 MYS  C13  C14   single  1.524  0.020  1.524
 MYS  C13  H131  single  0.970  0.020  1.090
 MYS  C13  H132  single  0.970  0.020  1.090
 MYS  C14  C15   single  1.523  0.020  1.523
 MYS  C14  H141  single  0.970  0.020  1.090
 MYS  C14  H142  single  0.970  0.020  1.090
 MYS  C15  H151  single  0.970  0.020  1.090
 MYS  C15  H152  single  0.970  0.020  1.090
 MYS  C15  H153  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
 MYS  H13   C1   H12   107.61  3.000
 MYS  H13   C1   H11   107.53  3.000
 MYS  H12   C1   H11   107.60  3.000
 MYS  H13   C1   C2    111.06  3.000
 MYS  H12   C1   C2    111.78  3.000
 MYS  H11   C1   C2    111.06  3.000
 MYS  H22   C2   H21   106.04  3.000
 MYS  H22   C2   C3    109.30  3.000
 MYS  H21   C2   C3    109.31  3.000
 MYS  H22   C2   C1    109.62  3.000
 MYS  H21   C2   C1    109.65  3.000
 MYS  C3    C2   C1    112.71  3.000
 MYS  H32   C3   H31   105.96  3.000
 MYS  H32   C3   C4    109.33  3.000
 MYS  H31   C3   C4    109.34  3.000
 MYS  H32   C3   C2    109.25  3.000
 MYS  H31   C3   C2    109.23  3.000
 MYS  C4    C3   C2    113.45  3.000
 MYS  H42   C4   H41   106.00  3.000
 MYS  H42   C4   C5    109.34  3.000
 MYS  H41   C4   C5    109.38  3.000
 MYS  H42   C4   C3    109.36  3.000
 MYS  H41   C4   C3    109.35  3.000
 MYS  C5    C4   C3    113.17  3.000
 MYS  H52   C5   H51   105.98  3.000
 MYS  H52   C5   C6    109.29  3.000
 MYS  H51   C5   C6    109.29  3.000
 MYS  H52   C5   C4    109.31  3.000
 MYS  H51   C5   C4    109.30  3.000
 MYS  C6    C5   C4    113.41  3.000
 MYS  H62   C6   H61   106.03  3.000
 MYS  H62   C6   C7    109.35  3.000
 MYS  H61   C6   C7    109.35  3.000
 MYS  H62   C6   C5    109.35  3.000
 MYS  H61   C6   C5    109.35  3.000
 MYS  C7    C6   C5    113.16  3.000
 MYS  H72   C7   H71   105.97  3.000
 MYS  H72   C7   C8    109.30  3.000
 MYS  H71   C7   C8    109.33  3.000
 MYS  H72   C7   C6    109.29  3.000
 MYS  H71   C7   C6    109.32  3.000
 MYS  C8    C7   C6    113.37  3.000
 MYS  H82   C8   H81   106.01  3.000
 MYS  H82   C8   C9    109.33  3.000
 MYS  H81   C8   C9    109.38  3.000
 MYS  H82   C8   C7    109.34  3.000
 MYS  H81   C8   C7    109.34  3.000
 MYS  C9    C8   C7    113.19  3.000
 MYS  H92   C9   H91   105.98  3.000
 MYS  H92   C9   C10   109.32  3.000
 MYS  H91   C9   C10   109.30  3.000
 MYS  H92   C9   C8    109.29  3.000
 MYS  H91   C9   C8    109.29  3.000
 MYS  C10   C9   C8    113.40  3.000
 MYS  H102  C10  H101  106.01  3.000
 MYS  H102  C10  C11   109.32  3.000
 MYS  H101  C10  C11   109.35  3.000
 MYS  H102  C10  C9    109.35  3.000
 MYS  H101  C10  C9    109.37  3.000
 MYS  C11   C10  C9    113.19  3.000
 MYS  H112  C11  H111  105.97  3.000
 MYS  H112  C11  C12   109.31  3.000
 MYS  H111  C11  C12   109.34  3.000
 MYS  H112  C11  C10   109.27  3.000
 MYS  H111  C11  C10   109.29  3.000
 MYS  C12   C11  C10   113.38  3.000
 MYS  H122  C12  H121  106.02  3.000
 MYS  H122  C12  C13   109.34  3.000
 MYS  H121  C12  C13   109.34  3.000
 MYS  H122  C12  C11   109.36  3.000
 MYS  H121  C12  C11   109.36  3.000
 MYS  C13   C12  C11   113.17  3.000
 MYS  H132  C13  H131  105.95  3.000
 MYS  H132  C13  C14   109.25  3.000
 MYS  H131  C13  C14   109.26  3.000
 MYS  H132  C13  C12   109.33  3.000
 MYS  H131  C13  C12   109.35  3.000
 MYS  C14   C13  C12   113.44  3.000
 MYS  H142  C14  H141  106.04  3.000
 MYS  H142  C14  C15   109.62  3.000
 MYS  H141  C14  C15   109.65  3.000
 MYS  H142  C14  C13   109.30  3.000
 MYS  H141  C14  C13   109.30  3.000
 MYS  C15   C14  C13   112.70  3.000
 MYS  H153  C15  H152  107.54  3.000
 MYS  H153  C15  H151  107.60  3.000
 MYS  H152  C15  H151  107.60  3.000
 MYS  H153  C15  C14   111.07  3.000
 MYS  H152  C15  C14   111.06  3.000
 MYS  H151  C15  C14   111.77  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
 MYS  Var_01  C4    C3   C2   C1    179.87  30.0  3
 MYS  Var_02  C5    C4   C3   C2    179.92  30.0  3
 MYS  Var_03  C6    C5   C4   C3    179.73  30.0  3
 MYS  Var_04  C7    C6   C5   C4    179.94  30.0  3
 MYS  Var_05  C8    C7   C6   C5   -179.96  30.0  3
 MYS  Var_06  C9    C8   C7   C6   -179.96  30.0  3
 MYS  Var_07  C10   C9   C8   C7   -179.92  30.0  3
 MYS  Var_08  C11   C10  C9   C8   -179.94  30.0  3
 MYS  Var_09  C12   C11  C10  C9   -179.98  30.0  3
 MYS  Var_10  C13   C12  C11  C10   179.44  30.0  3
 MYS  Var_11  C14   C13  C12  C11   179.98  30.0  3
 MYS  Var_12  C15   C14  C13  C12  -179.96  30.0  3
 MYS  Var_13  H11   C1   C2   C3     59.78  30.0  3
 MYS  Var_14  H151  C15  C14  C13  -179.94  30.0  3

