# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:14:51 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (9Z)-hexadec-9-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC\C=C/CCCCCCCC(O)=O
#
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
 PAM  PAM  '(9Z)-hexadec-9-enoic acid'  ligand  47  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PAM
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
 PAM  C1    C  C      0   0.409   1.4926  -0.5184  -7.0877
 PAM  O1    O  OC    -1  -0.635   2.3388  -0.0602  -7.8855
 PAM  O2    O  O      0  -0.610   0.8381  -1.5697  -7.2352
 PAM  C2    C  CH2    0  -0.580   1.2403   0.3164  -5.8205
 PAM  C3    C  CH2    0  -0.403   0.3562  -0.3194  -4.7600
 PAM  C4    C  CH2    0  -0.409   0.1734   0.5745  -3.5389
 PAM  C5    C  CH2    0  -0.411  -0.7072  -0.0420  -2.4590
 PAM  C6    C  CH2    0  -0.412  -0.8617   0.8523  -1.2352
 PAM  C7    C  CH2    0  -0.410  -1.7772   0.2681  -0.1671
 PAM  C8    C  CH2    0  -0.493  -1.8709   1.1543   1.0773
 PAM  C9    C  C1     0  -0.222  -2.8674   0.6464   2.0758
 PAM  C10   C  C1     0  -0.210  -2.6101  -0.1203   3.1344
 PAM  C11   C  CH2    0  -0.487  -1.2721  -0.6303   3.5705
 PAM  C12   C  CH2    0  -0.412  -0.7975   0.0029   4.8796
 PAM  C13   C  CH2    0  -0.412   0.5061  -0.6013   5.3858
 PAM  C14   C  CH2    0  -0.407   1.0073   0.0308   6.6782
 PAM  C15   C  CH2    0  -0.418   2.2942  -0.6022   7.1941
 PAM  C16   C  CH3    0  -0.662   2.7975   0.0312   8.4838
 PAM  H21   H  HCH2   0   0.218   0.8031   1.2745  -6.1289
 PAM  H22   H  HCH2   0   0.212   2.2092   0.5804  -5.3817
 PAM  H31   H  HCH2   0   0.199   0.7854  -1.2759  -4.4453
 PAM  H32   H  HCH2   0   0.200  -0.6233  -0.5556  -5.1855
 PAM  H41   H  HCH2   0   0.202  -0.2583   1.5332  -3.8488
 PAM  H42   H  HCH2   0   0.202   1.1546   0.8129  -3.1119
 PAM  H51   H  HCH2   0   0.205  -0.2870  -1.0070  -2.1545
 PAM  H52   H  HCH2   0   0.205  -1.6957  -0.2613  -2.8783
 PAM  H61   H  HCH2   0   0.208  -1.2504   1.8289  -1.5452
 PAM  H62   H  HCH2   0   0.207   0.1262   1.0449  -0.8016
 PAM  H71   H  HCH2   0   0.213  -1.4171  -0.7227   0.1286
 PAM  H72   H  HCH2   0   0.214  -2.7771   0.1161  -0.5872
 PAM  H81   H  HCH2   0   0.229  -2.1595   2.1645   0.7709
 PAM  H82   H  HCH2   0   0.227  -0.8781   1.2439   1.5263
 PAM  H9    H  H      0   0.227  -3.9023   0.9188   1.8875
 PAM  H10   H  H      0   0.227  -3.4454  -0.4105   3.7673
 PAM  H111  H  HCH2   0   0.228  -0.5187  -0.4736   2.7945
 PAM  H112  H  HCH2   0   0.227  -1.3404  -1.7145   3.7118
 PAM  H121  H  HCH2   0   0.213  -1.5742  -0.1116   5.6436
 PAM  H122  H  HCH2   0   0.214  -0.6737   1.0804   4.7310
 PAM  H131  H  HCH2   0   0.209   1.2759  -0.5051   4.6119
 PAM  H132  H  HCH2   0   0.208   0.3663  -1.6770   5.5399
 PAM  H141  H  HCH2   0   0.206   0.2310  -0.0481   7.4477
 PAM  H142  H  HCH2   0   0.206   1.1681   1.1031   6.5205
 PAM  H151  H  HCH2   0   0.210   3.0676  -0.5288   6.4232
 PAM  H152  H  HCH2   0   0.210   2.1292  -1.6722   7.3546
 PAM  H161  H  HCH3   0   0.225   3.7060  -0.4562   8.8394
 PAM  H162  H  HCH3   0   0.216   3.0245   1.0898   8.3438
 PAM  H163  H  HCH3   0   0.215   2.0511  -0.0425   9.2770

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
 PAM  C1   O1    deloc   1.250  0.020  1.250
 PAM  C1   O2    deloc   1.247  0.020  1.247
 PAM  C1   C2    single  1.538  0.020  1.538
 PAM  C2   C3    single  1.520  0.020  1.520
 PAM  C2   H21   single  0.970  0.020  1.090
 PAM  C2   H22   single  0.970  0.020  1.090
 PAM  C3   C4    single  1.524  0.020  1.524
 PAM  C3   H31   single  0.970  0.020  1.090
 PAM  C3   H32   single  0.970  0.020  1.090
 PAM  C4   C5    single  1.524  0.020  1.524
 PAM  C4   H41   single  0.970  0.020  1.090
 PAM  C4   H42   single  0.970  0.020  1.090
 PAM  C5   C6    single  1.524  0.020  1.524
 PAM  C5   H51   single  0.970  0.020  1.090
 PAM  C5   H52   single  0.970  0.020  1.090
 PAM  C6   C7    single  1.523  0.020  1.523
 PAM  C6   H61   single  0.970  0.020  1.090
 PAM  C6   H62   single  0.970  0.020  1.090
 PAM  C7   C8    single  1.531  0.020  1.531
 PAM  C7   H71   single  0.970  0.020  1.090
 PAM  C7   H72   single  0.970  0.020  1.090
 PAM  C8   C9    single  1.499  0.020  1.499
 PAM  C8   H81   single  0.970  0.020  1.090
 PAM  C8   H82   single  0.970  0.020  1.090
 PAM  C9   C10   double  1.332  0.020  1.332
 PAM  C9   H9    single  0.930  0.020  1.080
 PAM  C10  C11   single  1.497  0.020  1.497
 PAM  C10  H10   single  0.930  0.020  1.080
 PAM  C11  C12   single  1.530  0.020  1.530
 PAM  C11  H111  single  0.970  0.020  1.090
 PAM  C11  H112  single  0.970  0.020  1.090
 PAM  C12  C13   single  1.523  0.020  1.523
 PAM  C12  H121  single  0.970  0.020  1.090
 PAM  C12  H122  single  0.970  0.020  1.090
 PAM  C13  C14   single  1.524  0.020  1.524
 PAM  C13  H131  single  0.970  0.020  1.090
 PAM  C13  H132  single  0.970  0.020  1.090
 PAM  C14  C15   single  1.524  0.020  1.524
 PAM  C14  H141  single  0.970  0.020  1.090
 PAM  C14  H142  single  0.970  0.020  1.090
 PAM  C15  C16   single  1.523  0.020  1.523
 PAM  C15  H151  single  0.970  0.020  1.090
 PAM  C15  H152  single  0.970  0.020  1.090
 PAM  C16  H161  single  0.970  0.020  1.090
 PAM  C16  H162  single  0.970  0.020  1.090
 PAM  C16  H163  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
 PAM  C2    C1   O2    117.96  3.000
 PAM  C2    C1   O1    115.96  3.000
 PAM  O2    C1   O1    126.07  3.000
 PAM  H22   C2   H21   104.74  3.000
 PAM  H22   C2   C3    109.61  3.000
 PAM  H21   C2   C3    109.24  3.000
 PAM  H22   C2   C1    108.39  3.000
 PAM  H21   C2   C1    107.92  3.000
 PAM  C3    C2   C1    116.30  3.000
 PAM  H32   C3   H31   105.93  3.000
 PAM  H32   C3   C4    109.33  3.000
 PAM  H31   C3   C4    109.22  3.000
 PAM  H32   C3   C2    109.86  3.000
 PAM  H31   C3   C2    109.76  3.000
 PAM  C4    C3   C2    112.54  3.000
 PAM  H42   C4   H41   105.81  3.000
 PAM  H42   C4   C5    109.22  3.000
 PAM  H41   C4   C5    109.06  3.000
 PAM  H42   C4   C3    109.41  3.000
 PAM  H41   C4   C3    109.49  3.000
 PAM  C5    C4   C3    113.56  3.000
 PAM  H52   C5   H51   106.02  3.000
 PAM  H52   C5   C6    109.47  3.000
 PAM  H51   C5   C6    109.43  3.000
 PAM  H52   C5   C4    109.34  3.000
 PAM  H51   C5   C4    109.37  3.000
 PAM  C6    C5   C4    112.98  3.000
 PAM  H62   C6   H61   105.97  3.000
 PAM  H62   C6   C7    109.37  3.000
 PAM  H61   C6   C7    109.08  3.000
 PAM  H62   C6   C5    109.24  3.000
 PAM  H61   C6   C5    109.38  3.000
 PAM  C7    C6   C5    113.52  3.000
 PAM  H72   C7   H71   106.16  3.000
 PAM  H72   C7   C8    109.65  3.000
 PAM  H71   C7   C8    108.93  3.000
 PAM  H72   C7   C6    109.45  3.000
 PAM  H71   C7   C6    109.80  3.000
 PAM  C8    C7   C6    112.63  3.000
 PAM  H82   C8   H81   106.19  3.000
 PAM  H82   C8   C9    110.97  3.000
 PAM  H81   C8   C9    108.90  3.000
 PAM  H82   C8   C7    109.01  3.000
 PAM  H81   C8   C7    108.84  3.000
 PAM  C9    C8   C7    112.71  3.000
 PAM  H9    C9   C10   117.77  3.000
 PAM  H9    C9   C8    115.64  3.000
 PAM  C10   C9   C8    126.57  3.000
 PAM  H10   C10  C11   115.22  3.000
 PAM  H10   C10  C9    117.89  3.000
 PAM  C11   C10  C9    126.89  3.000
 PAM  H112  C11  H111  106.04  3.000
 PAM  H112  C11  C12   108.58  3.000
 PAM  H111  C11  C12   109.53  3.000
 PAM  H112  C11  C10   108.61  3.000
 PAM  H111  C11  C10   111.14  3.000
 PAM  C12   C11  C10   112.68  3.000
 PAM  H122  C12  H121  106.12  3.000
 PAM  H122  C12  C13   109.80  3.000
 PAM  H121  C12  C13   109.49  3.000
 PAM  H122  C12  C11   109.04  3.000
 PAM  H121  C12  C11   109.48  3.000
 PAM  C13   C12  C11   112.69  3.000
 PAM  H132  C13  H131  105.97  3.000
 PAM  H132  C13  C14   109.27  3.000
 PAM  H131  C13  C14   109.36  3.000
 PAM  H132  C13  C12   109.08  3.000
 PAM  H131  C13  C12   109.38  3.000
 PAM  C14   C13  C12   113.51  3.000
 PAM  H142  C14  H141  105.99  3.000
 PAM  H142  C14  C15   109.35  3.000
 PAM  H141  C14  C15   109.30  3.000
 PAM  H142  C14  C13   109.40  3.000
 PAM  H141  C14  C13   109.43  3.000
 PAM  C15   C14  C13   113.12  3.000
 PAM  H152  C15  H151  105.98  3.000
 PAM  H152  C15  C16   109.42  3.000
 PAM  H151  C15  C16   109.58  3.000
 PAM  H152  C15  C14   109.17  3.000
 PAM  H151  C15  C14   109.29  3.000
 PAM  C16   C15  C14   113.15  3.000
 PAM  H163  C16  H162  107.51  3.000
 PAM  H163  C16  H161  107.61  3.000
 PAM  H162  C16  H161  107.59  3.000
 PAM  H163  C16  C15   111.18  3.000
 PAM  H162  C16  C15   111.32  3.000
 PAM  H161  C16  C15   111.44  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
 PAM  Var_01  C11   C10  C9   C8      0.78   0.0  2
 PAM  Var_02  C4    C3   C2   C1    179.50  30.0  3
 PAM  Var_03  C3    C2   C1   O1   -172.11  30.0  3
 PAM  Var_04  C5    C4   C3   C2   -179.88  30.0  3
 PAM  Var_05  C6    C5   C4   C3    179.03  30.0  3
 PAM  Var_06  C7    C6   C5   C4    178.08  30.0  3
 PAM  Var_07  C8    C7   C6   C5    177.56  30.0  3
 PAM  Var_08  C9    C8   C7   C6    174.70  30.0  3
 PAM  Var_09  C10   C9   C8   C7     95.50  30.0  3
 PAM  Var_10  C12   C11  C10  C9    111.48  30.0  3
 PAM  Var_11  C13   C12  C11  C10   175.09  30.0  3
 PAM  Var_12  C14   C13  C12  C11   179.11  30.0  3
 PAM  Var_13  C15   C14  C13  C12   178.64  30.0  3
 PAM  Var_14  C16   C15  C14  C13   179.86  30.0  3
 PAM  Var_15  H161  C16  C15  C14   178.76  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
 PAM  plan-1  C1   0.020
 PAM  plan-1  O1   0.020
 PAM  plan-1  O2   0.020
 PAM  plan-1  C2   0.020
 PAM  plan-2  C8   0.020
 PAM  plan-2  C9   0.020
 PAM  plan-2  C10  0.020
 PAM  plan-2  C11  0.020
 PAM  plan-2  H9   0.020
 PAM  plan-2  H10  0.020

