# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 23:24:27 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  48  18  .  2021-08-20  2021-08-20  
;
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   0.550   1.3102  -0.6330  -7.0950
 PAM  O1    O  OH1   0  -0.599   2.1127  -0.0868  -8.0056
 PAM  O2    O  O     0  -0.446   0.8082  -1.7206  -7.2350
 PAM  C2    C  CH2   0  -0.580   1.1202   0.2654  -5.9050
 PAM  C3    C  CH2   0  -0.418   0.2573  -0.3384  -4.8092
 PAM  C4    C  CH2   0  -0.415   0.1100   0.6028  -3.6200
 PAM  C5    C  CH2   0  -0.413  -0.7475   0.0152  -2.5064
 PAM  C6    C  CH2   0  -0.414  -0.8884   0.9420  -1.3053
 PAM  C7    C  CH2   0  -0.410  -1.7685   0.3618  -0.2055
 PAM  C8    C  CH2   0  -0.493  -1.8692   1.2724   1.0209
 PAM  C9    C  C1    0  -0.227  -2.8186   0.7363   2.0500
 PAM  C10   C  C1    0  -0.204  -2.5064  -0.0070   3.1111
 PAM  C11   C  CH2   0  -0.485  -1.1403  -0.4526   3.5286
 PAM  C12   C  CH2   0  -0.413  -0.7771  -0.0007   4.9435
 PAM  C13   C  CH2   0  -0.411   0.5917  -0.5010   5.3872
 PAM  C14   C  CH2   0  -0.406   0.9584  -0.0845   6.8061
 PAM  C15   C  CH2   0  -0.418   2.3327  -0.5797   7.2410
 PAM  C16   C  CH3   0  -0.661   2.6929  -0.1682   8.6620
 PAM  HO1   H  HOH1  0   0.477   2.2138  -0.6881  -8.7581
 PAM  H21   H  HCH2  0   0.276   0.6886   1.2085  -6.2565
 PAM  H22   H  HCH2  0   0.274   2.1087   0.5273  -5.5140
 PAM  H31   H  HCH2  0   0.224   0.6948  -1.2823  -4.4729
 PAM  H32   H  HCH2  0   0.225  -0.7325  -0.5797  -5.2057
 PAM  H41   H  HCH2  0   0.213  -0.3278   1.5503  -3.9526
 PAM  H42   H  HCH2  0   0.212   1.1015   0.8489  -3.2242
 PAM  H51   H  HCH2  0   0.210  -0.3153  -0.9377  -2.1819
 PAM  H52   H  HCH2  0   0.209  -1.7416  -0.2214  -2.9015
 PAM  H61   H  HCH2  0   0.210  -1.3034   1.9023  -1.6309
 PAM  H62   H  HCH2  0   0.209   0.1049   1.1632  -0.8988
 PAM  H71   H  HCH2  0   0.215  -1.3741  -0.6109   0.1058
 PAM  H72   H  HCH2  0   0.215  -2.7704   0.1705  -0.6040
 PAM  H81   H  HCH2  0   0.229  -2.2088   2.2622   0.7008
 PAM  H82   H  HCH2  0   0.228  -0.8705   1.4131   1.4428
 PAM  H9    H  H     0   0.228  -3.8691   0.9539   1.8778
 PAM  H10   H  H     0   0.226  -3.3186  -0.3381   3.7541
 PAM  H111  H  HCH2  0   0.227  -0.3823  -0.0998   2.8250
 PAM  H112  H  HCH2  0   0.228  -1.1008  -1.5475   3.4924
 PAM  H121  H  HCH2  0   0.212  -1.5403  -0.3546   5.6450
 PAM  H122  H  HCH2  0   0.215  -0.8025   1.0927   4.9913
 PAM  H131  H  HCH2  0   0.208   1.3539  -0.1329   4.6915
 PAM  H132  H  HCH2  0   0.208   0.6173  -1.5939   5.3131
 PAM  H141  H  HCH2  0   0.206   0.2010  -0.4618   7.5022
 PAM  H142  H  HCH2  0   0.206   0.9251   1.0077   6.8858
 PAM  H151  H  HCH2  0   0.210   3.0893  -0.2006   6.5469
 PAM  H152  H  HCH2  0   0.210   2.3662  -1.6705   7.1576
 PAM  H161  H  HCH3  0   0.225   3.6768  -0.5407   8.9491
 PAM  H162  H  HCH3  0   0.215   2.7072   0.9182   8.7683
 PAM  H163  H  HCH3  0   0.215   1.9701  -0.5585   9.3811

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    single  1.331  0.020  1.331
 PAM  C1   O2    double  1.206  0.020  1.206
 PAM  C1   C2    single  1.503  0.020  1.503
 PAM  O1   HO1   single  0.850  0.020  0.980
 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  1.523  0.020  1.523
 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  1.333  0.020  1.333
 PAM  C9   H9    single  0.930  0.020  1.080
 PAM  C10  C11   single  1.496  0.020  1.496
 PAM  C10  H10   single  0.930  0.020  1.080
 PAM  C11  C12   single  1.529  0.020  1.529
 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    125.33  3.000
 PAM  C2    C1   O1    111.88  3.000
 PAM  O2    C1   O1    122.80  3.000
 PAM  HO1   O1   C1    109.86  3.000
 PAM  H22   C2   H21   105.33  3.000
 PAM  H22   C2   C3    110.50  3.000
 PAM  H21   C2   C3    110.47  3.000
 PAM  H22   C2   C1    108.15  3.000
 PAM  H21   C2   C1    108.08  3.000
 PAM  C3    C2   C1    113.90  3.000
 PAM  H32   C3   H31   106.46  3.000
 PAM  H32   C3   C4    109.38  3.000
 PAM  H31   C3   C4    109.38  3.000
 PAM  H32   C3   C2    109.89  3.000
 PAM  H31   C3   C2    109.72  3.000
 PAM  C4    C3   C2    111.85  3.000
 PAM  H42   C4   H41   106.08  3.000
 PAM  H42   C4   C5    109.39  3.000
 PAM  H41   C4   C5    109.30  3.000
 PAM  H42   C4   C3    109.47  3.000
 PAM  H41   C4   C3    109.63  3.000
 PAM  C5    C4   C3    112.75  3.000
 PAM  H52   C5   H51   106.08  3.000
 PAM  H52   C5   C6    109.37  3.000
 PAM  H51   C5   C6    109.40  3.000
 PAM  H52   C5   C4    109.29  3.000
 PAM  H51   C5   C4    109.27  3.000
 PAM  C6    C5   C4    113.19  3.000
 PAM  H62   C6   H61   106.06  3.000
 PAM  H62   C6   C7    109.43  3.000
 PAM  H61   C6   C7    109.24  3.000
 PAM  H62   C6   C5    109.35  3.000
 PAM  H61   C6   C5    109.51  3.000
 PAM  C7    C6   C5    113.01  3.000
 PAM  H72   C7   H71   106.13  3.000
 PAM  H72   C7   C8    109.59  3.000
 PAM  H71   C7   C8    108.93  3.000
 PAM  H72   C7   C6    109.41  3.000
 PAM  H71   C7   C6    109.61  3.000
 PAM  C8    C7   C6    112.95  3.000
 PAM  H82   C8   H81   106.26  3.000
 PAM  H82   C8   C9    111.07  3.000
 PAM  H81   C8   C9    109.13  3.000
 PAM  H82   C8   C7    109.00  3.000
 PAM  H81   C8   C7    108.91  3.000
 PAM  C9    C8   C7    112.26  3.000
 PAM  H9    C9   C10   117.67  3.000
 PAM  H9    C9   C8    115.58  3.000
 PAM  C10   C9   C8    126.70  3.000
 PAM  H10   C10  C11   115.22  3.000
 PAM  H10   C10  C9    117.75  3.000
 PAM  C11   C10  C9    127.02  3.000
 PAM  H112  C11  H111  106.04  3.000
 PAM  H112  C11  C12   108.49  3.000
 PAM  H111  C11  C12   109.61  3.000
 PAM  H112  C11  C10   108.73  3.000
 PAM  H111  C11  C10   110.94  3.000
 PAM  C12   C11  C10   112.77  3.000
 PAM  H122  C12  H121  106.18  3.000
 PAM  H122  C12  C13   109.65  3.000
 PAM  H121  C12  C13   109.48  3.000
 PAM  H122  C12  C11   109.27  3.000
 PAM  H121  C12  C11   109.36  3.000
 PAM  C13   C12  C11   112.70  3.000
 PAM  H132  C13  H131  106.02  3.000
 PAM  H132  C13  C14   109.27  3.000
 PAM  H131  C13  C14   109.39  3.000
 PAM  H132  C13  C12   109.20  3.000
 PAM  H131  C13  C12   109.26  3.000
 PAM  C14   C13  C12   113.44  3.000
 PAM  H142  C14  H141  106.02  3.000
 PAM  H142  C14  C15   109.30  3.000
 PAM  H141  C14  C15   109.28  3.000
 PAM  H142  C14  C13   109.45  3.000
 PAM  H141  C14  C13   109.34  3.000
 PAM  C15   C14  C13   113.20  3.000
 PAM  H152  C15  H151  106.00  3.000
 PAM  H152  C15  C16   109.46  3.000
 PAM  H151  C15  C16   109.55  3.000
 PAM  H152  C15  C14   109.25  3.000
 PAM  H151  C15  C14   109.26  3.000
 PAM  C16   C15  C14   113.07  3.000
 PAM  H163  C16  H162  107.47  3.000
 PAM  H163  C16  H161  107.57  3.000
 PAM  H162  C16  H161  107.61  3.000
 PAM  H163  C16  C15   111.19  3.000
 PAM  H162  C16  C15   111.28  3.000
 PAM  H161  C16  C15   111.52  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  CONST_01  HO1   O1   C1   O2      0.00   0.0  0
 PAM  Var_01    C11   C10  C9   C8      1.21   0.0  2
 PAM  Var_02    C4    C3   C2   C1    179.28  30.0  3
 PAM  Var_03    C3    C2   C1   O1   -177.58  30.0  3
 PAM  Var_04    C5    C4   C3   C2   -179.78  30.0  3
 PAM  Var_05    C6    C5   C4   C3    179.35  30.0  3
 PAM  Var_06    C7    C6   C5   C4    178.89  30.0  3
 PAM  Var_07    C8    C7   C6   C5    177.98  30.0  3
 PAM  Var_08    C9    C8   C7   C6    175.72  30.0  3
 PAM  Var_09    C10   C9   C8   C7     94.96  30.0  3
 PAM  Var_10    C12   C11  C10  C9    122.40  30.0  3
 PAM  Var_11    C13   C12  C11  C10   177.76  30.0  3
 PAM  Var_12    C14   C13  C12  C11  -178.80  30.0  3
 PAM  Var_13    C15   C14  C13  C12  -179.60  30.0  3
 PAM  Var_14    C16   C15  C14  C13  -179.69  30.0  3
 PAM  Var_15    H161  C16  C15  C14   179.62  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-1  HO1  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

