# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 14:53:56 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 10-methylundecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCCCCCCCC(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
 M12  M12  '10-methylundecanoic acid '  ligand  38  14  .  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_M12
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
 M12  C1    C  C     0   0.549  -5.7155  -0.1188  -0.0497
 M12  O1    O  O     0  -0.447  -5.8364  -1.2621  -0.4141
 M12  C2    C  CH2   0  -0.579  -4.4089   0.5985   0.1435
 M12  C3    C  CH2   0  -0.417  -3.1863  -0.2811  -0.0582
 M12  C4    C  CH2   0  -0.414  -1.8902   0.4945   0.1399
 M12  C5    C  CH2   0  -0.412  -0.6492  -0.3689  -0.0446
 M12  C6    C  CH2   0  -0.411   0.6514   0.3989   0.1533
 M12  C7    C  CH2   0  -0.409   1.8928  -0.4651  -0.0286
 M12  C8    C  CH2   0  -0.420   3.1954   0.2987   0.1769
 M12  C9    C  CH2   0  -0.393   4.4284  -0.5739  -0.0258
 M12  C10   C  CH1   0  -0.231   5.7643   0.1040   0.2848
 M12  C11   C  CH3   0  -0.650   6.9047  -0.9041   0.1748
 M12  C12   C  CH3   0  -0.657   6.0274   1.3083  -0.6140
 M12  OXT   O  OH1   0  -0.599  -6.7560   0.6643   0.2247
 M12  H21C  H  HCH2  0   0.276  -4.3900   1.4470  -0.5491
 M12  H22C  H  HCH2  0   0.273  -4.4045   1.0422   1.1441
 M12  HXT   H  HOH1  0   0.478  -7.5812   0.1762   0.0865
 M12  H31C  H  HCH2  0   0.224  -3.2161  -1.1212   0.6412
 M12  H32C  H  HCH2  0   0.224  -3.2010  -0.7139  -1.0620
 M12  H41C  H  HCH2  0   0.212  -1.8576   1.3344  -0.5628
 M12  H42C  H  HCH2  0   0.212  -1.8786   0.9373   1.1419
 M12  H51C  H  HCH2  0   0.208  -0.6838  -1.2086   0.6584
 M12  H52C  H  HCH2  0   0.208  -0.6602  -0.8123  -1.0465
 M12  H61C  H  HCH2  0   0.207   0.6863   1.2387  -0.5498
 M12  H62C  H  HCH2  0   0.206   0.6615   0.8430   1.1551
 M12  H71C  H  HCH2  0   0.206   1.8536  -1.3080   0.6706
 M12  H72C  H  HCH2  0   0.206   1.8848  -0.9050  -1.0323
 M12  H81C  H  HCH2  0   0.212   3.2174   1.1516  -0.5085
 M12  H82C  H  HCH2  0   0.205   3.2116   0.7218   1.1880
 M12  H91C  H  HCH2  0   0.210   4.3373  -1.4618   0.6101
 M12  H92C  H  HCH2  0   0.201   4.4479  -0.9440  -1.0583
 M12  H10   H  HCH1  0   0.207   5.7261   0.4577   1.3226
 M12  H111  H  HCH3  0   0.210   6.9906  -1.2866  -0.8455
 M12  H112  H  HCH3  0   0.222   7.8635  -0.4548   0.4392
 M12  H113  H  HCH3  0   0.221   6.7454  -1.7587   0.8349
 M12  H121  H  HCH3  0   0.210   6.0409   1.0115  -1.6660
 M12  H122  H  HCH3  0   0.227   5.2690   2.0830  -0.4977
 M12  H123  H  HCH3  0   0.223   6.9937   1.7624  -0.3868

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
 M12  C1   O1    double  1.206  0.020  1.206
 M12  C1   C2    single  1.503  0.020  1.503
 M12  C1   OXT   single  1.331  0.020  1.331
 M12  C2   C3    single  1.520  0.020  1.520
 M12  C3   C4    single  1.523  0.020  1.523
 M12  C4   C5    single  1.523  0.020  1.523
 M12  C5   C6    single  1.523  0.020  1.523
 M12  C6   C7    single  1.523  0.020  1.523
 M12  C7   C8    single  1.524  0.020  1.524
 M12  C8   C9    single  1.524  0.020  1.524
 M12  C9   C10   single  1.530  0.020  1.530
 M12  C10  C11   single  1.526  0.020  1.526
 M12  C10  C12   single  1.526  0.020  1.526
 M12  C2   H21C  single  0.970  0.020  1.090
 M12  C2   H22C  single  0.970  0.020  1.090
 M12  OXT  HXT   single  0.850  0.020  0.980
 M12  C3   H31C  single  0.970  0.020  1.090
 M12  C3   H32C  single  0.970  0.020  1.090
 M12  C4   H41C  single  0.970  0.020  1.090
 M12  C4   H42C  single  0.970  0.020  1.090
 M12  C5   H51C  single  0.970  0.020  1.090
 M12  C5   H52C  single  0.970  0.020  1.090
 M12  C6   H61C  single  0.970  0.020  1.090
 M12  C6   H62C  single  0.970  0.020  1.090
 M12  C7   H71C  single  0.970  0.020  1.090
 M12  C7   H72C  single  0.970  0.020  1.090
 M12  C8   H81C  single  0.970  0.020  1.090
 M12  C8   H82C  single  0.970  0.020  1.090
 M12  C9   H91C  single  0.970  0.020  1.090
 M12  C9   H92C  single  0.970  0.020  1.090
 M12  C10  H10   single  0.970  0.020  1.090
 M12  C11  H111  single  0.970  0.020  1.090
 M12  C11  H112  single  0.970  0.020  1.090
 M12  C11  H113  single  0.970  0.020  1.090
 M12  C12  H121  single  0.970  0.020  1.090
 M12  C12  H122  single  0.970  0.020  1.090
 M12  C12  H123  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
 M12  OXT   C1   C2    111.86  3.000
 M12  OXT   C1   O1    122.81  3.000
 M12  C2    C1   O1    125.34  3.000
 M12  H22C  C2   H21C  105.31  3.000
 M12  H22C  C2   C3    110.66  3.000
 M12  H21C  C2   C3    110.52  3.000
 M12  H22C  C2   C1    108.33  3.000
 M12  H21C  C2   C1    107.66  3.000
 M12  C3    C2   C1    113.96  3.000
 M12  H32C  C3   H31C  106.42  3.000
 M12  H32C  C3   C4    109.42  3.000
 M12  H31C  C3   C4    109.34  3.000
 M12  H32C  C3   C2    109.89  3.000
 M12  H31C  C3   C2    109.75  3.000
 M12  C4    C3   C2    111.87  3.000
 M12  H42C  C4   H41C  106.04  3.000
 M12  H42C  C4   C5    109.35  3.000
 M12  H41C  C4   C5    109.43  3.000
 M12  H42C  C4   C3    109.50  3.000
 M12  H41C  C4   C3    109.40  3.000
 M12  C5    C4   C3    112.89  3.000
 M12  H52C  C5   H51C  106.04  3.000
 M12  H52C  C5   C6    109.35  3.000
 M12  H51C  C5   C6    109.26  3.000
 M12  H52C  C5   C4    109.39  3.000
 M12  H51C  C5   C4    109.33  3.000
 M12  C6    C5   C4    113.22  3.000
 M12  H62C  C6   H61C  106.01  3.000
 M12  H62C  C6   C7    109.36  3.000
 M12  H61C  C6   C7    109.40  3.000
 M12  H62C  C6   C5    109.32  3.000
 M12  H61C  C6   C5    109.27  3.000
 M12  C7    C6   C5    113.22  3.000
 M12  H72C  C7   H71C  105.99  3.000
 M12  H72C  C7   C8    109.32  3.000
 M12  H71C  C7   C8    109.27  3.000
 M12  H72C  C7   C6    109.34  3.000
 M12  H71C  C7   C6    109.33  3.000
 M12  C8    C7   C6    113.33  3.000
 M12  H82C  C8   H81C  106.06  3.000
 M12  H82C  C8   C9    109.37  3.000
 M12  H81C  C8   C9    110.28  3.000
 M12  H82C  C8   C7    109.30  3.000
 M12  H81C  C8   C7    108.87  3.000
 M12  C9    C8   C7    112.74  3.000
 M12  H92C  C9   H91C  105.92  3.000
 M12  H92C  C9   C10   108.96  3.000
 M12  H91C  C9   C10   108.29  3.000
 M12  H92C  C9   C8    109.43  3.000
 M12  H91C  C9   C8    108.63  3.000
 M12  C10   C9   C8    115.19  3.000
 M12  H10   C10  C12   107.99  3.000
 M12  H10   C10  C11   107.89  3.000
 M12  C12   C10  C11   110.50  3.000
 M12  H10   C10  C9    107.72  3.000
 M12  C12   C10  C9    112.38  3.000
 M12  C11   C10  C9    110.19  3.000
 M12  H113  C11  H112  107.70  3.000
 M12  H113  C11  H111  107.58  3.000
 M12  H112  C11  H111  107.53  3.000
 M12  H113  C11  C10   111.38  3.000
 M12  H112  C11  C10   111.54  3.000
 M12  H111  C11  C10   110.93  3.000
 M12  H123  C12  H122  107.34  3.000
 M12  H123  C12  H121  107.60  3.000
 M12  H122  C12  H121  107.70  3.000
 M12  H123  C12  C10   111.00  3.000
 M12  H122  C12  C10   112.22  3.000
 M12  H121  C12  C10   110.77  3.000
 M12  HXT   OXT  C1    109.88  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
 M12  CONST_01  HXT   OXT  C1   O1     0.00   0.0  0
 M12  Var_01    C4    C3   C2   C1   179.63  30.0  3
 M12  Var_02    C3    C2   C1   O1    -4.57  30.0  3
 M12  Var_03    C5    C4   C3   C2   179.48  30.0  3
 M12  Var_04    C6    C5   C4   C3  -179.94  30.0  3
 M12  Var_05    C7    C6   C5   C4   179.89  30.0  3
 M12  Var_06    C8    C7   C6   C5  -179.66  30.0  3
 M12  Var_07    C9    C8   C7   C6  -179.27  30.0  3
 M12  Var_08    C10   C9   C8   C7  -174.93  30.0  3
 M12  Var_09    C11   C10  C9   C8   174.56  30.0  3
 M12  Var_10    H111  C11  C10  C9    62.91  30.0  3
 M12  Var_11    H121  C12  C10  C9   -59.41  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
 M12  plan-1  C1   0.020
 M12  plan-1  O1   0.020
 M12  plan-1  C2   0.020
 M12  plan-1  OXT  0.020
 M12  plan-1  HXT  0.020

