# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 22:53:38 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 12-imidazol-1-yldodecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCCCCCn1ccnc1
#
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
 LC4  LC4  '12-imidazol-1-yldodecanoic acid'  ligand  45  19  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LC4
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
 LC4  O1    O  O     0  -0.446   -8.4184  -1.5519  -0.0876
 LC4  C2    C  C     0   0.549   -8.3852  -0.3489  -0.0081
 LC4  O17   O  OH1   0  -0.599   -9.4829   0.3987   0.0776
 LC4  C3    C  CH2   0  -0.580   -7.1364   0.4877   0.0038
 LC4  C4    C  CH2   0  -0.418   -5.8511  -0.3229  -0.0193
 LC4  C5    C  CH2   0  -0.415   -4.6165   0.5704  -0.0093
 LC4  C6    C  CH2   0  -0.413   -3.3152  -0.2211  -0.0255
 LC4  C7    C  CH2   0  -0.412   -2.0747   0.6638  -0.0158
 LC4  C18   C  CH2   0  -0.413   -0.7730  -0.1278  -0.0228
 LC4  C19   C  CH2   0  -0.413    0.4680   0.7562  -0.0107
 LC4  C8    C  CH2   0  -0.413    1.7692  -0.0359  -0.0185
 LC4  C9    C  CH2   0  -0.423    3.0079   0.8512  -0.0019
 LC4  C10   C  CH2   0  -0.428    4.3056   0.0541  -0.0084
 LC4  C11   C  CH2   0  -0.296    5.5250   0.9652   0.0173
 LC4  N12   N  NR5   0  -0.397    6.7731   0.2270   0.0175
 LC4  C13   C  CR15  0  -0.109    7.3603  -0.3776  -1.0576
 LC4  C14   C  CR15  0  -0.220    8.4665  -1.0099  -0.5649
 LC4  N15   N  N     0  -0.459    8.5634  -0.8091   0.7827
 LC4  C16   C  CR15  0   0.093    7.5298  -0.0682   1.0946
 LC4  HO17  H  HOH1  0   0.478  -10.2694  -0.1666   0.0610
 LC4  H3    H  HCH2  0   0.276   -7.1778   1.1651  -0.8560
 LC4  H3A   H  HCH2  0   0.274   -7.1671   1.1362   0.8852
 LC4  H4    H  HCH2  0   0.224   -5.8199  -0.9929   0.8443
 LC4  H4A   H  HCH2  0   0.225   -5.8294  -0.9611  -0.9067
 LC4  H5    H  HCH2  0   0.212   -4.6448   1.2424  -0.8742
 LC4  H5A   H  HCH2  0   0.212   -4.6388   1.2150   0.8765
 LC4  H6    H  HCH2  0   0.209   -3.2881  -0.8929   0.8398
 LC4  H6A   H  HCH2  0   0.209   -3.2934  -0.8666  -0.9107
 LC4  H7    H  HCH2  0   0.207   -2.0989   1.3313  -0.8846
 LC4  H7A   H  HCH2  0   0.207   -2.0997   1.3138   0.8660
 LC4  H18   H  HCH2  0   0.207   -0.7502  -0.7964   0.8452
 LC4  H18A  H  HCH2  0   0.207   -0.7472  -0.7770  -0.9054
 LC4  H19   H  HCH2  0   0.208    0.4448   1.4256  -0.8781
 LC4  H19A  H  HCH2  0   0.208    0.4428   1.4044   0.8725
 LC4  H8    H  HCH2  0   0.211    1.7921  -0.7064   0.8478
 LC4  H8A   H  HCH2  0   0.211    1.7971  -0.6818  -0.9031
 LC4  H9    H  HCH2  0   0.217    2.9863   1.5210  -0.8685
 LC4  H9A   H  HCH2  0   0.217    2.9799   1.4965   0.8830
 LC4  H10   H  HCH2  0   0.229    4.3376  -0.6136   0.8579
 LC4  H10A  H  HCH2  0   0.231    4.3444  -0.5814  -0.8987
 LC4  H11   H  HCH2  0   0.260    5.5212   1.6327  -0.8456
 LC4  H11A  H  HCH2  0   0.261    5.5119   1.5937   0.9085
 LC4  H13   H  HCR5  0   0.286    6.9556  -0.3005  -2.0532
 LC4  H14   H  HCR5  0   0.248    9.1946  -1.5902  -1.1108
 LC4  H16   H  HCR5  0   0.277    7.2805   0.2901   2.0827

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
 LC4  O1   C2    double    1.206  0.020  1.206
 LC4  C2   C3    single    1.503  0.020  1.503
 LC4  C2   O17   single    1.331  0.020  1.331
 LC4  O17  HO17  single    0.850  0.020  0.980
 LC4  C4   C3    single    1.520  0.020  1.520
 LC4  C3   H3    single    0.970  0.020  1.090
 LC4  C3   H3A   single    0.970  0.020  1.090
 LC4  C4   C5    single    1.524  0.020  1.524
 LC4  C4   H4    single    0.970  0.020  1.090
 LC4  C4   H4A   single    0.970  0.020  1.090
 LC4  C5   C6    single    1.523  0.020  1.523
 LC4  C5   H5    single    0.970  0.020  1.090
 LC4  C5   H5A   single    0.970  0.020  1.090
 LC4  C6   C7    single    1.524  0.020  1.524
 LC4  C6   H6    single    0.970  0.020  1.090
 LC4  C6   H6A   single    0.970  0.020  1.090
 LC4  C7   C18   single    1.524  0.020  1.524
 LC4  C7   H7    single    0.970  0.020  1.090
 LC4  C7   H7A   single    0.970  0.020  1.090
 LC4  C18  C19   single    1.524  0.020  1.524
 LC4  C18  H18   single    0.970  0.020  1.090
 LC4  C18  H18A  single    0.970  0.020  1.090
 LC4  C19  C8    single    1.523  0.020  1.523
 LC4  C19  H19   single    0.970  0.020  1.090
 LC4  C19  H19A  single    0.970  0.020  1.090
 LC4  C8   C9    single    1.524  0.020  1.524
 LC4  C8   H8    single    0.970  0.020  1.090
 LC4  C8   H8A   single    0.970  0.020  1.090
 LC4  C9   C10   single    1.523  0.020  1.523
 LC4  C9   H9    single    0.970  0.020  1.090
 LC4  C9   H9A   single    0.970  0.020  1.090
 LC4  C10  C11   single    1.522  0.020  1.522
 LC4  C10  H10   single    0.970  0.020  1.090
 LC4  C10  H10A  single    0.970  0.020  1.090
 LC4  C11  N12   single    1.450  0.020  1.450
 LC4  C11  H11   single    0.970  0.020  1.090
 LC4  C11  H11A  single    0.970  0.020  1.090
 LC4  N12  C13   aromatic  1.366  0.020  1.366
 LC4  N12  C16   aromatic  1.349  0.020  1.349
 LC4  C13  C14   aromatic  1.366  0.020  1.366
 LC4  C13  H13   single    0.930  0.020  1.080
 LC4  C14  N15   aromatic  1.366  0.020  1.366
 LC4  C14  H14   single    0.930  0.020  1.080
 LC4  C16  N15   aromatic  1.309  0.020  1.309
 LC4  C16  H16   single    0.930  0.020  1.080

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
 LC4  C3    C2   O17  111.84  3.000
 LC4  O17   C2   O1   122.81  3.000
 LC4  C3    C2   O1   125.35  3.000
 LC4  HO17  O17  C2   109.92  3.000
 LC4  H3A   C3   H3   105.34  3.000
 LC4  H3A   C3   C4   110.61  3.000
 LC4  H3    C3   C4   110.48  3.000
 LC4  H3A   C3   C2   108.22  3.000
 LC4  H3    C3   C2   107.85  3.000
 LC4  C4    C3   C2   113.93  3.000
 LC4  H4A   C4   H4   106.43  3.000
 LC4  H4A   C4   C5   109.35  3.000
 LC4  H4    C4   C5   109.32  3.000
 LC4  H4A   C4   C3   109.91  3.000
 LC4  H4    C4   C3   109.82  3.000
 LC4  C5    C4   C3   111.86  3.000
 LC4  H5A   C5   H5   106.06  3.000
 LC4  H5A   C5   C6   109.37  3.000
 LC4  H5    C5   C6   109.41  3.000
 LC4  H5A   C5   C4   109.49  3.000
 LC4  H5    C5   C4   109.48  3.000
 LC4  C6    C5   C4   112.80  3.000
 LC4  H6A   C6   H6   106.04  3.000
 LC4  H6A   C6   C7   109.33  3.000
 LC4  H6    C6   C7   109.33  3.000
 LC4  H6A   C6   C5   109.37  3.000
 LC4  H6    C6   C5   109.34  3.000
 LC4  C7    C6   C5   113.19  3.000
 LC4  H7A   C7   H7   106.03  3.000
 LC4  H7A   C7   C18  109.35  3.000
 LC4  H7    C7   C18  109.37  3.000
 LC4  H7A   C7   C6   109.33  3.000
 LC4  H7    C7   C6   109.31  3.000
 LC4  C18   C7   C6   113.19  3.000
 LC4  H18A  C18  H18  106.02  3.000
 LC4  H18A  C18  C19  109.32  3.000
 LC4  H18   C18  C19  109.32  3.000
 LC4  H18A  C18  C7   109.36  3.000
 LC4  H18   C18  C7   109.34  3.000
 LC4  C19   C18  C7   113.23  3.000
 LC4  H19A  C19  H19  106.03  3.000
 LC4  H19A  C19  C8   109.35  3.000
 LC4  H19   C19  C8   109.37  3.000
 LC4  H19A  C19  C18  109.32  3.000
 LC4  H19   C19  C18  109.33  3.000
 LC4  C8    C19  C18  113.20  3.000
 LC4  H8A   C8   H8   106.09  3.000
 LC4  H8A   C8   C9   109.35  3.000
 LC4  H8    C8   C9   109.31  3.000
 LC4  H8A   C8   C19  109.41  3.000
 LC4  H8    C8   C19  109.39  3.000
 LC4  C9    C8   C19  113.05  3.000
 LC4  H9A   C9   H9   106.16  3.000
 LC4  H9A   C9   C10  109.48  3.000
 LC4  H9    C9   C10  109.48  3.000
 LC4  H9A   C9   C8   109.33  3.000
 LC4  H9    C9   C8   109.35  3.000
 LC4  C10   C9   C8   112.82  3.000
 LC4  H10A  C10  H10  106.78  3.000
 LC4  H10A  C10  C11  109.44  3.000
 LC4  H10   C10  C11  109.18  3.000
 LC4  H10A  C10  C9   109.73  3.000
 LC4  H10   C10  C9   109.93  3.000
 LC4  C11   C10  C9   111.66  3.000
 LC4  H11A  C11  H11  107.08  3.000
 LC4  H11A  C11  N12  107.67  3.000
 LC4  H11   C11  N12  108.34  3.000
 LC4  H11A  C11  C10  110.43  3.000
 LC4  H11   C11  C10  110.49  3.000
 LC4  N12   C11  C10  112.63  3.000
 LC4  C16   N12  C13  106.88  3.000
 LC4  C16   N12  C11  126.47  3.000
 LC4  C13   N12  C11  126.52  3.000
 LC4  H13   C13  C14  132.11  3.000
 LC4  H13   C13  N12  122.28  3.000
 LC4  C14   C13  N12  105.60  3.000
 LC4  H14   C14  N15  122.02  3.000
 LC4  H14   C14  C13  127.78  3.000
 LC4  N15   C14  C13  110.20  3.000
 LC4  C16   N15  C14  105.20  3.000
 LC4  H16   C16  N15  125.99  3.000
 LC4  H16   C16  N12  121.89  3.000
 LC4  N15   C16  N12  112.11  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
 LC4  CONST_01  N15   C14  C13  N12     0.00   0.0  0
 LC4  CONST_02  C14   N15  C16  N12     0.00   0.0  0
 LC4  CONST_03  N15   C16  N12  C13     0.00   0.0  0
 LC4  CONST_04  C16   N15  C14  C13     0.00   0.0  0
 LC4  CONST_05  C16   N12  C13  C14     0.00   0.0  0
 LC4  CONST_06  C14   C13  N12  C11   180.00   0.0  0
 LC4  CONST_07  N15   C16  N12  C11   180.00   0.0  0
 LC4  CONST_08  H14   C14  C13  N12   180.00   0.0  0
 LC4  CONST_09  H16   C16  N12  C13   180.00   0.0  0
 LC4  CONST_10  H13   C13  C14  N15   180.00   0.0  0
 LC4  CONST_11  HO17  O17  C2   O1      0.00   0.0  0
 LC4  Var_01    C13   N12  C11  C10    77.32  30.0  2
 LC4  Var_02    N12   C11  C10  C9    179.74  30.0  3
 LC4  Var_03    C4    C3   C2   O1     -3.16  30.0  3
 LC4  Var_04    C5    C4   C3   C2    179.87  30.0  1
 LC4  Var_05    C6    C5   C4   C3    179.73  30.0  3
 LC4  Var_06    C7    C6   C5   C4    179.99  30.0  3
 LC4  Var_07    C18   C7   C6   C5    179.62  30.0  3
 LC4  Var_08    C19   C18  C7   C6   -179.90  30.0  3
 LC4  Var_09    C8    C19  C18  C7   -179.97  30.0  3
 LC4  Var_10    C9    C8   C19  C18  -179.82  30.0  3
 LC4  Var_11    C10   C9   C8   C19   179.95  30.0  3
 LC4  Var_12    C11   C10  C9   C8   -179.64  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
 LC4  plan-1  C11   0.020
 LC4  plan-1  N12   0.020
 LC4  plan-1  C13   0.020
 LC4  plan-1  C14   0.020
 LC4  plan-1  N15   0.020
 LC4  plan-1  C16   0.020
 LC4  plan-1  H13   0.020
 LC4  plan-1  H14   0.020
 LC4  plan-1  H16   0.020
 LC4  plan-2  O1    0.020
 LC4  plan-2  C2    0.020
 LC4  plan-2  O17   0.020
 LC4  plan-2  C3    0.020
 LC4  plan-2  HO17  0.020

