# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 05:55:08 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: [5-(aminomethyl)-6-(2,2-dimethylpropyl)-2-ethyl-4-(4-methylphenyl)pyridin-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(CC(C)(C)C)c(CN)c(c2ccc(C)cc2)c1CC(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
 01T  01T  '[5-(aminomethyl)-6-(2,2-dimethylpropyl)-2-ethyl-4-(4-methylphenyl)pyridin-3-yl]acetic acid'  ligand  55  26  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_01T
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
 01T  C5    C  CR6    0   0.202  -2.0101  -0.1240  -0.3289
 01T  C6    C  CH2    0  -0.475  -3.3138  -0.7732  -0.7208
 01T  C7    C  CT     0  -0.082  -4.2847  -1.1066   0.4387
 01T  C8    C  CH3    0  -0.633  -4.7891   0.1659   1.1193
 01T  C10   C  CH3    0  -0.638  -5.4836  -1.8412  -0.1675
 01T  C15   C  CR6    0   0.051   0.2592   1.2569   0.4216
 01T  C17   C  C      0   0.448   2.4054   2.4217  -0.3753
 01T  C20   C  CR6    0  -0.027   1.6563  -0.7930   0.1744
 01T  C21   C  CR16   0  -0.268   2.1399  -1.2722   1.3901
 01T  C22   C  CR16   0  -0.290   3.3570  -1.9317   1.4601
 01T  C26   C  CR16   0  -0.208   2.4248  -0.9878  -0.9662
 01T  O19   O  OC    -1  -0.624   3.5240   2.8680  -0.0507
 01T  O18   O  O      0  -0.593   1.9544   2.2994  -1.5273
 01T  C16   C  CH2    0  -0.737   1.4879   2.0200   0.8074
 01T  C3    C  CR6    0   0.180  -1.0051   1.8501   0.3363
 01T  C2    C  CH2    0  -0.512  -1.2456   3.3129   0.6030
 01T  C1    C  CH3    0  -0.665  -0.9985   4.1674  -0.6398
 01T  N4    N  N      0  -0.440  -2.0836   1.1701  -0.0365
 01T  C9    C  CH3    0  -0.646  -3.6167  -2.0058   1.4784
 01T  C11   C  CR6    0  -0.017  -0.7958  -0.8160  -0.2778
 01T  C12   C  CH2    0  -0.415  -0.6937  -2.2639  -0.6801
 01T  N13   N  NH2    0  -0.781  -0.4326  -2.3711  -2.1113
 01T  C14   C  CR6    0   0.157   0.3439  -0.1003   0.1013
 01T  C25   C  CR16   0  -0.307   3.6440  -1.6483  -0.8920
 01T  C23   C  CR6    0   0.092   4.1321  -2.1316   0.3182
 01T  H6    H  HCH2   0   0.239  -3.8315  -0.0932  -1.4040
 01T  H6A   H  HCH2   0   0.230  -3.1292  -1.6896  -1.2870
 01T  H8    H  HCH3   0   0.214  -5.2629   0.8367   0.3991
 01T  H8A   H  HCH3   0   0.213  -5.5334  -0.0853   1.8787
 01T  H8B   H  HCH3   0   0.232  -3.9880   0.7204   1.6053
 01T  H10   H  HCH3   0   0.220  -5.1799  -2.7732  -0.6498
 01T  H10A  H  HCH3   0   0.223  -6.2199  -2.0870   0.6009
 01T  H10B  H  HCH3   0   0.221  -5.9837  -1.2247  -0.9179
 01T  H21   H  HCR6   0   0.243   1.5558  -1.1308   2.2921
 01T  H22   H  HCR6   0   0.243   3.7092  -2.2965   2.4183
 01T  H24   H  HCH3   0   0.244   6.1541  -2.3086   1.0386
 01T  H24A  H  HCH3   0   0.243   5.3344  -3.8444   0.8254
 01T  H24B  H  HCH3   0   0.242   5.9092  -2.9531  -0.5813
 01T  H26   H  HCR6   0   0.231   2.0632  -0.6279  -1.9187
 01T  H16   H  HCH2   0   0.249   1.2198   2.9398   1.3325
 01T  H16A  H  HCH2   0   0.248   2.0848   1.4468   1.5201
 01T  H2    H  HCH2   0   0.239  -2.2831   3.4297   0.9200
 01T  H2A   H  HCH2   0   0.234  -0.6262   3.6753   1.4255
 01T  H1    H  HCH3   0   0.225  -1.1813   5.2220  -0.4302
 01T  H1A   H  HCH3   0   0.235   0.0245   4.0594  -0.9982
 01T  H1B   H  HCH3   0   0.219  -1.6654   3.8678  -1.4498
 01T  H9    H  HCH3   0   0.226  -2.7264  -1.5387   1.9041
 01T  H9A   H  HCH3   0   0.226  -4.3026  -2.2136   2.3025
 01T  H9B   H  HCH3   0   0.223  -3.3172  -2.9645   1.0495
 01T  H12   H  HCH2   0   0.244   0.1382  -2.7309  -0.1517
 01T  H12A  H  HCH2   0   0.221  -1.5922  -2.8023  -0.3604
 01T  HN13  H  HNH2   0   0.348  -0.3527  -3.3500  -2.3591
 01T  HN1A  H  HNH2   0   0.340  -1.2333  -2.0230  -2.6261
 01T  H25   H  HCR6   0   0.241   4.2252  -1.7898  -1.7960
 01T  C24   C  CH3    0  -0.725   5.4500  -2.8458   0.4009

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
 01T  C11  C5    aromatic  1.399  0.020  1.399
 01T  N4   C5    aromatic  1.329  0.020  1.329
 01T  C5   C6    single    1.508  0.020  1.508
 01T  C7   C6    single    1.549  0.020  1.549
 01T  C6   H6    single    0.970  0.020  1.090
 01T  C6   H6A   single    0.970  0.020  1.090
 01T  C9   C7    single    1.528  0.020  1.528
 01T  C10  C7    single    1.531  0.020  1.531
 01T  C7   C8    single    1.529  0.020  1.529
 01T  C8   H8    single    0.970  0.020  1.090
 01T  C8   H8A   single    0.970  0.020  1.090
 01T  C8   H8B   single    0.970  0.020  1.090
 01T  C10  H10   single    0.970  0.020  1.090
 01T  C10  H10A  single    0.970  0.020  1.090
 01T  C10  H10B  single    0.970  0.020  1.090
 01T  C16  C15   single    1.497  0.020  1.497
 01T  C15  C14   aromatic  1.397  0.020  1.397
 01T  C15  C3    aromatic  1.399  0.020  1.399
 01T  C16  C17   single    1.550  0.020  1.550
 01T  O18  C17   deloc     1.243  0.020  1.243
 01T  C17  O19   deloc     1.247  0.020  1.247
 01T  C26  C20   aromatic  1.389  0.020  1.389
 01T  C20  C14   single    1.486  0.020  1.486
 01T  C20  C21   aromatic  1.393  0.020  1.393
 01T  C22  C21   aromatic  1.386  0.020  1.386
 01T  C21  H21   single    0.930  0.020  1.080
 01T  C23  C22   aromatic  1.394  0.020  1.394
 01T  C22  H22   single    0.930  0.020  1.080
 01T  C24  C23   single    1.501  0.020  1.501
 01T  C24  H24   single    0.970  0.020  1.090
 01T  C24  H24A  single    0.970  0.020  1.090
 01T  C24  H24B  single    0.970  0.020  1.090
 01T  C25  C26   aromatic  1.389  0.020  1.389
 01T  C26  H26   single    0.930  0.020  1.080
 01T  C16  H16   single    0.970  0.020  1.090
 01T  C16  H16A  single    0.970  0.020  1.090
 01T  C2   C3    single    1.506  0.020  1.506
 01T  C3   N4    aromatic  1.328  0.020  1.328
 01T  C1   C2    single    1.528  0.020  1.528
 01T  C2   H2    single    0.970  0.020  1.090
 01T  C2   H2A   single    0.970  0.020  1.090
 01T  C1   H1    single    0.970  0.020  1.090
 01T  C1   H1A   single    0.970  0.020  1.090
 01T  C1   H1B   single    0.970  0.020  1.090
 01T  C9   H9    single    0.970  0.020  1.090
 01T  C9   H9A   single    0.970  0.020  1.090
 01T  C9   H9B   single    0.970  0.020  1.090
 01T  C14  C11   aromatic  1.398  0.020  1.398
 01T  C11  C12   single    1.506  0.020  1.506
 01T  C12  N13   single    1.459  0.020  1.459
 01T  C12  H12   single    0.970  0.020  1.090
 01T  C12  H12A  single    0.970  0.020  1.090
 01T  N13  HN13  single    0.890  0.020  1.040
 01T  N13  HN1A  single    0.890  0.020  1.040
 01T  C25  C23   aromatic  1.391  0.020  1.391
 01T  C25  H25   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
 01T  C11   C5   N4    121.46  3.000
 01T  N4    C5   C6    115.38  3.000
 01T  C11   C5   C6    123.16  3.000
 01T  H6A   C6   H6    106.11  3.000
 01T  H6A   C6   C7    108.26  3.000
 01T  H6    C6   C7    107.74  3.000
 01T  H6A   C6   C5    110.46  3.000
 01T  H6    C6   C5    107.68  3.000
 01T  C7    C6   C5    116.11  3.000
 01T  C9    C7   C10   109.23  3.000
 01T  C10   C7   C8    108.50  3.000
 01T  C9    C7   C8    109.34  3.000
 01T  C8    C7   C6    111.16  3.000
 01T  C10   C7   C6    107.32  3.000
 01T  C9    C7   C6    111.22  3.000
 01T  H8B   C8   H8A   107.94  3.000
 01T  H8B   C8   H8    107.50  3.000
 01T  H8A   C8   H8    107.70  3.000
 01T  H8B   C8   C7    112.33  3.000
 01T  H8A   C8   C7    110.04  3.000
 01T  H8    C8   C7    111.15  3.000
 01T  H10B  C10  H10A  107.56  3.000
 01T  H10B  C10  H10   107.79  3.000
 01T  H10A  C10  H10   107.82  3.000
 01T  H10B  C10  C7    111.08  3.000
 01T  H10A  C10  C7    110.94  3.000
 01T  H10   C10  C7    111.49  3.000
 01T  C14   C15  C3    116.91  3.000
 01T  C3    C15  C16   122.77  3.000
 01T  C14   C15  C16   120.30  3.000
 01T  C16   C17  O18   117.83  3.000
 01T  O18   C17  O19   126.99  3.000
 01T  C16   C17  O19   115.15  3.000
 01T  C14   C20  C26   120.91  3.000
 01T  C14   C20  C21   120.66  3.000
 01T  C26   C20  C21   118.44  3.000
 01T  H21   C21  C22   119.56  3.000
 01T  H21   C21  C20   119.62  3.000
 01T  C22   C21  C20   120.83  3.000
 01T  H22   C22  C23   119.67  3.000
 01T  H22   C22  C21   119.34  3.000
 01T  C23   C22  C21   120.99  3.000
 01T  H26   C26  C25   119.96  3.000
 01T  H26   C26  C20   119.47  3.000
 01T  C25   C26  C20   120.57  3.000
 01T  H16A  C16  H16   105.21  3.000
 01T  H16A  C16  C17   108.09  3.000
 01T  H16   C16  C17   107.09  3.000
 01T  H16A  C16  C15   110.44  3.000
 01T  H16   C16  C15   110.58  3.000
 01T  C17   C16  C15   114.92  3.000
 01T  N4    C3   C2    114.66  3.000
 01T  N4    C3   C15   122.26  3.000
 01T  C2    C3   C15   123.04  3.000
 01T  H2A   C2   H2    106.56  3.000
 01T  H2A   C2   C1    109.60  3.000
 01T  H2    C2   C1    109.28  3.000
 01T  H2A   C2   C3    111.42  3.000
 01T  H2    C2   C3    107.89  3.000
 01T  C1    C2   C3    111.91  3.000
 01T  H1B   C1   H1A   107.61  3.000
 01T  H1B   C1   H1    107.80  3.000
 01T  H1A   C1   H1    108.45  3.000
 01T  H1B   C1   C2    110.57  3.000
 01T  H1A   C1   C2    111.34  3.000
 01T  H1    C1   C2    110.93  3.000
 01T  C3    N4   C5    121.03  3.000
 01T  H9B   C9   H9A   107.55  3.000
 01T  H9B   C9   H9    107.77  3.000
 01T  H9A   C9   H9    107.41  3.000
 01T  H9B   C9   C7    111.67  3.000
 01T  H9A   C9   C7    110.53  3.000
 01T  H9    C9   C7    111.71  3.000
 01T  C14   C11  C12   120.61  3.000
 01T  C12   C11  C5    121.65  3.000
 01T  C14   C11  C5    117.66  3.000
 01T  H12A  C12  H12   105.90  3.000
 01T  H12A  C12  N13   113.40  3.000
 01T  H12   C12  N13   107.90  3.000
 01T  H12A  C12  C11   109.82  3.000
 01T  H12   C12  C11   109.51  3.000
 01T  N13   C12  C11   110.17  3.000
 01T  HN1A  N13  HN13  105.66  3.000
 01T  HN1A  N13  C12   109.37  3.000
 01T  HN13  N13  C12   108.97  3.000
 01T  C11   C14  C20   119.65  3.000
 01T  C11   C14  C15   120.67  3.000
 01T  C20   C14  C15   119.68  3.000
 01T  H25   C25  C23   119.47  3.000
 01T  H25   C25  C26   119.22  3.000
 01T  C23   C25  C26   121.31  3.000
 01T  C25   C23  C24   121.40  3.000
 01T  C25   C23  C22   117.87  3.000
 01T  C24   C23  C22   120.73  3.000
 01T  H24B  C24  H24A  107.77  3.000
 01T  H24B  C24  H24   107.66  3.000
 01T  H24A  C24  H24   106.95  3.000
 01T  H24B  C24  C23   111.54  3.000
 01T  H24A  C24  C23   111.33  3.000
 01T  H24   C24  C23   111.37  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
 01T  CONST_01  C15   C14  C11  C5     0.00   0.0  0
 01T  CONST_02  C20   C14  C11  C5   180.00   0.0  0
 01T  CONST_03  C15   C3   N4   C5     0.00   0.0  0
 01T  CONST_06  C23   C25  C26  C20    0.00   0.0  0
 01T  CONST_07  C3    C15  C14  C20  180.00   0.0  0
 01T  CONST_08  C23   C22  C21  C20    0.00   0.0  0
 01T  CONST_09  C25   C26  C20  C21    0.00   0.0  0
 01T  CONST_11  C25   C23  C22  C21    0.00   0.0  0
 01T  CONST_12  C26   C20  C21  C22    0.00   0.0  0
 01T  CONST_13  C14   C20  C21  C22  180.00   0.0  0
 01T  CONST_14  C26   C25  C23  C22    0.00   0.0  0
 01T  CONST_16  C11   C14  C15  C3     0.00   0.0  0
 01T  CONST_17  C11   C5   N4   C3     0.00   0.0  0
 01T  CONST_18  C14   C11  C5   N4     0.00   0.0  0
 01T  CONST_19  C14   C15  C3   N4     0.00   0.0  0
 01T  CONST_20  C25   C26  C20  C14  180.00   0.0  0
 01T  CONST_21  C2    C3   N4   C5   180.00   0.0  0
 01T  CONST_22  C14   C11  C5   C6   180.00   0.0  0
 01T  CONST_23  C3    N4   C5   C6   180.00   0.0  0
 01T  CONST_24  C12   C11  C14  C15  180.00   0.0  0
 01T  CONST_25  C16   C15  C14  C20    0.00   0.0  0
 01T  CONST_26  C12   C11  C14  C20    0.00   0.0  0
 01T  CONST_27  C24   C23  C22  C21  180.00   0.0  0
 01T  CONST_28  C26   C25  C23  C24  180.00   0.0  0
 01T  CONST_29  C11   C14  C15  C16  180.00   0.0  0
 01T  CONST_30  N4    C3   C15  C16  180.00   0.0  0
 01T  CONST_31  C14   C15  C3   C2   180.00   0.0  0
 01T  CONST_32  C12   C11  C5   N4   180.00   0.0  0
 01T  CONST_33  H25   C25  C26  C20  180.00   0.0  0
 01T  CONST_34  H22   C22  C21  C20  180.00   0.0  0
 01T  CONST_35  H26   C26  C20  C21  180.00   0.0  0
 01T  CONST_36  H21   C21  C20  C26  180.00   0.0  0
 01T  Var_01    N13   C12  C11  C5    88.21  30.0  2
 01T  Var_02    C11   C5   C6   C7   103.05  30.0  2
 01T  Var_03    C1    C2   C3   C15   85.36  30.0  3
 01T  Var_04    C14   C15  C16  C17   77.33  30.0  2
 01T  Var_05    H24   C24  C23  C22  -61.93  30.0  2
 01T  Var_06    C9    C7   C6   C5   -56.62  30.0  2
 01T  Var_07    O18   C17  C16  C15   12.33  30.0  3
 01T  Var_08    H1    C1   C2   C3   179.75  30.0  3
 01T  Var_09    HN13  N13  C12  C11  179.11  30.0  3
 01T  Var_10    H9    C9   C7   C6    59.06  30.0  3
 01T  Var_11    H10   C10  C7   C6    61.03  30.0  3
 01T  Var_12    H8    C8   C7   C6    56.17  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
 01T  plan-1  C20  0.020
 01T  plan-1  C21  0.020
 01T  plan-1  C22  0.020
 01T  plan-1  C26  0.020
 01T  plan-1  C14  0.020
 01T  plan-1  C25  0.020
 01T  plan-1  C23  0.020
 01T  plan-1  H21  0.020
 01T  plan-1  H22  0.020
 01T  plan-1  H26  0.020
 01T  plan-1  H25  0.020
 01T  plan-1  C24  0.020
 01T  plan-2  C5   0.020
 01T  plan-2  C6   0.020
 01T  plan-2  C15  0.020
 01T  plan-2  C20  0.020
 01T  plan-2  C16  0.020
 01T  plan-2  C3   0.020
 01T  plan-2  C2   0.020
 01T  plan-2  N4   0.020
 01T  plan-2  C11  0.020
 01T  plan-2  C12  0.020
 01T  plan-2  C14  0.020
 01T  plan-3  C17  0.020
 01T  plan-3  O19  0.020
 01T  plan-3  O18  0.020
 01T  plan-3  C16  0.020

