# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 13:59:36 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Cc1nc(C)c(C(O)=O)c(c2ccc(C)cc2)c1CN
#
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
 10T  10T  '5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxylic acid'  ligand  46  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_10T
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
 10T  C4    C  CH2    0  -0.499   3.3746   0.8093  -0.7506
 10T  C5    C  CR6    0   0.215   2.1315   0.0058  -0.4847
 10T  C7    C  CR6    0   0.186   1.2657  -2.0891  -0.0668
 10T  C8    C  CH3    0  -0.735   1.5439  -3.5564   0.0855
 10T  C17   C  CR6    0  -0.019   0.8780   0.6120  -0.3497
 10T  C20   C  CR6    0   0.005  -1.5861   0.3402   0.0577
 10T  C21   C  CR16   0  -0.261  -2.1750   0.4583   1.3136
 10T  C22   C  CR16   0  -0.287  -3.4499   0.9869   1.4497
 10T  C26   C  CR16   0  -0.272  -2.3155   0.7422  -1.0556
 10T  O14   O  O      0  -0.596  -1.2840  -2.8925   1.5726
 10T  O15   O  OC    -1  -0.587  -1.9292  -2.7961  -0.5643
 10T  C12   C  CR6    0  -0.141  -0.0253  -1.5853   0.0844
 10T  C16   C  CR6    0   0.163  -0.2166  -0.2156  -0.0799
 10T  C23   C  CR6    0   0.088  -4.1799   1.4056   0.3389
 10T  C25   C  CR16   0  -0.292  -3.5927   1.2669  -0.9160
 10T  C18   C  CH2    0  -0.416   0.7172   2.1025  -0.5134
 10T  N19   N  NH2    0  -0.785   0.7149   2.4759  -1.9238
 10T  C2    C  CH1    0  -0.237   4.0458   1.3625   0.5175
 10T  C1    C  CH3    0  -0.643   4.5074   0.2540   1.4569
 10T  C3    C  CH3    0  -0.655   5.2141   2.2624   0.1295
 10T  N6    N  N      0  -0.448   2.3002  -1.3075  -0.3568
 10T  H4    H  HCH2   0   0.232   4.0929   0.1680  -1.2689
 10T  H4A   H  HCH2   0   0.243   3.1422   1.6358  -1.4264
 10T  H8    H  HCH3   0   0.245   1.3573  -3.8874   1.1083
 10T  H8A   H  HCH3   0   0.239   0.9002  -4.1544  -0.5619
 10T  H8B   H  HCH3   0   0.242   2.5801  -3.7746  -0.1643
 10T  H21   H  HCR6   0   0.243  -1.6315   0.1389   2.1938
 10T  H22   H  HCR6   0   0.244  -3.8837   1.0762   2.4391
 10T  H24   H  HCH3   0   0.247  -5.4793   3.0577   0.7887
 10T  H24A  H  HCH3   0   0.242  -6.1136   1.9646  -0.4318
 10T  H24B  H  HCH3   0   0.243  -6.1221   1.4966   1.2688
 10T  H26   H  HCR6   0   0.241  -1.8942   0.6259  -2.0471
 10T  H25   H  HCR6   0   0.245  -4.1420   1.5670  -1.8010
 10T  H18   H  HCH2   0   0.227  -0.1775   2.4328   0.0265
 10T  H18A  H  HCH2   0   0.242   1.5571   2.6142  -0.0397
 10T  HN19  H  HNH2   0   0.340  -0.1188   2.1112  -2.3675
 10T  HN1A  H  HNH2   0   0.350   0.6452   3.4835  -1.9978
 10T  H2    H  HCH1   0   0.221   3.3123   1.9745   1.0553
 10T  H1    H  HCH3   0   0.210   5.2165  -0.4113   0.9579
 10T  H1A   H  HCH3   0   0.220   5.0058   0.6741   2.3325
 10T  H1B   H  HCH3   0   0.229   3.6762  -0.3565   1.8089
 10T  H3    H  HCH3   0   0.224   4.8898   3.0861  -0.5094
 10T  H3A   H  HCH3   0   0.226   5.6921   2.6927   1.0110
 10T  H3B   H  HCH3   0   0.214   5.9739   1.6987  -0.4174
 10T  C13   C  C      0   0.332  -1.1907  -2.5079   0.3929
 10T  C24   C  CH3    0  -0.723  -5.5458   2.0074   0.4971

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
 10T  C2   C4    single    1.538  0.020  1.538
 10T  C5   C4    single    1.504  0.020  1.504
 10T  C4   H4    single    0.970  0.020  1.090
 10T  C4   H4A   single    0.970  0.020  1.090
 10T  C17  C5    aromatic  1.399  0.020  1.399
 10T  N6   C5    aromatic  1.330  0.020  1.330
 10T  C12  C7    aromatic  1.394  0.020  1.394
 10T  C7   C8    single    1.501  0.020  1.501
 10T  C7   N6    aromatic  1.329  0.020  1.329
 10T  C8   H8    single    0.970  0.020  1.090
 10T  C8   H8A   single    0.970  0.020  1.090
 10T  C8   H8B   single    0.970  0.020  1.090
 10T  O14  C13   deloc     1.244  0.020  1.244
 10T  C13  C12   single    1.518  0.020  1.518
 10T  C13  O15   deloc     1.243  0.020  1.243
 10T  C16  C17   aromatic  1.399  0.020  1.399
 10T  C17  C18   single    1.508  0.020  1.508
 10T  C21  C20   aromatic  1.392  0.020  1.392
 10T  C20  C16   single    1.484  0.020  1.484
 10T  C20  C26   aromatic  1.390  0.020  1.390
 10T  C22  C21   aromatic  1.387  0.020  1.387
 10T  C21  H21   single    0.930  0.020  1.080
 10T  C22  C23   aromatic  1.394  0.020  1.394
 10T  C22  H22   single    0.930  0.020  1.080
 10T  C24  C23   single    1.501  0.020  1.501
 10T  C24  H24   single    0.970  0.020  1.090
 10T  C24  H24A  single    0.970  0.020  1.090
 10T  C24  H24B  single    0.970  0.020  1.090
 10T  C25  C26   aromatic  1.388  0.020  1.388
 10T  C26  H26   single    0.930  0.020  1.080
 10T  C12  C16   aromatic  1.393  0.020  1.393
 10T  C23  C25   aromatic  1.392  0.020  1.392
 10T  C25  H25   single    0.930  0.020  1.080
 10T  C18  N19   single    1.459  0.020  1.459
 10T  C18  H18   single    0.970  0.020  1.090
 10T  C18  H18A  single    0.970  0.020  1.090
 10T  N19  HN19  single    0.890  0.020  1.040
 10T  N19  HN1A  single    0.890  0.020  1.040
 10T  C3   C2    single    1.525  0.020  1.525
 10T  C2   C1    single    1.525  0.020  1.525
 10T  C2   H2    single    0.970  0.020  1.090
 10T  C1   H1    single    0.970  0.020  1.090
 10T  C1   H1A   single    0.970  0.020  1.090
 10T  C1   H1B   single    0.970  0.020  1.090
 10T  C3   H3    single    0.970  0.020  1.090
 10T  C3   H3A   single    0.970  0.020  1.090
 10T  C3   H3B   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
 10T  H4A   C4   H4    106.86  3.000
 10T  H4A   C4   C2    109.32  3.000
 10T  H4    C4   C2    108.36  3.000
 10T  H4A   C4   C5    109.74  3.000
 10T  H4    C4   C5    108.26  3.000
 10T  C2    C4   C5    114.03  3.000
 10T  N6    C5   C17   122.15  3.000
 10T  N6    C5   C4    116.08  3.000
 10T  C17   C5   C4    121.75  3.000
 10T  N6    C7   C12   122.15  3.000
 10T  N6    C7   C8    116.93  3.000
 10T  C12   C7   C8    120.92  3.000
 10T  H8B   C8   H8A   108.40  3.000
 10T  H8B   C8   H8    108.50  3.000
 10T  H8A   C8   H8    106.80  3.000
 10T  H8B   C8   C7    110.44  3.000
 10T  H8A   C8   C7    111.47  3.000
 10T  H8    C8   C7    111.09  3.000
 10T  C18   C17  C16   121.49  3.000
 10T  C18   C17  C5    120.89  3.000
 10T  C16   C17  C5    117.61  3.000
 10T  C16   C20  C26   121.20  3.000
 10T  C26   C20  C21   118.42  3.000
 10T  C16   C20  C21   120.38  3.000
 10T  H21   C21  C22   119.61  3.000
 10T  H21   C21  C20   119.74  3.000
 10T  C22   C21  C20   120.65  3.000
 10T  H22   C22  C23   119.55  3.000
 10T  H22   C22  C21   119.27  3.000
 10T  C23   C22  C21   121.18  3.000
 10T  H26   C26  C25   119.37  3.000
 10T  H26   C26  C20   119.85  3.000
 10T  C25   C26  C20   120.77  3.000
 10T  C16   C12  C13   121.07  3.000
 10T  C16   C12  C7    118.03  3.000
 10T  C13   C12  C7    120.89  3.000
 10T  C12   C16  C20   118.95  3.000
 10T  C12   C16  C17   119.81  3.000
 10T  C20   C16  C17   121.23  3.000
 10T  C25   C23  C24   121.24  3.000
 10T  C25   C23  C22   117.88  3.000
 10T  C24   C23  C22   120.87  3.000
 10T  H25   C25  C23   119.64  3.000
 10T  H25   C25  C26   119.26  3.000
 10T  C23   C25  C26   121.09  3.000
 10T  H18A  C18  H18   105.85  3.000
 10T  H18A  C18  N19   107.50  3.000
 10T  H18   C18  N19   113.44  3.000
 10T  H18A  C18  C17   109.52  3.000
 10T  H18   C18  C17   109.35  3.000
 10T  N19   C18  C17   110.98  3.000
 10T  HN1A  N19  HN19  105.65  3.000
 10T  HN1A  N19  C18   108.99  3.000
 10T  HN19  N19  C18   109.44  3.000
 10T  H2    C2   C3    107.94  3.000
 10T  H2    C2   C1    107.83  3.000
 10T  C3    C2   C1    110.73  3.000
 10T  H2    C2   C4    108.26  3.000
 10T  C1    C2   C4    112.26  3.000
 10T  C3    C2   C4    109.69  3.000
 10T  H1B   C1   H1A   107.74  3.000
 10T  H1B   C1   H1    107.54  3.000
 10T  H1A   C1   H1    107.72  3.000
 10T  H1B   C1   C2    112.05  3.000
 10T  H1A   C1   C2    110.65  3.000
 10T  H1    C1   C2    110.96  3.000
 10T  H3B   C3   H3A   107.64  3.000
 10T  H3B   C3   H3    107.63  3.000
 10T  H3A   C3   H3    107.78  3.000
 10T  H3B   C3   C2    110.83  3.000
 10T  H3A   C3   C2    111.27  3.000
 10T  H3    C3   C2    111.51  3.000
 10T  C7    N6   C5    120.20  3.000
 10T  C12   C13  O15   116.14  3.000
 10T  O15   C13  O14   127.88  3.000
 10T  C12   C13  O14   115.97  3.000
 10T  H24B  C24  H24A  108.04  3.000
 10T  H24B  C24  H24   107.09  3.000
 10T  H24A  C24  H24   107.29  3.000
 10T  H24B  C24  C23   111.58  3.000
 10T  H24A  C24  C23   111.63  3.000
 10T  H24   C24  C23   110.99  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
 10T  CONST_01  C20   C16  C17  C5    180.00   0.0  0
 10T  CONST_02  C12   C16  C17  C5      0.00   0.0  0
 10T  CONST_03  C12   C7   N6   C5      0.00   0.0  0
 10T  CONST_04  C17   C16  C12  C7      0.00   0.0  0
 10T  CONST_05  C20   C16  C12  C7    180.00   0.0  0
 10T  CONST_06  C17   C5   N6   C7      0.00   0.0  0
 10T  CONST_09  C23   C22  C21  C20     0.00   0.0  0
 10T  CONST_10  C23   C25  C26  C20     0.00   0.0  0
 10T  CONST_12  C25   C26  C20  C21     0.00   0.0  0
 10T  CONST_13  C25   C23  C22  C21     0.00   0.0  0
 10T  CONST_14  C16   C20  C21  C22   180.00   0.0  0
 10T  CONST_15  C26   C20  C21  C22     0.00   0.0  0
 10T  CONST_16  C26   C25  C23  C22     0.00   0.0  0
 10T  CONST_18  N6    C5   C17  C16     0.00   0.0  0
 10T  CONST_19  C25   C26  C20  C16   180.00   0.0  0
 10T  CONST_20  N6    C7   C12  C16     0.00   0.0  0
 10T  CONST_21  C16   C17  C5   C4    180.00   0.0  0
 10T  CONST_22  C7    N6   C5   C4    180.00   0.0  0
 10T  CONST_23  C8    C7   N6   C5    180.00   0.0  0
 10T  CONST_24  C16   C12  C7   C8    180.00   0.0  0
 10T  CONST_25  N6    C7   C12  C13   180.00   0.0  0
 10T  CONST_26  C17   C16  C12  C13   180.00   0.0  0
 10T  CONST_27  C20   C16  C12  C13     0.00   0.0  0
 10T  CONST_28  C18   C17  C16  C20     0.00   0.0  0
 10T  CONST_29  C24   C23  C22  C21   180.00   0.0  0
 10T  CONST_30  C26   C25  C23  C24   180.00   0.0  0
 10T  CONST_31  C18   C17  C16  C12   180.00   0.0  0
 10T  CONST_32  N6    C5   C17  C18   180.00   0.0  0
 10T  CONST_33  H22   C22  C21  C20   180.00   0.0  0
 10T  CONST_34  H25   C25  C26  C20   180.00   0.0  0
 10T  CONST_35  H26   C26  C20  C21   180.00   0.0  0
 10T  CONST_36  H21   C21  C20  C26   180.00   0.0  0
 10T  Var_01    N19   C18  C17  C5     78.13  30.0  2
 10T  Var_02    O14   C13  C12  C7     77.70  30.0  2
 10T  Var_03    C2    C4   C5   C17    85.67  30.0  2
 10T  Var_04    H24   C24  C23  C22    79.96  30.0  2
 10T  Var_05    H8    C8   C7   C12   -65.23  30.0  2
 10T  Var_06    C3    C2   C4   C5   -174.81  30.0  1
 10T  Var_07    HN19  N19  C18  C17    67.30  30.0  3
 10T  Var_08    H3    C3   C2   C4     57.99  30.0  3
 10T  Var_09    H1    C1   C2   C4     58.79  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
 10T  plan-1  C4   0.020
 10T  plan-1  C5   0.020
 10T  plan-1  C7   0.020
 10T  plan-1  C8   0.020
 10T  plan-1  C17  0.020
 10T  plan-1  C20  0.020
 10T  plan-1  C12  0.020
 10T  plan-1  C16  0.020
 10T  plan-1  C18  0.020
 10T  plan-1  N6   0.020
 10T  plan-1  C13  0.020
 10T  plan-2  C20  0.020
 10T  plan-2  C21  0.020
 10T  plan-2  C22  0.020
 10T  plan-2  C26  0.020
 10T  plan-2  C16  0.020
 10T  plan-2  C23  0.020
 10T  plan-2  C25  0.020
 10T  plan-2  H21  0.020
 10T  plan-2  H22  0.020
 10T  plan-2  H26  0.020
 10T  plan-2  H25  0.020
 10T  plan-2  C24  0.020
 10T  plan-3  O14  0.020
 10T  plan-3  O15  0.020
 10T  plan-3  C12  0.020
 10T  plan-3  C13  0.020

