# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 21:51:57 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (2R)-3-[2-amino-6-(3-methylpyridin-2-yl)quinolin-3-yl]-N-(3,3-dimethylbutyl)-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cc1cc2cc(ccc2nc1N)c3ncccc3C)C(=O)NCCC(C)(C)C
#
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
 68M  68M  (2R)-3-[2-amino-6-(3-methylpyridin-2-yl)quinolin-3-yl]-N-(3,3-dimethylbutyl)-2-methylpropanamide  ligand  62  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_68M
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
 68M  C18  C  CH3   0  -0.645   -8.3830   2.0324  -0.4306
 68M  C16  C  CT    0  -0.098   -8.2345   0.9456   0.6365
 68M  C19  C  CH3   0  -0.635   -8.7694   1.4844   1.9651
 68M  C20  C  CH3   0  -0.648   -9.0469  -0.2887   0.2391
 68M  C15  C  CH2   0  -0.408   -6.7529   0.5864   0.8389
 68M  C14  C  CH2   0  -0.278   -6.0518  -0.0188  -0.3726
 68M  N3   N  NH1   0  -0.633   -4.6507  -0.2592  -0.0976
 68M  C13  C  C     0   0.571   -3.6341   0.2683  -0.7957
 68M  O1   O  O     0  -0.506   -3.7847   0.9573  -1.7974
 68M  C12  C  CH1   0  -0.385   -2.2487  -0.0227  -0.2427
 68M  C17  C  CH3   0  -0.650   -1.7061   1.2449   0.4147
 68M  C11  C  CH2   0  -0.539   -1.3327  -0.5185  -1.3770
 68M  C4   C  CR6   0   0.024    0.0079  -0.9740  -0.8823
 68M  C3   C  CR6   0   0.395    0.1841  -2.2650  -0.2649
 68M  N1   N  N     0  -0.501    1.3301  -2.6740   0.2287
 68M  N2   N  NH2   0  -0.837   -0.8532  -3.1361  -0.2174
 68M  C5   C  CR16  0  -0.254    1.1066  -0.1771  -0.9698
 68M  C1   C  CR66  0   0.105    2.3603  -0.5903  -0.4521
 68M  C6   C  CR16  0  -0.375    3.5137   0.2099  -0.5073
 68M  C2   C  CR66  0   0.199    2.4094  -1.8656   0.1543
 68M  C9   C  CR16  0  -0.298    3.6389  -2.2993   0.6946
 68M  C8   C  CR16  0  -0.288    4.7459  -1.4926   0.6472
 68M  C7   C  CR6   0   0.042    4.7007  -0.2138   0.0488
 68M  C10  C  CR6   0   0.173    5.9019   0.6498  -0.0266
 68M  N4   N  N     0  -0.418    6.1371   1.1970  -1.2196
 68M  C24  C  CR16  0  -0.088    7.1903   1.9841  -1.3787
 68M  C23  C  CR16  0  -0.319    8.0756   2.2715  -0.3533
 68M  C22  C  CR16  0  -0.185    7.8169   1.7284   0.8935
 68M  C21  C  CR6   0   0.023    6.7130   0.9052   1.0911
 68M  C25  C  CH3   0  -0.750    6.4188   0.3788   2.4658
 68M  H1   H  HCH3  0   0.226   -9.4280   2.3301  -0.5376
 68M  H2   H  HCH3  0   0.222   -7.8124   2.9244  -0.1613
 68M  H3   H  HCH3  0   0.224   -8.0396   1.7010  -1.4121
 68M  H4   H  HCH3  0   0.222   -8.6965   0.7339   2.7554
 68M  H5   H  HCH3  0   0.222   -8.2079   2.3641   2.2877
 68M  H6   H  HCH3  0   0.223   -9.8185   1.7744   1.8779
 68M  H7   H  HCH3  0   0.225   -8.7490  -0.6856  -0.7334
 68M  H8   H  HCH3  0   0.222   -8.9332  -1.0887   0.9745
 68M  H9   H  HCH3  0   0.226  -10.1102  -0.0471   0.1777
 68M  H10  H  HCH2  0   0.226   -6.2089   1.4885   1.1387
 68M  H11  H  HCH2  0   0.223   -6.6749  -0.1154   1.6775
 68M  H12  H  HCH2  0   0.240   -6.5276  -0.9578  -0.6651
 68M  H13  H  HCH2  0   0.243   -6.1067   0.6498  -1.2293
 68M  H14  H  HNH1  0   0.396   -4.4318  -0.8112   0.7164
 68M  H15  H  HCH1  0   0.253   -2.3227  -0.7963   0.5287
 68M  H16  H  HCH3  0   0.230   -1.6160   2.0538  -0.3113
 68M  H17  H  HCH3  0   0.243   -2.3599   1.5810   1.2203
 68M  H18  H  HCH3  0   0.245   -0.7214   1.0681   0.8460
 68M  H19  H  HCH2  0   0.265   -1.8275  -1.3253  -1.9266
 68M  H20  H  HCH2  0   0.269   -1.1921   0.2906  -2.0957
 68M  H21  H  HNH2  0   0.391   -0.7471  -3.9527   0.3609
 68M  H22  H  HNH2  0   0.404   -1.7976  -2.8276  -0.3593
 68M  H23  H  HCR6  0   0.260    1.0260   0.7973  -1.4395
 68M  H24  H  HCR6  0   0.249    3.4570   1.1817  -0.9841
 68M  H25  H  HCR6  0   0.252    3.6932  -3.2826   1.1448
 68M  H26  H  HCR6  0   0.254    5.6782  -1.8589   1.0571
 68M  H27  H  HCR6  0   0.258    7.3356   2.4044  -2.3678
 68M  H28  H  HCR6  0   0.268    8.9297   2.9128  -0.5225
 68M  H29  H  HCR6  0   0.265    8.4671   1.9575   1.7296
 68M  H30  H  HCH3  0   0.253    6.8143  -0.6274   2.6133
 68M  H31  H  HCH3  0   0.257    6.8773   1.0167   3.2205
 68M  H32  H  HCH3  0   0.251    5.3488   0.3367   2.6662

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
 68M  N2   C3   single    1.355  0.020  1.355
 68M  C3   N1   aromatic  1.313  0.020  1.313
 68M  C3   C4   aromatic  1.442  0.020  1.442
 68M  N1   C2   aromatic  1.351  0.020  1.351
 68M  C17  C12  single    1.528  0.020  1.528
 68M  C11  C12  single    1.540  0.020  1.540
 68M  C11  C4   single    1.500  0.020  1.500
 68M  C12  C13  single    1.520  0.020  1.520
 68M  C4   C5   aromatic  1.360  0.020  1.360
 68M  C2   C9   aromatic  1.411  0.020  1.411
 68M  C2   C1   aromatic  1.413  0.020  1.413
 68M  C9   C8   aromatic  1.370  0.020  1.370
 68M  C5   C1   aromatic  1.418  0.020  1.418
 68M  N3   C13  single    1.341  0.020  1.341
 68M  N3   C14  single    1.448  0.020  1.448
 68M  C13  O1   double    1.225  0.020  1.225
 68M  C1   C6   aromatic  1.405  0.020  1.405
 68M  C8   C7   aromatic  1.413  0.020  1.413
 68M  C14  C15  single    1.525  0.020  1.525
 68M  C15  C16  single    1.538  0.020  1.538
 68M  C6   C7   aromatic  1.378  0.020  1.378
 68M  C7   C10  single    1.481  0.020  1.481
 68M  C19  C16  single    1.530  0.020  1.530
 68M  C16  C20  single    1.530  0.020  1.530
 68M  C16  C18  single    1.530  0.020  1.530
 68M  N4   C10  aromatic  1.333  0.020  1.333
 68M  N4   C24  aromatic  1.324  0.020  1.324
 68M  C10  C21  aromatic  1.404  0.020  1.404
 68M  C24  C23  aromatic  1.385  0.020  1.385
 68M  C21  C25  single    1.501  0.020  1.501
 68M  C21  C22  aromatic  1.391  0.020  1.391
 68M  C23  C22  aromatic  1.384  0.020  1.384
 68M  C18  H1   single    0.970  0.020  1.090
 68M  C18  H2   single    0.970  0.020  1.090
 68M  C18  H3   single    0.970  0.020  1.090
 68M  C19  H4   single    0.970  0.020  1.090
 68M  C19  H5   single    0.970  0.020  1.090
 68M  C19  H6   single    0.970  0.020  1.090
 68M  C20  H7   single    0.970  0.020  1.090
 68M  C20  H8   single    0.970  0.020  1.090
 68M  C20  H9   single    0.970  0.020  1.090
 68M  C15  H10  single    0.970  0.020  1.090
 68M  C15  H11  single    0.970  0.020  1.090
 68M  C14  H12  single    0.970  0.020  1.090
 68M  C14  H13  single    0.970  0.020  1.090
 68M  N3   H14  single    0.860  0.020  1.020
 68M  C12  H15  single    0.970  0.020  1.090
 68M  C17  H16  single    0.970  0.020  1.090
 68M  C17  H17  single    0.970  0.020  1.090
 68M  C17  H18  single    0.970  0.020  1.090
 68M  C11  H19  single    0.970  0.020  1.090
 68M  C11  H20  single    0.970  0.020  1.090
 68M  N2   H21  single    0.890  0.020  1.040
 68M  N2   H22  single    0.890  0.020  1.040
 68M  C5   H23  single    0.930  0.020  1.080
 68M  C6   H24  single    0.930  0.020  1.080
 68M  C9   H25  single    0.930  0.020  1.080
 68M  C8   H26  single    0.930  0.020  1.080
 68M  C24  H27  single    0.930  0.020  1.080
 68M  C23  H28  single    0.930  0.020  1.080
 68M  C22  H29  single    0.930  0.020  1.080
 68M  C25  H30  single    0.970  0.020  1.090
 68M  C25  H31  single    0.970  0.020  1.090
 68M  C25  H32  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
 68M  H3   C18  H2   107.78  3.000
 68M  H3   C18  H1   107.21  3.000
 68M  H2   C18  H1   107.54  3.000
 68M  H3   C18  C16  112.39  3.000
 68M  H2   C18  C16  110.93  3.000
 68M  H1   C18  C16  110.78  3.000
 68M  C15  C16  C20  110.93  3.000
 68M  C20  C16  C19  108.90  3.000
 68M  C15  C16  C19  107.74  3.000
 68M  C20  C16  C18  109.89  3.000
 68M  C19  C16  C18  108.75  3.000
 68M  C15  C16  C18  110.56  3.000
 68M  H6   C19  H5   107.67  3.000
 68M  H6   C19  H4   107.72  3.000
 68M  H5   C19  H4   107.78  3.000
 68M  H6   C19  C16  111.10  3.000
 68M  H5   C19  C16  111.12  3.000
 68M  H4   C19  C16  111.28  3.000
 68M  H9   C20  H8   107.53  3.000
 68M  H9   C20  H7   107.22  3.000
 68M  H8   C20  H7   107.75  3.000
 68M  H9   C20  C16  110.68  3.000
 68M  H8   C20  C16  111.13  3.000
 68M  H7   C20  C16  112.32  3.000
 68M  H11  C15  H10  106.41  3.000
 68M  H11  C15  C14  108.72  3.000
 68M  H10  C15  C14  108.42  3.000
 68M  H11  C15  C16  108.59  3.000
 68M  H10  C15  C16  108.79  3.000
 68M  C14  C15  C16  115.53  3.000
 68M  H13  C14  H12  107.18  3.000
 68M  H13  C14  N3   107.48  3.000
 68M  H12  C14  N3   109.24  3.000
 68M  H13  C14  C15  111.01  3.000
 68M  H12  C14  C15  110.70  3.000
 68M  N3   C14  C15  111.09  3.000
 68M  H14  N3   C13  118.12  3.000
 68M  H14  N3   C14  117.04  3.000
 68M  C13  N3   C14  124.70  3.000
 68M  C12  C13  O1   121.15  3.000
 68M  O1   C13  N3   123.61  3.000
 68M  C12  C13  N3   115.23  3.000
 68M  H15  C12  C11  109.38  3.000
 68M  H15  C12  C17  107.88  3.000
 68M  C11  C12  C17  111.89  3.000
 68M  H15  C12  C13  109.27  3.000
 68M  C11  C12  C13  109.63  3.000
 68M  C17  C12  C13  108.75  3.000
 68M  H18  C17  H17  107.42  3.000
 68M  H18  C17  H16  108.01  3.000
 68M  H17  C17  H16  108.22  3.000
 68M  H18  C17  C12  110.90  3.000
 68M  H17  C17  C12  111.14  3.000
 68M  H16  C17  C12  110.99  3.000
 68M  H20  C11  H19  105.91  3.000
 68M  H20  C11  C4   109.10  3.000
 68M  H19  C11  C4   110.23  3.000
 68M  H20  C11  C12  108.85  3.000
 68M  H19  C11  C12  109.77  3.000
 68M  C4   C11  C12  112.74  3.000
 68M  C5   C4   C3   116.96  3.000
 68M  C5   C4   C11  121.53  3.000
 68M  C3   C4   C11  121.50  3.000
 68M  N2   C3   N1   117.04  3.000
 68M  N1   C3   C4   123.13  3.000
 68M  N2   C3   C4   119.80  3.000
 68M  C2   N1   C3   119.37  3.000
 68M  H22  N2   H21  115.46  3.000
 68M  H22  N2   C3   121.17  3.000
 68M  H21  N2   C3   117.46  3.000
 68M  H23  C5   C1   119.05  3.000
 68M  H23  C5   C4   119.61  3.000
 68M  C1   C5   C4   121.34  3.000
 68M  C2   C1   C6   120.16  3.000
 68M  C6   C1   C5   123.07  3.000
 68M  C2   C1   C5   116.77  3.000
 68M  H24  C6   C7   119.89  3.000
 68M  H24  C6   C1   119.01  3.000
 68M  C7   C6   C1   121.09  3.000
 68M  C9   C2   C1   118.16  3.000
 68M  C1   C2   N1   122.42  3.000
 68M  C9   C2   N1   119.42  3.000
 68M  H25  C9   C8   120.56  3.000
 68M  H25  C9   C2   118.81  3.000
 68M  C8   C9   C2   120.63  3.000
 68M  H26  C8   C7   119.63  3.000
 68M  H26  C8   C9   118.91  3.000
 68M  C7   C8   C9   121.45  3.000
 68M  C10  C7   C8   121.56  3.000
 68M  C10  C7   C6   119.92  3.000
 68M  C8   C7   C6   118.49  3.000
 68M  C21  C10  N4   122.38  3.000
 68M  C21  C10  C7   122.26  3.000
 68M  N4   C10  C7   115.33  3.000
 68M  C24  N4   C10  119.45  3.000
 68M  H27  C24  C23  120.61  3.000
 68M  H27  C24  N4   116.52  3.000
 68M  C23  C24  N4   122.88  3.000
 68M  H28  C23  C22  121.41  3.000
 68M  H28  C23  C24  120.81  3.000
 68M  C22  C23  C24  117.77  3.000
 68M  H29  C22  C21  119.44  3.000
 68M  H29  C22  C23  119.99  3.000
 68M  C21  C22  C23  120.56  3.000
 68M  C25  C21  C22  119.55  3.000
 68M  C22  C21  C10  116.93  3.000
 68M  C25  C21  C10  123.49  3.000
 68M  H32  C25  H31  107.97  3.000
 68M  H32  C25  H30  107.19  3.000
 68M  H31  C25  H30  107.08  3.000
 68M  H32  C25  C21  112.00  3.000
 68M  H31  C25  C21  110.28  3.000
 68M  H30  C25  C21  112.09  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
 68M  CONST_01  C2   N1   C3   C4      0.00   0.0  0
 68M  CONST_02  C2   C1   C5   C4      0.00   0.0  0
 68M  CONST_03  C6   C1   C5   C4    180.00   0.0  0
 68M  CONST_04  C9   C2   N1   C3    180.00   0.0  0
 68M  CONST_05  C1   C2   N1   C3      0.00   0.0  0
 68M  CONST_06  C1   C5   C4   C3      0.00   0.0  0
 68M  CONST_07  C5   C4   C3   N1      0.00   0.0  0
 68M  CONST_08  C8   C9   C2   N1    180.00   0.0  0
 68M  CONST_09  C5   C1   C2   N1      0.00   0.0  0
 68M  CONST_10  C6   C1   C2   N1    180.00   0.0  0
 68M  CONST_11  C9   C2   C1   C5    180.00   0.0  0
 68M  CONST_12  C7   C6   C1   C5    180.00   0.0  0
 68M  CONST_13  C8   C9   C2   C1      0.00   0.0  0
 68M  CONST_14  C8   C7   C6   C1      0.00   0.0  0
 68M  CONST_15  C10  C7   C6   C1    180.00   0.0  0
 68M  CONST_16  C9   C2   C1   C6      0.00   0.0  0
 68M  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 68M  CONST_20  C7   C8   C9   C2      0.00   0.0  0
 68M  CONST_21  C7   C6   C1   C2      0.00   0.0  0
 68M  CONST_22  C10  C7   C8   C9    180.00   0.0  0
 68M  CONST_25  C24  N4   C10  C7    180.00   0.0  0
 68M  CONST_26  C22  C21  C10  C7    180.00   0.0  0
 68M  CONST_27  C23  C24  N4   C10     0.00   0.0  0
 68M  CONST_28  C23  C22  C21  C10     0.00   0.0  0
 68M  CONST_29  C22  C21  C10  N4      0.00   0.0  0
 68M  CONST_30  C22  C23  C24  N4      0.00   0.0  0
 68M  CONST_31  C21  C10  N4   C24     0.00   0.0  0
 68M  CONST_32  C21  C22  C23  C24     0.00   0.0  0
 68M  CONST_33  N1   C3   C4   C11   180.00   0.0  0
 68M  CONST_34  C1   C5   C4   C11   180.00   0.0  0
 68M  CONST_35  C2   N1   C3   N2    180.00   0.0  0
 68M  CONST_36  C5   C4   C3   N2    180.00   0.0  0
 68M  CONST_37  C25  C21  C10  C7      0.00   0.0  0
 68M  CONST_38  C25  C21  C10  N4    180.00   0.0  0
 68M  CONST_39  C25  C21  C22  C23   180.00   0.0  0
 68M  CONST_40  H23  C5   C4   C3    180.00   0.0  0
 68M  CONST_41  H25  C9   C2   N1      0.00   0.0  0
 68M  CONST_42  H24  C6   C1   C5      0.00   0.0  0
 68M  CONST_43  H26  C8   C7   C6    180.00   0.0  0
 68M  CONST_44  H27  C24  N4   C10   180.00   0.0  0
 68M  CONST_45  H29  C22  C21  C10   180.00   0.0  0
 68M  CONST_46  H28  C23  C24  N4    180.00   0.0  0
 68M  CONST_47  H21  N2   C3   C4    180.00   0.0  0
 68M  CONST_49  C12  C13  N3   C14   180.00   0.0  0
 68M  CONST_50  O1   C13  N3   C14     0.00   0.0  0
 68M  CONST_51  H14  N3   C13  O1    180.00   0.0  0
 68M  Var_01    C3   C4   C11  C12    78.53  30.0  2
 68M  Var_02    H30  C25  C21  C10    85.67  30.0  2
 68M  Var_03    C14  C15  C16  C18   -63.36  30.0  3
 68M  Var_04    N3   C14  C15  C16   177.23  30.0  1
 68M  Var_05    C13  N3   C14  C15  -121.52  30.0  1
 68M  Var_06    H4   C19  C16  C18   179.16  30.0  3
 68M  Var_07    H7   C20  C16  C18    57.64  30.0  3
 68M  Var_08    H1   C18  C16  C19   -58.73  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 68M  chir_01  C12  C17  C11  C13  positiv

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
 68M  plan-1  C7   0.020
 68M  plan-1  C10  0.020
 68M  plan-1  N4   0.020
 68M  plan-1  C24  0.020
 68M  plan-1  C23  0.020
 68M  plan-1  C22  0.020
 68M  plan-1  C21  0.020
 68M  plan-1  C25  0.020
 68M  plan-1  H27  0.020
 68M  plan-1  H28  0.020
 68M  plan-1  H29  0.020
 68M  plan-2  C11  0.020
 68M  plan-2  C4   0.020
 68M  plan-2  C3   0.020
 68M  plan-2  N1   0.020
 68M  plan-2  N2   0.020
 68M  plan-2  C5   0.020
 68M  plan-2  C1   0.020
 68M  plan-2  C6   0.020
 68M  plan-2  C2   0.020
 68M  plan-2  C9   0.020
 68M  plan-2  C8   0.020
 68M  plan-2  C7   0.020
 68M  plan-2  C10  0.020
 68M  plan-2  H23  0.020
 68M  plan-2  H24  0.020
 68M  plan-2  H25  0.020
 68M  plan-2  H26  0.020
 68M  plan-3  C14  0.020
 68M  plan-3  N3   0.020
 68M  plan-3  C13  0.020
 68M  plan-3  O1   0.020
 68M  plan-3  C12  0.020
 68M  plan-3  H14  0.020
 68M  plan-4  C3   0.020
 68M  plan-4  N2   0.020
 68M  plan-4  H21  0.020
 68M  plan-4  H22  0.020

