# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:10:26 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-[1-(2,2-difluoroethyl)-4-(6-methylpyridin-2-yl)-1H-imidazol-5-yl]imidazo[1,2-a]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(n1)c2ncn(CC(F)F)c2c3ccc4nccn4c3
#
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
 QMY  QMY  6-[1-(2,2-difluoroethyl)-4-(6-methylpyridin-2-yl)-1H-imidazol-5-yl]imidazo[1,2-a]pyridine  ligand  40  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QMY
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
 QMY  C13  C  CH2   0  -0.451   2.7315  -1.4075  -0.9543
 QMY  C18  C  CR16  0  -0.126   0.2690   0.8545   1.2350
 QMY  C17  C  CR6   0  -0.105   0.4142   0.4045  -0.1094
 QMY  C19  C  CR16  0  -0.395   0.3801   2.1730   1.5442
 QMY  C20  C  CR56  0   0.524   0.6461   3.1045   0.5169
 QMY  C22  C  CR16  0   0.022   0.6701   1.3084  -1.0906
 QMY  C24  C  CR15  0  -0.204   1.0319   4.7871  -0.7273
 QMY  C11  C  CR16  0  -0.326  -3.1253  -2.5909   0.0382
 QMY  C12  C  CH3   0  -0.724  -3.9401   1.4784   0.8679
 QMY  C1   C  CR5   0   0.304   0.2895  -1.0193  -0.4363
 QMY  N2   N  NR5   0  -0.463   1.3421  -1.7870  -0.8737
 QMY  C3   C  CR15  0   0.099   0.8688  -3.0402  -1.0719
 QMY  N4   N  N     0  -0.452  -0.4015  -3.1273  -0.8037
 QMY  C5   C  CR5   0   0.061  -0.7863  -1.8776  -0.4061
 QMY  C6   C  CR6   0   0.141  -2.1678  -1.5806  -0.0334
 QMY  N7   N  N     0  -0.437  -2.4539  -0.3094   0.2381
 QMY  C8   C  CR6   0   0.226  -3.6852   0.0256   0.6012
 QMY  C9   C  CR16  0  -0.343  -4.7027  -0.9214   0.7076
 QMY  C10  C  CR16  0  -0.156  -4.4115  -2.2447   0.4171
 QMY  C14  C  CH1   0   0.546   3.4488  -1.7069   0.3458
 QMY  F15  F  F     0  -0.336   4.7295  -1.2616   0.2533
 QMY  F16  F  F     0  -0.333   2.8628  -1.0335   1.3723
 QMY  N21  N  N     0  -0.510   0.7839   2.6295  -0.7754
 QMY  N23  N  N     0  -0.481   0.7960   4.4144   0.5563
 QMY  C25  C  CR15  0  -0.123   1.0322   3.7142  -1.5761
 QMY  H34  H  HCH2  0   0.312   3.2038  -1.9678  -1.7606
 QMY  H33  H  HCH2  0   0.304   2.8168  -0.3474  -1.1910
 QMY  H37  H  HCR6  0   0.276   0.2725   2.5317   2.5584
 QMY  H38  H  HCR6  0   0.310   0.7782   1.0499  -2.1345
 QMY  H39  H  HCR5  0   0.257   1.1934   5.8202  -0.9960
 QMY  H29  H  HCR6  0   0.260  -2.8625  -3.6144  -0.1883
 QMY  H32  H  HCH3  0   0.251  -4.2302   1.9910  -0.0522
 QMY  H30  H  HCH3  0   0.241  -4.7448   1.6225   1.5877
 QMY  H31  H  HCH3  0   0.249  -3.0391   1.9625   1.2415
 QMY  H26  H  HCR5  0   0.293   1.5021  -3.8426  -1.4206
 QMY  H27  H  HCR6  0   0.260  -5.6976  -0.6233   1.0109
 QMY  H28  H  HCR6  0   0.266  -5.1802  -3.0031   0.4901
 QMY  H35  H  HCH1  0   0.207   3.4621  -2.7686   0.5954
 QMY  H40  H  HCR5  0   0.299   1.1777   3.6254  -2.6390
 QMY  H36  H  HCR6  0   0.257   0.0639   0.1292   2.0094

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
 QMY  N23  C24  aromatic  1.357  0.020  1.357
 QMY  N23  C20  aromatic  1.319  0.020  1.319
 QMY  C24  C25  aromatic  1.368  0.020  1.368
 QMY  C20  C19  aromatic  1.412  0.020  1.412
 QMY  C20  N21  aromatic  1.384  0.020  1.384
 QMY  C19  C18  aromatic  1.359  0.020  1.359
 QMY  C25  N21  aromatic  1.371  0.020  1.371
 QMY  N21  C22  aromatic  1.363  0.020  1.363
 QMY  C10  C9   aromatic  1.386  0.020  1.386
 QMY  C10  C11  aromatic  1.385  0.020  1.385
 QMY  C18  C17  aromatic  1.425  0.020  1.425
 QMY  C9   C8   aromatic  1.394  0.020  1.394
 QMY  C11  C6   aromatic  1.394  0.020  1.394
 QMY  C22  C17  aromatic  1.358  0.020  1.358
 QMY  C17  C1   single    1.466  0.020  1.466
 QMY  C8   C12  single    1.499  0.020  1.499
 QMY  C8   N7   aromatic  1.327  0.020  1.327
 QMY  C6   N7   aromatic  1.331  0.020  1.331
 QMY  C6   C5   single    1.461  0.020  1.461
 QMY  C1   C5   aromatic  1.377  0.020  1.377
 QMY  C1   N2   aromatic  1.374  0.020  1.374
 QMY  C5   N4   aromatic  1.367  0.020  1.367
 QMY  F16  C14  single    1.360  0.020  1.360
 QMY  N2   C13  single    1.443  0.020  1.443
 QMY  N2   C3   aromatic  1.354  0.020  1.354
 QMY  C13  C14  single    1.515  0.020  1.515
 QMY  N4   C3   aromatic  1.301  0.020  1.301
 QMY  C14  F15  single    1.359  0.020  1.359
 QMY  C13  H34  single    0.970  0.020  1.090
 QMY  C13  H33  single    0.970  0.020  1.090
 QMY  C18  H36  single    0.930  0.020  1.080
 QMY  C19  H37  single    0.930  0.020  1.080
 QMY  C22  H38  single    0.930  0.020  1.080
 QMY  C24  H39  single    0.930  0.020  1.080
 QMY  C11  H29  single    0.930  0.020  1.080
 QMY  C12  H32  single    0.970  0.020  1.090
 QMY  C12  H30  single    0.970  0.020  1.090
 QMY  C12  H31  single    0.970  0.020  1.090
 QMY  C3   H26  single    0.930  0.020  1.080
 QMY  C9   H27  single    0.930  0.020  1.080
 QMY  C10  H28  single    0.930  0.020  1.080
 QMY  C14  H35  single    0.970  0.020  1.090
 QMY  C25  H40  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
 QMY  H33  C13  H34  107.80  3.000
 QMY  H33  C13  C14  109.98  3.000
 QMY  H34  C13  C14  109.17  3.000
 QMY  H33  C13  N2   110.08  3.000
 QMY  H34  C13  N2   108.88  3.000
 QMY  C14  C13  N2   110.86  3.000
 QMY  H36  C18  C19  120.25  3.000
 QMY  H36  C18  C17  118.90  3.000
 QMY  C19  C18  C17  120.85  3.000
 QMY  C1   C17  C22  120.07  3.000
 QMY  C1   C17  C18  120.56  3.000
 QMY  C22  C17  C18  119.37  3.000
 QMY  H37  C19  C20  118.84  3.000
 QMY  H37  C19  C18  121.82  3.000
 QMY  C20  C19  C18  119.34  3.000
 QMY  N23  C20  N21  110.94  3.000
 QMY  N21  C20  C19  118.15  3.000
 QMY  N23  C20  C19  130.91  3.000
 QMY  H38  C22  N21  116.54  3.000
 QMY  H38  C22  C17  123.87  3.000
 QMY  N21  C22  C17  119.58  3.000
 QMY  H39  C24  C25  126.59  3.000
 QMY  H39  C24  N23  121.61  3.000
 QMY  C25  C24  N23  111.80  3.000
 QMY  H29  C11  C10  121.33  3.000
 QMY  H29  C11  C6   120.57  3.000
 QMY  C10  C11  C6   118.10  3.000
 QMY  H31  C12  H30  109.01  3.000
 QMY  H31  C12  H32  107.46  3.000
 QMY  H30  C12  H32  107.36  3.000
 QMY  H31  C12  C8   110.56  3.000
 QMY  H30  C12  C8   111.80  3.000
 QMY  H32  C12  C8   110.49  3.000
 QMY  C5   C1   N2   104.91  3.000
 QMY  N2   C1   C17  123.25  3.000
 QMY  C5   C1   C17  131.84  3.000
 QMY  C3   N2   C1   107.21  3.000
 QMY  C3   N2   C13  124.88  3.000
 QMY  C1   N2   C13  127.49  3.000
 QMY  H26  C3   N4   126.10  3.000
 QMY  H26  C3   N2   121.99  3.000
 QMY  N4   C3   N2   111.90  3.000
 QMY  C5   N4   C3   105.88  3.000
 QMY  C6   C5   N4   121.75  3.000
 QMY  N4   C5   C1   110.10  3.000
 QMY  C6   C5   C1   128.15  3.000
 QMY  N7   C6   C5   116.70  3.000
 QMY  C5   C6   C11  121.01  3.000
 QMY  N7   C6   C11  122.28  3.000
 QMY  C8   N7   C6   119.77  3.000
 QMY  C9   C8   N7   121.78  3.000
 QMY  N7   C8   C12  116.82  3.000
 QMY  C9   C8   C12  121.38  3.000
 QMY  H27  C9   C10  121.00  3.000
 QMY  H27  C9   C8   120.35  3.000
 QMY  C10  C9   C8   118.64  3.000
 QMY  H28  C10  C9   120.38  3.000
 QMY  H28  C10  C11  120.20  3.000
 QMY  C9   C10  C11  119.42  3.000
 QMY  H35  C14  F16  108.32  3.000
 QMY  H35  C14  F15  108.85  3.000
 QMY  F16  C14  F15  107.16  3.000
 QMY  H35  C14  C13  113.24  3.000
 QMY  F15  C14  C13  108.85  3.000
 QMY  F16  C14  C13  110.23  3.000
 QMY  C25  N21  C22  130.32  3.000
 QMY  C22  N21  C20  122.71  3.000
 QMY  C25  N21  C20  106.97  3.000
 QMY  C24  N23  C20  105.32  3.000
 QMY  H40  C25  N21  122.40  3.000
 QMY  H40  C25  C24  132.64  3.000
 QMY  N21  C25  C24  104.96  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
 QMY  CONST_01  N23  C20  C19  C18  180.00   0.0  0
 QMY  CONST_02  N21  C20  C19  C18    0.00   0.0  0
 QMY  CONST_03  N21  C22  C17  C18    0.00   0.0  0
 QMY  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 QMY  CONST_07  C20  N21  C22  C17    0.00   0.0  0
 QMY  CONST_08  C25  N21  C22  C17  180.00   0.0  0
 QMY  CONST_09  C6   C5   C1   C17    0.00   0.0  0
 QMY  CONST_10  N4   C5   C1   C17  180.00   0.0  0
 QMY  CONST_11  C3   N2   C1   C17  180.00   0.0  0
 QMY  CONST_12  C24  N23  C20  C19  180.00   0.0  0
 QMY  CONST_13  C25  N21  C20  C19  180.00   0.0  0
 QMY  CONST_14  C22  N21  C20  C19    0.00   0.0  0
 QMY  CONST_15  C22  C17  C18  C19    0.00   0.0  0
 QMY  CONST_16  C1   C17  C18  C19  180.00   0.0  0
 QMY  CONST_17  C25  C24  N23  C20    0.00   0.0  0
 QMY  CONST_18  C24  C25  N21  C20    0.00   0.0  0
 QMY  CONST_19  N23  C20  N21  C22  180.00   0.0  0
 QMY  CONST_20  C24  C25  N21  C22  180.00   0.0  0
 QMY  CONST_23  N21  C20  N23  C24    0.00   0.0  0
 QMY  CONST_24  C8   C9   C10  C11    0.00   0.0  0
 QMY  CONST_25  C8   N7   C6   C11    0.00   0.0  0
 QMY  CONST_26  C1   C5   C6   C11  180.00   0.0  0
 QMY  CONST_27  N4   C5   C6   C11    0.00   0.0  0
 QMY  CONST_28  N21  C22  C17  C1   180.00   0.0  0
 QMY  CONST_29  N7   C6   C5   C1     0.00   0.0  0
 QMY  CONST_30  C3   N4   C5   C1     0.00   0.0  0
 QMY  CONST_31  N4   C3   N2   C1     0.00   0.0  0
 QMY  CONST_32  C6   C5   C1   N2   180.00   0.0  0
 QMY  CONST_33  N4   C5   C1   N2     0.00   0.0  0
 QMY  CONST_34  C5   N4   C3   N2     0.00   0.0  0
 QMY  CONST_35  C5   C1   N2   C3     0.00   0.0  0
 QMY  CONST_36  C6   C5   N4   C3   180.00   0.0  0
 QMY  CONST_37  N7   C6   C5   N4   180.00   0.0  0
 QMY  CONST_38  C10  C11  C6   C5   180.00   0.0  0
 QMY  CONST_39  C8   N7   C6   C5   180.00   0.0  0
 QMY  CONST_40  C9   C10  C11  C6     0.00   0.0  0
 QMY  CONST_41  C9   C8   N7   C6     0.00   0.0  0
 QMY  CONST_42  C10  C9   C8   N7     0.00   0.0  0
 QMY  CONST_43  C10  C11  C6   N7     0.00   0.0  0
 QMY  CONST_44  N23  C24  C25  N21    0.00   0.0  0
 QMY  CONST_45  C25  N21  C20  N23    0.00   0.0  0
 QMY  CONST_46  C17  C1   N2   C13    0.00   0.0  0
 QMY  CONST_47  C5   C1   N2   C13  180.00   0.0  0
 QMY  CONST_48  N4   C3   N2   C13  180.00   0.0  0
 QMY  CONST_49  C10  C9   C8   C12  180.00   0.0  0
 QMY  CONST_50  C6   N7   C8   C12  180.00   0.0  0
 QMY  CONST_51  H38  C22  C17  C18  180.00   0.0  0
 QMY  CONST_52  H37  C19  C18  C17  180.00   0.0  0
 QMY  CONST_53  H39  C24  N23  C20  180.00   0.0  0
 QMY  CONST_54  H36  C18  C19  C20  180.00   0.0  0
 QMY  CONST_55  H40  C25  N21  C20  180.00   0.0  0
 QMY  CONST_56  H27  C9   C10  C11  180.00   0.0  0
 QMY  CONST_57  H26  C3   N2   C1   180.00   0.0  0
 QMY  CONST_58  H29  C11  C6   C5     0.00   0.0  0
 QMY  CONST_59  H28  C10  C11  C6   180.00   0.0  0
 QMY  Var_01    C14  C13  N2   C1    88.70  30.0  2
 QMY  Var_02    H32  C12  C8   N7    88.39  30.0  2
 QMY  Var_03    F16  C14  C13  N2   -59.11  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
 QMY  plan-1  C13  0.020
 QMY  plan-1  C17  0.020
 QMY  plan-1  C1   0.020
 QMY  plan-1  N2   0.020
 QMY  plan-1  C3   0.020
 QMY  plan-1  N4   0.020
 QMY  plan-1  C5   0.020
 QMY  plan-1  C6   0.020
 QMY  plan-1  H26  0.020
 QMY  plan-2  C11  0.020
 QMY  plan-2  C12  0.020
 QMY  plan-2  C5   0.020
 QMY  plan-2  C6   0.020
 QMY  plan-2  N7   0.020
 QMY  plan-2  C8   0.020
 QMY  plan-2  C9   0.020
 QMY  plan-2  C10  0.020
 QMY  plan-2  H29  0.020
 QMY  plan-2  H27  0.020
 QMY  plan-2  H28  0.020
 QMY  plan-3  C18  0.020
 QMY  plan-3  C17  0.020
 QMY  plan-3  C19  0.020
 QMY  plan-3  C20  0.020
 QMY  plan-3  C22  0.020
 QMY  plan-3  C24  0.020
 QMY  plan-3  C1   0.020
 QMY  plan-3  N21  0.020
 QMY  plan-3  N23  0.020
 QMY  plan-3  C25  0.020
 QMY  plan-3  H37  0.020
 QMY  plan-3  H38  0.020
 QMY  plan-3  H39  0.020
 QMY  plan-3  H40  0.020
 QMY  plan-3  H36  0.020

