# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:19:03 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: ~{N}-[6-[5-azanyl-6-[(2~{S})-1,1,1-tris(fluoranyl)propan-2-yl]oxy-pyrazin-2-yl]imidazo[1,2-a]pyridin-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Oc1nc(cnc1N)c2ccc3nc(NC(C)=O)cn3c2)C(F)(F)F
#
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
 5XV  5XV  ~{N}-[6-[5-azanyl-6-[(2~{S})-1,1,1-tris(fluoranyl)propan-2-yl]oxy-pyrazin-2-yl]imidazo[1,2-a]pyridin-2-yl]ethanamide  ligand  42  27  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5XV
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
 5XV  C1   C  CR16  0  -0.215  -1.4186   3.0354   0.4195
 5XV  C2   C  CR6   0  -0.086  -0.5893   1.9326   0.0665
 5XV  C3   C  CR16  0   0.039  -1.1768   0.7178  -0.1483
 5XV  C11  C  CR6   0   0.198   0.8681   2.0642  -0.0643
 5XV  C12  C  C     0   0.512  -5.9481  -2.0779  -0.2567
 5XV  C13  C  CH3   0  -0.783  -7.3705  -2.5684  -0.2234
 5XV  C16  C  CR6   0   0.451   2.8659   0.9914  -0.2622
 5XV  C17  C  CR6   0   0.369   3.5584   2.2396  -0.3162
 5XV  C19  C  CR16  0  -0.149   1.5296   3.2703  -0.1324
 5XV  C21  C  CH1   0  -0.175   3.0069  -1.3775  -0.2023
 5XV  C22  C  CT    0   1.004   4.0893  -2.2568   0.4019
 5XV  C23  C  CH3   0  -0.700   2.5000  -1.8978  -1.5335
 5XV  N4   N  N     0  -0.510  -2.5226   0.5844  -0.0300
 5XV  C5   C  CR56  0   0.528  -3.3528   1.6345   0.3041
 5XV  C6   C  CR16  0  -0.377  -2.7688   2.8935   0.5352
 5XV  C7   C  CR15  0  -0.139  -3.3120  -0.5280  -0.1974
 5XV  C8   C  CR5   0   0.340  -4.5879  -0.0753   0.0483
 5XV  N9   N  N     0  -0.511  -4.6129   1.2409   0.3535
 5XV  N10  N  NH1   0  -0.714  -5.7891  -0.7604   0.0226
 5XV  O14  O  O     0  -0.473  -5.0070  -2.8078  -0.5161
 5XV  N15  N  N     0  -0.454   1.5848   0.9237  -0.1398
 5XV  N18  N  N     0  -0.412   2.8596   3.3502  -0.2508
 5XV  N20  N  NH2   0  -0.824   4.9015   2.2859  -0.4750
 5XV  F24  F  F     0  -0.307   5.1635  -2.3593  -0.3875
 5XV  F25  F  F     0  -0.304   4.5099  -1.7837   1.5790
 5XV  F26  F  F     0  -0.306   3.6281  -3.4948   0.6112
 5XV  O27  O  O2    0  -0.496   3.6275  -0.1076  -0.3408
 5XV  H28  H  HCR6  0   0.265  -0.9793   4.0030   0.6177
 5XV  H29  H  HCR6  0   0.304  -0.6242  -0.1704  -0.4160
 5XV  H34  H  HCH3  0   0.255  -8.0943  -1.7930   0.0189
 5XV  H35  H  HCH3  0   0.273  -7.6281  -2.9900  -1.1948
 5XV  H33  H  HCH3  0   0.273  -7.4603  -3.3680   0.5116
 5XV  H36  H  HCR6  0   0.265   1.0016   4.2148  -0.0972
 5XV  H39  H  HCH1  0   0.293   2.1840  -1.3241   0.5171
 5XV  H42  H  HCH3  0   0.257   2.0872  -2.8999  -1.4282
 5XV  H41  H  HCH3  0   0.265   1.7002  -1.2545  -1.8958
 5XV  H40  H  HCH3  0   0.252   3.2887  -1.9221  -2.2842
 5XV  H30  H  HCR6  0   0.280  -3.4033   3.7241   0.8100
 5XV  H31  H  HCR5  0   0.304  -2.9046  -1.4831  -0.4678
 5XV  H32  H  HNH1  0   0.413  -6.6045  -0.2040   0.2296
 5XV  H37  H  HNH2  0   0.400   5.4502   1.4778  -0.2349
 5XV  H38  H  HNH2  0   0.396   5.3471   3.1709  -0.2956

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
 5XV  C13  C12  single    1.505  0.020  1.505
 5XV  C12  N10  single    1.356  0.020  1.356
 5XV  C12  O14  double    1.219  0.020  1.219
 5XV  N10  C8   single    1.383  0.020  1.383
 5XV  C8   N9   aromatic  1.351  0.020  1.351
 5XV  C8   C7   aromatic  1.376  0.020  1.376
 5XV  N9   C5   aromatic  1.321  0.020  1.321
 5XV  C7   N4   aromatic  1.374  0.020  1.374
 5XV  C5   C6   aromatic  1.407  0.020  1.407
 5XV  C5   N4   aromatic  1.380  0.020  1.380
 5XV  C6   C1   aromatic  1.363  0.020  1.363
 5XV  N4   C3   aromatic  1.357  0.020  1.357
 5XV  C1   C2   aromatic  1.424  0.020  1.424
 5XV  C3   C2   aromatic  1.366  0.020  1.366
 5XV  C2   C11  single    1.469  0.020  1.469
 5XV  C11  C19  aromatic  1.377  0.020  1.377
 5XV  C11  N15  aromatic  1.349  0.020  1.349
 5XV  C19  N18  aromatic  1.338  0.020  1.338
 5XV  N15  C16  aromatic  1.289  0.020  1.289
 5XV  N18  C17  aromatic  1.314  0.020  1.314
 5XV  C16  C17  aromatic  1.428  0.020  1.428
 5XV  C16  O27  single    1.339  0.020  1.339
 5XV  C21  C23  single    1.517  0.020  1.517
 5XV  C21  O27  single    1.420  0.020  1.420
 5XV  C21  C22  single    1.520  0.020  1.520
 5XV  C17  N20  single    1.353  0.020  1.353
 5XV  F25  C22  single    1.336  0.020  1.336
 5XV  F26  C22  single    1.338  0.020  1.338
 5XV  C22  F24  single    1.337  0.020  1.337
 5XV  C1   H28  single    0.930  0.020  1.080
 5XV  C3   H29  single    0.930  0.020  1.080
 5XV  C13  H34  single    0.970  0.020  1.090
 5XV  C13  H35  single    0.970  0.020  1.090
 5XV  C13  H33  single    0.970  0.020  1.090
 5XV  C19  H36  single    0.930  0.020  1.080
 5XV  C21  H39  single    0.970  0.020  1.090
 5XV  C23  H42  single    0.970  0.020  1.090
 5XV  C23  H41  single    0.970  0.020  1.090
 5XV  C23  H40  single    0.970  0.020  1.090
 5XV  C6   H30  single    0.930  0.020  1.080
 5XV  C7   H31  single    0.930  0.020  1.080
 5XV  N10  H32  single    0.860  0.020  1.020
 5XV  N20  H37  single    0.890  0.020  1.040
 5XV  N20  H38  single    0.890  0.020  1.040

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
 5XV  H28  C1   C6   118.71  3.000
 5XV  H28  C1   C2   120.12  3.000
 5XV  C6   C1   C2   121.16  3.000
 5XV  C11  C2   C3   119.49  3.000
 5XV  C11  C2   C1   122.03  3.000
 5XV  C3   C2   C1   118.48  3.000
 5XV  H29  C3   N4   116.62  3.000
 5XV  H29  C3   C2   123.38  3.000
 5XV  N4   C3   C2   120.00  3.000
 5XV  N15  C11  C19  118.84  3.000
 5XV  N15  C11  C2   117.14  3.000
 5XV  C19  C11  C2   124.01  3.000
 5XV  O14  C12  N10  122.35  3.000
 5XV  O14  C12  C13  122.63  3.000
 5XV  N10  C12  C13  115.01  3.000
 5XV  H33  C13  H35  107.33  3.000
 5XV  H33  C13  H34  108.53  3.000
 5XV  H35  C13  H34  108.48  3.000
 5XV  H33  C13  C12  109.39  3.000
 5XV  H35  C13  C12  109.26  3.000
 5XV  H34  C13  C12  113.67  3.000
 5XV  O27  C16  N15  121.85  3.000
 5XV  O27  C16  C17  116.05  3.000
 5XV  N15  C16  C17  122.10  3.000
 5XV  N20  C17  N18  120.32  3.000
 5XV  N20  C17  C16  121.03  3.000
 5XV  N18  C17  C16  118.62  3.000
 5XV  H36  C19  N18  115.83  3.000
 5XV  H36  C19  C11  121.88  3.000
 5XV  N18  C19  C11  122.29  3.000
 5XV  H39  C21  O27  110.43  3.000
 5XV  H39  C21  C23  110.03  3.000
 5XV  O27  C21  C23  111.54  3.000
 5XV  H39  C21  C22  107.61  3.000
 5XV  O27  C21  C22  104.17  3.000
 5XV  C23  C21  C22  112.86  3.000
 5XV  F26  C22  F25  107.36  3.000
 5XV  F26  C22  F24  107.36  3.000
 5XV  F25  C22  F24  107.12  3.000
 5XV  F24  C22  C21  112.44  3.000
 5XV  F26  C22  C21  110.62  3.000
 5XV  F25  C22  C21  111.68  3.000
 5XV  H40  C23  H41  108.41  3.000
 5XV  H40  C23  H42  108.71  3.000
 5XV  H41  C23  H42  107.31  3.000
 5XV  H40  C23  C21  111.75  3.000
 5XV  H41  C23  C21  109.57  3.000
 5XV  H42  C23  C21  110.95  3.000
 5XV  C7   N4   C5   107.45  3.000
 5XV  C5   N4   C3   122.88  3.000
 5XV  C7   N4   C3   129.68  3.000
 5XV  N9   C5   C6   131.03  3.000
 5XV  C6   C5   N4   118.10  3.000
 5XV  N9   C5   N4   110.87  3.000
 5XV  H30  C6   C5   119.06  3.000
 5XV  H30  C6   C1   121.55  3.000
 5XV  C5   C6   C1   119.38  3.000
 5XV  H31  C7   C8   133.63  3.000
 5XV  H31  C7   N4   122.21  3.000
 5XV  C8   C7   N4   104.16  3.000
 5XV  N10  C8   N9   118.07  3.000
 5XV  N9   C8   C7   112.21  3.000
 5XV  N10  C8   C7   129.72  3.000
 5XV  C8   N9   C5   105.31  3.000
 5XV  H32  N10  C8   115.16  3.000
 5XV  H32  N10  C12  118.91  3.000
 5XV  C8   N10  C12  125.93  3.000
 5XV  C16  N15  C11  119.27  3.000
 5XV  C19  N18  C17  118.87  3.000
 5XV  H38  N20  H37  114.97  3.000
 5XV  H38  N20  C17  116.64  3.000
 5XV  H37  N20  C17  119.07  3.000
 5XV  C21  O27  C16  118.65  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
 5XV  CONST_01  N9   C5   C6   C1   180.00   0.0  0
 5XV  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 5XV  CONST_03  N4   C3   C2   C1     0.00   0.0  0
 5XV  CONST_04  C19  C11  C2   C1     0.00   0.0  0
 5XV  CONST_05  N15  C11  C2   C1   180.00   0.0  0
 5XV  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 5XV  CONST_07  C7   N4   C3   C2   180.00   0.0  0
 5XV  CONST_08  C5   N4   C3   C2     0.00   0.0  0
 5XV  CONST_09  N18  C19  C11  C2   180.00   0.0  0
 5XV  CONST_10  C16  N15  C11  C2   180.00   0.0  0
 5XV  CONST_11  C8   C7   N4   C3   180.00   0.0  0
 5XV  CONST_12  N9   C5   N4   C3   180.00   0.0  0
 5XV  CONST_13  C6   C5   N4   C3     0.00   0.0  0
 5XV  CONST_14  C6   C1   C2   C3     0.00   0.0  0
 5XV  CONST_15  C19  C11  C2   C3   180.00   0.0  0
 5XV  CONST_16  N15  C11  C2   C3     0.00   0.0  0
 5XV  CONST_17  C6   C1   C2   C11  180.00   0.0  0
 5XV  CONST_18  N4   C3   C2   C11  180.00   0.0  0
 5XV  CONST_19  C17  N18  C19  C11    0.00   0.0  0
 5XV  CONST_20  C17  C16  N15  C11    0.00   0.0  0
 5XV  CONST_21  C19  C11  N15  C16    0.00   0.0  0
 5XV  CONST_22  C19  N18  C17  C16    0.00   0.0  0
 5XV  CONST_23  N9   C8   C7   N4     0.00   0.0  0
 5XV  CONST_24  C8   N9   C5   N4     0.00   0.0  0
 5XV  CONST_25  C7   C8   N9   C5     0.00   0.0  0
 5XV  CONST_26  C8   C7   N4   C5     0.00   0.0  0
 5XV  CONST_27  C8   N9   C5   C6   180.00   0.0  0
 5XV  CONST_28  C7   N4   C5   C6   180.00   0.0  0
 5XV  CONST_29  N9   C5   N4   C7     0.00   0.0  0
 5XV  CONST_30  N18  C19  C11  N15    0.00   0.0  0
 5XV  CONST_31  N18  C17  C16  N15    0.00   0.0  0
 5XV  CONST_32  O27  C16  N15  C11  180.00   0.0  0
 5XV  CONST_33  N20  C17  N18  C19  180.00   0.0  0
 5XV  CONST_34  N10  C8   C7   N4   180.00   0.0  0
 5XV  CONST_35  N10  C8   N9   C5   180.00   0.0  0
 5XV  CONST_36  N20  C17  C16  N15  180.00   0.0  0
 5XV  CONST_37  O27  C16  C17  N18  180.00   0.0  0
 5XV  CONST_38  H29  C3   C2   C1   180.00   0.0  0
 5XV  CONST_39  H30  C6   C1   C2   180.00   0.0  0
 5XV  CONST_40  H36  C19  C11  C2     0.00   0.0  0
 5XV  CONST_41  H31  C7   N4   C3     0.00   0.0  0
 5XV  CONST_42  H28  C1   C2   C3   180.00   0.0  0
 5XV  CONST_43  N9   C8   N10  C12  180.00   0.0  0
 5XV  CONST_44  C7   C8   N10  C12    0.00   0.0  0
 5XV  CONST_46  H38  N20  C17  C16  180.00   0.0  0
 5XV  CONST_47  H32  N10  C8   C7   180.00   0.0  0
 5XV  CONST_48  C8   N10  C12  C13  180.00   0.0  0
 5XV  CONST_49  O14  C12  N10  C8     0.00   0.0  0
 5XV  Var_01    N15  C16  O27  C21   -3.91  30.0  2
 5XV  Var_02    H34  C13  C12  N10    0.24  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
 5XV  chir_01  C21  C23  O27  C22  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
 5XV  plan-1  C2   0.020
 5XV  plan-1  C11  0.020
 5XV  plan-1  C16  0.020
 5XV  plan-1  C17  0.020
 5XV  plan-1  C19  0.020
 5XV  plan-1  N15  0.020
 5XV  plan-1  N18  0.020
 5XV  plan-1  N20  0.020
 5XV  plan-1  O27  0.020
 5XV  plan-1  H36  0.020
 5XV  plan-2  C1   0.020
 5XV  plan-2  C2   0.020
 5XV  plan-2  C3   0.020
 5XV  plan-2  C11  0.020
 5XV  plan-2  N4   0.020
 5XV  plan-2  C5   0.020
 5XV  plan-2  C6   0.020
 5XV  plan-2  C7   0.020
 5XV  plan-2  C8   0.020
 5XV  plan-2  N9   0.020
 5XV  plan-2  N10  0.020
 5XV  plan-2  H28  0.020
 5XV  plan-2  H29  0.020
 5XV  plan-2  H30  0.020
 5XV  plan-2  H31  0.020
 5XV  plan-3  C12  0.020
 5XV  plan-3  C13  0.020
 5XV  plan-3  C8   0.020
 5XV  plan-3  N10  0.020
 5XV  plan-3  O14  0.020
 5XV  plan-3  H32  0.020
 5XV  plan-4  C17  0.020
 5XV  plan-4  N20  0.020
 5XV  plan-4  H37  0.020
 5XV  plan-4  H38  0.020

