# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:44:53 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-ethyl-5-[3-({3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl}oxy)propoxy]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ncccc2N3CCC(CC3)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
 VYG  VYG  6-ethyl-5-[3-({3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl}oxy)propoxy]pyrimidine-2,4-diamine  ligand  58  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VYG
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
 VYG  C1   C  CH2   0  -0.501  -1.8846  -0.6773  15.9163
 VYG  C2   C  CR6   0   0.224  -1.4845  -0.3456  14.5089
 VYG  C3   C  CR6   0   0.507  -1.6389   1.0981  12.7601
 VYG  C4   C  CR6   0   0.434  -0.3534  -0.7461  12.4526
 VYG  C5   C  CR6   0   0.123  -0.6679  -1.1673  13.7637
 VYG  C6   C  CH2   0  -0.175  -0.9765  -3.4784  13.9813
 VYG  C7   C  CH2   0  -0.503  -0.3124  -4.7063  14.5644
 VYG  N1   N  NH2   0  -0.825  -2.1116   2.2691  12.2569
 VYG  C8   C  CH2   0  -0.171  -0.1155  -4.6875  16.0663
 VYG  C9   C  CR6   0   0.507  -1.4885  -4.7207  18.0038
 VYG  C10  C  CR16  0  -0.082  -0.4878  -4.9927  20.0374
 VYG  C11  C  CR16  0  -0.341  -1.6903  -4.9447  20.7010
 VYG  N2   N  N     0  -0.501  -0.8440   0.3847  11.9610
 VYG  C12  C  CR16  0  -0.228  -2.8533  -4.7869  19.9461
 VYG  C13  C  CR6   0   0.172  -2.7891  -4.6652  18.5684
 VYG  C14  C  CH2   0  -0.317  -5.0765  -3.8962  18.4124
 VYG  C15  C  CH2   0  -0.457  -6.0529  -3.3320  17.3941
 VYG  C16  C  CH1   0  -0.487  -6.4433  -4.3926  16.3658
 VYG  C17  C  CT    0   1.041  -7.3728  -3.8215  15.3232
 VYG  C18  C  CH2   0  -0.455  -5.1897  -5.0088  15.7454
 VYG  C19  C  CH2   0  -0.306  -4.2609  -5.5165  16.8362
 VYG  O1   O  O2    0  -0.476  -1.3994  -4.5928  16.6767
 VYG  N3   N  NH2   0  -0.823   0.4339  -1.4966  11.6564
 VYG  N    N  N     0  -0.498  -1.9739   0.7960  14.0086
 VYG  C    C  CH3   0  -0.676  -3.3684  -1.0164  16.0276
 VYG  O    O  O2    0  -0.493  -0.1544  -2.3406  14.2380
 VYG  F    F  F     0  -0.313  -7.8088  -4.7484  14.4556
 VYG  F1   F  F     0  -0.316  -6.7930  -2.8572  14.5893
 VYG  F2   F  F     0  -0.315  -8.4644  -3.2684  15.8747
 VYG  N4   N  N     0  -0.457  -0.3971  -4.8829  18.7093
 VYG  N5   N  NT    0  -0.495  -3.9039  -4.4385  17.7532
 VYG  H1   H  HCH2  0   0.246  -1.2878  -1.5023  16.3034
 VYG  H2   H  HCH2  0   0.248  -1.6683   0.1924  16.5414
 VYG  H3   H  HCH2  0   0.231  -1.1091  -3.6128  12.9020
 VYG  H4   H  HCH2  0   0.229  -1.9718  -3.3278  14.4129
 VYG  H5   H  HCH2  0   0.246  -0.9089  -5.5781  14.2831
 VYG  H6   H  HCH2  0   0.246   0.6689  -4.8469  14.1035
 VYG  H7   H  HNH2  0   0.384  -2.0939   2.3827  11.2577
 VYG  H8   H  HNH2  0   0.384  -2.8996   2.6822  12.7260
 VYG  H9   H  HCH2  0   0.238   0.3872  -5.6046  16.3819
 VYG  H10  H  HCH2  0   0.226   0.5123  -3.8491  16.3778
 VYG  H11  H  HCR6  0   0.255   0.4457  -5.1114  20.5750
 VYG  H12  H  HCR6  0   0.261  -1.7355  -5.0339  21.7775
 VYG  H13  H  HCR6  0   0.278  -3.8097  -4.7571  20.4510
 VYG  H14  H  HCH2  0   0.259  -4.7703  -3.0935  19.0850
 VYG  H15  H  HCH2  0   0.215  -5.5915  -4.6545  19.0240
 VYG  H16  H  HCH2  0   0.256  -5.5919  -2.4775  16.8956
 VYG  H17  H  HCH2  0   0.256  -6.9297  -2.9661  17.9302
 VYG  H18  H  HCH1  0   0.279  -6.9991  -5.1873  16.8788
 VYG  H19  H  HCH2  0   0.255  -5.4470  -5.8433  15.0910
 VYG  H20  H  HCH2  0   0.246  -4.6547  -4.2698  15.1427
 VYG  H21  H  HCH2  0   0.216  -4.7485  -6.3374  17.3847
 VYG  H22  H  HCH2  0   0.263  -3.3645  -5.9272  16.3781
 VYG  H23  H  HNH2  0   0.391   0.7776  -1.0791  10.8079
 VYG  H24  H  HNH2  0   0.399   1.0094  -2.2134  12.0645
 VYG  H25  H  HCH3  0   0.236  -3.6331  -1.2187  17.0654
 VYG  H26  H  HCH3  0   0.228  -3.9899  -0.1945  15.6741
 VYG  H27  H  HCH3  0   0.232  -3.6203  -1.9035  15.4449

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
 VYG  N3   C4   single    1.348  0.020  1.348
 VYG  N2   C4   aromatic  1.327  0.020  1.327
 VYG  N2   C3   aromatic  1.334  0.020  1.334
 VYG  C4   C5   aromatic  1.413  0.020  1.413
 VYG  N1   C3   single    1.359  0.020  1.359
 VYG  C3   N    aromatic  1.327  0.020  1.327
 VYG  C6   C7   single    1.513  0.020  1.513
 VYG  C6   O    single    1.427  0.020  1.427
 VYG  C5   O    single    1.366  0.020  1.366
 VYG  C5   C2   aromatic  1.377  0.020  1.377
 VYG  C7   C8   single    1.515  0.020  1.515
 VYG  F1   C17  single    1.343  0.020  1.343
 VYG  N    C2   aromatic  1.339  0.020  1.339
 VYG  F    C17  single    1.342  0.020  1.342
 VYG  C2   C1   single    1.500  0.020  1.500
 VYG  C17  F2   single    1.342  0.020  1.342
 VYG  C17  C16  single    1.509  0.020  1.509
 VYG  C8   O1   single    1.425  0.020  1.425
 VYG  C18  C16  single    1.528  0.020  1.528
 VYG  C18  C19  single    1.520  0.020  1.520
 VYG  C1   C    single    1.526  0.020  1.526
 VYG  O1   C9   single    1.336  0.020  1.336
 VYG  C16  C15  single    1.528  0.020  1.528
 VYG  C19  N5   single    1.460  0.020  1.460
 VYG  C15  C14  single    1.519  0.020  1.519
 VYG  N5   C14  single    1.450  0.020  1.450
 VYG  N5   C13  single    1.400  0.020  1.400
 VYG  C9   C13  aromatic  1.419  0.020  1.419
 VYG  C9   N4   aromatic  1.310  0.020  1.310
 VYG  C13  C12  aromatic  1.385  0.020  1.385
 VYG  N4   C10  aromatic  1.336  0.020  1.336
 VYG  C12  C11  aromatic  1.395  0.020  1.395
 VYG  C10  C11  aromatic  1.374  0.020  1.374
 VYG  C1   H1   single    0.970  0.020  1.090
 VYG  C1   H2   single    0.970  0.020  1.090
 VYG  C6   H3   single    0.970  0.020  1.090
 VYG  C6   H4   single    0.970  0.020  1.090
 VYG  C7   H5   single    0.970  0.020  1.090
 VYG  C7   H6   single    0.970  0.020  1.090
 VYG  N1   H7   single    0.890  0.020  1.040
 VYG  N1   H8   single    0.890  0.020  1.040
 VYG  C8   H9   single    0.970  0.020  1.090
 VYG  C8   H10  single    0.970  0.020  1.090
 VYG  C10  H11  single    0.930  0.020  1.080
 VYG  C11  H12  single    0.930  0.020  1.080
 VYG  C12  H13  single    0.930  0.020  1.080
 VYG  C14  H14  single    0.970  0.020  1.090
 VYG  C14  H15  single    0.970  0.020  1.090
 VYG  C15  H16  single    0.970  0.020  1.090
 VYG  C15  H17  single    0.970  0.020  1.090
 VYG  C16  H18  single    0.970  0.020  1.090
 VYG  C18  H19  single    0.970  0.020  1.090
 VYG  C18  H20  single    0.970  0.020  1.090
 VYG  C19  H21  single    0.970  0.020  1.090
 VYG  C19  H22  single    0.970  0.020  1.090
 VYG  N3   H23  single    0.890  0.020  1.040
 VYG  N3   H24  single    0.890  0.020  1.040
 VYG  C    H25  single    0.970  0.020  1.090
 VYG  C    H26  single    0.970  0.020  1.090
 VYG  C    H27  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
 VYG  H2   C1   H1   106.92  3.000
 VYG  H2   C1   C    109.12  3.000
 VYG  H1   C1   C    109.78  3.000
 VYG  H2   C1   C2   107.93  3.000
 VYG  H1   C1   C2   110.78  3.000
 VYG  C    C1   C2   112.14  3.000
 VYG  N    C2   C5   121.54  3.000
 VYG  N    C2   C1   116.20  3.000
 VYG  C5   C2   C1   122.26  3.000
 VYG  N    C3   N2   126.31  3.000
 VYG  N    C3   N1   117.16  3.000
 VYG  N2   C3   N1   116.49  3.000
 VYG  N3   C4   N2   118.14  3.000
 VYG  N2   C4   C5   121.04  3.000
 VYG  N3   C4   C5   120.81  3.000
 VYG  O    C5   C4   119.66  3.000
 VYG  O    C5   C2   123.19  3.000
 VYG  C4   C5   C2   117.15  3.000
 VYG  H4   C6   H3   107.16  3.000
 VYG  H4   C6   O    110.06  3.000
 VYG  H3   C6   O    110.17  3.000
 VYG  H4   C6   C7   111.02  3.000
 VYG  H3   C6   C7   109.46  3.000
 VYG  O    C6   C7   108.96  3.000
 VYG  H6   C7   H5   106.18  3.000
 VYG  H6   C7   C8   107.64  3.000
 VYG  H5   C7   C8   109.63  3.000
 VYG  H6   C7   C6   109.63  3.000
 VYG  H5   C7   C6   107.97  3.000
 VYG  C8   C7   C6   115.41  3.000
 VYG  H8   N1   H7   115.51  3.000
 VYG  H8   N1   C3   116.97  3.000
 VYG  H7   N1   C3   117.32  3.000
 VYG  H10  C8   H9   107.30  3.000
 VYG  H10  C8   O1   110.16  3.000
 VYG  H9   C8   O1   110.29  3.000
 VYG  H10  C8   C7   111.52  3.000
 VYG  H9   C8   C7   109.62  3.000
 VYG  O1   C8   C7   107.97  3.000
 VYG  N4   C9   O1   119.43  3.000
 VYG  N4   C9   C13  123.66  3.000
 VYG  O1   C9   C13  116.91  3.000
 VYG  H11  C10  N4   116.35  3.000
 VYG  H11  C10  C11  121.20  3.000
 VYG  N4   C10  C11  122.45  3.000
 VYG  H12  C11  C12  120.88  3.000
 VYG  H12  C11  C10  120.96  3.000
 VYG  C12  C11  C10  118.16  3.000
 VYG  C4   N2   C3   117.00  3.000
 VYG  H13  C12  C13  120.19  3.000
 VYG  H13  C12  C11  119.17  3.000
 VYG  C13  C12  C11  120.64  3.000
 VYG  N5   C13  C12  123.84  3.000
 VYG  C12  C13  C9   115.78  3.000
 VYG  N5   C13  C9   120.31  3.000
 VYG  H15  C14  H14  107.18  3.000
 VYG  H15  C14  N5   111.89  3.000
 VYG  H14  C14  N5   109.17  3.000
 VYG  H15  C14  C15  109.10  3.000
 VYG  H14  C14  C15  108.68  3.000
 VYG  N5   C14  C15  110.72  3.000
 VYG  H17  C15  H16  107.54  3.000
 VYG  H17  C15  C16  110.99  3.000
 VYG  H16  C15  C16  110.12  3.000
 VYG  H17  C15  C14  108.16  3.000
 VYG  H16  C15  C14  108.99  3.000
 VYG  C16  C15  C14  110.94  3.000
 VYG  H18  C16  C18  108.26  3.000
 VYG  H18  C16  C17  106.57  3.000
 VYG  C18  C16  C17  112.17  3.000
 VYG  H18  C16  C15  108.52  3.000
 VYG  C18  C16  C15  110.09  3.000
 VYG  C17  C16  C15  111.08  3.000
 VYG  F2   C17  F1   106.24  3.000
 VYG  F2   C17  F    106.62  3.000
 VYG  F1   C17  F    106.42  3.000
 VYG  F2   C17  C16  111.90  3.000
 VYG  F    C17  C16  112.66  3.000
 VYG  F1   C17  C16  112.53  3.000
 VYG  H20  C18  H19  107.55  3.000
 VYG  H20  C18  C19  108.81  3.000
 VYG  H19  C18  C19  108.61  3.000
 VYG  H20  C18  C16  110.64  3.000
 VYG  H19  C18  C16  110.99  3.000
 VYG  C19  C18  C16  110.16  3.000
 VYG  H22  C19  H21  107.06  3.000
 VYG  H22  C19  N5   110.01  3.000
 VYG  H21  C19  N5   110.24  3.000
 VYG  H22  C19  C18  109.12  3.000
 VYG  H21  C19  C18  109.63  3.000
 VYG  N5   C19  C18  110.71  3.000
 VYG  C9   O1   C8   118.63  3.000
 VYG  H24  N3   H23  116.26  3.000
 VYG  H24  N3   C4   119.43  3.000
 VYG  H23  N3   C4   117.81  3.000
 VYG  C3   N    C2   116.95  3.000
 VYG  H27  C    H26  107.96  3.000
 VYG  H27  C    H25  107.55  3.000
 VYG  H26  C    H25  108.09  3.000
 VYG  H27  C    C1   111.49  3.000
 VYG  H26  C    C1   111.31  3.000
 VYG  H25  C    C1   110.30  3.000
 VYG  C6   O    C5   113.95  3.000
 VYG  C10  N4   C9   119.29  3.000
 VYG  C19  N5   C14  111.35  3.000
 VYG  C14  N5   C13  116.09  3.000
 VYG  C19  N5   C13  116.17  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
 VYG  CONST_01  N2   C4   C5   C2      0.00   0.0  0
 VYG  CONST_02  N2   C3   N    C2      0.00   0.0  0
 VYG  CONST_03  C5   C4   N2   C3      0.00   0.0  0
 VYG  CONST_04  C5   C2   N    C3      0.00   0.0  0
 VYG  CONST_05  N    C3   N2   C4      0.00   0.0  0
 VYG  CONST_06  N    C2   C5   C4      0.00   0.0  0
 VYG  CONST_07  C11  C12  C13  C9      0.00   0.0  0
 VYG  CONST_08  C11  C10  N4   C9      0.00   0.0  0
 VYG  CONST_09  C13  C9   N4   C10     0.00   0.0  0
 VYG  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 VYG  CONST_11  N4   C9   C13  C12     0.00   0.0  0
 VYG  CONST_12  N4   C10  C11  C12     0.00   0.0  0
 VYG  CONST_13  N5   C13  C12  C11   180.00   0.0  0
 VYG  CONST_14  N5   C13  C9   N4    180.00   0.0  0
 VYG  CONST_15  C4   C5   C2   C1    180.00   0.0  0
 VYG  CONST_16  C3   N    C2   C1    180.00   0.0  0
 VYG  CONST_17  N3   C4   C5   C2    180.00   0.0  0
 VYG  CONST_18  N1   C3   N    C2    180.00   0.0  0
 VYG  CONST_19  N3   C4   N2   C3    180.00   0.0  0
 VYG  CONST_20  N1   C3   N2   C4    180.00   0.0  0
 VYG  CONST_21  O1   C9   N4   C10   180.00   0.0  0
 VYG  CONST_22  O    C5   C4   N2    180.00   0.0  0
 VYG  CONST_23  O1   C9   C13  C12   180.00   0.0  0
 VYG  CONST_24  N5   C13  C9   O1      0.00   0.0  0
 VYG  CONST_25  O    C5   C2   N     180.00   0.0  0
 VYG  CONST_26  H13  C12  C13  C9    180.00   0.0  0
 VYG  CONST_27  H11  C10  N4   C9    180.00   0.0  0
 VYG  CONST_28  H12  C11  C12  C13   180.00   0.0  0
 VYG  CONST_29  H23  N3   C4   C5    180.00   0.0  0
 VYG  Var_01    C19  N5   C13  C9     69.03  30.0  1
 VYG  Var_02    C18  C19  N5   C13  -163.02  30.0  1
 VYG  Var_03    C15  C14  N5   C13   163.84  30.0  1
 VYG  Var_04    N5   C19  C18  C16   -57.33  30.0  1
 VYG  Var_05    N5   C14  C15  C16    56.25  30.0  1
 VYG  Var_06    C    C1   C2   C5   -111.11  30.0  2
 VYG  Var_07    C13  C9   O1   C8   -177.94  30.0  2
 VYG  Var_08    C7   C6   O    C5   -179.38  30.0  2
 VYG  Var_09    H25  C    C1   C2   -178.07  30.0  3
 VYG  Var_10    H9   C8   O1   C9     52.36  30.0  2
 VYG  Var_11    O1   C8   C7   C6     60.98  30.0  3
 VYG  Var_12    O    C6   C7   C8     61.89  30.0  2

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
 VYG  chir_01  C16  C17  C18  C15  negativ

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
 VYG  plan-1  C9   0.020
 VYG  plan-1  C10  0.020
 VYG  plan-1  C11  0.020
 VYG  plan-1  C12  0.020
 VYG  plan-1  C13  0.020
 VYG  plan-1  O1   0.020
 VYG  plan-1  N4   0.020
 VYG  plan-1  N5   0.020
 VYG  plan-1  H11  0.020
 VYG  plan-1  H12  0.020
 VYG  plan-1  H13  0.020
 VYG  plan-2  C1   0.020
 VYG  plan-2  C2   0.020
 VYG  plan-2  C3   0.020
 VYG  plan-2  C4   0.020
 VYG  plan-2  C5   0.020
 VYG  plan-2  N1   0.020
 VYG  plan-2  N2   0.020
 VYG  plan-2  N3   0.020
 VYG  plan-2  N    0.020
 VYG  plan-2  O    0.020
 VYG  plan-3  C3   0.020
 VYG  plan-3  N1   0.020
 VYG  plan-3  H7   0.020
 VYG  plan-3  H8   0.020
 VYG  plan-4  C4   0.020
 VYG  plan-4  N3   0.020
 VYG  plan-4  H23  0.020
 VYG  plan-4  H24  0.020

