# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:16:10 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[(1-{2-[(3,5-dimethylphenyl)amino]pyrimidin-4-yl}-3-methyl-1H-pyrazol-4-yl)methyl]azetidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)cc(Nc2nccc(n2)n3cc(CN4CC(O)C4)c(C)n3)c1
#
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
 X6G  X6G  1-[(1-{2-[(3,5-dimethylphenyl)amino]pyrimidin-4-yl}-3-methyl-1H-pyrazol-4-yl)methyl]azetidin-3-ol  ligand  51  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X6G
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
 X6G  C4   C  CR6   0   0.577  -0.2093   1.5656   0.3217
 X6G  C5   C  CR16  0  -0.424   0.2227   2.8713   0.0912
 X6G  C6   C  CR16  0   0.009   1.5769   2.9984  -0.1313
 X6G  N1   N  N     0  -0.474   2.4292   1.9792  -0.1240
 X6G  N3   N  N     0  -0.509   0.6077   0.5365   0.3339
 X6G  CAR  C  CR6   0   0.127   5.9315  -2.0126   0.3419
 X6G  CAH  C  CR16  0  -0.423   4.5774  -1.7298   0.4295
 X6G  CAG  C  CR16  0  -0.376   6.7953  -1.0262  -0.1312
 X6G  CAS  C  CR6   0   0.129   6.3112   0.2160  -0.5215
 X6G  CAB  C  CH3   0  -0.725   7.2404   1.2627  -1.0672
 X6G  CAI  C  CR16  0  -0.377   4.9475   0.4891  -0.4304
 X6G  CAT  C  CR6   0   0.399   4.0708  -0.4823   0.0486
 X6G  C2   C  CR6   0   0.616   1.9036   0.7839   0.1168
 X6G  NBA  N  NR5   0  -0.399  -1.5488   1.2788   0.5531
 X6G  CAJ  C  CR15  0   0.061  -2.1093   0.0521   0.7180
 X6G  NAP  N  N     0  -0.307  -2.4539   2.2642   0.6503
 X6G  CAU  C  CR5   0   0.301  -3.6011   1.6686   0.8777
 X6G  CAC  C  CH3   0  -0.746  -4.8557   2.4493   1.0549
 X6G  CAV  C  CR5   0  -0.188  -3.4420   0.2547   0.9326
 X6G  CAK  C  CH2   0  -0.386  -4.4939  -0.7864   1.1278
 X6G  NAZ  N  N     0  -0.409  -4.8493  -1.4135  -0.1237
 X6G  CAM  C  C     0  -0.304  -5.5817  -0.6169  -1.1122
 X6G  CAL  C  C     0  -0.301  -5.9209  -2.4131  -0.1077
 X6G  CAY  C  C     0   0.009  -6.3646  -1.8785  -1.4817
 X6G  OAD  O  OH1   0  -0.660  -7.7206  -1.6774  -1.7368
 X6G  H1   H  HCR6  0   0.288  -0.4446   3.7171   0.0798
 X6G  H2   H  HCR6  0   0.278   2.0024   3.9755  -0.3288
 X6G  H3   H  HCH3  0   0.249   6.4395  -4.0482  -0.1187
 X6G  H4   H  HCH3  0   0.243   7.4774  -3.3125   1.0929
 X6G  H5   H  HCH3  0   0.243   5.8403  -3.8172   1.5163
 X6G  H6   H  HCR6  0   0.256   3.8982  -2.4873   0.8076
 X6G  H7   H  HCR6  0   0.236   7.8587  -1.2309  -0.1925
 X6G  H8   H  HCH3  0   0.247   7.1958   1.2901  -2.1580
 X6G  H9   H  HCH3  0   0.243   6.9771   2.2586  -0.7110
 X6G  H10  H  HCH3  0   0.242   8.2748   1.0658  -0.7883
 X6G  H11  H  HCR6  0   0.271   4.5773   1.4575  -0.7282
 X6G  H13  H  HCR5  0   0.300  -1.5235  -0.8504   0.6720
 X6G  H14  H  HCH3  0   0.254  -5.5510   2.2781   0.2320
 X6G  H15  H  HCH3  0   0.252  -5.3688   2.1673   1.9746
 X6G  H16  H  HCH3  0   0.258  -4.6434   3.5160   1.0965
 X6G  H17  H  HCH2  0   0.252  -4.1271  -1.5643   1.8024
 X6G  H18  H  HCH2  0   0.209  -5.3707  -0.3348   1.6207
 X6G  H20  H  H     0   0.206  -6.2499   0.1277  -0.6547
 X6G  H21  H  H     0   0.234  -4.9747  -0.1271  -1.8768
 X6G  H22  H  H     0   0.229  -5.5931  -3.4519  -0.0229
 X6G  H23  H  H     0   0.205  -6.6891  -2.2159   0.6536
 X6G  H24  H  H     0   0.217  -5.8723  -2.4279  -2.2912
 X6G  H25  H  HOH1  0   0.455  -8.1084  -2.5158  -2.0051
 X6G  NAQ  N  NH1   0  -0.771   2.6918  -0.3210   0.1688
 X6G  CAA  C  CH3   0  -0.724   6.4501  -3.3663   0.7339
 X6G  H12  H  HNH1  0   0.409   2.1823  -1.1585   0.4075

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
 X6G  N1   C6   aromatic  1.329  0.020  1.329
 X6G  N1   C2   aromatic  1.328  0.020  1.328
 X6G  CAB  CAS  single    1.502  0.020  1.502
 X6G  C6   C5   aromatic  1.378  0.020  1.378
 X6G  CAI  CAS  aromatic  1.394  0.020  1.394
 X6G  CAI  CAT  aromatic  1.393  0.020  1.393
 X6G  NAQ  C2   single    1.358  0.020  1.358
 X6G  NAQ  CAT  single    1.394  0.020  1.394
 X6G  C2   N3   aromatic  1.337  0.020  1.337
 X6G  CAS  CAG  aromatic  1.389  0.020  1.389
 X6G  CAT  CAH  aromatic  1.399  0.020  1.399
 X6G  C5   C4   aromatic  1.395  0.020  1.395
 X6G  N3   C4   aromatic  1.314  0.020  1.314
 X6G  CAG  CAR  aromatic  1.394  0.020  1.394
 X6G  C4   NBA  single    1.389  0.020  1.389
 X6G  CAH  CAR  aromatic  1.386  0.020  1.386
 X6G  CAR  CAA  single    1.502  0.020  1.502
 X6G  NBA  NAP  aromatic  1.342  0.020  1.342
 X6G  NBA  CAJ  aromatic  1.359  0.020  1.359
 X6G  NAP  CAU  aromatic  1.313  0.020  1.313
 X6G  CAJ  CAV  aromatic  1.365  0.020  1.365
 X6G  CAM  CAY  single    1.530  0.020  1.530
 X6G  CAM  NAZ  single    1.466  0.020  1.466
 X6G  CAY  OAD  single    1.394  0.020  1.394
 X6G  CAY  CAL  single    1.540  0.020  1.540
 X6G  CAU  CAV  aromatic  1.424  0.020  1.424
 X6G  CAU  CAC  single    1.488  0.020  1.488
 X6G  CAV  CAK  single    1.493  0.020  1.493
 X6G  NAZ  CAL  single    1.466  0.020  1.466
 X6G  NAZ  CAK  single    1.444  0.020  1.444
 X6G  C5   H1   single    0.930  0.020  1.080
 X6G  C6   H2   single    0.930  0.020  1.080
 X6G  CAA  H3   single    0.970  0.020  1.090
 X6G  CAA  H4   single    0.970  0.020  1.090
 X6G  CAA  H5   single    0.970  0.020  1.090
 X6G  CAH  H6   single    0.930  0.020  1.080
 X6G  CAG  H7   single    0.930  0.020  1.080
 X6G  CAB  H8   single    0.970  0.020  1.090
 X6G  CAB  H9   single    0.970  0.020  1.090
 X6G  CAB  H10  single    0.970  0.020  1.090
 X6G  CAI  H11  single    0.930  0.020  1.080
 X6G  NAQ  H12  single    0.860  0.020  1.020
 X6G  CAJ  H13  single    0.930  0.020  1.080
 X6G  CAC  H14  single    0.970  0.020  1.090
 X6G  CAC  H15  single    0.970  0.020  1.090
 X6G  CAC  H16  single    0.970  0.020  1.090
 X6G  CAK  H17  single    0.970  0.020  1.090
 X6G  CAK  H18  single    0.970  0.020  1.090
 X6G  CAM  H20  single    0.970  0.020  1.090
 X6G  CAM  H21  single    0.970  0.020  1.090
 X6G  CAL  H22  single    0.970  0.020  1.090
 X6G  CAL  H23  single    0.970  0.020  1.090
 X6G  CAY  H24  single    0.970  0.020  1.090
 X6G  OAD  H25  single    0.850  0.020  0.980

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
 X6G  NBA  C4   N3   115.87  3.000
 X6G  NBA  C4   C5   121.30  3.000
 X6G  N3   C4   C5   122.84  3.000
 X6G  H1   C5   C6   122.31  3.000
 X6G  H1   C5   C4   123.02  3.000
 X6G  C6   C5   C4   114.67  3.000
 X6G  H2   C6   N1   116.15  3.000
 X6G  H2   C6   C5   119.89  3.000
 X6G  N1   C6   C5   123.97  3.000
 X6G  C2   N1   C6   115.95  3.000
 X6G  C2   N3   C4   117.14  3.000
 X6G  CAG  CAR  CAH  118.85  3.000
 X6G  CAH  CAR  CAA  120.32  3.000
 X6G  CAG  CAR  CAA  120.83  3.000
 X6G  H6   CAH  CAT  119.37  3.000
 X6G  H6   CAH  CAR  119.41  3.000
 X6G  CAT  CAH  CAR  121.22  3.000
 X6G  H7   CAG  CAS  119.64  3.000
 X6G  H7   CAG  CAR  119.55  3.000
 X6G  CAS  CAG  CAR  120.81  3.000
 X6G  CAI  CAS  CAB  119.50  3.000
 X6G  CAI  CAS  CAG  119.86  3.000
 X6G  CAB  CAS  CAG  120.63  3.000
 X6G  H10  CAB  H9   108.11  3.000
 X6G  H10  CAB  H8   107.40  3.000
 X6G  H9   CAB  H8   107.08  3.000
 X6G  H10  CAB  CAS  111.61  3.000
 X6G  H9   CAB  CAS  111.62  3.000
 X6G  H8   CAB  CAS  110.80  3.000
 X6G  H11  CAI  CAT  120.32  3.000
 X6G  H11  CAI  CAS  119.58  3.000
 X6G  CAT  CAI  CAS  120.10  3.000
 X6G  NAQ  CAT  CAI  124.86  3.000
 X6G  NAQ  CAT  CAH  115.98  3.000
 X6G  CAI  CAT  CAH  119.16  3.000
 X6G  NAQ  C2   N3   113.94  3.000
 X6G  N3   C2   N1   125.43  3.000
 X6G  NAQ  C2   N1   120.63  3.000
 X6G  NAP  NBA  CAJ  112.09  3.000
 X6G  CAJ  NBA  C4   127.18  3.000
 X6G  NAP  NBA  C4   120.73  3.000
 X6G  H13  CAJ  CAV  131.46  3.000
 X6G  H13  CAJ  NBA  121.81  3.000
 X6G  CAV  CAJ  NBA  106.73  3.000
 X6G  CAU  NAP  NBA  105.60  3.000
 X6G  CAV  CAU  CAC  127.63  3.000
 X6G  CAC  CAU  NAP  121.29  3.000
 X6G  CAV  CAU  NAP  111.08  3.000
 X6G  H16  CAC  H15  108.24  3.000
 X6G  H16  CAC  H14  107.87  3.000
 X6G  H15  CAC  H14  107.20  3.000
 X6G  H16  CAC  CAU  110.75  3.000
 X6G  H15  CAC  CAU  111.19  3.000
 X6G  H14  CAC  CAU  111.42  3.000
 X6G  CAK  CAV  CAU  128.23  3.000
 X6G  CAK  CAV  CAJ  127.23  3.000
 X6G  CAU  CAV  CAJ  104.50  3.000
 X6G  H18  CAK  H17  106.40  3.000
 X6G  H18  CAK  NAZ  111.69  3.000
 X6G  H17  CAK  NAZ  107.96  3.000
 X6G  H18  CAK  CAV  109.46  3.000
 X6G  H17  CAK  CAV  109.91  3.000
 X6G  NAZ  CAK  CAV  111.28  3.000
 X6G  CAL  NAZ  CAM   90.73  3.000
 X6G  CAL  NAZ  CAK  117.81  3.000
 X6G  CAM  NAZ  CAK  118.13  3.000
 X6G  H21  CAM  H20  108.98  3.000
 X6G  H21  CAM  CAY  119.02  3.000
 X6G  H20  CAM  CAY  110.35  3.000
 X6G  H21  CAM  NAZ  115.98  3.000
 X6G  H20  CAM  NAZ  113.01  3.000
 X6G  CAY  CAM  NAZ   88.30  3.000
 X6G  H23  CAL  H22  109.06  3.000
 X6G  H23  CAL  CAY  110.75  3.000
 X6G  H22  CAL  CAY  119.07  3.000
 X6G  H23  CAL  NAZ  113.34  3.000
 X6G  H22  CAL  NAZ  115.46  3.000
 X6G  CAY  CAL  NAZ   87.94  3.000
 X6G  H24  CAY  OAD  111.98  3.000
 X6G  H24  CAY  CAL  110.85  3.000
 X6G  OAD  CAY  CAL  119.58  3.000
 X6G  H24  CAY  CAM  111.23  3.000
 X6G  CAL  CAY  CAM   85.61  3.000
 X6G  OAD  CAY  CAM  115.01  3.000
 X6G  H25  OAD  CAY  108.50  3.000
 X6G  H12  NAQ  C2   113.03  3.000
 X6G  H12  NAQ  CAT  115.09  3.000
 X6G  C2   NAQ  CAT  131.69  3.000
 X6G  H5   CAA  H4   108.15  3.000
 X6G  H5   CAA  H3   107.27  3.000
 X6G  H4   CAA  H3   107.29  3.000
 X6G  H5   CAA  CAR  111.54  3.000
 X6G  H4   CAA  CAR  111.54  3.000
 X6G  H3   CAA  CAR  110.84  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
 X6G  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 X6G  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 X6G  CONST_03  CAU  NAP  NBA  C4   180.00   0.0  0
 X6G  CONST_04  CAV  CAJ  NBA  C4   180.00   0.0  0
 X6G  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 X6G  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 X6G  CONST_07  NAP  NBA  C4   C5     0.00   0.0  0
 X6G  CONST_08  CAJ  NBA  C4   C5   180.00   0.0  0
 X6G  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 X6G  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 X6G  CONST_11  NBA  C4   C5   C6   180.00   0.0  0
 X6G  CONST_12  NAP  NBA  C4   N3   180.00   0.0  0
 X6G  CONST_13  CAJ  NBA  C4   N3     0.00   0.0  0
 X6G  CONST_14  CAI  CAS  CAG  CAR    0.00   0.0  0
 X6G  CONST_15  CAI  CAT  CAH  CAR    0.00   0.0  0
 X6G  CONST_16  CAS  CAI  CAT  CAH    0.00   0.0  0
 X6G  CONST_17  CAS  CAG  CAR  CAH    0.00   0.0  0
 X6G  CONST_18  CAT  CAI  CAS  CAG    0.00   0.0  0
 X6G  CONST_19  CAT  CAH  CAR  CAG    0.00   0.0  0
 X6G  CONST_20  NBA  C4   N3   C2   180.00   0.0  0
 X6G  CONST_21  CAV  CAU  NAP  NBA    0.00   0.0  0
 X6G  CONST_22  CAU  CAV  CAJ  NBA    0.00   0.0  0
 X6G  CONST_23  CAU  NAP  NBA  CAJ    0.00   0.0  0
 X6G  CONST_24  NAP  CAU  CAV  CAJ    0.00   0.0  0
 X6G  CONST_25  CAV  CAJ  NBA  NAP    0.00   0.0  0
 X6G  CONST_26  NAQ  C2   N3   C4   180.00   0.0  0
 X6G  CONST_27  NAQ  C2   N1   C6   180.00   0.0  0
 X6G  CONST_28  CAS  CAG  CAR  CAA  180.00   0.0  0
 X6G  CONST_29  CAT  CAH  CAR  CAA  180.00   0.0  0
 X6G  CONST_30  CAB  CAS  CAG  CAR  180.00   0.0  0
 X6G  CONST_31  NAQ  CAT  CAH  CAR  180.00   0.0  0
 X6G  CONST_32  NAQ  CAT  CAI  CAS  180.00   0.0  0
 X6G  CONST_33  CAT  CAI  CAS  CAB  180.00   0.0  0
 X6G  CONST_34  CAC  CAU  NAP  NBA  180.00   0.0  0
 X6G  CONST_35  CAK  CAV  CAJ  NBA  180.00   0.0  0
 X6G  CONST_36  CAC  CAU  CAV  CAJ  180.00   0.0  0
 X6G  CONST_37  CAK  CAV  CAU  NAP  180.00   0.0  0
 X6G  CONST_38  H2   C6   C5   C4   180.00   0.0  0
 X6G  CONST_39  H13  CAJ  NBA  C4     0.00   0.0  0
 X6G  CONST_40  H1   C5   C6   N1   180.00   0.0  0
 X6G  CONST_41  H11  CAI  CAT  CAH  180.00   0.0  0
 X6G  CONST_42  H7   CAG  CAR  CAH  180.00   0.0  0
 X6G  CONST_43  H6   CAH  CAR  CAG  180.00   0.0  0
 X6G  Var_01    CAY  CAL  NAZ  CAM   20.80  30.0  1
 X6G  Var_02    CAT  NAQ  C2   N1     2.23  30.0  1
 X6G  Var_03    C2   NAQ  CAT  CAH  167.14  30.0  2
 X6G  Var_04    NAZ  CAK  CAV  CAJ  -75.97  30.0  2
 X6G  Var_05    CAM  NAZ  CAK  CAV  -69.62  30.0  1
 X6G  Var_06    H3   CAA  CAR  CAH   89.12  30.0  2
 X6G  Var_07    H8   CAB  CAS  CAG   99.75  30.0  2
 X6G  Var_08    H14  CAC  CAU  NAP  112.78  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
 X6G  chir_01  CAY  CAM  OAD  CAL  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
 X6G  plan-1  C4   0.020
 X6G  plan-1  NBA  0.020
 X6G  plan-1  CAJ  0.020
 X6G  plan-1  NAP  0.020
 X6G  plan-1  CAU  0.020
 X6G  plan-1  CAC  0.020
 X6G  plan-1  CAV  0.020
 X6G  plan-1  CAK  0.020
 X6G  plan-1  H13  0.020
 X6G  plan-2  C4   0.020
 X6G  plan-2  C5   0.020
 X6G  plan-2  C6   0.020
 X6G  plan-2  N1   0.020
 X6G  plan-2  N3   0.020
 X6G  plan-2  C2   0.020
 X6G  plan-2  NBA  0.020
 X6G  plan-2  H1   0.020
 X6G  plan-2  H2   0.020
 X6G  plan-2  NAQ  0.020
 X6G  plan-3  CAR  0.020
 X6G  plan-3  CAH  0.020
 X6G  plan-3  CAG  0.020
 X6G  plan-3  CAS  0.020
 X6G  plan-3  CAB  0.020
 X6G  plan-3  CAI  0.020
 X6G  plan-3  CAT  0.020
 X6G  plan-3  H6   0.020
 X6G  plan-3  H7   0.020
 X6G  plan-3  H11  0.020
 X6G  plan-3  NAQ  0.020
 X6G  plan-3  CAA  0.020

