# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:13:25 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5-(4-phenoxyphenyl)-7-(tetrahydro-2H-pyran-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cc(c3ccc(Oc4ccccc4)cc3)c12)C5CCOCC5
#
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
 VSF  VSF  5-(4-phenoxyphenyl)-7-(tetrahydro-2H-pyran-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  51  29  .  2021-08-24  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VSF
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
 VSF  NAK  N  NH2   0  -0.824   0.4460   3.0813  -0.0693
 VSF  C6   C  CR6   0   0.394  -0.8708   2.8158  -0.1149
 VSF  N1   N  N     0  -0.474  -1.7045   3.8570  -0.1835
 VSF  C2   C  CR16  0   0.041  -3.0153   3.6290  -0.2025
 VSF  N3   N  N     0  -0.463  -3.6371   2.4704  -0.1427
 VSF  C4   C  CR56  0   0.509  -2.7977   1.4343  -0.0897
 VSF  C5   C  CR56  0  -0.114  -1.3983   1.5070  -0.1072
 VSF  NAG  N  NR5   0  -0.521  -3.1588   0.1294   0.0031
 VSF  CAQ  C  CH1   0  -0.118  -4.5195  -0.3781   0.0394
 VSF  CAV  C  CH2   0  -0.455  -4.7902  -1.1757   1.3119
 VSF  CAU  C  CH2   0  -0.185  -6.2062  -1.7324   1.2728
 VSF  OAT  O  O2    0  -0.482  -6.4331  -2.5185   0.1240
 VSF  CAS  C  CH2   0  -0.185  -6.2524  -1.7835  -1.0662
 VSF  CAR  C  CH2   0  -0.454  -4.8393  -1.2313  -1.1851
 VSF  CAH  C  CR15  0  -0.051  -2.0192  -0.6328   0.0355
 VSF  CAI  C  CR5   0  -0.010  -0.9068   0.1612  -0.0339
 VSF  CAJ  C  CR6   0   0.019   0.4731  -0.3322  -0.0583
 VSF  CAL  C  CR16  0  -0.312   0.8880  -1.3295   0.8249
 VSF  CAM  C  CR16  0  -0.306   2.1817  -1.8278   0.7901
 VSF  CAN  C  CR6   0   0.306   3.0837  -1.3283  -0.1363
 VSF  CAO  C  CR16  0  -0.283   2.6949  -0.3398  -1.0310
 VSF  CAP  C  CR16  0  -0.343   1.3982   0.1449  -0.9913
 VSF  OBD  O  O2    0  -0.512   4.3411  -1.8696  -0.1847
 VSF  CBE  C  CR6   0   0.352   5.4275  -1.0619  -0.0070
 VSF  CBJ  C  CR16  0  -0.330   5.3825   0.1103   0.7392
 VSF  CBI  C  CR16  0  -0.246   6.5439   0.8539   0.9056
 VSF  CBH  C  CR16  0  -0.271   7.7419   0.4379   0.3416
 VSF  CBG  C  CR16  0  -0.247   7.7734  -0.7388  -0.3965
 VSF  CBF  C  CR16  0  -0.330   6.6213  -1.4891  -0.5776
 VSF  H1   H  HNH2  0   0.406   1.1017   2.3683   0.1991
 VSF  H2   H  HNH2  0   0.397   0.7328   4.0344   0.0793
 VSF  H3   H  HCR6  0   0.246  -3.6439   4.5116  -0.2647
 VSF  H4   H  HCH1  0   0.269  -5.1685   0.5012   0.0330
 VSF  H5   H  HCH2  0   0.238  -4.0740  -1.9977   1.3999
 VSF  H6   H  HCH2  0   0.253  -4.6744  -0.5403   2.1926
 VSF  H7   H  HCH2  0   0.243  -6.3874  -2.3698   2.1393
 VSF  H8   H  HCH2  0   0.203  -6.9261  -0.9017   1.3170
 VSF  H9   H  HCH2  0   0.243  -6.4682  -2.4580  -1.8958
 VSF  H10  H  HCH2  0   0.203  -6.9735  -0.9544  -1.1177
 VSF  H11  H  HCH2  0   0.252  -4.7578  -0.6366  -2.0977
 VSF  H12  H  HCH2  0   0.238  -4.1263  -2.0571  -1.2630
 VSF  H13  H  HCR5  0   0.300  -2.0736  -1.7093   0.0805
 VSF  H14  H  HCR6  0   0.256   0.1973  -1.7129   1.5653
 VSF  H15  H  HCR6  0   0.272   2.4893  -2.5976   1.4863
 VSF  H16  H  HCR6  0   0.279   3.3902   0.0421  -1.7680
 VSF  H17  H  HCR6  0   0.270   1.0983   0.8882  -1.7196
 VSF  H18  H  HCR6  0   0.276   4.4604   0.4471   1.1951
 VSF  H19  H  HCR6  0   0.262   6.5060   1.7651   1.4884
 VSF  H20  H  HCR6  0   0.256   8.6418   1.0226   0.4773
 VSF  H21  H  HCR6  0   0.261   8.7001  -1.0754  -0.8430
 VSF  H22  H  HCR6  0   0.268   6.6434  -2.4039  -1.1566

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
 VSF  CAV  CAU  single    1.522  0.020  1.522
 VSF  CAV  CAQ  single    1.526  0.020  1.526
 VSF  C2   N3   aromatic  1.316  0.020  1.316
 VSF  C2   N1   aromatic  1.331  0.020  1.331
 VSF  N3   C4   aromatic  1.335  0.020  1.335
 VSF  CAU  OAT  single    1.410  0.020  1.410
 VSF  N1   C6   aromatic  1.336  0.020  1.336
 VSF  OAT  CAS  single    1.410  0.020  1.410
 VSF  C4   NAG  aromatic  1.357  0.020  1.357
 VSF  C4   C5   aromatic  1.401  0.020  1.401
 VSF  CAQ  NAG  single    1.453  0.020  1.453
 VSF  CAQ  CAR  single    1.526  0.020  1.526
 VSF  C6   C5   aromatic  1.411  0.020  1.411
 VSF  C6   NAK  single    1.344  0.020  1.344
 VSF  NAG  CAH  aromatic  1.371  0.020  1.371
 VSF  C5   CAI  aromatic  1.435  0.020  1.435
 VSF  CAP  CAO  aromatic  1.385  0.020  1.385
 VSF  CAP  CAJ  aromatic  1.398  0.020  1.398
 VSF  CAH  CAI  aromatic  1.368  0.020  1.368
 VSF  CAI  CAJ  single    1.466  0.020  1.466
 VSF  CAS  CAR  single    1.522  0.020  1.522
 VSF  CAO  CAN  aromatic  1.389  0.020  1.389
 VSF  CAJ  CAL  aromatic  1.395  0.020  1.395
 VSF  CAN  OBD  single    1.370  0.020  1.370
 VSF  CAN  CAM  aromatic  1.386  0.020  1.386
 VSF  CAL  CAM  aromatic  1.387  0.020  1.387
 VSF  OBD  CBE  single    1.365  0.020  1.365
 VSF  CBE  CBJ  aromatic  1.390  0.020  1.390
 VSF  CBE  CBF  aromatic  1.390  0.020  1.390
 VSF  CBJ  CBI  aromatic  1.389  0.020  1.389
 VSF  CBF  CBG  aromatic  1.387  0.020  1.387
 VSF  CBI  CBH  aromatic  1.388  0.020  1.388
 VSF  CBG  CBH  aromatic  1.389  0.020  1.389
 VSF  NAK  H1   single    0.890  0.020  1.040
 VSF  NAK  H2   single    0.890  0.020  1.040
 VSF  C2   H3   single    0.930  0.020  1.080
 VSF  CAQ  H4   single    0.970  0.020  1.090
 VSF  CAV  H5   single    0.970  0.020  1.090
 VSF  CAV  H6   single    0.970  0.020  1.090
 VSF  CAU  H7   single    0.970  0.020  1.090
 VSF  CAU  H8   single    0.970  0.020  1.090
 VSF  CAS  H9   single    0.970  0.020  1.090
 VSF  CAS  H10  single    0.970  0.020  1.090
 VSF  CAR  H11  single    0.970  0.020  1.090
 VSF  CAR  H12  single    0.970  0.020  1.090
 VSF  CAH  H13  single    0.930  0.020  1.080
 VSF  CAL  H14  single    0.930  0.020  1.080
 VSF  CAM  H15  single    0.930  0.020  1.080
 VSF  CAO  H16  single    0.930  0.020  1.080
 VSF  CAP  H17  single    0.930  0.020  1.080
 VSF  CBJ  H18  single    0.930  0.020  1.080
 VSF  CBI  H19  single    0.930  0.020  1.080
 VSF  CBH  H20  single    0.930  0.020  1.080
 VSF  CBG  H21  single    0.930  0.020  1.080
 VSF  CBF  H22  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
 VSF  H2   NAK  H1   116.52  3.000
 VSF  H2   NAK  C6   118.11  3.000
 VSF  H1   NAK  C6   120.54  3.000
 VSF  C5   C6   N1   119.34  3.000
 VSF  C5   C6   NAK  123.31  3.000
 VSF  N1   C6   NAK  117.34  3.000
 VSF  C2   N1   C6   118.82  3.000
 VSF  H3   C2   N3   116.41  3.000
 VSF  H3   C2   N1   115.60  3.000
 VSF  N3   C2   N1   127.99  3.000
 VSF  C4   N3   C2   112.83  3.000
 VSF  NAG  C4   C5   108.45  3.000
 VSF  C5   C4   N3   125.97  3.000
 VSF  NAG  C4   N3   125.58  3.000
 VSF  CAI  C5   C4   107.02  3.000
 VSF  CAI  C5   C6   137.93  3.000
 VSF  C4   C5   C6   114.93  3.000
 VSF  CAH  NAG  CAQ  125.70  3.000
 VSF  CAH  NAG  C4   108.35  3.000
 VSF  CAQ  NAG  C4   125.94  3.000
 VSF  H4   CAQ  CAR  108.70  3.000
 VSF  H4   CAQ  CAV  108.67  3.000
 VSF  CAR  CAQ  CAV  109.86  3.000
 VSF  H4   CAQ  NAG  105.96  3.000
 VSF  CAR  CAQ  NAG  111.81  3.000
 VSF  CAV  CAQ  NAG  111.69  3.000
 VSF  H6   CAV  H5   107.63  3.000
 VSF  H6   CAV  CAU  109.40  3.000
 VSF  H5   CAV  CAU  109.66  3.000
 VSF  H6   CAV  CAQ  110.46  3.000
 VSF  H5   CAV  CAQ  110.11  3.000
 VSF  CAU  CAV  CAQ  109.56  3.000
 VSF  H8   CAU  H7   107.50  3.000
 VSF  H8   CAU  OAT  110.39  3.000
 VSF  H7   CAU  OAT  107.13  3.000
 VSF  H8   CAU  CAV  109.36  3.000
 VSF  H7   CAU  CAV  110.36  3.000
 VSF  OAT  CAU  CAV  111.99  3.000
 VSF  CAS  OAT  CAU  112.10  3.000
 VSF  H10  CAS  H9   107.50  3.000
 VSF  H10  CAS  CAR  109.37  3.000
 VSF  H9   CAS  CAR  110.40  3.000
 VSF  H10  CAS  OAT  110.38  3.000
 VSF  H9   CAS  OAT  107.11  3.000
 VSF  CAR  CAS  OAT  111.96  3.000
 VSF  H12  CAR  H11  107.63  3.000
 VSF  H12  CAR  CAS  109.69  3.000
 VSF  H11  CAR  CAS  109.40  3.000
 VSF  H12  CAR  CAQ  110.04  3.000
 VSF  H11  CAR  CAQ  110.51  3.000
 VSF  CAS  CAR  CAQ  109.55  3.000
 VSF  H13  CAH  CAI  128.46  3.000
 VSF  H13  CAH  NAG  120.91  3.000
 VSF  CAI  CAH  NAG  110.60  3.000
 VSF  CAJ  CAI  CAH  124.81  3.000
 VSF  CAJ  CAI  C5   129.60  3.000
 VSF  CAH  CAI  C5   105.57  3.000
 VSF  CAP  CAJ  CAL  118.01  3.000
 VSF  CAL  CAJ  CAI  120.66  3.000
 VSF  CAP  CAJ  CAI  121.29  3.000
 VSF  H14  CAL  CAM  119.01  3.000
 VSF  H14  CAL  CAJ  119.76  3.000
 VSF  CAM  CAL  CAJ  121.22  3.000
 VSF  H15  CAM  CAN  120.08  3.000
 VSF  H15  CAM  CAL  120.29  3.000
 VSF  CAN  CAM  CAL  119.63  3.000
 VSF  OBD  CAN  CAO  121.03  3.000
 VSF  OBD  CAN  CAM  118.59  3.000
 VSF  CAO  CAN  CAM  120.32  3.000
 VSF  H16  CAO  CAP  119.82  3.000
 VSF  H16  CAO  CAN  120.65  3.000
 VSF  CAP  CAO  CAN  119.52  3.000
 VSF  H17  CAP  CAO  118.70  3.000
 VSF  H17  CAP  CAJ  119.99  3.000
 VSF  CAO  CAP  CAJ  121.29  3.000
 VSF  CBE  OBD  CAN  119.48  3.000
 VSF  CBF  CBE  CBJ  120.47  3.000
 VSF  CBF  CBE  OBD  116.62  3.000
 VSF  CBJ  CBE  OBD  122.88  3.000
 VSF  H18  CBJ  CBI  119.69  3.000
 VSF  H18  CBJ  CBE  121.06  3.000
 VSF  CBI  CBJ  CBE  119.25  3.000
 VSF  H19  CBI  CBH  120.09  3.000
 VSF  H19  CBI  CBJ  119.07  3.000
 VSF  CBH  CBI  CBJ  120.84  3.000
 VSF  H20  CBH  CBG  120.37  3.000
 VSF  H20  CBH  CBI  120.34  3.000
 VSF  CBG  CBH  CBI  119.30  3.000
 VSF  H21  CBG  CBF  119.29  3.000
 VSF  H21  CBG  CBH  120.13  3.000
 VSF  CBF  CBG  CBH  120.58  3.000
 VSF  H22  CBF  CBG  120.66  3.000
 VSF  H22  CBF  CBE  119.77  3.000
 VSF  CBG  CBF  CBE  119.57  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
 VSF  CONST_01  N3   C2   N1   C6     0.00   0.0  0
 VSF  CONST_02  N3   C4   C5   C6     0.00   0.0  0
 VSF  CONST_03  NAG  C4   C5   C6   180.00   0.0  0
 VSF  CONST_04  CAH  CAI  C5   C6   180.00   0.0  0
 VSF  CONST_05  CAJ  CAI  C5   C6     0.00   0.0  0
 VSF  CONST_06  C4   N3   C2   N1     0.00   0.0  0
 VSF  CONST_07  C4   C5   C6   N1     0.00   0.0  0
 VSF  CONST_08  CAI  C5   C6   N1   180.00   0.0  0
 VSF  CONST_09  NAG  C4   N3   C2   180.00   0.0  0
 VSF  CONST_10  C5   C4   N3   C2     0.00   0.0  0
 VSF  CONST_11  C5   C6   N1   C2     0.00   0.0  0
 VSF  CONST_12  CAH  NAG  C4   N3   180.00   0.0  0
 VSF  CONST_13  CAI  C5   C4   N3   180.00   0.0  0
 VSF  CONST_14  CAI  CAH  NAG  C4     0.00   0.0  0
 VSF  CONST_15  CAH  CAI  C5   C4     0.00   0.0  0
 VSF  CONST_16  CAJ  CAI  C5   C4   180.00   0.0  0
 VSF  CONST_17  CAH  NAG  C4   C5     0.00   0.0  0
 VSF  CONST_18  NAG  CAH  CAI  C5     0.00   0.0  0
 VSF  CONST_21  CAI  C5   C4   NAG    0.00   0.0  0
 VSF  CONST_22  CAJ  CAI  CAH  NAG  180.00   0.0  0
 VSF  CONST_25  CAO  CAP  CAJ  CAI  180.00   0.0  0
 VSF  CONST_26  CAM  CAL  CAJ  CAI  180.00   0.0  0
 VSF  CONST_27  CAN  CAO  CAP  CAJ    0.00   0.0  0
 VSF  CONST_28  CAN  CAM  CAL  CAJ    0.00   0.0  0
 VSF  CONST_29  CAO  CAP  CAJ  CAL    0.00   0.0  0
 VSF  CONST_30  CAO  CAN  CAM  CAL    0.00   0.0  0
 VSF  CONST_31  CAP  CAO  CAN  CAM    0.00   0.0  0
 VSF  CONST_32  CAP  CAJ  CAL  CAM    0.00   0.0  0
 VSF  CONST_33  CBH  CBI  CBJ  CBE    0.00   0.0  0
 VSF  CONST_34  CBH  CBG  CBF  CBE    0.00   0.0  0
 VSF  CONST_35  CBG  CBF  CBE  CBJ    0.00   0.0  0
 VSF  CONST_36  CBG  CBH  CBI  CBJ    0.00   0.0  0
 VSF  CONST_37  CBF  CBE  CBJ  CBI    0.00   0.0  0
 VSF  CONST_38  CBF  CBG  CBH  CBI    0.00   0.0  0
 VSF  CONST_39  CAQ  NAG  C4   N3     0.00   0.0  0
 VSF  CONST_40  CAQ  NAG  C4   C5   180.00   0.0  0
 VSF  CONST_41  CAI  CAH  NAG  CAQ  180.00   0.0  0
 VSF  CONST_42  C2   N1   C6   NAK  180.00   0.0  0
 VSF  CONST_43  C4   C5   C6   NAK  180.00   0.0  0
 VSF  CONST_44  CAI  C5   C6   NAK    0.00   0.0  0
 VSF  CONST_45  OBD  CAN  CAM  CAL  180.00   0.0  0
 VSF  CONST_46  OBD  CAN  CAO  CAP  180.00   0.0  0
 VSF  CONST_47  CBI  CBJ  CBE  OBD  180.00   0.0  0
 VSF  CONST_48  CBG  CBF  CBE  OBD  180.00   0.0  0
 VSF  CONST_49  H3   C2   N1   C6   180.00   0.0  0
 VSF  CONST_50  H13  CAH  NAG  C4   180.00   0.0  0
 VSF  CONST_51  H17  CAP  CAJ  CAI    0.00   0.0  0
 VSF  CONST_52  H14  CAL  CAJ  CAI    0.00   0.0  0
 VSF  CONST_53  H16  CAO  CAP  CAJ  180.00   0.0  0
 VSF  CONST_54  H15  CAM  CAL  CAJ  180.00   0.0  0
 VSF  CONST_55  H19  CBI  CBJ  CBE  180.00   0.0  0
 VSF  CONST_56  H21  CBG  CBF  CBE  180.00   0.0  0
 VSF  CONST_57  H22  CBF  CBE  CBJ  180.00   0.0  0
 VSF  CONST_58  H20  CBH  CBI  CBJ  180.00   0.0  0
 VSF  CONST_59  H18  CBJ  CBI  CBH  180.00   0.0  0
 VSF  CONST_60  H1   NAK  C6   N1   180.00   0.0  0
 VSF  CONST_61  H2   NAK  C6   N1     0.00   0.0  0
 VSF  Var_01    OAT  CAU  CAV  CAQ   56.31  30.0  1
 VSF  Var_02    OAT  CAS  CAR  CAQ  -56.37  30.0  1
 VSF  Var_03    CAR  CAS  OAT  CAU   60.08  30.0  1
 VSF  Var_04    CBJ  CBE  OBD  CAN   27.43  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
 VSF  chir_01  CAQ  CAV  NAG  CAR  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
 VSF  plan-1  CAI  0.020
 VSF  plan-1  CAJ  0.020
 VSF  plan-1  CAL  0.020
 VSF  plan-1  CAM  0.020
 VSF  plan-1  CAN  0.020
 VSF  plan-1  CAO  0.020
 VSF  plan-1  CAP  0.020
 VSF  plan-1  OBD  0.020
 VSF  plan-1  H14  0.020
 VSF  plan-1  H15  0.020
 VSF  plan-1  H16  0.020
 VSF  plan-1  H17  0.020
 VSF  plan-2  OBD  0.020
 VSF  plan-2  CBE  0.020
 VSF  plan-2  CBJ  0.020
 VSF  plan-2  CBI  0.020
 VSF  plan-2  CBH  0.020
 VSF  plan-2  CBG  0.020
 VSF  plan-2  CBF  0.020
 VSF  plan-2  H18  0.020
 VSF  plan-2  H19  0.020
 VSF  plan-2  H20  0.020
 VSF  plan-2  H21  0.020
 VSF  plan-2  H22  0.020
 VSF  plan-3  NAK  0.020
 VSF  plan-3  C6   0.020
 VSF  plan-3  N1   0.020
 VSF  plan-3  C2   0.020
 VSF  plan-3  N3   0.020
 VSF  plan-3  C4   0.020
 VSF  plan-3  C5   0.020
 VSF  plan-3  NAG  0.020
 VSF  plan-3  CAQ  0.020
 VSF  plan-3  CAH  0.020
 VSF  plan-3  CAI  0.020
 VSF  plan-3  CAJ  0.020
 VSF  plan-3  H3   0.020
 VSF  plan-3  H13  0.020
 VSF  plan-4  NAK  0.020
 VSF  plan-4  C6   0.020
 VSF  plan-4  H1   0.020
 VSF  plan-4  H2   0.020

