# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 18:28:46 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-(4-chlorophenyl)-7-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)c2cn(c3ccccc3)c4N=CNC(=O)c24
#
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
 BKS  BKS  5-(4-chlorophenyl)-7-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one  ligand  35  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BKS
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
 BKS  C    C   CR16  0  -0.253  -5.5870   2.2541  -0.0126
 BKS  N    N   NR5   0  -0.612  -1.9120   0.2449  -0.0372
 BKS  O    O   O     0  -0.464   1.2616  -3.1112  -0.0090
 BKS  CL   CL  CL    0  -0.132   6.1116   1.4292   0.0627
 BKS  C1   C   CR16  0  -0.253  -4.5719   2.6412   0.8516
 BKS  N1   N   N     0  -0.443  -2.6946  -2.0186   0.0662
 BKS  C2   C   CR16  0  -0.290  -3.3600   1.9662   0.8534
 BKS  N2   N   NR16  0  -0.660  -0.9592  -3.5823   0.0768
 BKS  C3   C   CR6   0   0.326  -3.1601   0.9111  -0.0288
 BKS  C4   C   CR16  0  -0.277  -4.1667   0.5241  -0.9052
 BKS  C5   C   CR16  0  -0.255  -5.3807   1.1948  -0.8868
 BKS  C6   C   CR15  0  -0.065  -0.6874   0.8688  -0.0523
 BKS  C7   C   CR5   0   0.009   0.3160  -0.0610  -0.0103
 BKS  C8   C   CR56  0  -0.204  -0.3367  -1.3334   0.0376
 BKS  C9   C   CR56  0   0.496  -1.7086  -1.0985   0.0203
 BKS  C10  C   CR16  0   0.157  -2.2645  -3.2346   0.0963
 BKS  C11  C   CR6   0   0.491   0.1158  -2.6935   0.0324
 BKS  C12  C   CR6   0   0.058   1.7443   0.2657  -0.0098
 BKS  C13  C   CR16  0  -0.328   2.2213   1.3144  -0.7982
 BKS  C14  C   CR16  0  -0.196   3.5577   1.6811  -0.7791
 BKS  C15  C   CR6   0  -0.057   4.4361   0.9841   0.0344
 BKS  C16  C   CR16  0  -0.199   3.9934  -0.0649   0.8254
 BKS  C17  C   CR16  0  -0.309   2.6538  -0.4175   0.7989
 BKS  H    H   HCR6  0   0.263  -6.5340   2.7773  -0.0068
 BKS  H1   H   HCR6  0   0.266  -4.7225   3.4645   1.5370
 BKS  H2   H   HCR6  0   0.278  -2.5778   2.2549   1.5439
 BKS  HN2  H   HNR6  0   0.432  -0.7348  -4.5690   0.0850
 BKS  H4   H   HCR6  0   0.273  -4.0051  -0.2860  -1.6025
 BKS  H5   H   HCR6  0   0.266  -6.1644   0.8927  -1.5688
 BKS  H6   H   HCR5  0   0.306  -0.6218   1.9445  -0.0917
 BKS  H10  H   HCR6  0   0.301  -2.9668  -4.0564   0.1375
 BKS  H13  H   HCR6  0   0.261   1.5435   1.8481  -1.4522
 BKS  H14  H   HCR6  0   0.280   3.9075   2.4953  -1.3993
 BKS  H16  H   HCR6  0   0.279   4.6817  -0.5990   1.4663
 BKS  H17  H   HCR6  0   0.256   2.3162  -1.2283   1.4278

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
 BKS  C    C1   aromatic  1.388  0.020  1.388
 BKS  C    C5   aromatic  1.389  0.020  1.389
 BKS  N    C3   single    1.415  0.020  1.415
 BKS  N    C6   aromatic  1.374  0.020  1.374
 BKS  N    C9   aromatic  1.360  0.020  1.360
 BKS  O    C11  double    1.220  0.020  1.220
 BKS  CL   C15  single    1.734  0.020  1.734
 BKS  C1   C2   aromatic  1.387  0.020  1.387
 BKS  N1   C9   single    1.349  0.020  1.349
 BKS  N1   C10  double    1.290  0.020  1.290
 BKS  C2   C3   aromatic  1.390  0.020  1.390
 BKS  N2   C10  single    1.351  0.020  1.351
 BKS  N2   C11  single    1.396  0.020  1.396
 BKS  C3   C4   aromatic  1.390  0.020  1.390
 BKS  C4   C5   aromatic  1.387  0.020  1.387
 BKS  C6   C7   aromatic  1.369  0.020  1.369
 BKS  C7   C8   aromatic  1.431  0.020  1.431
 BKS  C7   C12  single    1.465  0.020  1.465
 BKS  C8   C9   aromatic  1.392  0.020  1.392
 BKS  C8   C11  single    1.433  0.020  1.433
 BKS  C12  C13  aromatic  1.396  0.020  1.396
 BKS  C12  C17  aromatic  1.396  0.020  1.396
 BKS  C13  C14  aromatic  1.386  0.020  1.386
 BKS  C14  C15  aromatic  1.385  0.020  1.385
 BKS  C15  C16  aromatic  1.386  0.020  1.386
 BKS  C16  C17  aromatic  1.385  0.020  1.385
 BKS  C    H    single    0.930  0.020  1.080
 BKS  C1   H1   single    0.930  0.020  1.080
 BKS  C2   H2   single    0.930  0.020  1.080
 BKS  N2   HN2  single    0.860  0.020  1.020
 BKS  C4   H4   single    0.930  0.020  1.080
 BKS  C5   H5   single    0.930  0.020  1.080
 BKS  C6   H6   single    0.930  0.020  1.080
 BKS  C10  H10  single    0.930  0.020  1.080
 BKS  C13  H13  single    0.930  0.020  1.080
 BKS  C14  H14  single    0.930  0.020  1.080
 BKS  C16  H16  single    0.930  0.020  1.080
 BKS  C17  H17  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
 BKS  H    C    C5   120.15  3.000
 BKS  H    C    C1   120.12  3.000
 BKS  C5   C    C1   119.73  3.000
 BKS  C9   N    C6   108.40  3.000
 BKS  C9   N    C3   126.65  3.000
 BKS  C6   N    C3   124.91  3.000
 BKS  H1   C1   C2   119.41  3.000
 BKS  H1   C1   C    120.32  3.000
 BKS  C2   C1   C    120.26  3.000
 BKS  C10  N1   C9   113.57  3.000
 BKS  H2   C2   C3   120.23  3.000
 BKS  H2   C2   C1   120.15  3.000
 BKS  C3   C2   C1   119.62  3.000
 BKS  HN2  N2   C11  116.78  3.000
 BKS  HN2  N2   C10  117.72  3.000
 BKS  C11  N2   C10  125.51  3.000
 BKS  C4   C3   C2   120.50  3.000
 BKS  C4   C3   N    120.27  3.000
 BKS  C2   C3   N    119.22  3.000
 BKS  H4   C4   C5   120.12  3.000
 BKS  H4   C4   C3   120.48  3.000
 BKS  C5   C4   C3   119.40  3.000
 BKS  H5   C5   C4   119.38  3.000
 BKS  H5   C5   C    120.14  3.000
 BKS  C4   C5   C    120.48  3.000
 BKS  H6   C6   C7   129.35  3.000
 BKS  H6   C6   N    120.49  3.000
 BKS  C7   C6   N    110.15  3.000
 BKS  C12  C7   C8   130.01  3.000
 BKS  C12  C7   C6   124.28  3.000
 BKS  C8   C7   C6   105.71  3.000
 BKS  C11  C8   C9   118.11  3.000
 BKS  C11  C8   C7   134.40  3.000
 BKS  C9   C8   C7   107.40  3.000
 BKS  C8   C9   N1   127.20  3.000
 BKS  C8   C9   N    108.34  3.000
 BKS  N1   C9   N    124.45  3.000
 BKS  H10  C10  N2   115.62  3.000
 BKS  H10  C10  N1   120.03  3.000
 BKS  N2   C10  N1   124.36  3.000
 BKS  C8   C11  N2   111.17  3.000
 BKS  C8   C11  O    128.41  3.000
 BKS  N2   C11  O    120.42  3.000
 BKS  C17  C12  C13  118.18  3.000
 BKS  C17  C12  C7   121.75  3.000
 BKS  C13  C12  C7   120.02  3.000
 BKS  H13  C13  C14  118.79  3.000
 BKS  H13  C13  C12  119.84  3.000
 BKS  C14  C13  C12  121.36  3.000
 BKS  H14  C14  C15  120.69  3.000
 BKS  H14  C14  C13  120.21  3.000
 BKS  C15  C14  C13  119.10  3.000
 BKS  C16  C15  C14  120.88  3.000
 BKS  C16  C15  CL   119.57  3.000
 BKS  C14  C15  CL   119.55  3.000
 BKS  H16  C16  C17  120.07  3.000
 BKS  H16  C16  C15  120.57  3.000
 BKS  C17  C16  C15  119.37  3.000
 BKS  H17  C17  C16  118.82  3.000
 BKS  H17  C17  C12  120.07  3.000
 BKS  C16  C17  C12  121.10  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
 BKS  CONST_01  C3   C2   C1   C      0.00  0.0  0
 BKS  CONST_02  C3   C4   C5   C      0.00  0.0  0
 BKS  CONST_03  C1   C2   C3   N    180.00  0.0  0
 BKS  CONST_04  C5   C4   C3   N    180.00  0.0  0
 BKS  CONST_05  C8   C7   C6   N      0.00  0.0  0
 BKS  CONST_06  C12  C7   C6   N    180.00  0.0  0
 BKS  CONST_07  C7   C8   C9   N      0.00  0.0  0
 BKS  CONST_08  C4   C5   C    C1     0.00  0.0  0
 BKS  CONST_09  C4   C3   C2   C1     0.00  0.0  0
 BKS  CONST_10  C5   C    C1   C2     0.00  0.0  0
 BKS  CONST_13  C5   C4   C3   C2     0.00  0.0  0
 BKS  CONST_14  C7   C6   N    C3   180.00  0.0  0
 BKS  CONST_15  C8   C9   N    C3   180.00  0.0  0
 BKS  CONST_18  C8   C9   N    C6     0.00  0.0  0
 BKS  CONST_19  C9   C8   C7   C6     0.00  0.0  0
 BKS  CONST_22  C9   N    C6   C7     0.00  0.0  0
 BKS  CONST_23  C14  C13  C12  C7   180.00  0.0  0
 BKS  CONST_24  C16  C17  C12  C7   180.00  0.0  0
 BKS  CONST_27  C12  C7   C8   C9   180.00  0.0  0
 BKS  CONST_28  C15  C14  C13  C12    0.00  0.0  0
 BKS  CONST_29  C15  C16  C17  C12    0.00  0.0  0
 BKS  CONST_30  C16  C17  C12  C13    0.00  0.0  0
 BKS  CONST_31  C16  C15  C14  C13    0.00  0.0  0
 BKS  CONST_32  C17  C12  C13  C14    0.00  0.0  0
 BKS  CONST_33  C17  C16  C15  C14    0.00  0.0  0
 BKS  CONST_34  C3   N    C9   N1     0.00  0.0  0
 BKS  CONST_35  C12  C7   C8   C11    0.00  0.0  0
 BKS  CONST_36  C11  N2   C10  N1     0.00  0.0  0
 BKS  CONST_37  C9   N1   C10  N2     0.00  0.0  0
 BKS  CONST_38  C10  N2   C11  C8     0.00  0.0  0
 BKS  CONST_39  C13  C14  C15  CL   180.00  0.0  0
 BKS  CONST_40  C17  C16  C15  CL   180.00  0.0  0
 BKS  CONST_41  C10  N2   C11  O    180.00  0.0  0
 BKS  CONST_42  H2   C2   C1   C    180.00  0.0  0
 BKS  CONST_43  H4   C4   C5   C    180.00  0.0  0
 BKS  CONST_44  H5   C5   C    C1   180.00  0.0  0
 BKS  CONST_45  H    C    C1   C2   180.00  0.0  0
 BKS  CONST_46  H6   C6   N    C3     0.00  0.0  0
 BKS  CONST_47  H1   C1   C2   C3   180.00  0.0  0
 BKS  CONST_48  H13  C13  C12  C7     0.00  0.0  0
 BKS  CONST_49  H17  C17  C12  C7     0.00  0.0  0
 BKS  CONST_50  H14  C14  C13  C12  180.00  0.0  0
 BKS  CONST_51  H16  C16  C17  C12  180.00  0.0  0
 BKS  CONST_52  HN2  N2   C10  N1   180.00  0.0  0
 BKS  CONST_53  H10  C10  N1   C9   180.00  0.0  0

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
 BKS  plan-1  C    0.020
 BKS  plan-1  N    0.020
 BKS  plan-1  C1   0.020
 BKS  plan-1  C2   0.020
 BKS  plan-1  C3   0.020
 BKS  plan-1  C4   0.020
 BKS  plan-1  C5   0.020
 BKS  plan-1  H    0.020
 BKS  plan-1  H1   0.020
 BKS  plan-1  H2   0.020
 BKS  plan-1  H4   0.020
 BKS  plan-1  H5   0.020
 BKS  plan-2  CL   0.020
 BKS  plan-2  C7   0.020
 BKS  plan-2  C12  0.020
 BKS  plan-2  C13  0.020
 BKS  plan-2  C14  0.020
 BKS  plan-2  C15  0.020
 BKS  plan-2  C16  0.020
 BKS  plan-2  C17  0.020
 BKS  plan-2  H13  0.020
 BKS  plan-2  H14  0.020
 BKS  plan-2  H16  0.020
 BKS  plan-2  H17  0.020
 BKS  plan-3  N    0.020
 BKS  plan-3  O    0.020
 BKS  plan-3  N1   0.020
 BKS  plan-3  N2   0.020
 BKS  plan-3  C3   0.020
 BKS  plan-3  C6   0.020
 BKS  plan-3  C7   0.020
 BKS  plan-3  C8   0.020
 BKS  plan-3  C9   0.020
 BKS  plan-3  C10  0.020
 BKS  plan-3  C11  0.020
 BKS  plan-3  C12  0.020
 BKS  plan-3  HN2  0.020
 BKS  plan-3  H6   0.020
 BKS  plan-3  H10  0.020

