# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 12:14:54 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-(hydroxymethyl)-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](n1nc(CO)c2C(=O)NC(=O)Nc12)c3ccc(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
 FKJ  FKJ  3-(hydroxymethyl)-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione  ligand  38  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FKJ
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
 FKJ  C2   C  CR5   0   0.300   2.4573   1.7857   0.4040
 FKJ  C3   C  CH1   0  -0.222   0.1671  -0.3623   2.0140
 FKJ  C5   C  CR16  0  -0.278  -1.6412   0.7341   0.6307
 FKJ  C7   C  CR6   0  -0.203  -3.4644  -0.5431  -0.2771
 FKJ  C9   C  CR16  0  -0.307  -1.7598  -1.6292   1.0148
 FKJ  C10  C  CT    0   1.052  -4.7175  -0.5750  -1.0933
 FKJ  C11  C  CH3   0  -0.648  -0.0245   0.3625   3.3367
 FKJ  C12  C  CH2   0  -0.238   3.0415   3.1426   0.2154
 FKJ  C13  C  CR6   0   0.530   3.6697   0.2287  -1.3526
 FKJ  O2   O  O     0  -0.437   4.4201   0.9575  -1.9674
 FKJ  C1   C  CR56  0  -0.369   2.7885   0.5928  -0.2806
 FKJ  N2   N  NR16  0  -0.736   3.5806  -1.1292  -1.6630
 FKJ  C14  C  CR6   0   0.678   2.7776  -2.0992  -1.1054
 FKJ  O1   O  O     0  -0.464   2.7944  -3.2527  -1.4740
 FKJ  N3   N  NR16  0  -0.752   1.9483  -1.6617  -0.0983
 FKJ  C    C  CR56  0   0.782   1.9713  -0.3606   0.2867
 FKJ  N1   N  NR5   0  -0.356   1.2434   0.2347   1.2336
 FKJ  N    N  N     0  -0.290   1.5328   1.5534   1.3018
 FKJ  O    O  OH1   0  -0.666   4.3917   3.1061   0.6173
 FKJ  C4   C  CR6   0   0.151  -1.1047  -0.4204   1.1974
 FKJ  C8   C  CR16  0  -0.264  -2.9376  -1.6967   0.2815
 FKJ  F2   F  F     0  -0.314  -4.4745  -0.2854  -2.3806
 FKJ  F1   F  F     0  -0.301  -5.3196  -1.7670  -1.0693
 FKJ  F    F  F     0  -0.313  -5.6125   0.3263  -0.6649
 FKJ  C6   C  CR16  0  -0.248  -2.8112   0.6753  -0.1023
 FKJ  H1   H  HCH1  0   0.290   0.4841  -1.3840   2.2399
 FKJ  H2   H  HCR6  0   0.269  -1.1460   1.6885   0.7581
 FKJ  H3   H  HCR6  0   0.272  -1.3551  -2.5366   1.4467
 FKJ  H4   H  HCH3  0   0.248  -0.3528   1.3902   3.1958
 FKJ  H5   H  HCH3  0   0.256  -0.7842  -0.1631   3.9127
 FKJ  H6   H  HCH3  0   0.255   0.8989   0.3654   3.9144
 FKJ  H7   H  HCH2  0   0.224   2.9415   3.4255  -0.8376
 FKJ  H8   H  HCH2  0   0.219   2.4556   3.8606   0.8008
 FKJ  H9   H  HNR6  0   0.430   4.1757  -1.4563  -2.4140
 FKJ  H10  H  HNR6  0   0.436   1.3431  -2.3459   0.3327
 FKJ  H11  H  HOH1  0   0.460   4.8458   3.8433   0.2000
 FKJ  H12  H  HCR6  0   0.275  -3.4225  -2.6547   0.1554
 FKJ  H13  H  HCR6  0   0.279  -3.2085   1.5856  -0.5328

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
 FKJ  O1   C14  double    1.211  0.020  1.211
 FKJ  C14  N2   single    1.377  0.020  1.377
 FKJ  C14  N3   single    1.376  0.020  1.376
 FKJ  N2   C13  single    1.396  0.020  1.396
 FKJ  N3   C    single    1.357  0.020  1.357
 FKJ  C13  O2   double    1.213  0.020  1.213
 FKJ  C13  C1   single    1.435  0.020  1.435
 FKJ  C    C1   aromatic  1.378  0.020  1.378
 FKJ  C    N1   aromatic  1.335  0.020  1.335
 FKJ  C1   C2   aromatic  1.415  0.020  1.415
 FKJ  C9   C8   aromatic  1.389  0.020  1.389
 FKJ  C9   C4   aromatic  1.387  0.020  1.387
 FKJ  N1   C3   single    1.457  0.020  1.457
 FKJ  N1   N    aromatic  1.352  0.020  1.352
 FKJ  C8   C7   aromatic  1.386  0.020  1.386
 FKJ  C3   C4   single    1.513  0.020  1.513
 FKJ  C3   C11  single    1.520  0.020  1.520
 FKJ  C2   N    aromatic  1.309  0.020  1.309
 FKJ  C2   C12  single    1.489  0.020  1.489
 FKJ  C4   C5   aromatic  1.394  0.020  1.394
 FKJ  O    C12  single    1.409  0.020  1.409
 FKJ  F    C10  single    1.340  0.020  1.340
 FKJ  C7   C10  single    1.496  0.020  1.496
 FKJ  C7   C6   aromatic  1.393  0.020  1.393
 FKJ  F1   C10  single    1.336  0.020  1.336
 FKJ  C10  F2   single    1.342  0.020  1.342
 FKJ  C5   C6   aromatic  1.382  0.020  1.382
 FKJ  C3   H1   single    0.970  0.020  1.090
 FKJ  C5   H2   single    0.930  0.020  1.080
 FKJ  C9   H3   single    0.930  0.020  1.080
 FKJ  C11  H4   single    0.970  0.020  1.090
 FKJ  C11  H5   single    0.970  0.020  1.090
 FKJ  C11  H6   single    0.970  0.020  1.090
 FKJ  C12  H7   single    0.970  0.020  1.090
 FKJ  C12  H8   single    0.970  0.020  1.090
 FKJ  N2   H9   single    0.860  0.020  1.020
 FKJ  N3   H10  single    0.860  0.020  1.020
 FKJ  O    H11  single    0.850  0.020  0.980
 FKJ  C8   H12  single    0.930  0.020  1.080
 FKJ  C6   H13  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
 FKJ  N    C2   C1   110.34  3.000
 FKJ  N    C2   C12  121.69  3.000
 FKJ  C1   C2   C12  127.96  3.000
 FKJ  H1   C3   C4   108.63  3.000
 FKJ  H1   C3   N1   106.22  3.000
 FKJ  C4   C3   N1   110.34  3.000
 FKJ  H1   C3   C11  107.59  3.000
 FKJ  C4   C3   C11  112.46  3.000
 FKJ  N1   C3   C11  111.32  3.000
 FKJ  H2   C5   C6   119.16  3.000
 FKJ  H2   C5   C4   120.42  3.000
 FKJ  C6   C5   C4   120.42  3.000
 FKJ  C6   C7   C8   119.94  3.000
 FKJ  C6   C7   C10  118.67  3.000
 FKJ  C8   C7   C10  121.38  3.000
 FKJ  H3   C9   C8   119.11  3.000
 FKJ  H3   C9   C4   120.07  3.000
 FKJ  C8   C9   C4   120.82  3.000
 FKJ  F    C10  F1   107.06  3.000
 FKJ  F1   C10  F2   106.95  3.000
 FKJ  F    C10  F2   106.40  3.000
 FKJ  F2   C10  C7   111.54  3.000
 FKJ  F1   C10  C7   112.76  3.000
 FKJ  F    C10  C7   111.75  3.000
 FKJ  H6   C11  H5   108.20  3.000
 FKJ  H6   C11  H4   108.78  3.000
 FKJ  H5   C11  H4   108.30  3.000
 FKJ  H6   C11  C3   110.85  3.000
 FKJ  H5   C11  C3   108.55  3.000
 FKJ  H4   C11  C3   112.06  3.000
 FKJ  H8   C12  H7   107.19  3.000
 FKJ  H8   C12  O    112.14  3.000
 FKJ  H7   C12  O    111.62  3.000
 FKJ  H8   C12  C2   108.64  3.000
 FKJ  H7   C12  C2   108.74  3.000
 FKJ  O    C12  C2   108.43  3.000
 FKJ  N2   C13  C1   111.96  3.000
 FKJ  C1   C13  O2   127.30  3.000
 FKJ  N2   C13  O2   120.74  3.000
 FKJ  C    C1   C13  119.75  3.000
 FKJ  C    C1   C2   104.20  3.000
 FKJ  C13  C1   C2   136.01  3.000
 FKJ  H9   N2   C14  114.55  3.000
 FKJ  H9   N2   C13  116.21  3.000
 FKJ  C14  N2   C13  129.23  3.000
 FKJ  N3   C14  O1   122.27  3.000
 FKJ  N3   C14  N2   115.08  3.000
 FKJ  O1   C14  N2   122.65  3.000
 FKJ  H10  N3   C    122.59  3.000
 FKJ  H10  N3   C14  117.26  3.000
 FKJ  C    N3   C14  120.15  3.000
 FKJ  N1   C    N3   128.30  3.000
 FKJ  N1   C    C1   107.88  3.000
 FKJ  N3   C    C1   123.83  3.000
 FKJ  N    N1   C    110.74  3.000
 FKJ  N    N1   C3   122.06  3.000
 FKJ  C    N1   C3   126.87  3.000
 FKJ  N1   N    C2   106.84  3.000
 FKJ  H11  O    C12  108.00  3.000
 FKJ  C9   C4   C5   119.12  3.000
 FKJ  C5   C4   C3   120.76  3.000
 FKJ  C9   C4   C3   120.11  3.000
 FKJ  H12  C8   C9   119.01  3.000
 FKJ  H12  C8   C7   121.34  3.000
 FKJ  C9   C8   C7   119.65  3.000
 FKJ  H13  C6   C7   120.89  3.000
 FKJ  H13  C6   C5   119.07  3.000
 FKJ  C7   C6   C5   120.04  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
 FKJ  CONST_01  N1   C    C1   C2     0.00   0.0  0
 FKJ  CONST_02  C    N1   N    C2     0.00   0.0  0
 FKJ  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 FKJ  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 FKJ  CONST_05  C4   C9   C8   C7     0.00   0.0  0
 FKJ  CONST_06  C4   C5   C6   C7     0.00   0.0  0
 FKJ  CONST_07  C6   C7   C8   C9     0.00   0.0  0
 FKJ  CONST_08  C6   C5   C4   C9     0.00   0.0  0
 FKJ  CONST_09  N    N1   C    C1     0.00   0.0  0
 FKJ  CONST_10  N1   N    C2   C1     0.00   0.0  0
 FKJ  CONST_11  N    C2   C1   C      0.00   0.0  0
 FKJ  CONST_12  N3   C14  N2   C13    0.00   0.0  0
 FKJ  CONST_13  C14  N2   C13  C1     0.00   0.0  0
 FKJ  CONST_14  C    N3   C14  N2     0.00   0.0  0
 FKJ  CONST_15  C3   N1   N    C2   180.00   0.0  0
 FKJ  CONST_16  N3   C    N1   C3     0.00   0.0  0
 FKJ  CONST_17  C1   C    N1   C3   180.00   0.0  0
 FKJ  CONST_18  C8   C9   C4   C3   180.00   0.0  0
 FKJ  CONST_19  C6   C5   C4   C3   180.00   0.0  0
 FKJ  CONST_20  C10  C7   C6   C5   180.00   0.0  0
 FKJ  CONST_21  C10  C7   C8   C9   180.00   0.0  0
 FKJ  CONST_22  C13  C1   C2   C12    0.00   0.0  0
 FKJ  CONST_23  C    C1   C2   C12  180.00   0.0  0
 FKJ  CONST_24  N1   N    C2   C12  180.00   0.0  0
 FKJ  CONST_25  O1   C14  N2   C13  180.00   0.0  0
 FKJ  CONST_26  C14  N2   C13  O2   180.00   0.0  0
 FKJ  CONST_27  C    N3   C14  O1   180.00   0.0  0
 FKJ  CONST_28  H3   C9   C4   C5   180.00   0.0  0
 FKJ  CONST_29  H2   C5   C6   C7   180.00   0.0  0
 FKJ  CONST_30  H12  C8   C9   C4   180.00   0.0  0
 FKJ  CONST_31  H13  C6   C5   C4   180.00   0.0  0
 FKJ  CONST_32  H9   N2   C13  C1   180.00   0.0  0
 FKJ  CONST_33  H10  N3   C14  N2   180.00   0.0  0
 FKJ  Var_01    O    C12  C2   C1   -66.14  30.0  2
 FKJ  Var_02    F    C10  C7   C8   128.33  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
 FKJ  chir_01  C3  N1  C4  C11  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
 FKJ  plan-1  C3   0.020
 FKJ  plan-1  C5   0.020
 FKJ  plan-1  C7   0.020
 FKJ  plan-1  C9   0.020
 FKJ  plan-1  C10  0.020
 FKJ  plan-1  C4   0.020
 FKJ  plan-1  C8   0.020
 FKJ  plan-1  C6   0.020
 FKJ  plan-1  H2   0.020
 FKJ  plan-1  H3   0.020
 FKJ  plan-1  H12  0.020
 FKJ  plan-1  H13  0.020
 FKJ  plan-2  C2   0.020
 FKJ  plan-2  C3   0.020
 FKJ  plan-2  C12  0.020
 FKJ  plan-2  C13  0.020
 FKJ  plan-2  O2   0.020
 FKJ  plan-2  C1   0.020
 FKJ  plan-2  N2   0.020
 FKJ  plan-2  C14  0.020
 FKJ  plan-2  O1   0.020
 FKJ  plan-2  N3   0.020
 FKJ  plan-2  C    0.020
 FKJ  plan-2  N1   0.020
 FKJ  plan-2  N    0.020
 FKJ  plan-2  H9   0.020
 FKJ  plan-2  H10  0.020

