# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:27:58 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(propan-2-yl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1ncc2C(=O)NC(=Nc12)[C@@H]3CN(C[C@H]3C)Cc4ccccc4
#
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
 JAR  JAR  6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(propan-2-yl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  51  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JAR
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
 JAR  C1    C  CH3   0  -0.648  -2.5585  -3.6634   0.3857
 JAR  C2    C  CH1   0  -0.123  -1.6918  -2.6859  -0.3929
 JAR  C3    C  CH3   0  -0.657  -1.0936  -3.3033  -1.6487
 JAR  N4    N  NR5   0  -0.368  -2.4467  -1.4852  -0.7250
 JAR  N5    N  N     0  -0.258  -3.4966  -1.5358  -1.5598
 JAR  C6    C  CR15  0  -0.075  -3.9429  -0.3083  -1.6853
 JAR  C7    C  CR56  0  -0.341  -3.1661   0.5783  -0.9143
 JAR  C8    C  CR6   0   0.510  -3.1401   1.9823  -0.6507
 JAR  O9    O  O     0  -0.462  -3.8874   2.8448  -1.0781
 JAR  N10   N  NR16  0  -0.717  -2.0925   2.3001   0.2160
 JAR  C11   C  CR6   0   0.561  -1.1993   1.4249   0.7610
 JAR  N12   N  N     0  -0.443  -1.2306   0.1522   0.5326
 JAR  C13   C  CR56  0   0.609  -2.2120  -0.2324  -0.3092
 JAR  C14   C  CR15  0  -0.402  -0.1276   2.0313   1.6172
 JAR  C16   C  CH2   0  -0.263   1.0644   2.4249   0.7336
 JAR  N17   N  NR5   0  -0.415   1.7269   1.1575   0.5594
 JAR  C18   C  CH2   0  -0.311   2.9708   1.1739  -0.1570
 JAR  C19   C  CR6   0   0.082   3.3787  -0.2033  -0.6227
 JAR  C20   C  CR16  0  -0.300   2.4217  -1.1640  -0.9446
 JAR  C21   C  CR16  0  -0.244   2.8047  -2.4146  -1.4099
 JAR  C22   C  CR16  0  -0.270   4.1507  -2.7240  -1.5637
 JAR  C23   C  CR16  0  -0.243   5.1105  -1.7736  -1.2428
 JAR  C24   C  CR16  0  -0.311   4.7246  -0.5248  -0.7719
 JAR  C25   C  CH2   0  -0.242   1.7644   0.5254   1.8645
 JAR  C26   C  CR15  0  -0.245   0.5056   1.0267   2.6005
 JAR  C28   C  CH3   0  -0.672   0.8370   1.6848   3.9331
 JAR  H1    H  HCH3  0   0.240  -2.9308  -3.2123   1.3054
 JAR  H1A   H  HCH3  0   0.234  -3.4117  -3.9923  -0.2079
 JAR  H1B   H  HCH3  0   0.238  -1.9747  -4.5435   0.6541
 JAR  H2    H  HCH1  0   0.266  -0.8813  -2.3368   0.2493
 JAR  H3    H  HCH3  0   0.239  -1.8691  -3.6825  -2.3141
 JAR  H3A   H  HCH3  0   0.238  -0.4927  -2.5777  -2.1986
 JAR  H3B   H  HCH3  0   0.240  -0.4482  -4.1378  -1.3745
 JAR  H6    H  HCR5  0   0.275  -4.7943  -0.0949  -2.3132
 JAR  HN10  H  HNR6  0   0.427  -2.0032   3.2779   0.4620
 JAR  H14   H  HCR5  0   0.285  -0.5340   2.9021   2.1382
 JAR  H16   H  HCH2  0   0.252   0.7756   2.8602  -0.2263
 JAR  H16A  H  HCH2  0   0.216   1.6737   3.1767   1.2630
 JAR  H18   H  HCH2  0   0.254   2.8526   1.8171  -1.0357
 JAR  H18A  H  HCH2  0   0.209   3.7915   1.6166   0.4333
 JAR  H20   H  HCR6  0   0.259   1.3726  -0.9256  -0.8109
 JAR  H21   H  HCR6  0   0.248   2.0509  -3.1536  -1.6525
 JAR  H22   H  HCR6  0   0.253   4.4491  -3.6995  -1.9254
 JAR  H23   H  HCR6  0   0.253   6.1622  -2.0063  -1.3515
 JAR  H24   H  HCR6  0   0.245   5.4819   0.2076  -0.5149
 JAR  H25   H  HCH2  0   0.233   1.7833  -0.5616   1.7668
 JAR  H25A  H  HCH2  0   0.199   2.6694   0.8162   2.4235
 JAR  H26   H  HCR5  0   0.256  -0.1812   0.1994   2.7799
 JAR  H28   H  HCH3  0   0.221   1.4885   2.5522   3.8038
 JAR  H28A  H  HCH3  0   0.233  -0.0671   2.0181   4.4446
 JAR  H28B  H  HCH3  0   0.236   1.3525   0.9846   4.5920

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
 JAR  C1   C2    single    1.521  0.020  1.521
 JAR  C1   H1    single    0.970  0.020  1.090
 JAR  C1   H1A   single    0.970  0.020  1.090
 JAR  C1   H1B   single    0.970  0.020  1.090
 JAR  C3   C2    single    1.522  0.020  1.522
 JAR  C2   N4    single    1.457  0.020  1.457
 JAR  C2   H2    single    0.970  0.020  1.090
 JAR  C3   H3    single    0.970  0.020  1.090
 JAR  C3   H3A   single    0.970  0.020  1.090
 JAR  C3   H3B   single    0.970  0.020  1.090
 JAR  N4   C13   aromatic  1.341  0.020  1.341
 JAR  N4   N5    aromatic  1.342  0.020  1.342
 JAR  N5   C6    aromatic  1.312  0.020  1.312
 JAR  C7   C6    aromatic  1.409  0.020  1.409
 JAR  C6   H6    single    0.930  0.020  1.080
 JAR  C13  C7    aromatic  1.391  0.020  1.391
 JAR  C7   C8    single    1.429  0.020  1.429
 JAR  N10  C8    single    1.396  0.020  1.396
 JAR  C8   O9    double    1.219  0.020  1.219
 JAR  C11  N10   single    1.364  0.020  1.364
 JAR  N10  HN10  single    0.860  0.020  1.020
 JAR  C14  C11   single    1.500  0.020  1.500
 JAR  N12  C11   double    1.293  0.020  1.293
 JAR  N12  C13   single    1.349  0.020  1.349
 JAR  C16  C14   single    1.535  0.020  1.535
 JAR  C26  C14   single    1.542  0.020  1.542
 JAR  C14  H14   single    0.970  0.020  1.090
 JAR  N17  C16   single    1.441  0.020  1.441
 JAR  C16  H16   single    0.970  0.020  1.090
 JAR  C16  H16A  single    0.970  0.020  1.090
 JAR  C18  N17   single    1.436  0.020  1.436
 JAR  N17  C25   single    1.451  0.020  1.451
 JAR  C19  C18   single    1.510  0.020  1.510
 JAR  C18  H18   single    0.970  0.020  1.090
 JAR  C18  H18A  single    0.970  0.020  1.090
 JAR  C24  C19   aromatic  1.392  0.020  1.392
 JAR  C19  C20   aromatic  1.394  0.020  1.394
 JAR  C21  C20   aromatic  1.388  0.020  1.388
 JAR  C20  H20   single    0.930  0.020  1.080
 JAR  C22  C21   aromatic  1.390  0.020  1.390
 JAR  C21  H21   single    0.930  0.020  1.080
 JAR  C23  C22   aromatic  1.388  0.020  1.388
 JAR  C22  H22   single    0.930  0.020  1.080
 JAR  C23  C24   aromatic  1.389  0.020  1.389
 JAR  C23  H23   single    0.930  0.020  1.080
 JAR  C24  H24   single    0.930  0.020  1.080
 JAR  C25  C26   single    1.542  0.020  1.542
 JAR  C25  H25   single    0.970  0.020  1.090
 JAR  C25  H25A  single    0.970  0.020  1.090
 JAR  C26  C28   single    1.523  0.020  1.523
 JAR  C26  H26   single    0.970  0.020  1.090
 JAR  C28  H28   single    0.970  0.020  1.090
 JAR  C28  H28A  single    0.970  0.020  1.090
 JAR  C28  H28B  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
 JAR  H1B   C1   H1A   108.05  3.000
 JAR  H1B   C1   H1    108.03  3.000
 JAR  H1A   C1   H1    108.48  3.000
 JAR  H1B   C1   C2    109.87  3.000
 JAR  H1A   C1   C2    111.17  3.000
 JAR  H1    C1   C2    111.14  3.000
 JAR  H2    C2   N4    104.79  3.000
 JAR  H2    C2   C3    108.87  3.000
 JAR  N4    C2   C3    110.49  3.000
 JAR  H2    C2   C1    109.13  3.000
 JAR  N4    C2   C1    110.56  3.000
 JAR  C3    C2   C1    112.69  3.000
 JAR  H3B   C3   H3A   108.05  3.000
 JAR  H3B   C3   H3    107.97  3.000
 JAR  H3A   C3   H3    108.39  3.000
 JAR  H3B   C3   C2    109.62  3.000
 JAR  H3A   C3   C2    111.26  3.000
 JAR  H3    C3   C2    111.43  3.000
 JAR  C13   N4   N5    111.41  3.000
 JAR  N5    N4   C2    121.07  3.000
 JAR  C13   N4   C2    127.51  3.000
 JAR  C6    N5   N4    106.87  3.000
 JAR  H6    C6   C7    128.99  3.000
 JAR  H6    C6   N5    120.60  3.000
 JAR  C7    C6   N5    110.42  3.000
 JAR  C13   C7   C8    118.69  3.000
 JAR  C8    C7   C6    136.85  3.000
 JAR  C13   C7   C6    104.46  3.000
 JAR  N10   C8   O9    121.11  3.000
 JAR  O9    C8   C7    128.29  3.000
 JAR  N10   C8   C7    110.60  3.000
 JAR  HN10  N10  C11   117.70  3.000
 JAR  HN10  N10  C8    115.91  3.000
 JAR  C11   N10  C8    126.39  3.000
 JAR  C14   C11  N12   121.06  3.000
 JAR  N12   C11  N10   123.02  3.000
 JAR  C14   C11  N10   115.89  3.000
 JAR  C13   N12  C11   114.10  3.000
 JAR  N12   C13  C7    127.19  3.000
 JAR  N12   C13  N4    125.97  3.000
 JAR  C7    C13  N4    106.84  3.000
 JAR  H14   C14  C26   111.58  3.000
 JAR  H14   C14  C16   111.03  3.000
 JAR  C26   C14  C16   102.43  3.000
 JAR  H14   C14  C11   109.18  3.000
 JAR  C26   C14  C11   113.21  3.000
 JAR  C16   C14  C11   109.26  3.000
 JAR  H16A  C16  H16   107.22  3.000
 JAR  H16A  C16  N17   113.80  3.000
 JAR  H16   C16  N17   111.45  3.000
 JAR  H16A  C16  C14   109.11  3.000
 JAR  H16   C16  C14   113.74  3.000
 JAR  N17   C16  C14   101.60  3.000
 JAR  C25   N17  C18   115.57  3.000
 JAR  C25   N17  C16   106.64  3.000
 JAR  C18   N17  C16   116.67  3.000
 JAR  H18A  C18  H18   105.89  3.000
 JAR  H18A  C18  C19   109.26  3.000
 JAR  H18   C18  C19   108.51  3.000
 JAR  H18A  C18  N17   112.46  3.000
 JAR  H18   C18  N17   108.27  3.000
 JAR  C19   C18  N17   112.19  3.000
 JAR  C24   C19  C20   118.68  3.000
 JAR  C20   C19  C18   120.96  3.000
 JAR  C24   C19  C18   120.34  3.000
 JAR  H20   C20  C21   120.43  3.000
 JAR  H20   C20  C19   118.97  3.000
 JAR  C21   C20  C19   120.59  3.000
 JAR  H21   C21  C22   119.82  3.000
 JAR  H21   C21  C20   119.85  3.000
 JAR  C22   C21  C20   120.33  3.000
 JAR  H22   C22  C23   120.24  3.000
 JAR  H22   C22  C21   120.31  3.000
 JAR  C23   C22  C21   119.45  3.000
 JAR  H23   C23  C24   119.81  3.000
 JAR  H23   C23  C22   120.08  3.000
 JAR  C24   C23  C22   120.11  3.000
 JAR  H24   C24  C23   119.56  3.000
 JAR  H24   C24  C19   119.60  3.000
 JAR  C23   C24  C19   120.84  3.000
 JAR  H25A  C25  H25   107.08  3.000
 JAR  H25A  C25  C26   110.02  3.000
 JAR  H25   C25  C26   112.38  3.000
 JAR  H25A  C25  N17   111.24  3.000
 JAR  H25   C25  N17   110.72  3.000
 JAR  C26   C25  N17   105.47  3.000
 JAR  H26   C26  C28   108.73  3.000
 JAR  H26   C26  C25   110.25  3.000
 JAR  C28   C26  C25   112.37  3.000
 JAR  H26   C26  C14   109.92  3.000
 JAR  C28   C26  C14   111.46  3.000
 JAR  C25   C26  C14   104.05  3.000
 JAR  H28B  C28  H28A  107.73  3.000
 JAR  H28B  C28  H28   107.42  3.000
 JAR  H28A  C28  H28   107.89  3.000
 JAR  H28B  C28  C26   110.73  3.000
 JAR  H28A  C28  C26   111.22  3.000
 JAR  H28   C28  C26   111.68  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
 JAR  CONST_01  C6    C7   C13  N4      0.00   0.0  0
 JAR  CONST_02  C7    C6   N5   N4      0.00   0.0  0
 JAR  CONST_03  C7    C13  N4   N5      0.00   0.0  0
 JAR  CONST_04  C13   C7   C6   N5      0.00   0.0  0
 JAR  CONST_05  C13   N4   N5   C6      0.00   0.0  0
 JAR  CONST_06  C22   C23  C24  C19     0.00   0.0  0
 JAR  CONST_07  C22   C21  C20  C19     0.00   0.0  0
 JAR  CONST_08  C23   C24  C19  C20     0.00   0.0  0
 JAR  CONST_09  C23   C22  C21  C20     0.00   0.0  0
 JAR  CONST_10  C24   C19  C20  C21     0.00   0.0  0
 JAR  CONST_11  C24   C23  C22  C21     0.00   0.0  0
 JAR  CONST_12  C11   N10  C8   C7      0.00   0.0  0
 JAR  CONST_13  C14   C11  N10  C8    180.00   0.0  0
 JAR  CONST_14  N12   C11  N10  C8      0.00   0.0  0
 JAR  CONST_15  C13   N12  C11  N10     0.00   0.0  0
 JAR  CONST_16  C14   C11  N12  C13   180.00   0.0  0
 JAR  CONST_17  C7    C13  N4   C2    180.00   0.0  0
 JAR  CONST_18  N12   C13  N4   C2      0.00   0.0  0
 JAR  CONST_19  C6    N5   N4   C2    180.00   0.0  0
 JAR  CONST_20  C23   C24  C19  C18   180.00   0.0  0
 JAR  CONST_21  C21   C20  C19  C18   180.00   0.0  0
 JAR  CONST_22  C11   N10  C8   O9    180.00   0.0  0
 JAR  CONST_23  H6    C6   N5   N4    180.00   0.0  0
 JAR  CONST_24  H23   C23  C24  C19   180.00   0.0  0
 JAR  CONST_25  H21   C21  C20  C19   180.00   0.0  0
 JAR  CONST_26  H24   C24  C19  C20   180.00   0.0  0
 JAR  CONST_27  H22   C22  C21  C20   180.00   0.0  0
 JAR  CONST_28  H20   C20  C21  C22   180.00   0.0  0
 JAR  CONST_29  HN10  N10  C8   C7    180.00   0.0  0
 JAR  Var_01    C25   N17  C16  C14   -44.69  30.0  1
 JAR  Var_02    C26   C25  N17  C16    30.51  30.0  1
 JAR  Var_03    C19   C18  N17  C16  -163.76  30.0  2
 JAR  Var_04    C24   C19  C18  N17  -150.87  30.0  2
 JAR  Var_05    C13   N4   C2   C1    116.19  30.0  2
 JAR  Var_06    H1    C1   C2   N4    -58.80  30.0  3
 JAR  Var_07    H3    C3   C2   N4    -66.41  30.0  3

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
 JAR  chir_01  C14  C11  C16  C26  positiv
 JAR  chir_02  C26  C14  C25  C28  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
 JAR  plan-1  C18   0.020
 JAR  plan-1  C19   0.020
 JAR  plan-1  C20   0.020
 JAR  plan-1  C21   0.020
 JAR  plan-1  C22   0.020
 JAR  plan-1  C23   0.020
 JAR  plan-1  C24   0.020
 JAR  plan-1  H20   0.020
 JAR  plan-1  H21   0.020
 JAR  plan-1  H22   0.020
 JAR  plan-1  H23   0.020
 JAR  plan-1  H24   0.020
 JAR  plan-2  C2    0.020
 JAR  plan-2  N4    0.020
 JAR  plan-2  N5    0.020
 JAR  plan-2  C6    0.020
 JAR  plan-2  C7    0.020
 JAR  plan-2  C8    0.020
 JAR  plan-2  O9    0.020
 JAR  plan-2  N10   0.020
 JAR  plan-2  C11   0.020
 JAR  plan-2  N12   0.020
 JAR  plan-2  C13   0.020
 JAR  plan-2  C14   0.020
 JAR  plan-2  H6    0.020
 JAR  plan-2  HN10  0.020

