# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:17:02 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N~2~-(1-cyclopentyl-4-oxo-4,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl)-N-(4-methoxyphenyl)-D-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)[C@@H](C)NC2=NC(=O)c3cnn(C4CCCC4)c3N2)cc1
#
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
 35O  35O  N~2~-(1-cyclopentyl-4-oxo-4,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl)-N-(4-methoxyphenyl)-D-alaninamide  ligand  53  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_35O
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
 35O  C4   C  CH2   0  -0.454    6.3400  -1.7039   1.3696
 35O  C1   C  CH2   0  -0.440    7.4589  -2.1982   0.4573
 35O  C2   C  CH2   0  -0.452    6.7269  -3.1476  -0.4871
 35O  C3   C  CH2   0  -0.450    5.4331  -2.3986  -0.8131
 35O  C5   C  CH1   0  -0.102    5.1028  -1.5805   0.4572
 35O  N8   N  NR5   0  -0.375    4.7871  -0.1969   0.1447
 35O  C11  C  CR56  0   0.752    3.6019   0.4162   0.1414
 35O  N13  N  NR16  0  -0.762    2.3750  -0.0648   0.4685
 35O  N9   N  N     0  -0.267    5.7566   0.6469  -0.2704
 35O  C10  C  CR15  0  -0.069    5.1718   1.7938  -0.5180
 35O  C12  C  CR56  0  -0.395    3.7858   1.7186  -0.2752
 35O  C16  C  CR6   0   0.434    2.6470   2.6049  -0.3640
 35O  O17  O  O     0  -0.484    2.7266   3.7745  -0.7202
 35O  N15  N  N     0  -0.552    1.4383   2.0516  -0.0175
 35O  C14  C  CR6   0   0.766    1.3221   0.8074   0.3595
 35O  N18  N  NH1   0  -0.678    0.1209   0.3026   0.6595
 35O  C19  C  CH1   0  -0.208   -1.0841   1.0930   0.6351
 35O  C20  C  CH3   0  -0.652   -1.2586   1.9253   1.9076
 35O  C21  C  C     0   0.546   -2.2624   0.1368   0.4723
 35O  O22  O  O     0  -0.467   -2.1867  -1.0322   0.8094
 35O  N23  N  NH1   0  -0.740   -3.3659   0.7258  -0.0285
 35O  C24  C  CR6   0   0.346   -4.6564   0.1931  -0.1847
 35O  C29  C  CR16  0  -0.327   -5.6945   1.1002  -0.4123
 35O  C28  C  CR16  0  -0.329   -6.9922   0.6689  -0.5915
 35O  C27  C  CR6   0   0.371   -7.2974  -0.6925  -0.5434
 35O  O30  O  O2    0  -0.472   -8.5914  -1.0257  -0.7195
 35O  C31  C  CH3   0  -0.436   -8.9443  -2.3932  -0.6756
 35O  C26  C  CR16  0  -0.373   -6.2679  -1.6000  -0.3231
 35O  C25  C  CR16  0  -0.296   -4.9583  -1.1631  -0.1474
 35O  H1   H  HCH2  0   0.246    6.1327  -2.4571   2.1320
 35O  H2   H  HCH2  0   0.251    6.5686  -0.7728   1.8872
 35O  H3   H  HCH2  0   0.227    7.8830  -1.3630  -0.1048
 35O  H4   H  HCH2  0   0.235    8.2691  -2.6787   1.0068
 35O  H5   H  HCH2  0   0.239    7.2972  -3.3966  -1.3826
 35O  H6   H  HCH2  0   0.226    6.5038  -4.0850   0.0297
 35O  H7   H  HCH2  0   0.245    5.6000  -1.7160  -1.6482
 35O  H8   H  HCH2  0   0.250    4.6135  -3.0597  -1.0941
 35O  H9   H  HCH1  0   0.267    4.2270  -1.9844   0.9657
 35O  H10  H  HNR6  0   0.435    2.2263  -1.0250   0.7431
 35O  H11  H  HCR5  0   0.273    5.7477   2.6401  -0.8602
 35O  H12  H  HNH1  0   0.408    0.0434  -0.6419   1.0069
 35O  H13  H  HCH1  0   0.289   -1.0353   1.7636  -0.2253
 35O  H14  H  HCH3  0   0.256   -0.4101   2.5977   2.0253
 35O  H15  H  HCH3  0   0.241   -2.1620   2.5330   1.8612
 35O  H16  H  HCH3  0   0.240   -1.3204   1.2841   2.7868
 35O  H17  H  HNH1  0   0.420   -3.2804   1.7019  -0.2708
 35O  H18  H  HCR6  0   0.273   -5.4862   2.1632  -0.4473
 35O  H19  H  HCR6  0   0.268   -7.7807   1.3905  -0.7645
 35O  H20  H  HCH3  0   0.259  -10.0219  -2.4400  -0.8122
 35O  H21  H  HCH3  0   0.228   -8.4649  -2.9658  -1.4744
 35O  H22  H  HCH3  0   0.227   -8.6914  -2.8500   0.2848
 35O  H23  H  HCR6  0   0.281   -6.4518  -2.6651  -0.2869
 35O  H24  H  HCR6  0   0.280   -4.1893  -1.9012   0.0109

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
 35O  O30  C31  single    1.413  0.020  1.413
 35O  O30  C27  single    1.348  0.020  1.348
 35O  C28  C27  aromatic  1.396  0.020  1.396
 35O  C28  C29  aromatic  1.379  0.020  1.379
 35O  C27  C26  aromatic  1.390  0.020  1.390
 35O  C29  C24  aromatic  1.397  0.020  1.397
 35O  C26  C25  aromatic  1.392  0.020  1.392
 35O  C24  C25  aromatic  1.390  0.020  1.390
 35O  C24  N23  single    1.405  0.020  1.405
 35O  C1   C2   single    1.526  0.020  1.526
 35O  C1   C4   single    1.526  0.020  1.526
 35O  N23  C21  single    1.347  0.020  1.347
 35O  C2   C3   single    1.530  0.020  1.530
 35O  O22  C21  double    1.219  0.020  1.219
 35O  C21  C19  single    1.526  0.020  1.526
 35O  C20  C19  single    1.530  0.020  1.530
 35O  C4   C5   single    1.542  0.020  1.542
 35O  C19  N18  single    1.441  0.020  1.441
 35O  C3   C5   single    1.547  0.020  1.547
 35O  C5   N8   single    1.453  0.020  1.453
 35O  N13  C11  single    1.358  0.020  1.358
 35O  N13  C14  single    1.372  0.020  1.372
 35O  N18  C14  single    1.337  0.020  1.337
 35O  N8   C11  aromatic  1.334  0.020  1.334
 35O  N8   N9   aromatic  1.351  0.020  1.351
 35O  C11  C12  aromatic  1.380  0.020  1.380
 35O  C14  N15  double    1.305  0.020  1.305
 35O  N9   C10  aromatic  1.311  0.020  1.311
 35O  C12  C10  aromatic  1.409  0.020  1.409
 35O  C12  C16  single    1.446  0.020  1.446
 35O  N15  C16  single    1.374  0.020  1.374
 35O  C16  O17  double    1.225  0.020  1.225
 35O  C4   H1   single    0.970  0.020  1.090
 35O  C4   H2   single    0.970  0.020  1.090
 35O  C1   H3   single    0.970  0.020  1.090
 35O  C1   H4   single    0.970  0.020  1.090
 35O  C2   H5   single    0.970  0.020  1.090
 35O  C2   H6   single    0.970  0.020  1.090
 35O  C3   H7   single    0.970  0.020  1.090
 35O  C3   H8   single    0.970  0.020  1.090
 35O  C5   H9   single    0.970  0.020  1.090
 35O  N13  H10  single    0.860  0.020  1.020
 35O  C10  H11  single    0.930  0.020  1.080
 35O  N18  H12  single    0.860  0.020  1.020
 35O  C19  H13  single    0.970  0.020  1.090
 35O  C20  H14  single    0.970  0.020  1.090
 35O  C20  H15  single    0.970  0.020  1.090
 35O  C20  H16  single    0.970  0.020  1.090
 35O  N23  H17  single    0.860  0.020  1.020
 35O  C29  H18  single    0.930  0.020  1.080
 35O  C28  H19  single    0.930  0.020  1.080
 35O  C31  H20  single    0.970  0.020  1.090
 35O  C31  H21  single    0.970  0.020  1.090
 35O  C31  H22  single    0.970  0.020  1.090
 35O  C26  H23  single    0.930  0.020  1.080
 35O  C25  H24  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
 35O  H2   C4   H1   107.32  3.000
 35O  H2   C4   C5   112.40  3.000
 35O  H1   C4   C5   108.43  3.000
 35O  H2   C4   C1   114.02  3.000
 35O  H1   C4   C1   109.47  3.000
 35O  C5   C4   C1   105.09  3.000
 35O  H4   C1   H3   107.92  3.000
 35O  H4   C1   C2   113.21  3.000
 35O  H3   C1   C2   110.09  3.000
 35O  H4   C1   C4   112.72  3.000
 35O  H3   C1   C4   110.16  3.000
 35O  C2   C1   C4   102.70  3.000
 35O  H6   C2   H5   107.40  3.000
 35O  H6   C2   C3   110.36  3.000
 35O  H5   C2   C3   112.27  3.000
 35O  H6   C2   C1   109.80  3.000
 35O  H5   C2   C1   113.54  3.000
 35O  C3   C2   C1   103.47  3.000
 35O  H8   C3   H7   107.28  3.000
 35O  H8   C3   C5   111.85  3.000
 35O  H7   C3   C5   109.29  3.000
 35O  H8   C3   C2   113.20  3.000
 35O  H7   C3   C2   109.87  3.000
 35O  C5   C3   C2   105.34  3.000
 35O  H9   C5   N8   106.17  3.000
 35O  H9   C5   C3   111.01  3.000
 35O  N8   C5   C3   111.93  3.000
 35O  H9   C5   C4   109.80  3.000
 35O  N8   C5   C4   112.19  3.000
 35O  C3   C5   C4   105.81  3.000
 35O  N9   N8   C11  110.47  3.000
 35O  N9   N8   C5   120.33  3.000
 35O  C11  N8   C5   129.12  3.000
 35O  C12  C11  N13  121.84  3.000
 35O  C12  C11  N8   108.42  3.000
 35O  N13  C11  N8   129.73  3.000
 35O  H10  N13  C14  120.89  3.000
 35O  H10  N13  C11  122.37  3.000
 35O  C14  N13  C11  116.69  3.000
 35O  C10  N9   N8   106.52  3.000
 35O  H11  C10  C12  128.41  3.000
 35O  H11  C10  N9   120.52  3.000
 35O  C12  C10  N9   111.07  3.000
 35O  C16  C12  C10  137.01  3.000
 35O  C16  C12  C11  119.49  3.000
 35O  C10  C12  C11  103.50  3.000
 35O  N15  C16  O17  120.99  3.000
 35O  O17  C16  C12  123.50  3.000
 35O  N15  C16  C12  115.51  3.000
 35O  C14  N15  C16  122.35  3.000
 35O  N18  C14  N15  120.32  3.000
 35O  N15  C14  N13  124.11  3.000
 35O  N18  C14  N13  115.57  3.000
 35O  H12  N18  C19  117.05  3.000
 35O  H12  N18  C14  119.97  3.000
 35O  C19  N18  C14  122.70  3.000
 35O  H13  C19  C21  109.58  3.000
 35O  H13  C19  C20  109.05  3.000
 35O  C21  C19  C20  109.96  3.000
 35O  H13  C19  N18  108.23  3.000
 35O  C20  C19  N18  112.30  3.000
 35O  C21  C19  N18  107.68  3.000
 35O  H16  C20  H15  108.38  3.000
 35O  H16  C20  H14  108.68  3.000
 35O  H15  C20  H14  107.83  3.000
 35O  H16  C20  C19  110.93  3.000
 35O  H15  C20  C19  111.25  3.000
 35O  H14  C20  C19  109.68  3.000
 35O  N23  C21  O22  124.95  3.000
 35O  O22  C21  C19  121.56  3.000
 35O  N23  C21  C19  113.45  3.000
 35O  H17  N23  C24  114.70  3.000
 35O  H17  N23  C21  116.27  3.000
 35O  C24  N23  C21  128.89  3.000
 35O  C25  C24  C29  118.46  3.000
 35O  C25  C24  N23  124.51  3.000
 35O  C29  C24  N23  117.03  3.000
 35O  H18  C29  C28  118.90  3.000
 35O  H18  C29  C24  119.95  3.000
 35O  C28  C29  C24  121.15  3.000
 35O  H19  C28  C27  119.75  3.000
 35O  H19  C28  C29  119.84  3.000
 35O  C27  C28  C29  120.41  3.000
 35O  C26  C27  O30  124.78  3.000
 35O  C26  C27  C28  118.70  3.000
 35O  O30  C27  C28  116.52  3.000
 35O  C31  O30  C27  118.36  3.000
 35O  H22  C31  H21  108.76  3.000
 35O  H22  C31  H20  108.76  3.000
 35O  H21  C31  H20  108.67  3.000
 35O  H22  C31  O30  111.96  3.000
 35O  H21  C31  O30  112.00  3.000
 35O  H20  C31  O30  106.58  3.000
 35O  H23  C26  C25  117.71  3.000
 35O  H23  C26  C27  121.49  3.000
 35O  C25  C26  C27  120.80  3.000
 35O  H24  C25  C26  118.36  3.000
 35O  H24  C25  C24  121.15  3.000
 35O  C26  C25  C24  120.49  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
 35O  CONST_01  C10  C12  C11  N8     0.00   0.0  0
 35O  CONST_02  C12  C10  N9   N8     0.00   0.0  0
 35O  CONST_03  C10  N9   N8   C11    0.00   0.0  0
 35O  CONST_04  N9   C10  C12  C11    0.00   0.0  0
 35O  CONST_05  C12  C11  N8   N9     0.00   0.0  0
 35O  CONST_06  C27  C28  C29  C24    0.00   0.0  0
 35O  CONST_07  C27  C26  C25  C24    0.00   0.0  0
 35O  CONST_08  C26  C27  C28  C29    0.00   0.0  0
 35O  CONST_09  C26  C25  C24  C29    0.00   0.0  0
 35O  CONST_10  C25  C26  C27  C28    0.00   0.0  0
 35O  CONST_11  C25  C24  C29  C28    0.00   0.0  0
 35O  CONST_12  N13  C11  N8   C5     0.00   0.0  0
 35O  CONST_13  C12  C11  N8   C5   180.00   0.0  0
 35O  CONST_14  C10  N9   N8   C5   180.00   0.0  0
 35O  CONST_15  N15  C14  N13  C11    0.00   0.0  0
 35O  CONST_16  C16  N15  C14  N13    0.00   0.0  0
 35O  CONST_17  C28  C29  C24  N23  180.00   0.0  0
 35O  CONST_18  C26  C25  C24  N23  180.00   0.0  0
 35O  CONST_19  O30  C27  C28  C29  180.00   0.0  0
 35O  CONST_20  C25  C26  C27  O30  180.00   0.0  0
 35O  CONST_21  N18  C14  N13  C11  180.00   0.0  0
 35O  CONST_22  N18  C14  N15  C16  180.00   0.0  0
 35O  CONST_23  H11  C10  N9   N8   180.00   0.0  0
 35O  CONST_24  H19  C28  C29  C24  180.00   0.0  0
 35O  CONST_25  H23  C26  C25  C24  180.00   0.0  0
 35O  CONST_26  H24  C25  C24  C29  180.00   0.0  0
 35O  CONST_27  H18  C29  C28  C27  180.00   0.0  0
 35O  CONST_28  H10  N13  C14  N15  180.00   0.0  0
 35O  CONST_31  C19  N18  C14  N13  180.00   0.0  0
 35O  CONST_32  C19  N18  C14  N15    0.00   0.0  0
 35O  CONST_33  H17  N23  C24  C29    0.00   0.0  0
 35O  CONST_34  H12  N18  C14  N13    0.00   0.0  0
 35O  CONST_35  C24  N23  C21  C19  180.00   0.0  0
 35O  CONST_36  C24  N23  C21  O22    0.00   0.0  0
 35O  Var_01    C3   C2   C1   C4    42.24  30.0  1
 35O  Var_02    C5   C3   C2   C1   -31.87  30.0  1
 35O  Var_03    C5   C4   C1   C2   -36.38  30.0  1
 35O  Var_04    C26  C27  O30  C31    0.22  30.0  2
 35O  Var_05    H20  C31  O30  C27  178.55  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
 35O  chir_01  C5   C4   C3   N8   positiv
 35O  chir_02  C19  N18  C20  C21  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
 35O  plan-1  N23  0.020
 35O  plan-1  C24  0.020
 35O  plan-1  C29  0.020
 35O  plan-1  C28  0.020
 35O  plan-1  C27  0.020
 35O  plan-1  O30  0.020
 35O  plan-1  C26  0.020
 35O  plan-1  C25  0.020
 35O  plan-1  H18  0.020
 35O  plan-1  H19  0.020
 35O  plan-1  H23  0.020
 35O  plan-1  H24  0.020
 35O  plan-2  C5   0.020
 35O  plan-2  N8   0.020
 35O  plan-2  C11  0.020
 35O  plan-2  N13  0.020
 35O  plan-2  N9   0.020
 35O  plan-2  C10  0.020
 35O  plan-2  C12  0.020
 35O  plan-2  C16  0.020
 35O  plan-2  O17  0.020
 35O  plan-2  N15  0.020
 35O  plan-2  C14  0.020
 35O  plan-2  N18  0.020
 35O  plan-2  C19  0.020
 35O  plan-2  H10  0.020
 35O  plan-2  H11  0.020
 35O  plan-2  H12  0.020
 35O  plan-3  C19  0.020
 35O  plan-3  C21  0.020
 35O  plan-3  O22  0.020
 35O  plan-3  N23  0.020
 35O  plan-3  C24  0.020
 35O  plan-3  H17  0.020

