# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:12:37 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC1=Nc2n(ncc2C(=O)N1)C3CCCC3)c4ccc(Cl)cc4
#
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
 49E  49E  6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  45  25  .  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_49E
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
 49E  C2   C   CH2   0  -0.455  -4.7360  -3.4032   0.9246
 49E  C3   C   CH2   0  -0.440  -4.5337  -1.8976   1.1226
 49E  C4   C   CH2   0  -0.443  -4.2115  -2.3046  -1.2178
 49E  C5   C   CR15  0  -0.094  -3.6379  -1.5038  -0.0504
 49E  N8   N   NR5   0  -0.383  -3.5680  -0.0795  -0.2886
 49E  C11  C   CR56  0   0.617  -2.4864   0.7114  -0.2090
 49E  N13  N   N     0  -0.524  -1.2406   0.3158   0.1006
 49E  N9   N   N     0  -0.274  -4.6749   0.6239  -0.6081
 49E  C10  C   CR15  0  -0.068  -4.3013   1.8721  -0.7374
 49E  C12  C   CR56  0  -0.370  -2.9190   2.0038  -0.4974
 49E  C16  C   CR6   0   0.514  -1.9677   3.0660  -0.4771
 49E  O17  O   O     0  -0.466  -2.1529   4.2500  -0.7013
 49E  N15  N   NR16  0  -0.750  -0.6945   2.5955  -0.1506
 49E  C14  C   CR6   0   0.777  -0.3693   1.2911   0.1200
 49E  N18  N   NH1   0  -0.679   0.9165   1.0459   0.3987
 49E  C19  C   CH1   0  -0.160   1.4100  -0.2796   0.7513
 49E  C20  C   CH3   0  -0.654   1.1127  -0.6345   2.2048
 49E  C24  C   CR6   0   0.144   2.8821  -0.3413   0.4160
 49E  C29  C   CR16  0  -0.321   3.3178  -1.0499  -0.6980
 49E  C28  C   CR16  0  -0.193   4.6628  -1.1047  -1.0342
 49E  C27  C   CR6   0  -0.053   5.5810  -0.4332  -0.2437
 49E  C26  C   CR16  0  -0.193   5.1752   0.2840   0.8711
 49E  C25  C   CR16  0  -0.305   3.8273   0.3223   1.1938
 49E  C1   C   CH2   0  -0.454  -4.5481  -3.6636  -0.5920
 49E  CL   CL  CL    0  -0.128   7.2640  -0.4920  -0.6535
 49E  H1   H   HCH2  0   0.233  -3.9952  -3.9619   1.4981
 49E  H2   H   HCH2  0   0.237  -5.7145  -3.7254   1.2798
 49E  H3   H   HCH2  0   0.233  -5.4825  -1.3620   1.0420
 49E  H4   H   HCH2  0   0.243  -4.0946  -1.6455   2.0887
 49E  H5   H   HCH2  0   0.235  -5.1164  -1.8092  -1.5758
 49E  H6   H   HCH2  0   0.244  -3.5178  -2.3762  -2.0561
 49E  H7   H   HCR5  0   0.266  -2.6122  -1.8221   0.1492
 49E  H8   H   HCR5  0   0.270  -5.0186   2.6365  -0.9954
 49E  H9   H   HNR6  0   0.423   0.0402   3.2908  -0.1254
 49E  H10  H   HNH1  0   0.413   1.5477   1.8257   0.4964
 49E  H11  H   HCH1  0   0.274   0.8876  -0.9940   0.1131
 49E  H12  H   HCH3  0   0.229   1.5745   0.0699   2.8970
 49E  H13  H   HCH3  0   0.247   0.0376  -0.6283   2.3794
 49E  H14  H   HCH3  0   0.240   1.4878  -1.6321   2.4326
 49E  H15  H   HCR6  0   0.267   2.6007  -1.5755  -1.3166
 49E  H16  H   HCR6  0   0.282   4.9863  -1.6594  -1.9042
 49E  H17  H   HCR6  0   0.282   5.8971   0.8056   1.4840
 49E  H18  H   HCR6  0   0.268   3.5237   0.8787   2.0724
 49E  H19  H   HCH2  0   0.233  -3.7355  -4.3725  -0.7566
 49E  H20  H   HCH2  0   0.236  -5.4383  -4.0975  -1.0468

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
 49E  CL   C27  single    1.733  0.020  1.733
 49E  C27  C26  aromatic  1.386  0.020  1.386
 49E  C27  C28  aromatic  1.385  0.020  1.385
 49E  C26  C25  aromatic  1.387  0.020  1.387
 49E  C28  C29  aromatic  1.387  0.020  1.387
 49E  C25  C24  aromatic  1.392  0.020  1.392
 49E  C2   C1   single    1.550  0.020  1.550
 49E  C2   C3   single    1.532  0.020  1.532
 49E  C29  C24  aromatic  1.390  0.020  1.390
 49E  C1   C4   single    1.534  0.020  1.534
 49E  C24  C19  single    1.511  0.020  1.511
 49E  C4   C5   single    1.527  0.020  1.527
 49E  C20  C19  single    1.525  0.020  1.525
 49E  C19  N18  single    1.458  0.020  1.458
 49E  C5   C3   single    1.528  0.020  1.528
 49E  C5   N8   single    1.446  0.020  1.446
 49E  N13  C11  single    1.343  0.020  1.343
 49E  N13  C14  double    1.308  0.020  1.308
 49E  N18  C14  single    1.338  0.020  1.338
 49E  N8   C11  aromatic  1.342  0.020  1.342
 49E  N8   N9   aromatic  1.350  0.020  1.350
 49E  C11  C12  aromatic  1.393  0.020  1.393
 49E  C14  N15  single    1.371  0.020  1.371
 49E  N9   C10  aromatic  1.309  0.020  1.309
 49E  C12  C10  aromatic  1.409  0.020  1.409
 49E  C12  C16  single    1.426  0.020  1.426
 49E  N15  C16  single    1.396  0.020  1.396
 49E  C16  O17  double    1.219  0.020  1.219
 49E  C2   H1   single    0.970  0.020  1.090
 49E  C2   H2   single    0.970  0.020  1.090
 49E  C3   H3   single    0.970  0.020  1.090
 49E  C3   H4   single    0.970  0.020  1.090
 49E  C4   H5   single    0.970  0.020  1.090
 49E  C4   H6   single    0.970  0.020  1.090
 49E  C5   H7   single    0.970  0.020  1.090
 49E  C10  H8   single    0.930  0.020  1.080
 49E  N15  H9   single    0.860  0.020  1.020
 49E  N18  H10  single    0.860  0.020  1.020
 49E  C19  H11  single    0.970  0.020  1.090
 49E  C20  H12  single    0.970  0.020  1.090
 49E  C20  H13  single    0.970  0.020  1.090
 49E  C20  H14  single    0.970  0.020  1.090
 49E  C29  H15  single    0.930  0.020  1.080
 49E  C28  H16  single    0.930  0.020  1.080
 49E  C26  H17  single    0.930  0.020  1.080
 49E  C25  H18  single    0.930  0.020  1.080
 49E  C1   H19  single    0.970  0.020  1.090
 49E  C1   H20  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
 49E  H2   C2   H1   106.68  3.000
 49E  H2   C2   C1   112.22  3.000
 49E  H1   C2   C1   110.24  3.000
 49E  H2   C2   C3   111.53  3.000
 49E  H1   C2   C3   110.23  3.000
 49E  C1   C2   C3   105.99  3.000
 49E  H4   C3   H3   107.56  3.000
 49E  H4   C3   C5   112.61  3.000
 49E  H3   C3   C5   109.05  3.000
 49E  H4   C3   C2   113.25  3.000
 49E  H3   C3   C2   110.95  3.000
 49E  C5   C3   C2   103.39  3.000
 49E  H6   C4   H5   107.76  3.000
 49E  H6   C4   C1   113.27  3.000
 49E  H5   C4   C1   110.73  3.000
 49E  H6   C4   C5   112.52  3.000
 49E  H5   C4   C5   108.90  3.000
 49E  C1   C4   C5   103.60  3.000
 49E  H7   C5   N8   105.77  3.000
 49E  H7   C5   C4   109.85  3.000
 49E  N8   C5   C4   114.13  3.000
 49E  H7   C5   C3   109.58  3.000
 49E  N8   C5   C3   114.13  3.000
 49E  C4   C5   C3   103.39  3.000
 49E  N9   N8   C11  111.57  3.000
 49E  N9   N8   C5   120.85  3.000
 49E  C11  N8   C5   127.57  3.000
 49E  C12  C11  N13  127.51  3.000
 49E  C12  C11  N8   106.51  3.000
 49E  N13  C11  N8   125.98  3.000
 49E  C14  N13  C11  113.68  3.000
 49E  C10  N9   N8   106.63  3.000
 49E  H8   C10  C12  128.78  3.000
 49E  H8   C10  N9   120.60  3.000
 49E  C12  C10  N9   110.62  3.000
 49E  C16  C12  C10  136.59  3.000
 49E  C16  C12  C11  118.75  3.000
 49E  C10  C12  C11  104.66  3.000
 49E  N15  C16  O17  120.59  3.000
 49E  O17  C16  C12  128.27  3.000
 49E  N15  C16  C12  111.14  3.000
 49E  H9   N15  C14  118.46  3.000
 49E  H9   N15  C16  115.88  3.000
 49E  C14  N15  C16  125.66  3.000
 49E  N18  C14  N15  116.31  3.000
 49E  N15  C14  N13  123.26  3.000
 49E  N18  C14  N13  120.43  3.000
 49E  H10  N18  C19  117.90  3.000
 49E  H10  N18  C14  118.69  3.000
 49E  C19  N18  C14  122.84  3.000
 49E  H11  C19  C24  108.05  3.000
 49E  H11  C19  C20  108.16  3.000
 49E  C24  C19  C20  113.07  3.000
 49E  H11  C19  N18  106.97  3.000
 49E  C20  C19  N18  112.09  3.000
 49E  C24  C19  N18  108.26  3.000
 49E  H14  C20  H13  108.14  3.000
 49E  H14  C20  H12  108.24  3.000
 49E  H13  C20  H12  108.22  3.000
 49E  H14  C20  C19  110.18  3.000
 49E  H13  C20  C19  110.11  3.000
 49E  H12  C20  C19  111.85  3.000
 49E  C25  C24  C29  118.54  3.000
 49E  C29  C24  C19  120.26  3.000
 49E  C25  C24  C19  121.19  3.000
 49E  H15  C29  C28  118.96  3.000
 49E  H15  C29  C24  119.83  3.000
 49E  C28  C29  C24  121.20  3.000
 49E  H16  C28  C27  120.63  3.000
 49E  H16  C28  C29  120.35  3.000
 49E  C27  C28  C29  119.02  3.000
 49E  CL   C27  C26  119.47  3.000
 49E  C26  C27  C28  121.05  3.000
 49E  CL   C27  C28  119.49  3.000
 49E  H17  C26  C25  120.25  3.000
 49E  H17  C26  C27  120.67  3.000
 49E  C25  C26  C27  119.08  3.000
 49E  H18  C25  C26  118.38  3.000
 49E  H18  C25  C24  120.50  3.000
 49E  C26  C25  C24  121.11  3.000
 49E  H20  C1   H19  106.67  3.000
 49E  H20  C1   C4   111.21  3.000
 49E  H19  C1   C4   110.54  3.000
 49E  H20  C1   C2   112.09  3.000
 49E  H19  C1   C2   110.31  3.000
 49E  C4   C1   C2   106.08  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
 49E  CONST_01  C10  C12  C11  N8     0.00   0.0  0
 49E  CONST_02  C12  C10  N9   N8     0.00   0.0  0
 49E  CONST_03  C10  N9   N8   C11    0.00   0.0  0
 49E  CONST_04  N9   C10  C12  C11    0.00   0.0  0
 49E  CONST_05  C12  C11  N8   N9     0.00   0.0  0
 49E  CONST_06  C27  C26  C25  C24    0.00   0.0  0
 49E  CONST_07  C27  C28  C29  C24    0.00   0.0  0
 49E  CONST_08  C26  C27  C28  C29    0.00   0.0  0
 49E  CONST_09  C26  C25  C24  C29    0.00   0.0  0
 49E  CONST_10  C25  C26  C27  C28    0.00   0.0  0
 49E  CONST_11  C25  C24  C29  C28    0.00   0.0  0
 49E  CONST_12  N13  C11  N8   C5     0.00   0.0  0
 49E  CONST_13  C12  C11  N8   C5   180.00   0.0  0
 49E  CONST_14  C10  N9   N8   C5   180.00   0.0  0
 49E  CONST_15  N15  C14  N13  C11    0.00   0.0  0
 49E  CONST_16  C16  N15  C14  N13    0.00   0.0  0
 49E  CONST_17  C14  N15  C16  C12    0.00   0.0  0
 49E  CONST_18  C26  C25  C24  C19  180.00   0.0  0
 49E  CONST_19  C28  C29  C24  C19  180.00   0.0  0
 49E  CONST_20  CL   C27  C28  C29  180.00   0.0  0
 49E  CONST_21  CL   C27  C26  C25  180.00   0.0  0
 49E  CONST_22  N18  C14  N13  C11  180.00   0.0  0
 49E  CONST_23  N18  C14  N15  C16  180.00   0.0  0
 49E  CONST_24  C14  N15  C16  O17  180.00   0.0  0
 49E  CONST_25  H8   C10  N9   N8   180.00   0.0  0
 49E  CONST_26  H17  C26  C25  C24  180.00   0.0  0
 49E  CONST_27  H16  C28  C29  C24  180.00   0.0  0
 49E  CONST_28  H18  C25  C24  C29  180.00   0.0  0
 49E  CONST_29  H15  C29  C28  C27  180.00   0.0  0
 49E  CONST_30  H9   N15  C14  N13  180.00   0.0  0
 49E  CONST_31  C19  N18  C14  N13    0.00   0.0  0
 49E  CONST_32  C19  N18  C14  N15  180.00   0.0  0
 49E  CONST_33  H10  N18  C14  N13  180.00   0.0  0
 49E  Var_01    C5   C4   C1   C2    23.67  30.0  1
 49E  Var_02    C4   C1   C2   C3     1.25  30.0  1
 49E  Var_03    C1   C2   C3   C5   -25.68  30.0  1

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
 49E  chir_01  C5   C4   C3   N8   positiv
 49E  chir_02  C19  N18  C24  C20  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
 49E  plan-1  C19  0.020
 49E  plan-1  C24  0.020
 49E  plan-1  C29  0.020
 49E  plan-1  C28  0.020
 49E  plan-1  C27  0.020
 49E  plan-1  C26  0.020
 49E  plan-1  C25  0.020
 49E  plan-1  CL   0.020
 49E  plan-1  H15  0.020
 49E  plan-1  H16  0.020
 49E  plan-1  H17  0.020
 49E  plan-1  H18  0.020
 49E  plan-2  C5   0.020
 49E  plan-2  N8   0.020
 49E  plan-2  C11  0.020
 49E  plan-2  N13  0.020
 49E  plan-2  N9   0.020
 49E  plan-2  C10  0.020
 49E  plan-2  C12  0.020
 49E  plan-2  C16  0.020
 49E  plan-2  O17  0.020
 49E  plan-2  N15  0.020
 49E  plan-2  C14  0.020
 49E  plan-2  N18  0.020
 49E  plan-2  C19  0.020
 49E  plan-2  H8   0.020
 49E  plan-2  H9   0.020
 49E  plan-2  H10  0.020

