# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:06:25 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6-{[(1S)-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
 49D  49D  6-{[(1S)-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_49D
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
 49D  C2   C   CH2   0  -0.454  -4.5524  -3.6513   0.5875
 49D  C3   C   CH2   0  -0.443  -4.2067  -2.2933   1.2116
 49D  C4   C   CH2   0  -0.440  -4.5371  -1.8872  -1.1280
 49D  C5   C   CR15  0  -0.094  -3.6375  -1.4929   0.0418
 49D  N8   N   NR5   0  -0.383  -3.5675  -0.0687   0.2799
 49D  C11  C   CR56  0   0.617  -2.4849   0.7213   0.2063
 49D  N13  N   N     0  -0.524  -1.2378   0.3248  -0.0963
 49D  N9   N   N     0  -0.274  -4.6751   0.6350   0.5964
 49D  C10  C   CR15  0  -0.068  -4.3012   1.8827   0.7289
 49D  C12  C   CR56  0  -0.370  -2.9178   2.0137   0.4944
 49D  C16  C   CR6   0   0.514  -1.9655   3.0750   0.4800
 49D  O17  O   O     0  -0.466  -2.1507   4.2589   0.7047
 49D  N15  N   NR16  0  -0.751  -0.6913   2.6039   0.1582
 49D  C14  C   CR6   0   0.777  -0.3652   1.2991  -0.1089
 49D  N18  N   NH1   0  -0.680   0.9227   1.0518  -0.3760
 49D  C19  C   CH1   0  -0.161   1.4143  -0.2731  -0.7336
 49D  C20  C   CH3   0  -0.652   1.1276  -0.6173  -2.1919
 49D  C24  C   CR6   0   0.146   2.8842  -0.3444  -0.3921
 49D  C29  C   CR16  0  -0.306   3.8310   0.3507  -1.1402
 49D  C28  C   CR16  0  -0.194   5.1782   0.2991  -0.8164
 49D  C27  C   CR6   0  -0.054   5.5819  -0.4653   0.2675
 49D  C26  C   CR16  0  -0.193   4.6624  -1.1708   1.0261
 49D  C25  C   CR16  0  -0.323   3.3178  -1.1006   0.6907
 49D  C1   C   CH2   0  -0.456  -4.7331  -3.3933  -0.9304
 49D  CL   CL  CL    0  -0.128   7.2642  -0.5422   0.6771
 49D  H1   H   HCH2  0   0.233  -3.7469  -4.3671   0.7566
 49D  H2   H   HCH2  0   0.236  -5.4480  -4.0759   1.0404
 49D  H3   H   HCH2  0   0.235  -5.1072  -1.7951   1.5765
 49D  H4   H   HCH2  0   0.244  -3.5079  -2.3684   2.0453
 49D  H5   H   HCH2  0   0.233  -5.4874  -1.3550  -1.0428
 49D  H6   H   HCH2  0   0.243  -4.1027  -1.6328  -2.0956
 49D  H7   H   HCR5  0   0.266  -2.6124  -1.8108  -0.1611
 49D  H8   H   HCR5  0   0.270  -5.0186   2.6473   0.9855
 49D  H9   H   HNR6  0   0.423   0.0428   3.2997   0.1309
 49D  H10  H   HNH1  0   0.413   1.5584   1.8299  -0.4560
 49D  H11  H   HCH1  0   0.274   0.8850  -0.9902  -0.1042
 49D  H12  H   HCH3  0   0.229   1.6047   0.0853  -2.8755
 49D  H13  H   HCH3  0   0.240   1.4946  -1.6178  -2.4204
 49D  H14  H   HCH3  0   0.247   0.0545  -0.5996  -2.3780
 49D  H15  H   HCR6  0   0.268   3.5291   0.9419  -1.9964
 49D  H16  H   HCR6  0   0.282   5.9014   0.8469  -1.4049
 49D  H17  H   HCR6  0   0.282   4.9838  -1.7655   1.8703
 49D  H18  H   HCR6  0   0.267   2.5997  -1.6524   1.2848
 49D  H19  H   HCH2  0   0.233  -3.9850  -3.9475  -1.4988
 49D  H20  H   HCH2  0   0.237  -5.7073  -3.7216  -1.2916

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
 49D  CL   C27  single    1.733  0.020  1.733
 49D  C2   C1   single    1.550  0.020  1.550
 49D  C2   C3   single    1.534  0.020  1.534
 49D  C28  C27  aromatic  1.386  0.020  1.386
 49D  C28  C29  aromatic  1.386  0.020  1.386
 49D  C27  C26  aromatic  1.385  0.020  1.385
 49D  C29  C24  aromatic  1.393  0.020  1.393
 49D  C26  C25  aromatic  1.388  0.020  1.388
 49D  C20  C19  single    1.526  0.020  1.526
 49D  C1   C4   single    1.532  0.020  1.532
 49D  C24  C25  aromatic  1.390  0.020  1.390
 49D  C24  C19  single    1.511  0.020  1.511
 49D  C4   C5   single    1.527  0.020  1.527
 49D  C19  N18  single    1.458  0.020  1.458
 49D  C3   C5   single    1.527  0.020  1.527
 49D  C5   N8   single    1.446  0.020  1.446
 49D  N18  C14  single    1.338  0.020  1.338
 49D  N13  C14  double    1.308  0.020  1.308
 49D  N13  C11  single    1.343  0.020  1.343
 49D  N8   C11  aromatic  1.342  0.020  1.342
 49D  N8   N9   aromatic  1.350  0.020  1.350
 49D  C14  N15  single    1.371  0.020  1.371
 49D  C11  C12  aromatic  1.393  0.020  1.393
 49D  N9   C10  aromatic  1.309  0.020  1.309
 49D  N15  C16  single    1.396  0.020  1.396
 49D  C12  C10  aromatic  1.409  0.020  1.409
 49D  C12  C16  single    1.426  0.020  1.426
 49D  C16  O17  double    1.219  0.020  1.219
 49D  C2   H1   single    0.970  0.020  1.090
 49D  C2   H2   single    0.970  0.020  1.090
 49D  C3   H3   single    0.970  0.020  1.090
 49D  C3   H4   single    0.970  0.020  1.090
 49D  C4   H5   single    0.970  0.020  1.090
 49D  C4   H6   single    0.970  0.020  1.090
 49D  C5   H7   single    0.970  0.020  1.090
 49D  C10  H8   single    0.930  0.020  1.080
 49D  N15  H9   single    0.860  0.020  1.020
 49D  N18  H10  single    0.860  0.020  1.020
 49D  C19  H11  single    0.970  0.020  1.090
 49D  C20  H12  single    0.970  0.020  1.090
 49D  C20  H13  single    0.970  0.020  1.090
 49D  C20  H14  single    0.970  0.020  1.090
 49D  C29  H15  single    0.930  0.020  1.080
 49D  C28  H16  single    0.930  0.020  1.080
 49D  C26  H17  single    0.930  0.020  1.080
 49D  C25  H18  single    0.930  0.020  1.080
 49D  C1   H19  single    0.970  0.020  1.090
 49D  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
 49D  H2   C2   H1   106.66  3.000
 49D  H2   C2   C1   112.08  3.000
 49D  H1   C2   C1   110.31  3.000
 49D  H2   C2   C3   111.16  3.000
 49D  H1   C2   C3   110.58  3.000
 49D  C1   C2   C3   106.10  3.000
 49D  H4   C3   H3   107.73  3.000
 49D  H4   C3   C5   112.51  3.000
 49D  H3   C3   C5   108.91  3.000
 49D  H4   C3   C2   113.23  3.000
 49D  H3   C3   C2   110.73  3.000
 49D  C5   C3   C2   103.67  3.000
 49D  H6   C4   H5   107.58  3.000
 49D  H6   C4   C1   113.25  3.000
 49D  H5   C4   C1   110.95  3.000
 49D  H6   C4   C5   112.62  3.000
 49D  H5   C4   C5   109.08  3.000
 49D  C1   C4   C5   103.32  3.000
 49D  H7   C5   N8   105.77  3.000
 49D  H7   C5   C4   109.59  3.000
 49D  N8   C5   C4   114.14  3.000
 49D  H7   C5   C3   109.85  3.000
 49D  N8   C5   C3   114.09  3.000
 49D  C4   C5   C3   103.41  3.000
 49D  N9   N8   C11  111.58  3.000
 49D  N9   N8   C5   120.83  3.000
 49D  C11  N8   C5   127.58  3.000
 49D  C12  C11  N13  127.52  3.000
 49D  C12  C11  N8   106.50  3.000
 49D  N13  C11  N8   125.98  3.000
 49D  C14  N13  C11  113.68  3.000
 49D  C10  N9   N8   106.63  3.000
 49D  H8   C10  C12  128.77  3.000
 49D  H8   C10  N9   120.62  3.000
 49D  C12  C10  N9   110.62  3.000
 49D  C16  C12  C10  136.59  3.000
 49D  C16  C12  C11  118.74  3.000
 49D  C10  C12  C11  104.67  3.000
 49D  N15  C16  O17  120.59  3.000
 49D  O17  C16  C12  128.27  3.000
 49D  N15  C16  C12  111.14  3.000
 49D  H9   N15  C14  118.46  3.000
 49D  H9   N15  C16  115.87  3.000
 49D  C14  N15  C16  125.67  3.000
 49D  N18  C14  N15  116.33  3.000
 49D  N15  C14  N13  123.25  3.000
 49D  N18  C14  N13  120.42  3.000
 49D  H10  N18  C19  118.00  3.000
 49D  H10  N18  C14  118.69  3.000
 49D  C19  N18  C14  122.78  3.000
 49D  H11  C19  C24  108.09  3.000
 49D  H11  C19  C20  108.18  3.000
 49D  C24  C19  C20  112.85  3.000
 49D  H11  C19  N18  106.99  3.000
 49D  C24  C19  N18  108.39  3.000
 49D  C20  C19  N18  112.09  3.000
 49D  H14  C20  H13  108.11  3.000
 49D  H14  C20  H12  108.27  3.000
 49D  H13  C20  H12  108.23  3.000
 49D  H14  C20  C19  110.17  3.000
 49D  H13  C20  C19  110.13  3.000
 49D  H12  C20  C19  111.83  3.000
 49D  C25  C24  C29  118.55  3.000
 49D  C25  C24  C19  120.34  3.000
 49D  C29  C24  C19  121.10  3.000
 49D  H15  C29  C28  118.40  3.000
 49D  H15  C29  C24  120.49  3.000
 49D  C28  C29  C24  121.10  3.000
 49D  H16  C28  C27  120.67  3.000
 49D  H16  C28  C29  120.25  3.000
 49D  C27  C28  C29  119.08  3.000
 49D  CL   C27  C26  119.49  3.000
 49D  C26  C27  C28  121.05  3.000
 49D  CL   C27  C28  119.46  3.000
 49D  H17  C26  C25  120.30  3.000
 49D  H17  C26  C27  120.69  3.000
 49D  C25  C26  C27  119.02  3.000
 49D  H18  C25  C26  118.95  3.000
 49D  H18  C25  C24  119.84  3.000
 49D  C26  C25  C24  121.20  3.000
 49D  H20  C1   H19  106.70  3.000
 49D  H20  C1   C4   111.59  3.000
 49D  H19  C1   C4   110.16  3.000
 49D  H20  C1   C2   112.25  3.000
 49D  H19  C1   C2   110.23  3.000
 49D  C4   C1   C2   105.96  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
 49D  CONST_01  C10  C12  C11  N8     0.00   0.0  0
 49D  CONST_02  C12  C10  N9   N8     0.00   0.0  0
 49D  CONST_03  C10  N9   N8   C11    0.00   0.0  0
 49D  CONST_04  N9   C10  C12  C11    0.00   0.0  0
 49D  CONST_05  C12  C11  N8   N9     0.00   0.0  0
 49D  CONST_06  C27  C28  C29  C24    0.00   0.0  0
 49D  CONST_07  C27  C26  C25  C24    0.00   0.0  0
 49D  CONST_08  C26  C27  C28  C29    0.00   0.0  0
 49D  CONST_09  C26  C25  C24  C29    0.00   0.0  0
 49D  CONST_10  C25  C26  C27  C28    0.00   0.0  0
 49D  CONST_11  C25  C24  C29  C28    0.00   0.0  0
 49D  CONST_12  N13  C11  N8   C5     0.00   0.0  0
 49D  CONST_13  C12  C11  N8   C5   180.00   0.0  0
 49D  CONST_14  C10  N9   N8   C5   180.00   0.0  0
 49D  CONST_15  N15  C14  N13  C11    0.00   0.0  0
 49D  CONST_16  C16  N15  C14  N13    0.00   0.0  0
 49D  CONST_17  C14  N15  C16  C12    0.00   0.0  0
 49D  CONST_18  C28  C29  C24  C19  180.00   0.0  0
 49D  CONST_19  C26  C25  C24  C19  180.00   0.0  0
 49D  CONST_20  CL   C27  C28  C29  180.00   0.0  0
 49D  CONST_21  CL   C27  C26  C25  180.00   0.0  0
 49D  CONST_22  N18  C14  N13  C11  180.00   0.0  0
 49D  CONST_23  N18  C14  N15  C16  180.00   0.0  0
 49D  CONST_24  C14  N15  C16  O17  180.00   0.0  0
 49D  CONST_25  H8   C10  N9   N8   180.00   0.0  0
 49D  CONST_26  H16  C28  C29  C24  180.00   0.0  0
 49D  CONST_27  H17  C26  C25  C24  180.00   0.0  0
 49D  CONST_28  H18  C25  C24  C29  180.00   0.0  0
 49D  CONST_29  H15  C29  C28  C27  180.00   0.0  0
 49D  CONST_30  H9   N15  C14  N13  180.00   0.0  0
 49D  CONST_31  C19  N18  C14  N13    0.00   0.0  0
 49D  CONST_32  C19  N18  C14  N15  180.00   0.0  0
 49D  CONST_33  H10  N18  C14  N13  180.00   0.0  0
 49D  Var_01    C5   C4   C1   C2    26.27  30.0  1
 49D  Var_02    C4   C1   C2   C3    -2.02  30.0  1
 49D  Var_03    C1   C2   C3   C5   -23.03  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
 49D  chir_01  C5   C4   C3   N8   positiv
 49D  chir_02  C19  N18  C20  C24  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
 49D  plan-1  C19  0.020
 49D  plan-1  C24  0.020
 49D  plan-1  C29  0.020
 49D  plan-1  C28  0.020
 49D  plan-1  C27  0.020
 49D  plan-1  C26  0.020
 49D  plan-1  C25  0.020
 49D  plan-1  CL   0.020
 49D  plan-1  H15  0.020
 49D  plan-1  H16  0.020
 49D  plan-1  H17  0.020
 49D  plan-1  H18  0.020
 49D  plan-2  C5   0.020
 49D  plan-2  N8   0.020
 49D  plan-2  C11  0.020
 49D  plan-2  N13  0.020
 49D  plan-2  N9   0.020
 49D  plan-2  C10  0.020
 49D  plan-2  C12  0.020
 49D  plan-2  C16  0.020
 49D  plan-2  O17  0.020
 49D  plan-2  N15  0.020
 49D  plan-2  C14  0.020
 49D  plan-2  N18  0.020
 49D  plan-2  C19  0.020
 49D  plan-2  H8   0.020
 49D  plan-2  H9   0.020
 49D  plan-2  H10  0.020

