# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:42:26 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (1-phenyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1nn(c2ccccc2)c3CCCc13
#
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
 BQ5  BQ5  (1-phenyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)methanamine  ligand  31  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BQ5
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
 BQ5  N1   N  NR5   0  -0.479  -0.2421  -0.1177  -0.0327
 BQ5  C4   C  CR55  0  -0.129   1.8696   0.4625  -0.1025
 BQ5  C5   C  CR5   0   0.236   1.7284  -0.9355  -0.1971
 BQ5  C6   C  CR6   0   0.349  -1.6465  -0.1556  -0.0011
 BQ5  C7   C  CH2   0  -0.505   2.8770   1.5614  -0.1627
 BQ5  C8   C  CH2   0  -0.499   0.5209   2.4339   0.0223
 BQ5  C13  C  CR16  0  -0.305  -2.3175  -1.2729  -0.4953
 BQ5  C15  C  CR16  0  -0.249  -3.7594   0.8643   0.5294
 BQ5  C12  C  CR16  0  -0.310  -2.3726   0.9117   0.5185
 BQ5  C16  C  CR16  0  -0.266  -4.4333  -0.2454   0.0407
 BQ5  C14  C  CR16  0  -0.246  -3.7025  -1.3126  -0.4655
 BQ5  N2   N  N     0  -0.314   0.4518  -1.2670  -0.1426
 BQ5  C3   C  CR55  0   0.378   0.5999   0.9443   0.0009
 BQ5  C11  C  CH2   0  -0.462   2.0201   2.8075   0.1955
 BQ5  C9   C  CH2   0  -0.371   2.7919  -1.9737  -0.3344
 BQ5  N10  N  NH2   0  -0.790   3.8643  -1.7316   0.6179
 BQ5  H1   H  HCH2  0   0.241   3.7061   1.4260   0.5325
 BQ5  H2   H  HCH2  0   0.237   3.3142   1.6468  -1.1613
 BQ5  H3   H  HCH2  0   0.260   0.1006   2.8197  -0.9107
 BQ5  H4   H  HCH2  0   0.263  -0.0808   2.8415   0.8352
 BQ5  H5   H  HCR6  0   0.272  -1.7597  -2.1050  -0.8998
 BQ5  H6   H  HCR6  0   0.263  -4.3110   1.7018   0.9358
 BQ5  H7   H  HCR6  0   0.270  -1.8723   1.7755   0.9304
 BQ5  H8   H  HCR6  0   0.259  -5.5144  -0.2802   0.0565
 BQ5  H9   H  HCR6  0   0.262  -4.2123  -2.1856  -0.8515
 BQ5  H10  H  HCH2  0   0.246   2.1946   3.0747   1.2379
 BQ5  H11  H  HCH2  0   0.242   2.2879   3.6756  -0.4049
 BQ5  H12  H  HCH2  0   0.216   2.3282  -2.9659  -0.2584
 BQ5  H13  H  HCH2  0   0.237   3.2188  -1.9117  -1.3397
 BQ5  H14  H  HNH2  0   0.343   3.5308  -1.9181   1.5551
 BQ5  H15  H  HNH2  0   0.352   4.6130  -2.3919   0.4519

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
 BQ5  C16  C15  aromatic  1.387  0.020  1.387
 BQ5  C16  C14  aromatic  1.389  0.020  1.389
 BQ5  C15  C12  aromatic  1.388  0.020  1.388
 BQ5  C14  C13  aromatic  1.386  0.020  1.386
 BQ5  C12  C6   aromatic  1.392  0.020  1.392
 BQ5  C13  C6   aromatic  1.394  0.020  1.394
 BQ5  C6   N1   single    1.405  0.020  1.405
 BQ5  N1   N2   aromatic  1.347  0.020  1.347
 BQ5  N1   C3   aromatic  1.356  0.020  1.356
 BQ5  C8   C3   single    1.492  0.020  1.492
 BQ5  C8   C11  single    1.555  0.020  1.555
 BQ5  N2   C5   aromatic  1.320  0.020  1.320
 BQ5  C3   C4   aromatic  1.362  0.020  1.362
 BQ5  C5   C4   aromatic  1.408  0.020  1.408
 BQ5  C5   C9   single    1.492  0.020  1.492
 BQ5  C4   C7   single    1.492  0.020  1.492
 BQ5  C11  C7   single    1.554  0.020  1.554
 BQ5  N10  C9   single    1.454  0.020  1.454
 BQ5  C7   H1   single    0.970  0.020  1.090
 BQ5  C7   H2   single    0.970  0.020  1.090
 BQ5  C8   H3   single    0.970  0.020  1.090
 BQ5  C8   H4   single    0.970  0.020  1.090
 BQ5  C13  H5   single    0.930  0.020  1.080
 BQ5  C15  H6   single    0.930  0.020  1.080
 BQ5  C12  H7   single    0.930  0.020  1.080
 BQ5  C16  H8   single    0.930  0.020  1.080
 BQ5  C14  H9   single    0.930  0.020  1.080
 BQ5  C11  H10  single    0.970  0.020  1.090
 BQ5  C11  H11  single    0.970  0.020  1.090
 BQ5  C9   H12  single    0.970  0.020  1.090
 BQ5  C9   H13  single    0.970  0.020  1.090
 BQ5  N10  H14  single    0.890  0.020  1.040
 BQ5  N10  H15  single    0.890  0.020  1.040

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
 BQ5  C3   N1   N2   110.52  3.000
 BQ5  C3   N1   C6   129.88  3.000
 BQ5  N2   N1   C6   119.58  3.000
 BQ5  C3   C4   C7   111.84  3.000
 BQ5  C7   C4   C5   142.76  3.000
 BQ5  C3   C4   C5   105.24  3.000
 BQ5  C9   C5   N2   121.21  3.000
 BQ5  C9   C5   C4   128.70  3.000
 BQ5  N2   C5   C4   110.09  3.000
 BQ5  C12  C6   C13  119.74  3.000
 BQ5  C13  C6   N1   119.65  3.000
 BQ5  C12  C6   N1   120.61  3.000
 BQ5  H2   C7   H1   106.73  3.000
 BQ5  H2   C7   C11  111.61  3.000
 BQ5  H1   C7   C11  111.83  3.000
 BQ5  H2   C7   C4   111.36  3.000
 BQ5  H1   C7   C4   113.34  3.000
 BQ5  C11  C7   C4   102.06  3.000
 BQ5  H4   C8   H3   106.98  3.000
 BQ5  H4   C8   C11  111.05  3.000
 BQ5  H3   C8   C11  112.39  3.000
 BQ5  H4   C8   C3   114.40  3.000
 BQ5  H3   C8   C3   111.13  3.000
 BQ5  C11  C8   C3   100.98  3.000
 BQ5  H5   C13  C14  120.13  3.000
 BQ5  H5   C13  C6   120.10  3.000
 BQ5  C14  C13  C6   119.77  3.000
 BQ5  H6   C15  C16  120.25  3.000
 BQ5  H6   C15  C12  119.07  3.000
 BQ5  C16  C15  C12  120.67  3.000
 BQ5  H7   C12  C15  119.17  3.000
 BQ5  H7   C12  C6   120.94  3.000
 BQ5  C15  C12  C6   119.88  3.000
 BQ5  H8   C16  C14  120.43  3.000
 BQ5  H8   C16  C15  120.40  3.000
 BQ5  C14  C16  C15  119.17  3.000
 BQ5  H9   C14  C16  120.13  3.000
 BQ5  H9   C14  C13  119.10  3.000
 BQ5  C16  C14  C13  120.77  3.000
 BQ5  C5   N2   N1   106.70  3.000
 BQ5  C8   C3   C4   113.81  3.000
 BQ5  C4   C3   N1   107.45  3.000
 BQ5  C8   C3   N1   138.56  3.000
 BQ5  H11  C11  H10  107.01  3.000
 BQ5  H11  C11  C8   111.54  3.000
 BQ5  H10  C11  C8   108.65  3.000
 BQ5  H11  C11  C7   112.12  3.000
 BQ5  H10  C11  C7   109.19  3.000
 BQ5  C8   C11  C7   108.26  3.000
 BQ5  H13  C9   H12  106.23  3.000
 BQ5  H13  C9   N10  107.73  3.000
 BQ5  H12  C9   N10  114.61  3.000
 BQ5  H13  C9   C5   108.86  3.000
 BQ5  H12  C9   C5   108.75  3.000
 BQ5  N10  C9   C5   110.45  3.000
 BQ5  H15  N10  H14  105.98  3.000
 BQ5  H15  N10  C9   109.24  3.000
 BQ5  H14  N10  C9   109.43  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
 BQ5  CONST_01  C15  C12  C6   N1    180.00   0.0  0
 BQ5  CONST_02  C14  C13  C6   N1    180.00   0.0  0
 BQ5  CONST_03  C4   C5   N2   N1      0.00   0.0  0
 BQ5  CONST_04  C5   C4   C3   N1      0.00   0.0  0
 BQ5  CONST_05  C6   N1   C3   C4    180.00   0.0  0
 BQ5  CONST_06  N2   N1   C3   C4      0.00   0.0  0
 BQ5  CONST_07  C6   N1   N2   C5    180.00   0.0  0
 BQ5  CONST_08  C3   N1   N2   C5      0.00   0.0  0
 BQ5  CONST_09  C16  C15  C12  C6      0.00   0.0  0
 BQ5  CONST_10  C16  C14  C13  C6      0.00   0.0  0
 BQ5  CONST_11  C15  C16  C14  C13     0.00   0.0  0
 BQ5  CONST_12  C15  C12  C6   C13     0.00   0.0  0
 BQ5  CONST_15  C14  C16  C15  C12     0.00   0.0  0
 BQ5  CONST_16  C14  C13  C6   C12     0.00   0.0  0
 BQ5  CONST_19  C3   C4   C5   N2      0.00   0.0  0
 BQ5  CONST_20  C8   C3   N1   C6      0.00   0.0  0
 BQ5  CONST_21  C9   C5   N2   N1    180.00   0.0  0
 BQ5  CONST_22  C9   C5   C4   C7      0.00   0.0  0
 BQ5  CONST_23  C9   C5   C4   C3    180.00   0.0  0
 BQ5  CONST_24  H7   C12  C6   N1      0.00   0.0  0
 BQ5  CONST_25  H5   C13  C6   N1      0.00   0.0  0
 BQ5  CONST_26  H6   C15  C12  C6    180.00   0.0  0
 BQ5  CONST_27  H9   C14  C13  C6    180.00   0.0  0
 BQ5  CONST_28  H8   C16  C14  C13   180.00   0.0  0
 BQ5  Var_01    C11  C8   C3   N1    174.86  30.0  1
 BQ5  Var_02    C8   C11  C7   C4    -16.80  30.0  1
 BQ5  Var_03    C11  C7   C4   C5   -175.30  30.0  1
 BQ5  Var_04    C3   C8   C11  C7     16.74  30.0  1
 BQ5  Var_05    N10  C9   C5   C4     46.70  30.0  2
 BQ5  Var_06    H14  N10  C9   C5     69.60  30.0  3

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
 BQ5  plan-1  N1   0.020
 BQ5  plan-1  C6   0.020
 BQ5  plan-1  C13  0.020
 BQ5  plan-1  C15  0.020
 BQ5  plan-1  C12  0.020
 BQ5  plan-1  C16  0.020
 BQ5  plan-1  C14  0.020
 BQ5  plan-1  H5   0.020
 BQ5  plan-1  H6   0.020
 BQ5  plan-1  H7   0.020
 BQ5  plan-1  H8   0.020
 BQ5  plan-1  H9   0.020
 BQ5  plan-2  N1   0.020
 BQ5  plan-2  C4   0.020
 BQ5  plan-2  C5   0.020
 BQ5  plan-2  C6   0.020
 BQ5  plan-2  C7   0.020
 BQ5  plan-2  C8   0.020
 BQ5  plan-2  N2   0.020
 BQ5  plan-2  C3   0.020
 BQ5  plan-2  C9   0.020

