# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 04:35:41 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 4-(2-phenylhydrazinyl)-1H-pyrazolo[3,4-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N(Nc1ncnc2[nH]ncc12)c3ccccc3
#
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
 12R  12R  4-(2-phenylhydrazinyl)-1H-pyrazolo[3,4-d]pyrimidine  ligand  27  17  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_12R
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
 12R  C4   C  CR6   0   0.506   0.7323  -0.1192   0.4926
 12R  C14  C  CR16  0  -0.343  -3.4181  -1.1416   0.6050
 12R  C5   C  CR56  0  -0.207   1.9661   0.5506   0.3645
 12R  C6   C  CR56  0   0.542   2.8144   0.0564  -0.6285
 12R  C10  C  CR15  0  -0.121   2.6825   1.6249   0.9464
 12R  C13  C  CR6   0   0.345  -2.3860  -0.2033   0.6739
 12R  N1   N  N     0  -0.449   2.5546  -0.9705  -1.4450
 12R  N3   N  N     0  -0.469   0.4607  -1.1416  -0.3074
 12R  C2   C  CR16  0   0.060   1.3729  -1.5009  -1.2160
 12R  N7   N  NR15  0  -0.511   3.9198   0.8180  -0.5843
 12R  N9   N  N     0  -0.231   3.8459   1.7637   0.3630
 12R  N11  N  NH1   0  -0.529  -0.1798   0.2553   1.4106
 12R  N12  N  NH1   0  -0.535  -1.3594  -0.4054   1.5957
 12R  C15  C  CR16  0  -0.247  -4.4873  -0.9431  -0.2533
 12R  C16  C  CR16  0  -0.284  -4.5499   0.1868  -1.0600
 12R  C17  C  CR16  0  -0.249  -3.5213   1.1165  -0.9911
 12R  C18  C  CR16  0  -0.311  -2.4451   0.9314  -0.1341
 12R  H2   H  HCR5  0   0.274   2.3922   2.2822   1.7518
 12R  H3   H  HCR6  0   0.258   1.0945  -2.3424  -1.8415
 12R  H4   H  HNR5  0   0.422   4.7457   0.7371  -1.1565
 12R  H5   H  HNH1  0   0.414   0.0402   0.9779   2.0772
 12R  H6   H  HNH1  0   0.389  -1.2349  -1.3658   1.8860
 12R  H7   H  HCR6  0   0.255  -5.2761  -1.6833  -0.2933
 12R  H8   H  HCR6  0   0.249  -5.3851   0.3388  -1.7306
 12R  H9   H  HCR6  0   0.254  -3.5505   2.0034  -1.6114
 12R  H10  H  HCR6  0   0.259  -1.6576   1.6720  -0.0955
 12R  H1   H  HCR6  0   0.259  -3.3840  -2.0287   1.2271

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
 12R  C14  C15  aromatic  1.385  0.020  1.385
 12R  C14  C13  aromatic  1.397  0.020  1.397
 12R  C15  C16  aromatic  1.390  0.020  1.390
 12R  N12  C13  single    1.394  0.020  1.394
 12R  N12  N11  single    1.365  0.020  1.365
 12R  C10  N9   aromatic  1.309  0.020  1.309
 12R  C10  C5   aromatic  1.416  0.020  1.416
 12R  N9   N7   aromatic  1.341  0.020  1.341
 12R  C13  C18  aromatic  1.394  0.020  1.394
 12R  N11  C4   single    1.347  0.020  1.347
 12R  C5   C4   aromatic  1.410  0.020  1.410
 12R  C5   C6   aromatic  1.396  0.020  1.396
 12R  N7   C6   aromatic  1.343  0.020  1.343
 12R  C16  C17  aromatic  1.388  0.020  1.388
 12R  C4   N3   aromatic  1.326  0.020  1.326
 12R  C6   N1   aromatic  1.337  0.020  1.337
 12R  C18  C17  aromatic  1.388  0.020  1.388
 12R  N3   C2   aromatic  1.337  0.020  1.337
 12R  N1   C2   aromatic  1.315  0.020  1.315
 12R  C14  H1   single    0.930  0.020  1.080
 12R  C10  H2   single    0.930  0.020  1.080
 12R  C2   H3   single    0.930  0.020  1.080
 12R  N7   H4   single    0.860  0.020  1.020
 12R  N11  H5   single    0.860  0.020  1.020
 12R  N12  H6   single    0.890  0.020  1.040
 12R  C15  H7   single    0.930  0.020  1.080
 12R  C16  H8   single    0.930  0.020  1.080
 12R  C17  H9   single    0.930  0.020  1.080
 12R  C18  H10  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
 12R  N11  C4   N3   119.12  3.000
 12R  N3   C4   C5   119.39  3.000
 12R  N11  C4   C5   121.49  3.000
 12R  H1   C14  C15  119.80  3.000
 12R  H1   C14  C13  119.88  3.000
 12R  C15  C14  C13  120.31  3.000
 12R  C10  C5   C6   104.68  3.000
 12R  C6   C5   C4   115.35  3.000
 12R  C10  C5   C4   139.98  3.000
 12R  N7   C6   N1   127.98  3.000
 12R  N1   C6   C5   126.01  3.000
 12R  N7   C6   C5   106.01  3.000
 12R  H2   C10  N9   120.47  3.000
 12R  H2   C10  C5   129.23  3.000
 12R  N9   C10  C5   110.30  3.000
 12R  C18  C13  N12  122.16  3.000
 12R  C18  C13  C14  119.13  3.000
 12R  N12  C13  C14  118.64  3.000
 12R  C2   N1   C6   112.20  3.000
 12R  C2   N3   C4   118.52  3.000
 12R  H3   C2   N3   115.17  3.000
 12R  H3   C2   N1   116.29  3.000
 12R  N3   C2   N1   128.54  3.000
 12R  H4   N7   N9   120.19  3.000
 12R  H4   N7   C6   127.60  3.000
 12R  N9   N7   C6   112.20  3.000
 12R  N7   N9   C10  106.81  3.000
 12R  H5   N11  N12  116.50  3.000
 12R  H5   N11  C4   120.16  3.000
 12R  N12  N11  C4   122.90  3.000
 12R  H6   N12  N11  113.10  3.000
 12R  H6   N12  C13  114.72  3.000
 12R  N11  N12  C13  118.46  3.000
 12R  H7   C15  C16  120.11  3.000
 12R  H7   C15  C14  119.17  3.000
 12R  C16  C15  C14  120.72  3.000
 12R  H8   C16  C17  120.58  3.000
 12R  H8   C16  C15  120.59  3.000
 12R  C17  C16  C15  118.83  3.000
 12R  H9   C17  C18  118.94  3.000
 12R  H9   C17  C16  120.01  3.000
 12R  C18  C17  C16  121.05  3.000
 12R  H10  C18  C17  119.68  3.000
 12R  H10  C18  C13  120.37  3.000
 12R  C17  C18  C13  119.95  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
 12R  CONST_01  N9   C10  C5   C4   180.00  0.0  0
 12R  CONST_02  N7   C6   C5   C4   180.00  0.0  0
 12R  CONST_03  N1   C6   C5   C4     0.00  0.0  0
 12R  CONST_04  N1   C2   N3   C4     0.00  0.0  0
 12R  CONST_05  C17  C16  C15  C14    0.00  0.0  0
 12R  CONST_06  C17  C18  C13  C14    0.00  0.0  0
 12R  CONST_07  N7   N9   C10  C5     0.00  0.0  0
 12R  CONST_08  C2   N3   C4   C5     0.00  0.0  0
 12R  CONST_09  N9   N7   C6   C5     0.00  0.0  0
 12R  CONST_10  C2   N1   C6   C5     0.00  0.0  0
 12R  CONST_11  N9   C10  C5   C6     0.00  0.0  0
 12R  CONST_12  N3   C4   C5   C6     0.00  0.0  0
 12R  CONST_13  C10  N9   N7   C6     0.00  0.0  0
 12R  CONST_14  N3   C2   N1   C6     0.00  0.0  0
 12R  CONST_15  N3   C4   C5   C10  180.00  0.0  0
 12R  CONST_16  N7   C6   C5   C10    0.00  0.0  0
 12R  CONST_17  N1   C6   C5   C10  180.00  0.0  0
 12R  CONST_18  C16  C15  C14  C13    0.00  0.0  0
 12R  CONST_19  C16  C17  C18  C13    0.00  0.0  0
 12R  CONST_20  N9   N7   C6   N1   180.00  0.0  0
 12R  CONST_21  N7   C6   N1   C2   180.00  0.0  0
 12R  CONST_22  C18  C13  C14  C15    0.00  0.0  0
 12R  CONST_23  C18  C17  C16  C15    0.00  0.0  0
 12R  CONST_24  N11  C4   C5   C6   180.00  0.0  0
 12R  CONST_25  N11  C4   C5   C10    0.00  0.0  0
 12R  CONST_26  N11  C4   N3   C2   180.00  0.0  0
 12R  CONST_27  C15  C14  C13  N12  180.00  0.0  0
 12R  CONST_28  C17  C18  C13  N12  180.00  0.0  0
 12R  CONST_29  H2   C10  C5   C4     0.00  0.0  0
 12R  CONST_30  H3   C2   N3   C4   180.00  0.0  0
 12R  CONST_31  H8   C16  C15  C14  180.00  0.0  0
 12R  CONST_32  H10  C18  C13  C14  180.00  0.0  0
 12R  CONST_33  H4   N7   C6   C5   180.00  0.0  0
 12R  CONST_34  H7   C15  C14  C13  180.00  0.0  0
 12R  CONST_35  H9   C17  C18  C13  180.00  0.0  0
 12R  CONST_36  H1   C14  C15  C16  180.00  0.0  0
 12R  CONST_39  N12  N11  C4   C5   180.00  0.0  0
 12R  CONST_40  N12  N11  C4   N3     0.00  0.0  0
 12R  CONST_43  H5   N11  C4   C5     0.00  0.0  0

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
 12R  plan-1  C14  0.020
 12R  plan-1  C13  0.020
 12R  plan-1  N12  0.020
 12R  plan-1  C15  0.020
 12R  plan-1  C16  0.020
 12R  plan-1  C17  0.020
 12R  plan-1  C18  0.020
 12R  plan-1  H7   0.020
 12R  plan-1  H8   0.020
 12R  plan-1  H9   0.020
 12R  plan-1  H10  0.020
 12R  plan-1  H1   0.020
 12R  plan-2  C4   0.020
 12R  plan-2  C5   0.020
 12R  plan-2  C6   0.020
 12R  plan-2  C10  0.020
 12R  plan-2  N1   0.020
 12R  plan-2  N3   0.020
 12R  plan-2  C2   0.020
 12R  plan-2  N7   0.020
 12R  plan-2  N9   0.020
 12R  plan-2  N11  0.020
 12R  plan-2  H2   0.020
 12R  plan-2  H3   0.020
 12R  plan-2  H4   0.020
 12R  plan-3  C13  0.020
 12R  plan-3  N11  0.020
 12R  plan-3  N12  0.020
 12R  plan-3  H6   0.020
 12R  plan-4  C4   0.020
 12R  plan-4  N11  0.020
 12R  plan-4  N12  0.020
 12R  plan-4  H5   0.020

