# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:21:08 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-methyl-5-(pyridin-3-yl)-2H-pyrazolo[3,4-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc2cnc(cc12)c3cccnc3
#
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
 5E5  5E5  3-methyl-5-(pyridin-3-yl)-2H-pyrazolo[3,4-c]pyridine  ligand  26  16  .  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_5E5
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
 5E5  C7   C  CR16  0  -0.391  -0.4191  -0.7085   0.0464
 5E5  C2   C  CR5   0   0.361  -2.9932  -1.0552   0.0868
 5E5  C10  C  CR16  0  -0.093  -1.1329   1.9613  -0.2620
 5E5  N3   N  NR15  0  -0.449  -3.9244  -0.1001  -0.0304
 5E5  C6   C  CR56  0  -0.026  -1.7819  -0.3663   0.0045
 5E5  C1   C  CH3   0  -0.737  -3.2992  -2.4930   0.2867
 5E5  N4   N  N     0  -0.296  -3.4789   1.1390  -0.1775
 5E5  C5   C  CR56  0   0.146  -2.1549   0.9906  -0.1571
 5E5  C8   C  CR6   0   0.192   0.4899   0.3126  -0.0858
 5E5  N9   N  N     0  -0.432   0.1209   1.6213  -0.2262
 5E5  C11  C  CR6   0  -0.018   1.9451   0.0700  -0.0632
 5E5  C12  C  CR16  0  -0.179   2.8406   1.0720   0.3072
 5E5  C13  C  CR16  0  -0.314   4.1970   0.7972   0.3289
 5E5  C14  C  CR16  0  -0.074   4.6249  -0.4727  -0.0274
 5E5  N15  N  N     0  -0.399   3.7896  -1.4353  -0.4015
 5E5  C16  C  CR16  0  -0.113   2.4928  -1.1633  -0.4209
 5E5  H1   H  HCR6  0   0.266  -0.1038  -1.7328   0.1969
 5E5  H2   H  HCR6  0   0.269  -1.3720   3.0144  -0.3740
 5E5  H3   H  HNR5  0   0.432  -4.9231  -0.2559  -0.0162
 5E5  H4   H  HCH3  0   0.268  -3.4277  -2.7256   1.3450
 5E5  H5   H  HCH3  0   0.266  -4.2108  -2.7863  -0.2326
 5E5  H6   H  HCH3  0   0.263  -2.4839  -3.1081  -0.0899
 5E5  H7   H  HCR6  0   0.265   2.4748   2.0518   0.5826
 5E5  H8   H  HCR6  0   0.271   4.9140   1.5531   0.6191
 5E5  H9   H  HCR6  0   0.265   5.6804  -0.7204  -0.0170
 5E5  H10  H  HCR6  0   0.257   1.8478  -1.9679  -0.7588

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
 5E5  C13  C12  aromatic  1.384  0.020  1.384
 5E5  C13  C14  aromatic  1.387  0.020  1.387
 5E5  C1   C2   single    1.484  0.020  1.484
 5E5  C12  C11  aromatic  1.394  0.020  1.394
 5E5  C14  N15  aromatic  1.328  0.020  1.328
 5E5  C7   C6   aromatic  1.406  0.020  1.406
 5E5  C7   C8   aromatic  1.373  0.020  1.373
 5E5  C2   C6   aromatic  1.396  0.020  1.396
 5E5  C2   N3   aromatic  1.339  0.020  1.339
 5E5  C11  C8   single    1.475  0.020  1.475
 5E5  C11  C16  aromatic  1.396  0.020  1.396
 5E5  C6   C5   aromatic  1.416  0.020  1.416
 5E5  N15  C16  aromatic  1.325  0.020  1.325
 5E5  C8   N9   aromatic  1.367  0.020  1.367
 5E5  N3   N4   aromatic  1.325  0.020  1.325
 5E5  C5   N4   aromatic  1.332  0.020  1.332
 5E5  C5   C10  aromatic  1.413  0.020  1.413
 5E5  N9   C10  aromatic  1.300  0.020  1.300
 5E5  C7   H1   single    0.930  0.020  1.080
 5E5  C10  H2   single    0.930  0.020  1.080
 5E5  N3   H3   single    0.860  0.020  1.020
 5E5  C1   H4   single    0.970  0.020  1.090
 5E5  C1   H5   single    0.970  0.020  1.090
 5E5  C1   H6   single    0.970  0.020  1.090
 5E5  C12  H7   single    0.930  0.020  1.080
 5E5  C13  H8   single    0.930  0.020  1.080
 5E5  C14  H9   single    0.930  0.020  1.080
 5E5  C16  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
 5E5  H1   C7   C8   121.62  3.000
 5E5  H1   C7   C6   121.13  3.000
 5E5  C8   C7   C6   117.24  3.000
 5E5  C1   C2   C6   131.70  3.000
 5E5  C6   C2   N3   104.25  3.000
 5E5  C1   C2   N3   124.03  3.000
 5E5  H2   C10  N9   117.97  3.000
 5E5  H2   C10  C5   120.98  3.000
 5E5  N9   C10  C5   121.05  3.000
 5E5  H3   N3   N4   118.55  3.000
 5E5  H3   N3   C2   125.16  3.000
 5E5  N4   N3   C2   116.29  3.000
 5E5  C5   C6   C2   104.54  3.000
 5E5  C5   C6   C7   119.46  3.000
 5E5  C2   C6   C7   136.00  3.000
 5E5  H6   C1   H5   108.04  3.000
 5E5  H6   C1   H4   107.66  3.000
 5E5  H5   C1   H4   107.84  3.000
 5E5  H6   C1   C2   110.27  3.000
 5E5  H5   C1   C2   111.68  3.000
 5E5  H4   C1   C2   111.20  3.000
 5E5  C5   N4   N3   103.19  3.000
 5E5  N4   C5   C6   111.72  3.000
 5E5  N4   C5   C10  129.85  3.000
 5E5  C6   C5   C10  118.43  3.000
 5E5  C11  C8   N9   115.16  3.000
 5E5  N9   C8   C7   122.89  3.000
 5E5  C11  C8   C7   121.94  3.000
 5E5  C8   N9   C10  120.91  3.000
 5E5  C16  C11  C12  116.81  3.000
 5E5  C16  C11  C8   121.89  3.000
 5E5  C12  C11  C8   121.30  3.000
 5E5  H7   C12  C13  120.49  3.000
 5E5  H7   C12  C11  120.11  3.000
 5E5  C13  C12  C11  119.41  3.000
 5E5  H8   C13  C14  120.29  3.000
 5E5  H8   C13  C12  121.00  3.000
 5E5  C14  C13  C12  118.70  3.000
 5E5  H9   C14  N15  116.70  3.000
 5E5  H9   C14  C13  120.48  3.000
 5E5  N15  C14  C13  122.81  3.000
 5E5  C16  N15  C14  118.09  3.000
 5E5  H10  C16  N15  115.73  3.000
 5E5  H10  C16  C11  120.11  3.000
 5E5  N15  C16  C11  124.16  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
 5E5  CONST_01  N3   C2   C6   C7   180.00   0.0  0
 5E5  CONST_02  N4   C5   C6   C7   180.00   0.0  0
 5E5  CONST_03  C10  C5   C6   C7     0.00   0.0  0
 5E5  CONST_06  C10  N9   C8   C7     0.00   0.0  0
 5E5  CONST_07  C8   C7   C6   C2   180.00   0.0  0
 5E5  CONST_08  N4   C5   C6   C2     0.00   0.0  0
 5E5  CONST_09  C10  C5   C6   C2   180.00   0.0  0
 5E5  CONST_10  C5   N4   N3   C2     0.00   0.0  0
 5E5  CONST_11  N3   N4   C5   C10  180.00   0.0  0
 5E5  CONST_12  C11  C8   N9   C10  180.00   0.0  0
 5E5  CONST_13  C5   C6   C2   N3     0.00   0.0  0
 5E5  CONST_14  C6   C5   N4   N3     0.00   0.0  0
 5E5  CONST_15  C11  C8   C7   C6   180.00   0.0  0
 5E5  CONST_16  N9   C8   C7   C6     0.00   0.0  0
 5E5  CONST_17  N4   N3   C2   C6     0.00   0.0  0
 5E5  CONST_18  N9   C10  C5   C6     0.00   0.0  0
 5E5  CONST_19  N9   C10  C5   N4   180.00   0.0  0
 5E5  CONST_20  C8   C7   C6   C5     0.00   0.0  0
 5E5  CONST_21  C8   N9   C10  C5     0.00   0.0  0
 5E5  CONST_22  C13  C12  C11  C8   180.00   0.0  0
 5E5  CONST_23  N15  C16  C11  C8   180.00   0.0  0
 5E5  CONST_26  C14  C13  C12  C11    0.00   0.0  0
 5E5  CONST_27  C14  N15  C16  C11    0.00   0.0  0
 5E5  CONST_28  N15  C14  C13  C12    0.00   0.0  0
 5E5  CONST_29  N15  C16  C11  C12    0.00   0.0  0
 5E5  CONST_30  C16  C11  C12  C13    0.00   0.0  0
 5E5  CONST_31  C16  N15  C14  C13    0.00   0.0  0
 5E5  CONST_32  C1   C2   C6   C7     0.00   0.0  0
 5E5  CONST_33  C5   C6   C2   C1   180.00   0.0  0
 5E5  CONST_34  N4   N3   C2   C1   180.00   0.0  0
 5E5  CONST_35  H1   C7   C6   C2     0.00   0.0  0
 5E5  CONST_36  H3   N3   C2   C6   180.00   0.0  0
 5E5  CONST_37  H2   C10  C5   C6   180.00   0.0  0
 5E5  CONST_38  H7   C12  C11  C8     0.00   0.0  0
 5E5  CONST_39  H10  C16  C11  C8     0.00   0.0  0
 5E5  CONST_40  H8   C13  C12  C11  180.00   0.0  0
 5E5  CONST_41  H9   C14  C13  C12  180.00   0.0  0
 5E5  Var_01    H4   C1   C2   N3   -86.49  30.0  2

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
 5E5  plan-1  C8   0.020
 5E5  plan-1  C11  0.020
 5E5  plan-1  C12  0.020
 5E5  plan-1  C13  0.020
 5E5  plan-1  C14  0.020
 5E5  plan-1  N15  0.020
 5E5  plan-1  C16  0.020
 5E5  plan-1  H7   0.020
 5E5  plan-1  H8   0.020
 5E5  plan-1  H9   0.020
 5E5  plan-1  H10  0.020
 5E5  plan-2  C7   0.020
 5E5  plan-2  C2   0.020
 5E5  plan-2  C10  0.020
 5E5  plan-2  N3   0.020
 5E5  plan-2  C6   0.020
 5E5  plan-2  C1   0.020
 5E5  plan-2  N4   0.020
 5E5  plan-2  C5   0.020
 5E5  plan-2  C8   0.020
 5E5  plan-2  N9   0.020
 5E5  plan-2  C11  0.020
 5E5  plan-2  H1   0.020
 5E5  plan-2  H2   0.020
 5E5  plan-2  H3   0.020

