# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:27:20 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1C(=O)/C=C/N2CCc3c[nH]nc3C2
#
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
 2XD  2XD  (2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one  ligand  35  20  .  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_2XD
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
 2XD  C4   C  CR16  0  -0.311   2.9644   1.5163  -0.3555
 2XD  C14  C  CH2   0  -0.340  -2.2296   0.5407  -0.8472
 2XD  C5   C  CR6   0  -0.166   3.0646   0.1425  -0.1014
 2XD  C6   C  C     0   0.423   1.8910  -0.7654  -0.0974
 2XD  C11  C  CR5   0  -0.128  -4.2930  -0.3083   0.4070
 2XD  C7   C  C1    0  -0.551   0.5881  -0.2497  -0.3766
 2XD  C8   C  C1    0   0.136  -0.4856  -1.1034  -0.3839
 2XD  C9   C  CH2   0  -0.328  -2.7646  -1.8720  -0.6716
 2XD  C10  C  CH2   0  -0.498  -3.8190  -1.7214   0.4198
 2XD  C12  C  CR15  0  -0.018  -5.4246   0.3167   0.8810
 2XD  C13  C  CR5   0   0.228  -3.5560   0.7285  -0.1852
 2XD  N1   N  NR15  0  -0.425  -5.2980   1.6152   0.5590
 2XD  N2   N  N     0  -0.302  -4.1723   1.8918  -0.0889
 2XD  C3   C  CR16  0  -0.270   4.0713   2.3403  -0.3550
 2XD  O1   O  O     0  -0.546   2.0834  -1.9772   0.1526
 2XD  C2   C  CR16  0  -0.241   5.3268   1.7937  -0.0948
 2XD  C1   C  CR16  0  -0.345   5.4652   0.4452   0.1624
 2XD  C    C  CR6   0   0.360   4.3462  -0.3936   0.1640
 2XD  O    O  OH1   0  -0.638   4.5322  -1.6862   0.4192
 2XD  N    N  NT    0  -0.433  -1.7631  -0.8139  -0.5926
 2XD  H1   H  HCR6  0   0.263   1.9997   1.9592  -0.5597
 2XD  H3   H  HCH2  0   0.283  -1.5091   1.2549  -0.4509
 2XD  H4   H  H     0   0.271   0.4617   0.7988  -0.5925
 2XD  H5   H  H     0   0.289  -0.2994  -2.1555  -0.1994
 2XD  H6   H  HCH2  0   0.273  -2.2588  -2.8327  -0.5961
 2XD  H7   H  HCH2  0   0.263  -3.2401  -1.8300  -1.6559
 2XD  H8   H  HCH2  0   0.252  -3.3871  -1.9869   1.3886
 2XD  H9   H  HCH2  0   0.258  -4.6318  -2.4246   0.2307
 2XD  H10  H  HCR5  0   0.288  -6.2873  -0.0587   1.4068
 2XD  H11  H  HNR5  0   0.421  -5.9509   2.3543   0.7639
 2XD  H12  H  HCR6  0   0.257   3.9625   3.3976  -0.5530
 2XD  H13  H  HCR6  0   0.263   6.2034   2.4287  -0.0927
 2XD  H14  H  HCR6  0   0.263   6.4392   0.0189   0.3677
 2XD  H15  H  HOH1  0   0.474   3.6217  -2.0973   0.3782
 2XD  H2   H  HCH2  0   0.276  -2.2957   0.7133  -1.9269

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
 2XD  N1   N2   aromatic  1.328  0.020  1.328
 2XD  N1   C12  aromatic  1.344  0.020  1.344
 2XD  N2   C13  aromatic  1.320  0.020  1.320
 2XD  C12  C11  aromatic  1.377  0.020  1.377
 2XD  C13  C11  aromatic  1.403  0.020  1.403
 2XD  C13  C14  single    1.494  0.020  1.494
 2XD  C11  C10  single    1.491  0.020  1.491
 2XD  C14  N    single    1.455  0.020  1.455
 2XD  C10  C9   single    1.525  0.020  1.525
 2XD  C9   N    single    1.459  0.020  1.459
 2XD  N    C8   single    1.326  0.020  1.326
 2XD  C8   C7   double    1.372  0.020  1.372
 2XD  C7   C6   single    1.429  0.020  1.429
 2XD  C6   O1   double    1.252  0.020  1.252
 2XD  C6   C5   single    1.484  0.020  1.484
 2XD  C4   C5   aromatic  1.401  0.020  1.401
 2XD  C4   C3   aromatic  1.380  0.020  1.380
 2XD  C5   C    aromatic  1.414  0.020  1.414
 2XD  C3   C2   aromatic  1.394  0.020  1.394
 2XD  C    O    single    1.331  0.020  1.331
 2XD  C    C1   aromatic  1.398  0.020  1.398
 2XD  C2   C1   aromatic  1.380  0.020  1.380
 2XD  C4   H1   single    0.930  0.020  1.080
 2XD  C14  H2   single    0.970  0.020  1.090
 2XD  C14  H3   single    0.970  0.020  1.090
 2XD  C7   H4   single    0.930  0.020  1.080
 2XD  C8   H5   single    0.930  0.020  1.080
 2XD  C9   H6   single    0.970  0.020  1.090
 2XD  C9   H7   single    0.970  0.020  1.090
 2XD  C10  H8   single    0.970  0.020  1.090
 2XD  C10  H9   single    0.970  0.020  1.090
 2XD  C12  H10  single    0.930  0.020  1.080
 2XD  N1   H11  single    0.860  0.020  1.020
 2XD  C3   H12  single    0.930  0.020  1.080
 2XD  C2   H13  single    0.930  0.020  1.080
 2XD  C1   H14  single    0.930  0.020  1.080
 2XD  O    H15  single    0.850  0.020  0.980

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
 2XD  H1   C4   C3   118.11  3.000
 2XD  H1   C4   C5   120.00  3.000
 2XD  C3   C4   C5   121.89  3.000
 2XD  H3   C14  H2   107.17  3.000
 2XD  H3   C14  N    109.55  3.000
 2XD  H2   C14  N    109.79  3.000
 2XD  H3   C14  C13  110.09  3.000
 2XD  H2   C14  C13  111.31  3.000
 2XD  N    C14  C13  108.91  3.000
 2XD  C    C5   C6   118.97  3.000
 2XD  C    C5   C4   118.07  3.000
 2XD  C6   C5   C4   122.96  3.000
 2XD  O1   C6   C7   121.90  3.000
 2XD  O1   C6   C5   118.11  3.000
 2XD  C7   C6   C5   119.99  3.000
 2XD  C13  C11  C12  103.98  3.000
 2XD  C13  C11  C10  122.49  3.000
 2XD  C12  C11  C10  133.53  3.000
 2XD  H4   C7   C8   120.83  3.000
 2XD  H4   C7   C6   119.81  3.000
 2XD  C8   C7   C6   119.35  3.000
 2XD  H5   C8   N    113.83  3.000
 2XD  H5   C8   C7   117.94  3.000
 2XD  N    C8   C7   128.23  3.000
 2XD  H7   C9   H6   107.36  3.000
 2XD  H7   C9   N    108.62  3.000
 2XD  H6   C9   N    108.51  3.000
 2XD  H7   C9   C10  109.85  3.000
 2XD  H6   C9   C10  111.03  3.000
 2XD  N    C9   C10  111.36  3.000
 2XD  H9   C10  H8   106.93  3.000
 2XD  H9   C10  C9   109.11  3.000
 2XD  H8   C10  C9   109.70  3.000
 2XD  H9   C10  C11  111.87  3.000
 2XD  H8   C10  C11  111.30  3.000
 2XD  C9   C10  C11  107.90  3.000
 2XD  H10  C12  N1   121.93  3.000
 2XD  H10  C12  C11  131.89  3.000
 2XD  N1   C12  C11  106.18  3.000
 2XD  N2   C13  C11  112.04  3.000
 2XD  C11  C13  C14  124.08  3.000
 2XD  N2   C13  C14  123.89  3.000
 2XD  H11  N1   N2   119.73  3.000
 2XD  H11  N1   C12  126.82  3.000
 2XD  N2   N1   C12  113.45  3.000
 2XD  N1   N2   C13  104.35  3.000
 2XD  H12  C3   C2   120.55  3.000
 2XD  H12  C3   C4   120.21  3.000
 2XD  C2   C3   C4   119.24  3.000
 2XD  H13  C2   C1   119.46  3.000
 2XD  H13  C2   C3   119.99  3.000
 2XD  C1   C2   C3   120.56  3.000
 2XD  H14  C1   C    118.91  3.000
 2XD  H14  C1   C2   120.68  3.000
 2XD  C    C1   C2   120.41  3.000
 2XD  O    C    C1   118.10  3.000
 2XD  C1   C    C5   119.84  3.000
 2XD  O    C    C5   122.06  3.000
 2XD  H15  O    C    105.33  3.000
 2XD  C9   N    C8   120.75  3.000
 2XD  C8   N    C14  122.65  3.000
 2XD  C9   N    C14  116.46  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
 2XD  CONST_01  C1   C    C5   C4     0.00   0.0  0
 2XD  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 2XD  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 2XD  CONST_04  C2   C1   C    C5     0.00   0.0  0
 2XD  CONST_05  N2   N1   C12  C11    0.00   0.0  0
 2XD  CONST_06  N1   N2   C13  C11    0.00   0.0  0
 2XD  CONST_07  C13  N2   N1   C12    0.00   0.0  0
 2XD  CONST_08  N2   C13  C11  C12    0.00   0.0  0
 2XD  CONST_09  N1   C12  C11  C13    0.00   0.0  0
 2XD  CONST_10  C    C5   C4   C3     0.00   0.0  0
 2XD  CONST_11  C    C1   C2   C3     0.00   0.0  0
 2XD  CONST_12  O    C    C5   C4   180.00   0.0  0
 2XD  CONST_13  C3   C4   C5   C6   180.00   0.0  0
 2XD  CONST_14  C1   C    C5   C6   180.00   0.0  0
 2XD  CONST_15  O    C    C1   C2   180.00   0.0  0
 2XD  CONST_16  H13  C2   C3   C4   180.00   0.0  0
 2XD  CONST_17  H12  C3   C4   C5   180.00   0.0  0
 2XD  CONST_18  H14  C1   C    C5   180.00   0.0  0
 2XD  CONST_19  H11  N1   C12  C11  180.00   0.0  0
 2XD  CONST_20  H10  C12  C11  C10    0.00   0.0  0
 2XD  CONST_21  H1   C4   C3   C2   180.00   0.0  0
 2XD  Var_01    C10  C9   N    C14  -65.13  30.0  1
 2XD  Var_02    N    C14  C13  C11   -8.52  30.0  1
 2XD  Var_03    N    C9   C10  C11   49.05  30.0  1
 2XD  Var_04    C12  C11  C10  C9   159.87  30.0  1
 2XD  Var_05    C13  C14  N    C9    41.07  30.0  1
 2XD  Var_06    C7   C6   C5   C4     0.75  30.0  2
 2XD  Var_07    C7   C8   N    C14   -0.60  30.0  2
 2XD  Var_08    N    C8   C7   C6   178.53   0.0  2
 2XD  Var_09    C8   C7   C6   C5   179.29  30.0  1

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
 2XD  plan-1  C4   0.020
 2XD  plan-1  C5   0.020
 2XD  plan-1  C6   0.020
 2XD  plan-1  C3   0.020
 2XD  plan-1  C2   0.020
 2XD  plan-1  C1   0.020
 2XD  plan-1  C    0.020
 2XD  plan-1  O    0.020
 2XD  plan-1  H1   0.020
 2XD  plan-1  H12  0.020
 2XD  plan-1  H13  0.020
 2XD  plan-1  H14  0.020
 2XD  plan-2  C14  0.020
 2XD  plan-2  C11  0.020
 2XD  plan-2  C10  0.020
 2XD  plan-2  C12  0.020
 2XD  plan-2  C13  0.020
 2XD  plan-2  N1   0.020
 2XD  plan-2  N2   0.020
 2XD  plan-2  H10  0.020
 2XD  plan-2  H11  0.020
 2XD  plan-3  C5   0.020
 2XD  plan-3  C6   0.020
 2XD  plan-3  C7   0.020
 2XD  plan-3  O1   0.020
 2XD  plan-4  C6   0.020
 2XD  plan-4  C7   0.020
 2XD  plan-4  C8   0.020
 2XD  plan-4  N    0.020
 2XD  plan-4  H4   0.020
 2XD  plan-4  H5   0.020

