# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 06:03:01 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-[1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCc2n(CC3CC3)nc(c2C1)c4cccc5[nH]ccc45
#
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
 BKD  BKD  1-[1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]ethan-1-one  ligand  47  25  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BKD
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
 BKD  C14  C  CH2   0  -0.491  -2.4879   4.5950   0.7968
 BKD  C5   C  CH2   0  -0.330  -3.2582  -1.7844  -1.0698
 BKD  C6   C  CH2   0  -0.512  -3.2347  -0.2755  -0.8181
 BKD  C7   C  CR5   0   0.432  -1.8066   0.1383  -0.7761
 BKD  C8   C  CR5   0  -0.216  -0.7346  -0.7146  -0.6668
 BKD  C9   C  CR5   0   0.222   0.3978   0.1315  -0.6559
 BKD  C12  C  CH2   0  -0.325  -2.0478   2.6305  -0.8273
 BKD  C13  C  CH1   0  -0.249  -2.3395   3.1233   0.5646
 BKD  C1   C  CH3   0  -0.811  -1.6683  -3.6802   1.8215
 BKD  C15  C  CH2   0  -0.482  -1.2842   3.8698   1.3177
 BKD  C16  C  CR6   0   0.025   1.8105  -0.2333  -0.5512
 BKD  C17  C  CR16  0  -0.375   2.2575  -1.4678  -1.0030
 BKD  C18  C  CR16  0  -0.266   3.6012  -1.8551  -0.9059
 BKD  C19  C  CR16  0  -0.319   4.5494  -1.0199  -0.3516
 BKD  C2   C  C     0   0.522  -2.7217  -3.0664   0.9302
 BKD  C20  C  CR56  0   0.352   4.1122   0.2231   0.1024
 BKD  C21  C  CR56  0   0.042   2.7636   0.6409   0.0125
 BKD  C22  C  CR15  0  -0.450   2.7039   1.9478   0.5903
 BKD  C23  C  CR15  0  -0.024   3.9715   2.2601   0.9898
 BKD  C26  C  CH2   0  -0.379  -0.9151  -2.1956  -0.5412
 BKD  N10  N  N     0  -0.312   0.0196   1.4003  -0.7436
 BKD  N11  N  NR5   0  -0.337  -1.3066   1.3873  -0.8245
 BKD  N24  N  NR15  0  -0.679   4.8150   1.2293   0.6964
 BKD  N4   N  NT    0  -0.450  -2.3051  -2.4668  -0.2106
 BKD  O3   O  O     0  -0.502  -3.9075  -3.1263   1.2287
 BKD  H1   H  HCH2  0   0.248  -2.3575   5.2573  -0.0505
 BKD  H2   H  HCH2  0   0.255  -3.2378   4.9249   1.5038
 BKD  H3   H  HCH2  0   0.273  -4.2531  -2.1888  -0.9105
 BKD  H4   H  HCH2  0   0.260  -2.9812  -1.9845  -2.1077
 BKD  H5   H  HCH2  0   0.268  -3.7832   0.2376  -1.6118
 BKD  H6   H  HCH2  0   0.265  -3.7383  -0.0380   0.1232
 BKD  H7   H  HCH2  0   0.266  -2.9739   2.4717  -1.3820
 BKD  H8   H  HCH2  0   0.269  -1.4594   3.3620  -1.3823
 BKD  H9   H  HCH1  0   0.264  -2.9855   2.4755   1.1488
 BKD  H10  H  HCH3  0   0.267  -1.0126  -4.3635   1.2818
 BKD  H11  H  HCH3  0   0.268  -1.0397  -2.9135   2.2772
 BKD  H12  H  HCH3  0   0.271  -2.1595  -4.2317   2.6188
 BKD  H13  H  HCH2  0   0.252  -0.3342   4.0379   0.8254
 BKD  H14  H  HCH2  0   0.252  -1.2083   3.7037   2.3845
 BKD  H15  H  HCR6  0   0.244   1.5624  -2.1520  -1.4722
 BKD  H16  H  HCR6  0   0.251   3.8966  -2.8266  -1.2796
 BKD  H17  H  HCR6  0   0.260   5.5876  -1.3167  -0.2749
 BKD  H18  H  HCR5  0   0.253   1.8361   2.5772   0.6842
 BKD  H19  H  HCR5  0   0.280   4.3436   3.1533   1.4652
 BKD  H20  H  HCH2  0   0.260  -0.6643  -2.7091  -1.4760
 BKD  H21  H  HCH2  0   0.281  -0.2526  -2.6034   0.2196
 BKD  H25  H  HNR5  0   0.410   5.8013   1.2149   0.8951

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
 BKD  C15  C14  single    1.499  0.020  1.499
 BKD  C15  C13  single    1.496  0.020  1.496
 BKD  C14  C13  single    1.497  0.020  1.497
 BKD  C13  C12  single    1.505  0.020  1.505
 BKD  C12  N11  single    1.447  0.020  1.447
 BKD  C6   C7   single    1.487  0.020  1.487
 BKD  C6   C5   single    1.530  0.020  1.530
 BKD  N11  C7   aromatic  1.346  0.020  1.346
 BKD  N11  N10  aromatic  1.329  0.020  1.329
 BKD  C7   C8   aromatic  1.374  0.020  1.374
 BKD  C5   N4   single    1.453  0.020  1.453
 BKD  N10  C9   aromatic  1.327  0.020  1.327
 BKD  C8   C9   aromatic  1.414  0.020  1.414
 BKD  C8   C26  single    1.497  0.020  1.497
 BKD  O3   C2   double    1.224  0.020  1.224
 BKD  C9   C16  single    1.463  0.020  1.463
 BKD  N4   C2   single    1.355  0.020  1.355
 BKD  N4   C26  single    1.454  0.020  1.454
 BKD  C2   C1   single    1.510  0.020  1.510
 BKD  C22  C21  aromatic  1.430  0.020  1.430
 BKD  C22  C23  aromatic  1.365  0.020  1.365
 BKD  C16  C21  aromatic  1.411  0.020  1.411
 BKD  C16  C17  aromatic  1.388  0.020  1.388
 BKD  C21  C20  aromatic  1.415  0.020  1.415
 BKD  C23  N24  aromatic  1.364  0.020  1.364
 BKD  C17  C18  aromatic  1.402  0.020  1.402
 BKD  C20  N24  aromatic  1.364  0.020  1.364
 BKD  C20  C19  aromatic  1.394  0.020  1.394
 BKD  C18  C19  aromatic  1.380  0.020  1.380
 BKD  C14  H1   single    0.970  0.020  1.090
 BKD  C14  H2   single    0.970  0.020  1.090
 BKD  C5   H3   single    0.970  0.020  1.090
 BKD  C5   H4   single    0.970  0.020  1.090
 BKD  C6   H5   single    0.970  0.020  1.090
 BKD  C6   H6   single    0.970  0.020  1.090
 BKD  C12  H7   single    0.970  0.020  1.090
 BKD  C12  H8   single    0.970  0.020  1.090
 BKD  C13  H9   single    0.970  0.020  1.090
 BKD  C1   H10  single    0.970  0.020  1.090
 BKD  C1   H11  single    0.970  0.020  1.090
 BKD  C1   H12  single    0.970  0.020  1.090
 BKD  C15  H13  single    0.970  0.020  1.090
 BKD  C15  H14  single    0.970  0.020  1.090
 BKD  C17  H15  single    0.930  0.020  1.080
 BKD  C18  H16  single    0.930  0.020  1.080
 BKD  C19  H17  single    0.930  0.020  1.080
 BKD  C22  H18  single    0.930  0.020  1.080
 BKD  C23  H19  single    0.930  0.020  1.080
 BKD  C26  H20  single    0.970  0.020  1.090
 BKD  C26  H21  single    0.970  0.020  1.090
 BKD  N24  H25  single    0.860  0.020  1.020

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
 BKD  H2   C14  H1   114.09  3.000
 BKD  H2   C14  C15  118.48  3.000
 BKD  H1   C14  C15  118.10  3.000
 BKD  H2   C14  C13  118.01  3.000
 BKD  H1   C14  C13  117.88  3.000
 BKD  C15  C14  C13   59.91  3.000
 BKD  H4   C5   H3   107.66  3.000
 BKD  H4   C5   N4   108.02  3.000
 BKD  H3   C5   N4   109.84  3.000
 BKD  H4   C5   C6   109.45  3.000
 BKD  H3   C5   C6   110.94  3.000
 BKD  N4   C5   C6   110.84  3.000
 BKD  H6   C6   H5   106.98  3.000
 BKD  H6   C6   C7   110.94  3.000
 BKD  H5   C6   C7   111.83  3.000
 BKD  H6   C6   C5   110.41  3.000
 BKD  H5   C6   C5   109.63  3.000
 BKD  C7   C6   C5   107.08  3.000
 BKD  N11  C7   C8   106.79  3.000
 BKD  C8   C7   C6   125.35  3.000
 BKD  N11  C7   C6   127.86  3.000
 BKD  C26  C8   C9   133.47  3.000
 BKD  C26  C8   C7   121.77  3.000
 BKD  C9   C8   C7   104.71  3.000
 BKD  N10  C9   C16  121.23  3.000
 BKD  C16  C9   C8   128.67  3.000
 BKD  N10  C9   C8   110.09  3.000
 BKD  H8   C12  H7   107.27  3.000
 BKD  H8   C12  N11  107.51  3.000
 BKD  H7   C12  N11  108.10  3.000
 BKD  H8   C12  C13  110.83  3.000
 BKD  H7   C12  C13  110.69  3.000
 BKD  N11  C12  C13  112.25  3.000
 BKD  H9   C13  C15  116.53  3.000
 BKD  H9   C13  C12  114.69  3.000
 BKD  C15  C13  C12  119.49  3.000
 BKD  H9   C13  C14  116.37  3.000
 BKD  C12  C13  C14  118.98  3.000
 BKD  C15  C13  C14   60.09  3.000
 BKD  H12  C1   H11  108.09  3.000
 BKD  H12  C1   H10  108.49  3.000
 BKD  H11  C1   H10  107.50  3.000
 BKD  H12  C1   C2   108.90  3.000
 BKD  H11  C1   C2   111.27  3.000
 BKD  H10  C1   C2   112.47  3.000
 BKD  H14  C15  H13  114.22  3.000
 BKD  H14  C15  C13  117.98  3.000
 BKD  H13  C15  C13  117.86  3.000
 BKD  H14  C15  C14  118.24  3.000
 BKD  H13  C15  C14  118.12  3.000
 BKD  C13  C15  C14   60.00  3.000
 BKD  C21  C16  C17  117.61  3.000
 BKD  C17  C16  C9   120.62  3.000
 BKD  C21  C16  C9   121.76  3.000
 BKD  H15  C17  C18  118.09  3.000
 BKD  H15  C17  C16  119.76  3.000
 BKD  C18  C17  C16  122.12  3.000
 BKD  H16  C18  C19  119.64  3.000
 BKD  H16  C18  C17  119.07  3.000
 BKD  C19  C18  C17  121.29  3.000
 BKD  H17  C19  C20  121.49  3.000
 BKD  H17  C19  C18  121.44  3.000
 BKD  C20  C19  C18  117.07  3.000
 BKD  O3   C2   N4   121.67  3.000
 BKD  N4   C2   C1   117.54  3.000
 BKD  O3   C2   C1   120.79  3.000
 BKD  N24  C20  C21  107.52  3.000
 BKD  N24  C20  C19  129.67  3.000
 BKD  C21  C20  C19  122.81  3.000
 BKD  C22  C21  C20  106.50  3.000
 BKD  C20  C21  C16  119.10  3.000
 BKD  C22  C21  C16  134.38  3.000
 BKD  H18  C22  C23  126.12  3.000
 BKD  H18  C22  C21  127.11  3.000
 BKD  C23  C22  C21  106.77  3.000
 BKD  H19  C23  N24  120.50  3.000
 BKD  H19  C23  C22  129.72  3.000
 BKD  N24  C23  C22  109.78  3.000
 BKD  H21  C26  H20  106.35  3.000
 BKD  H21  C26  N4   110.68  3.000
 BKD  H20  C26  N4   108.99  3.000
 BKD  H21  C26  C8   110.85  3.000
 BKD  H20  C26  C8   111.38  3.000
 BKD  N4   C26  C8   108.59  3.000
 BKD  N11  N10  C9   106.21  3.000
 BKD  N10  N11  C12  120.19  3.000
 BKD  N10  N11  C7   112.19  3.000
 BKD  C12  N11  C7   127.35  3.000
 BKD  H25  N24  C23  125.07  3.000
 BKD  H25  N24  C20  125.50  3.000
 BKD  C23  N24  C20  109.43  3.000
 BKD  C26  N4   C2   124.62  3.000
 BKD  C26  N4   C5   113.88  3.000
 BKD  C2   N4   C5   120.27  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
 BKD  CONST_01  C9   N10  N11  C7      0.00   0.0  0
 BKD  CONST_02  N10  C9   C8   C7      0.00   0.0  0
 BKD  CONST_03  C16  C9   C8   C7    180.00   0.0  0
 BKD  CONST_04  N10  N11  C7   C8      0.00   0.0  0
 BKD  CONST_05  N11  N10  C9   C8      0.00   0.0  0
 BKD  CONST_08  N11  C7   C8   C9      0.00   0.0  0
 BKD  CONST_09  C22  C21  C16  C9      0.00   0.0  0
 BKD  CONST_10  C20  C21  C16  C9    180.00   0.0  0
 BKD  CONST_11  C18  C17  C16  C9    180.00   0.0  0
 BKD  CONST_12  N11  N10  C9   C16   180.00   0.0  0
 BKD  CONST_13  C23  C22  C21  C16   180.00   0.0  0
 BKD  CONST_14  N24  C20  C21  C16   180.00   0.0  0
 BKD  CONST_15  C19  C20  C21  C16     0.00   0.0  0
 BKD  CONST_16  C19  C18  C17  C16     0.00   0.0  0
 BKD  CONST_18  C22  C21  C16  C17   180.00   0.0  0
 BKD  CONST_19  C20  C21  C16  C17     0.00   0.0  0
 BKD  CONST_20  C20  C19  C18  C17     0.00   0.0  0
 BKD  CONST_21  C21  C16  C17  C18     0.00   0.0  0
 BKD  CONST_22  C21  C20  C19  C18     0.00   0.0  0
 BKD  CONST_23  N24  C20  C19  C18   180.00   0.0  0
 BKD  CONST_24  C22  C21  C20  C19   180.00   0.0  0
 BKD  CONST_25  C23  N24  C20  C19   180.00   0.0  0
 BKD  CONST_26  C23  C22  C21  C20     0.00   0.0  0
 BKD  CONST_27  C22  C23  N24  C20     0.00   0.0  0
 BKD  CONST_28  N24  C23  C22  C21     0.00   0.0  0
 BKD  CONST_30  C23  N24  C20  C21     0.00   0.0  0
 BKD  CONST_31  N24  C20  C21  C22     0.00   0.0  0
 BKD  CONST_32  C26  C8   C9   C16     0.00   0.0  0
 BKD  CONST_33  C12  N11  C7   C6      0.00   0.0  0
 BKD  CONST_34  C12  N11  C7   C8    180.00   0.0  0
 BKD  CONST_35  C12  N11  N10  C9    180.00   0.0  0
 BKD  CONST_36  H15  C17  C16  C9      0.00   0.0  0
 BKD  CONST_37  H18  C22  C21  C16     0.00   0.0  0
 BKD  CONST_38  H16  C18  C17  C16   180.00   0.0  0
 BKD  CONST_39  H17  C19  C18  C17   180.00   0.0  0
 BKD  CONST_40  H25  N24  C20  C19     0.00   0.0  0
 BKD  CONST_41  H19  C23  N24  C20   180.00   0.0  0
 BKD  CONST_42  O3   C2   N4   C5      0.00   0.0  0
 BKD  CONST_43  C1   C2   N4   C5    180.00   0.0  0
 BKD  CONST_44  C26  N4   C2   C1      0.00   0.0  0
 BKD  CONST_45  O3   C2   N4   C26   180.00   0.0  0
 BKD  Var_01    N11  C7   C6   C5    166.72  30.0  1
 BKD  Var_02    C8   C26  N4   C5     49.40  30.0  1
 BKD  Var_03    C26  N4   C5   C6    -69.07  30.0  1
 BKD  Var_04    N4   C5   C6   C7     46.03  30.0  1
 BKD  Var_05    N4   C26  C8   C7    -14.66  30.0  1
 BKD  Var_06    C12  C13  C15  C14   108.47  30.0  1
 BKD  Var_07    N11  C12  C13  C14   151.46  30.0  3
 BKD  Var_08    C13  C12  N11  C7     87.57  30.0  2
 BKD  Var_09    H1   C14  C15  C13  -107.66  30.0  1
 BKD  Var_10    H10  C1   C2   N4    -52.28  30.0  3

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
 BKD  chir_01  C13  C15  C14  C12  both

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
 BKD  plan-1  C9   0.020
 BKD  plan-1  C16  0.020
 BKD  plan-1  C17  0.020
 BKD  plan-1  C18  0.020
 BKD  plan-1  C19  0.020
 BKD  plan-1  C20  0.020
 BKD  plan-1  C21  0.020
 BKD  plan-1  C22  0.020
 BKD  plan-1  C23  0.020
 BKD  plan-1  N24  0.020
 BKD  plan-1  H15  0.020
 BKD  plan-1  H16  0.020
 BKD  plan-1  H17  0.020
 BKD  plan-1  H18  0.020
 BKD  plan-1  H19  0.020
 BKD  plan-1  H25  0.020
 BKD  plan-2  C6   0.020
 BKD  plan-2  C7   0.020
 BKD  plan-2  C8   0.020
 BKD  plan-2  C9   0.020
 BKD  plan-2  C12  0.020
 BKD  plan-2  C16  0.020
 BKD  plan-2  C26  0.020
 BKD  plan-2  N10  0.020
 BKD  plan-2  N11  0.020
 BKD  plan-3  C5   0.020
 BKD  plan-3  C1   0.020
 BKD  plan-3  C2   0.020
 BKD  plan-3  C26  0.020
 BKD  plan-3  N4   0.020
 BKD  plan-3  O3   0.020

