# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:00:01 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-azanyl-3-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c2ccc3ccn(Cc4ccccn4)c3c2)c1C#N
#
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
 JD2  JD2  5-azanyl-3-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  38  24  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JD2
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
 JD2  C10  C  CR56  0   0.409   0.8524  -1.2718  -0.2165
 JD2  C13  C  CR6   0   0.258   3.5401   0.7031  -0.5641
 JD2  C15  C  CR16  0  -0.074   3.4315   2.1951   1.1562
 JD2  C17  C  CR16  0  -0.145   5.5284   1.8584   0.0844
 JD2  C20  C  CR15  0  -0.426   1.8300  -3.2275   0.4333
 JD2  C21  C  CR16  0  -0.338  -0.1254  -0.2943  -0.3586
 JD2  C22  C  CR5   0  -0.285  -3.8325   0.2810  -0.0344
 JD2  C02  C  CR5   0   0.618  -4.3692   1.5675  -0.1575
 JD2  N03  N  NR15  0  -0.491  -3.3174   2.3906  -0.1226
 JD2  N04  N  N     0  -0.300  -2.1372   1.7539   0.0195
 JD2  C05  C  CR5   0   0.320  -2.4233   0.4778   0.0718
 JD2  C06  C  CR6   0   0.037  -1.3739  -0.5362   0.1964
 JD2  C07  C  CR16  0  -0.333  -1.6215  -1.7350   0.8983
 JD2  C08  C  CR16  0  -0.331  -0.6436  -2.6943   1.0487
 JD2  C09  C  CR56  0   0.049   0.6185  -2.4756   0.4866
 JD2  N11  N  NR5   0  -0.522   2.1358  -1.3093  -0.6886
 JD2  C12  C  CH2   0  -0.401   2.8051  -0.2768  -1.4429
 JD2  N14  N  N     0  -0.402   2.8213   1.3226   0.3665
 JD2  C16  C  CR16  0  -0.328   4.7817   2.5028   1.0569
 JD2  C18  C  CR16  0  -0.345   4.8972   0.9386  -0.7406
 JD2  C19  C  CR15  0  -0.019   2.7175  -2.4806  -0.2843
 JD2  C23  C  CSP   0  -0.037  -4.5722  -0.9073  -0.0906
 JD2  N24  N  NS    0  -0.267  -5.2040  -1.8744  -0.1430
 JD2  H1   H  HCR6  0   0.264   2.8156   2.6797   1.9057
 JD2  H2   H  HCR6  0   0.276   6.5845   2.0633  -0.0297
 JD2  H3   H  HCR5  0   0.250   2.0168  -4.1999   0.8600
 JD2  H4   H  HCR6  0   0.256   0.0715   0.6309  -0.8835
 JD2  H5   H  HNH2  0   0.408  -5.8326   2.8888  -0.6179
 JD2  H6   H  HNH2  0   0.408  -6.3279   1.2845  -0.5251
 JD2  H7   H  HNR5  0   0.429  -3.3360   3.3976  -0.1638
 JD2  H8   H  HCR6  0   0.247  -2.5888  -1.8986   1.3551
 JD2  H9   H  HCR6  0   0.249  -0.8521  -3.6017   1.6013
 JD2  H10  H  HCH2  0   0.288   2.0639   0.2501  -2.0469
 JD2  H11  H  HCH2  0   0.289   3.4947  -0.7517  -2.1409
 JD2  H12  H  HCR6  0   0.272   5.2288   3.2259   1.7250
 JD2  H13  H  HCR6  0   0.271   5.4502   0.4094  -1.5054
 JD2  H14  H  HCR5  0   0.287   3.7385  -2.6989  -0.5560
 JD2  N01  N  NH2   0  -0.841  -5.6534   1.9742  -0.2353

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
 JD2  N01  C02  single    1.349  0.020  1.349
 JD2  C02  N03  aromatic  1.336  0.020  1.336
 JD2  C02  C22  aromatic  1.399  0.020  1.399
 JD2  N03  N04  aromatic  1.348  0.020  1.348
 JD2  N24  C23  triple    1.156  0.020  1.156
 JD2  C23  C22  single    1.401  0.020  1.401
 JD2  C22  C05  aromatic  1.427  0.020  1.427
 JD2  N04  C05  aromatic  1.309  0.020  1.309
 JD2  C05  C06  single    1.465  0.020  1.465
 JD2  C06  C07  aromatic  1.411  0.020  1.411
 JD2  C06  C21  aromatic  1.388  0.020  1.388
 JD2  C07  C08  aromatic  1.378  0.020  1.378
 JD2  C21  C10  aromatic  1.390  0.020  1.390
 JD2  C08  C09  aromatic  1.399  0.020  1.399
 JD2  C10  C09  aromatic  1.414  0.020  1.414
 JD2  C10  N11  aromatic  1.368  0.020  1.368
 JD2  C09  C20  aromatic  1.427  0.020  1.427
 JD2  N11  C12  single    1.443  0.020  1.443
 JD2  N11  C19  aromatic  1.369  0.020  1.369
 JD2  C12  C13  single    1.508  0.020  1.508
 JD2  C20  C19  aromatic  1.364  0.020  1.364
 JD2  C13  C18  aromatic  1.389  0.020  1.389
 JD2  C13  N14  aromatic  1.329  0.020  1.329
 JD2  C18  C17  aromatic  1.387  0.020  1.387
 JD2  N14  C15  aromatic  1.326  0.020  1.326
 JD2  C17  C16  aromatic  1.385  0.020  1.385
 JD2  C15  C16  aromatic  1.388  0.020  1.388
 JD2  C15  H1   single    0.930  0.020  1.080
 JD2  C17  H2   single    0.930  0.020  1.080
 JD2  C20  H3   single    0.930  0.020  1.080
 JD2  C21  H4   single    0.930  0.020  1.080
 JD2  N01  H5   single    0.890  0.020  1.040
 JD2  N01  H6   single    0.890  0.020  1.040
 JD2  N03  H7   single    0.860  0.020  1.020
 JD2  C07  H8   single    0.930  0.020  1.080
 JD2  C08  H9   single    0.930  0.020  1.080
 JD2  C12  H10  single    0.970  0.020  1.090
 JD2  C12  H11  single    0.970  0.020  1.090
 JD2  C16  H12  single    0.930  0.020  1.080
 JD2  C18  H13  single    0.930  0.020  1.080
 JD2  C19  H14  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
 JD2  N11  C10  C09  107.67  3.000
 JD2  N11  C10  C21  130.09  3.000
 JD2  C09  C10  C21  122.24  3.000
 JD2  C18  C13  N14  122.58  3.000
 JD2  N14  C13  C12  116.58  3.000
 JD2  C18  C13  C12  120.84  3.000
 JD2  H1   C15  C16  120.18  3.000
 JD2  H1   C15  N14  116.39  3.000
 JD2  C16  C15  N14  123.43  3.000
 JD2  H2   C17  C18  120.46  3.000
 JD2  H2   C17  C16  120.81  3.000
 JD2  C18  C17  C16  118.73  3.000
 JD2  H3   C20  C19  126.11  3.000
 JD2  H3   C20  C09  127.42  3.000
 JD2  C19  C20  C09  106.47  3.000
 JD2  H4   C21  C06  120.46  3.000
 JD2  H4   C21  C10  121.54  3.000
 JD2  C06  C21  C10  118.00  3.000
 JD2  C23  C22  C05  129.91  3.000
 JD2  C05  C22  C02  104.98  3.000
 JD2  C23  C22  C02  125.02  3.000
 JD2  N03  C02  N01  124.41  3.000
 JD2  N03  C02  C22  105.20  3.000
 JD2  N01  C02  C22  130.33  3.000
 JD2  H7   N03  N04  119.48  3.000
 JD2  H7   N03  C02  126.86  3.000
 JD2  N04  N03  C02  113.63  3.000
 JD2  C05  N04  N03  105.86  3.000
 JD2  C06  C05  N04  121.46  3.000
 JD2  C06  C05  C22  128.21  3.000
 JD2  N04  C05  C22  110.33  3.000
 JD2  C07  C06  C05  120.32  3.000
 JD2  C07  C06  C21  120.33  3.000
 JD2  C05  C06  C21  119.33  3.000
 JD2  H8   C07  C08  118.88  3.000
 JD2  H8   C07  C06  119.69  3.000
 JD2  C08  C07  C06  121.41  3.000
 JD2  H9   C08  C09  120.65  3.000
 JD2  H9   C08  C07  120.17  3.000
 JD2  C09  C08  C07  119.18  3.000
 JD2  C08  C09  C20  134.32  3.000
 JD2  C20  C09  C10  106.84  3.000
 JD2  C08  C09  C10  118.83  3.000
 JD2  C19  N11  C12  124.72  3.000
 JD2  C19  N11  C10  108.67  3.000
 JD2  C12  N11  C10  126.57  3.000
 JD2  H11  C12  H10  106.59  3.000
 JD2  H11  C12  N11  108.44  3.000
 JD2  H10  C12  N11  108.64  3.000
 JD2  H11  C12  C13  110.36  3.000
 JD2  H10  C12  C13  109.87  3.000
 JD2  N11  C12  C13  112.73  3.000
 JD2  C15  N14  C13  118.36  3.000
 JD2  H12  C16  C17  121.47  3.000
 JD2  H12  C16  C15  120.41  3.000
 JD2  C17  C16  C15  118.12  3.000
 JD2  H13  C18  C17  120.80  3.000
 JD2  H13  C18  C13  120.42  3.000
 JD2  C17  C18  C13  118.78  3.000
 JD2  H14  C19  N11  120.06  3.000
 JD2  H14  C19  C20  129.60  3.000
 JD2  N11  C19  C20  110.33  3.000
 JD2  N24  C23  C22  180.00  3.000
 JD2  H6   N01  H5   113.16  3.000
 JD2  H6   N01  C02  116.59  3.000
 JD2  H5   N01  C02  117.70  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
 JD2  CONST_01  C05  C06  C21  C10  180.00   0.0  0
 JD2  CONST_02  C07  C06  C21  C10    0.00   0.0  0
 JD2  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 JD2  CONST_04  C19  C20  C09  C10    0.00   0.0  0
 JD2  CONST_05  C20  C19  N11  C10    0.00   0.0  0
 JD2  CONST_06  C16  C17  C18  C13    0.00   0.0  0
 JD2  CONST_07  C16  C15  N14  C13    0.00   0.0  0
 JD2  CONST_08  C18  C13  N14  C15    0.00   0.0  0
 JD2  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 JD2  CONST_10  N14  C13  C18  C17    0.00   0.0  0
 JD2  CONST_11  N14  C15  C16  C17    0.00   0.0  0
 JD2  CONST_12  C07  C08  C09  C20  180.00   0.0  0
 JD2  CONST_13  C21  C10  C09  C20  180.00   0.0  0
 JD2  CONST_14  N11  C10  C09  C20    0.00   0.0  0
 JD2  CONST_17  C08  C07  C06  C21    0.00   0.0  0
 JD2  CONST_18  C08  C09  C10  C21    0.00   0.0  0
 JD2  CONST_19  C19  N11  C10  C21  180.00   0.0  0
 JD2  CONST_20  N04  N03  C02  C22    0.00   0.0  0
 JD2  CONST_21  N03  N04  C05  C22    0.00   0.0  0
 JD2  CONST_23  C05  N04  N03  C02    0.00   0.0  0
 JD2  CONST_24  N04  C05  C22  C02    0.00   0.0  0
 JD2  CONST_25  C06  C05  C22  C02  180.00   0.0  0
 JD2  CONST_26  C05  C22  C02  N03    0.00   0.0  0
 JD2  CONST_27  C06  C05  N04  N03  180.00   0.0  0
 JD2  CONST_29  C08  C07  C06  C05  180.00   0.0  0
 JD2  CONST_30  C09  C08  C07  C06    0.00   0.0  0
 JD2  CONST_31  C09  C10  C21  C06    0.00   0.0  0
 JD2  CONST_32  N11  C10  C21  C06  180.00   0.0  0
 JD2  CONST_33  N11  C10  C09  C08  180.00   0.0  0
 JD2  CONST_34  C19  C20  C09  C08  180.00   0.0  0
 JD2  CONST_35  C19  N11  C10  C09    0.00   0.0  0
 JD2  CONST_36  N11  C19  C20  C09    0.00   0.0  0
 JD2  CONST_37  C12  C13  N14  C15  180.00   0.0  0
 JD2  CONST_38  C12  C13  C18  C17  180.00   0.0  0
 JD2  CONST_39  C12  N11  C19  C20  180.00   0.0  0
 JD2  CONST_40  C12  N11  C10  C21    0.00   0.0  0
 JD2  CONST_41  N04  N03  C02  N01  180.00   0.0  0
 JD2  CONST_42  C05  C22  C02  N01  180.00   0.0  0
 JD2  CONST_43  C23  C22  C02  N03  180.00   0.0  0
 JD2  CONST_44  C23  C22  C05  N04  180.00   0.0  0
 JD2  CONST_45  C23  C22  C05  C06    0.00   0.0  0
 JD2  CONST_46  C12  N11  C10  C09  180.00   0.0  0
 JD2  CONST_47  H9   C08  C09  C10  180.00   0.0  0
 JD2  CONST_48  H3   C20  C09  C10  180.00   0.0  0
 JD2  CONST_49  H14  C19  N11  C10  180.00   0.0  0
 JD2  CONST_50  H2   C17  C18  C13  180.00   0.0  0
 JD2  CONST_51  H1   C15  N14  C13  180.00   0.0  0
 JD2  CONST_52  H8   C07  C06  C21  180.00   0.0  0
 JD2  CONST_53  H7   N03  C02  C22  180.00   0.0  0
 JD2  CONST_54  H4   C21  C06  C05    0.00   0.0  0
 JD2  CONST_55  H13  C18  C13  N14  180.00   0.0  0
 JD2  CONST_56  H12  C16  C15  N14  180.00   0.0  0
 JD2  Var_01    C13  C12  N11  C10   90.63  30.0  2
 JD2  Var_02    C18  C13  C12  N11  124.00  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
 JD2  plan-1  C22  0.020
 JD2  plan-1  C02  0.020
 JD2  plan-1  N03  0.020
 JD2  plan-1  N04  0.020
 JD2  plan-1  C05  0.020
 JD2  plan-1  C06  0.020
 JD2  plan-1  C23  0.020
 JD2  plan-1  N24  0.020
 JD2  plan-1  H7   0.020
 JD2  plan-1  N01  0.020
 JD2  plan-2  C13  0.020
 JD2  plan-2  C15  0.020
 JD2  plan-2  C17  0.020
 JD2  plan-2  C12  0.020
 JD2  plan-2  N14  0.020
 JD2  plan-2  C16  0.020
 JD2  plan-2  C18  0.020
 JD2  plan-2  H1   0.020
 JD2  plan-2  H2   0.020
 JD2  plan-2  H12  0.020
 JD2  plan-2  H13  0.020
 JD2  plan-3  C10  0.020
 JD2  plan-3  C20  0.020
 JD2  plan-3  C21  0.020
 JD2  plan-3  C05  0.020
 JD2  plan-3  C06  0.020
 JD2  plan-3  C07  0.020
 JD2  plan-3  C08  0.020
 JD2  plan-3  C09  0.020
 JD2  plan-3  N11  0.020
 JD2  plan-3  C12  0.020
 JD2  plan-3  C19  0.020
 JD2  plan-3  H3   0.020
 JD2  plan-3  H4   0.020
 JD2  plan-3  H8   0.020
 JD2  plan-3  H9   0.020
 JD2  plan-3  H14  0.020
 JD2  plan-4  C02  0.020
 JD2  plan-4  H5   0.020
 JD2  plan-4  H6   0.020
 JD2  plan-4  N01  0.020

