# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:56:40 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (5-methoxy-6-pyridin-4-yl-1~{H}-indazol-3-yl)-(4-methylpiperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2c([nH]nc2C(=O)N3CCN(C)CC3)cc1c4ccncc4
#
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
 I5B  I5B  "(5-methoxy-6-pyridin-4-yl-1~{H}-indazol-3-yl)-(4-methylpiperazin-1-yl)methanone"
  ligand  47  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I5B
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
 I5B  C1   C  CR6   0   0.376  15.1118  -25.5822  17.0122
 I5B  C2   C  CR6   0  -0.057  15.8481  -26.6445  16.4031
 I5B  C3   C  CR16  0  -0.312  17.1340  -26.9241  16.8086
 I5B  C11  C  CH3   0  -0.438  13.0599  -24.3967  17.0973
 I5B  C12  C  CR6   0   0.177  15.2407  -27.4721  15.3397
 I5B  C13  C  CR16  0  -0.349  14.6950  -26.9201  14.1828
 I5B  C14  C  CR16  0  -0.063  14.1931  -27.7655  13.2074
 I5B  C16  C  CR16  0  -0.059  14.7120  -29.6167  14.4074
 I5B  C17  C  CR16  0  -0.364  15.2428  -28.8604  15.4414
 I5B  C21  C  CH2   0  -0.316  18.3370  -21.6642  21.7894
 I5B  C22  C  CH2   0  -0.274  19.4194  -21.8271  22.8443
 I5B  C24  C  CH2   0  -0.273  20.9539  -22.6048  21.1846
 I5B  C25  C  CH2   0  -0.316  19.8886  -22.4317  20.1177
 I5B  C26  C  CH3   0  -0.515  21.7722  -21.7656  23.2743
 I5B  C4   C  CR56  0   0.412  17.6927  -26.1277  17.8097
 I5B  C5   C  CR56  0  -0.023  16.9858  -25.0771  18.4026
 I5B  C6   C  CR16  0  -0.485  15.6688  -24.8030  18.0028
 I5B  N7   N  NR15  0  -0.542  18.9146  -26.1423  18.4025
 I5B  N8   N  N     0  -0.228  19.0419  -25.1945  19.3120
 I5B  C9   C  CR5   0   0.045  17.9076  -24.5242  19.3372
 I5B  O10  O  O2    0  -0.465  13.8503  -25.4387  16.5644
 I5B  N15  N  N     0  -0.404  14.1918  -29.0909  13.3060
 I5B  O19  O  O     0  -0.488  16.4458  -23.3703  20.7204
 I5B  N20  N  NT    0  -0.464  18.5699  -22.6000  20.7029
 I5B  N23  N  NT    0  -0.415  20.7398  -21.6667  22.2691
 I5B  H1   H  HCR6  0   0.279  17.6969  -27.7256  16.3476
 I5B  H2   H  HCH3  0   0.261  12.1002  -24.4472  16.5893
 I5B  H3   H  HCH3  0   0.229  12.8977  -24.5170  18.1717
 I5B  H4   H  HCH3  0   0.229  13.5047  -23.4143  16.9162
 I5B  H5   H  HCR6  0   0.265  14.6755  -25.8511  14.0238
 I5B  H6   H  HCR6  0   0.262  13.7730  -27.3473  12.2992
 I5B  H7   H  HCR6  0   0.262  14.7068  -30.6988  14.4796
 I5B  H8   H  HCR6  0   0.269  15.6425  -29.3525  16.3185
 I5B  H9   H  HCH2  0   0.240  18.3532  -20.6431  21.3945
 I5B  H10  H  HCH2  0   0.267  17.3584  -21.8383  22.2270
 I5B  H11  H  HCH2  0   0.242  19.2720  -21.0675  23.6158
 I5B  H12  H  HCH2  0   0.196  19.2997  -22.8107  23.3311
 I5B  H13  H  HCH2  0   0.196  20.9454  -23.6520  21.5337
 I5B  H14  H  HCH2  0   0.241  21.9351  -22.4180  20.7420
 I5B  H15  H  HCH2  0   0.275  20.0505  -23.1305  19.3060
 I5B  H16  H  HCH2  0   0.244  19.9507  -21.4186  19.7070
 I5B  H17  H  HCH3  0   0.233  21.6177  -21.0071  24.0431
 I5B  H18  H  HCH3  0   0.193  21.8020  -22.7471  23.7724
 I5B  H19  H  HCH3  0   0.233  22.7506  -21.5910  22.8242
 I5B  H20  H  HCR6  0   0.277  15.1155  -24.0063  18.4775
 I5B  H21  H  HNR5  0   0.422  19.6755  -26.7833  18.2394
 I5B  C18  C  C     0   0.527  17.5981  -23.4435  20.3050

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
 I5B  C14  N15  aromatic  1.329  0.020  1.329
 I5B  C14  C13  aromatic  1.385  0.020  1.385
 I5B  N15  C16  aromatic  1.327  0.020  1.327
 I5B  C13  C12  aromatic  1.393  0.020  1.393
 I5B  C16  C17  aromatic  1.387  0.020  1.387
 I5B  C12  C17  aromatic  1.392  0.020  1.392
 I5B  C12  C2   single    1.478  0.020  1.478
 I5B  C2   C3   aromatic  1.377  0.020  1.377
 I5B  C2   C1   aromatic  1.429  0.020  1.429
 I5B  O10  C1   single    1.346  0.020  1.346
 I5B  O10  C11  single    1.412  0.020  1.412
 I5B  C3   C4   aromatic  1.396  0.020  1.396
 I5B  C1   C6   aromatic  1.378  0.020  1.378
 I5B  C4   N7   aromatic  1.358  0.020  1.358
 I5B  C4   C5   aromatic  1.398  0.020  1.398
 I5B  C6   C5   aromatic  1.403  0.020  1.403
 I5B  N7   N8   aromatic  1.320  0.020  1.320
 I5B  C5   C9   aromatic  1.424  0.020  1.424
 I5B  N8   C9   aromatic  1.318  0.020  1.318
 I5B  C9   C18  single    1.483  0.020  1.483
 I5B  C25  N20  single    1.452  0.020  1.452
 I5B  C25  C24  single    1.518  0.020  1.518
 I5B  C18  N20  single    1.347  0.020  1.347
 I5B  C18  O19  double    1.227  0.020  1.227
 I5B  N20  C21  single    1.453  0.020  1.453
 I5B  C24  N23  single    1.450  0.020  1.450
 I5B  C21  C22  single    1.520  0.020  1.520
 I5B  N23  C22  single    1.449  0.020  1.449
 I5B  N23  C26  single    1.444  0.020  1.444
 I5B  C3   H1   single    0.930  0.020  1.080
 I5B  C11  H2   single    0.970  0.020  1.090
 I5B  C11  H3   single    0.970  0.020  1.090
 I5B  C11  H4   single    0.970  0.020  1.090
 I5B  C13  H5   single    0.930  0.020  1.080
 I5B  C14  H6   single    0.930  0.020  1.080
 I5B  C16  H7   single    0.930  0.020  1.080
 I5B  C17  H8   single    0.930  0.020  1.080
 I5B  C21  H9   single    0.970  0.020  1.090
 I5B  C21  H10  single    0.970  0.020  1.090
 I5B  C22  H11  single    0.970  0.020  1.090
 I5B  C22  H12  single    0.970  0.020  1.090
 I5B  C24  H13  single    0.970  0.020  1.090
 I5B  C24  H14  single    0.970  0.020  1.090
 I5B  C25  H15  single    0.970  0.020  1.090
 I5B  C25  H16  single    0.970  0.020  1.090
 I5B  C26  H17  single    0.970  0.020  1.090
 I5B  C26  H18  single    0.970  0.020  1.090
 I5B  C26  H19  single    0.970  0.020  1.090
 I5B  C6   H20  single    0.930  0.020  1.080
 I5B  N7   H21  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
 I5B  O10  C1   C6   123.90  3.000
 I5B  C6   C1   C2   121.23  3.000
 I5B  O10  C1   C2   114.86  3.000
 I5B  C12  C2   C3   118.81  3.000
 I5B  C3   C2   C1   120.44  3.000
 I5B  C12  C2   C1   120.74  3.000
 I5B  H1   C3   C4   121.32  3.000
 I5B  H1   C3   C2   120.70  3.000
 I5B  C4   C3   C2   117.97  3.000
 I5B  H4   C11  H3   108.78  3.000
 I5B  H4   C11  H2   108.88  3.000
 I5B  H3   C11  H2   108.85  3.000
 I5B  H4   C11  O10  111.89  3.000
 I5B  H3   C11  O10  111.88  3.000
 I5B  H2   C11  O10  106.47  3.000
 I5B  C17  C12  C13  117.16  3.000
 I5B  C17  C12  C2   120.35  3.000
 I5B  C13  C12  C2   122.45  3.000
 I5B  H5   C13  C14  119.57  3.000
 I5B  H5   C13  C12  121.40  3.000
 I5B  C14  C13  C12  119.01  3.000
 I5B  H6   C14  N15  116.51  3.000
 I5B  H6   C14  C13  119.66  3.000
 I5B  N15  C14  C13  123.84  3.000
 I5B  H7   C16  N15  116.66  3.000
 I5B  H7   C16  C17  119.76  3.000
 I5B  N15  C16  C17  123.57  3.000
 I5B  H8   C17  C16  119.85  3.000
 I5B  H8   C17  C12  120.88  3.000
 I5B  C16  C17  C12  119.27  3.000
 I5B  H10  C21  H9   107.95  3.000
 I5B  H10  C21  N20  110.03  3.000
 I5B  H9   C21  N20  109.18  3.000
 I5B  H10  C21  C22  110.17  3.000
 I5B  H9   C21  C22  109.86  3.000
 I5B  N20  C21  C22  109.62  3.000
 I5B  H12  C22  H11  107.06  3.000
 I5B  H12  C22  N23  111.87  3.000
 I5B  H11  C22  N23  109.04  3.000
 I5B  H12  C22  C21  108.92  3.000
 I5B  H11  C22  C21  108.63  3.000
 I5B  N23  C22  C21  111.19  3.000
 I5B  H14  C24  H13  107.30  3.000
 I5B  H14  C24  N23  108.97  3.000
 I5B  H13  C24  N23  112.09  3.000
 I5B  H14  C24  C25  109.03  3.000
 I5B  H13  C24  C25  108.97  3.000
 I5B  N23  C24  C25  110.39  3.000
 I5B  H16  C25  H15  107.90  3.000
 I5B  H16  C25  N20  108.05  3.000
 I5B  H15  C25  N20  111.28  3.000
 I5B  H16  C25  C24  109.23  3.000
 I5B  H15  C25  C24  110.38  3.000
 I5B  N20  C25  C24  109.93  3.000
 I5B  H19  C26  H18  107.76  3.000
 I5B  H19  C26  H17  107.85  3.000
 I5B  H18  C26  H17  107.75  3.000
 I5B  H19  C26  N23  110.06  3.000
 I5B  H18  C26  N23  113.28  3.000
 I5B  H17  C26  N23  109.97  3.000
 I5B  N7   C4   C5   106.13  3.000
 I5B  C5   C4   C3   122.04  3.000
 I5B  N7   C4   C3   131.83  3.000
 I5B  C9   C5   C6   135.92  3.000
 I5B  C9   C5   C4   104.05  3.000
 I5B  C6   C5   C4   120.03  3.000
 I5B  H20  C6   C5   119.98  3.000
 I5B  H20  C6   C1   121.74  3.000
 I5B  C5   C6   C1   118.28  3.000
 I5B  H21  N7   N8   119.69  3.000
 I5B  H21  N7   C4   127.97  3.000
 I5B  N8   N7   C4   112.32  3.000
 I5B  C9   N8   N7   107.19  3.000
 I5B  N8   C9   C5   110.30  3.000
 I5B  N8   C9   C18  124.24  3.000
 I5B  C5   C9   C18  125.16  3.000
 I5B  C11  O10  C1   118.52  3.000
 I5B  C16  N15  C14  117.16  3.000
 I5B  C25  N20  C21  111.85  3.000
 I5B  C21  N20  C18  120.58  3.000
 I5B  C25  N20  C18  127.49  3.000
 I5B  C26  N23  C24  111.76  3.000
 I5B  C26  N23  C22  111.56  3.000
 I5B  C24  N23  C22  111.09  3.000
 I5B  N20  C18  O19  122.70  3.000
 I5B  O19  C18  C9   117.40  3.000
 I5B  N20  C18  C9   119.90  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
 I5B  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 I5B  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 I5B  CONST_05  C9   C5   C6   C1    180.00   0.0  0
 I5B  CONST_06  C14  C13  C12  C2    180.00   0.0  0
 I5B  CONST_07  C16  C17  C12  C2    180.00   0.0  0
 I5B  CONST_08  N7   C4   C3   C2    180.00   0.0  0
 I5B  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 I5B  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 I5B  CONST_13  C6   C1   C2   C3      0.00   0.0  0
 I5B  CONST_14  N8   N7   C4   C3    180.00   0.0  0
 I5B  CONST_15  C6   C5   C4   C3      0.00   0.0  0
 I5B  CONST_16  C9   C5   C4   C3    180.00   0.0  0
 I5B  CONST_17  N15  C14  C13  C12     0.00   0.0  0
 I5B  CONST_18  N15  C16  C17  C12     0.00   0.0  0
 I5B  CONST_19  C4   C3   C2   C12   180.00   0.0  0
 I5B  CONST_20  C6   C1   C2   C12   180.00   0.0  0
 I5B  CONST_21  C16  N15  C14  C13     0.00   0.0  0
 I5B  CONST_22  C16  C17  C12  C13     0.00   0.0  0
 I5B  CONST_23  C17  C16  N15  C14     0.00   0.0  0
 I5B  CONST_24  C17  C12  C13  C14     0.00   0.0  0
 I5B  CONST_25  C9   N8   N7   C4      0.00   0.0  0
 I5B  CONST_26  N8   C9   C5   C4      0.00   0.0  0
 I5B  CONST_27  N8   N7   C4   C5      0.00   0.0  0
 I5B  CONST_28  N7   N8   C9   C5      0.00   0.0  0
 I5B  CONST_29  N7   C4   C5   C6    180.00   0.0  0
 I5B  CONST_30  N8   C9   C5   C6    180.00   0.0  0
 I5B  CONST_31  C9   C5   C4   N7      0.00   0.0  0
 I5B  CONST_32  O10  C1   C2   C3    180.00   0.0  0
 I5B  CONST_33  O10  C1   C2   C12     0.00   0.0  0
 I5B  CONST_34  C4   C5   C9   C18   180.00   0.0  0
 I5B  CONST_35  C6   C5   C9   C18     0.00   0.0  0
 I5B  CONST_36  N7   N8   C9   C18   180.00   0.0  0
 I5B  CONST_37  O10  C1   C6   C5    180.00   0.0  0
 I5B  CONST_38  C9   C18  N20  C21   180.00   0.0  0
 I5B  CONST_39  C9   C18  N20  C25     0.00   0.0  0
 I5B  CONST_40  H1   C3   C2   C1    180.00   0.0  0
 I5B  CONST_41  H5   C13  C12  C2      0.00   0.0  0
 I5B  CONST_42  H8   C17  C12  C2      0.00   0.0  0
 I5B  CONST_43  H20  C6   C1   C2    180.00   0.0  0
 I5B  CONST_44  H21  N7   C4   C3      0.00   0.0  0
 I5B  CONST_45  H6   C14  C13  C12   180.00   0.0  0
 I5B  CONST_46  H7   C16  C17  C12   180.00   0.0  0
 I5B  CONST_47  H1   C3   C2   C12     0.00   0.0  0
 I5B  CONST_48  H8   C17  C12  C13   180.00   0.0  0
 I5B  CONST_49  H7   C16  N15  C14   180.00   0.0  0
 I5B  CONST_50  H6   C14  N15  C16   180.00   0.0  0
 I5B  CONST_51  H5   C13  C12  C17   180.00   0.0  0
 I5B  CONST_52  H20  C6   C5   C4    180.00   0.0  0
 I5B  CONST_53  H1   C3   C4   C5    180.00   0.0  0
 I5B  CONST_54  H21  N7   C4   C5    180.00   0.0  0
 I5B  CONST_55  H1   C3   C4   N7      0.00   0.0  0
 I5B  CONST_56  H20  C6   C5   C9      0.00   0.0  0
 I5B  CONST_57  H21  N7   N8   C9    180.00   0.0  0
 I5B  CONST_58  H5   C13  C14  N15   180.00   0.0  0
 I5B  CONST_59  H8   C17  C16  N15   180.00   0.0  0
 I5B  CONST_60  O19  C18  N20  C21     0.00   0.0  0
 I5B  CONST_61  O19  C18  N20  C25   180.00   0.0  0
 I5B  Var_01    C24  C25  N20  C21    57.67  30.0  1
 I5B  Var_02    C24  N23  C22  C21   -56.93  30.0  1
 I5B  Var_03    C25  N20  C21  C22   -56.74  30.0  1
 I5B  Var_04    C25  C24  N23  C22    57.24  30.0  1
 I5B  Var_05    N23  C24  C25  N20   -57.06  30.0  1
 I5B  Var_06    N23  C22  C21  N20    55.85  30.0  1
 I5B  Var_07    C24  C25  N20  C18  -125.69  30.0  1
 I5B  Var_08    C22  C21  N20  C18   126.36  30.0  1
 I5B  Var_09    C26  N23  C22  C21   177.65  30.0  1
 I5B  Var_10    C26  N23  C24  C25  -177.45  30.0  1
 I5B  Var_11    N20  C18  C9   C5   -150.49  30.0  2
 I5B  Var_12    N20  C18  C9   N8     36.34  30.0  2
 I5B  Var_13    H15  C25  N20  C21  -179.74  30.0  1
 I5B  Var_14    H16  C25  N20  C21   -61.45  30.0  1
 I5B  Var_15    H13  C24  N23  C22   -64.44  30.0  1
 I5B  Var_16    H14  C24  N23  C22   176.95  30.0  1
 I5B  Var_17    H11  C22  N23  C24  -176.68  30.0  1
 I5B  Var_18    H12  C22  N23  C24    65.09  30.0  1
 I5B  Var_19    H9   C21  N20  C25    63.65  30.0  1
 I5B  Var_20    H10  C21  N20  C25  -178.05  30.0  1
 I5B  Var_21    H13  C24  C25  N20    66.45  30.0  1
 I5B  Var_22    H14  C24  C25  N20  -176.73  30.0  1
 I5B  Var_23    H11  C22  C21  N20   175.84  30.0  1
 I5B  Var_24    H12  C22  C21  N20   -67.87  30.0  1
 I5B  Var_25    H15  C25  C24  N23   179.82  30.0  1
 I5B  Var_26    H16  C25  C24  N23    61.34  30.0  1
 I5B  Var_27    H9   C21  C22  N23   -64.13  30.0  1
 I5B  Var_28    H10  C21  C22  N23   177.08  30.0  1
 I5B  Var_29    C11  O10  C1   C2   -178.90  30.0  2
 I5B  Var_30    C6   C1   O10  C11     2.64  30.0  2
 I5B  Var_31    O19  C18  C9   C5     30.17  30.0  2
 I5B  Var_32    O19  C18  C9   N8   -143.00  30.0  2
 I5B  Var_33    H15  C25  N20  C18    -3.10  30.0  1
 I5B  Var_34    H16  C25  N20  C18   115.18  30.0  1
 I5B  Var_35    H9   C21  N20  C18  -113.25  30.0  1
 I5B  Var_36    H10  C21  N20  C18     5.05  30.0  1
 I5B  Var_37    H17  C26  N23  C22   -58.45  30.0  3
 I5B  Var_38    H18  C26  N23  C22    62.17  30.0  3
 I5B  Var_39    H19  C26  N23  C22  -177.13  30.0  3
 I5B  Var_40    H17  C26  N23  C24   176.50  30.0  3
 I5B  Var_41    H18  C26  N23  C24   -62.88  30.0  3
 I5B  Var_42    H19  C26  N23  C24    57.82  30.0  3
 I5B  Var_43    H13  C24  N23  C26    60.87  30.0  1
 I5B  Var_44    H14  C24  N23  C26   -57.74  30.0  1
 I5B  Var_45    H11  C22  N23  C26    57.90  30.0  1
 I5B  Var_46    H12  C22  N23  C26   -60.33  30.0  1
 I5B  Var_47    H2   C11  O10  C1    178.78  30.0  3
 I5B  Var_48    H3   C11  O10  C1    -62.42  30.0  3
 I5B  Var_49    H4   C11  O10  C1     59.94  30.0  3

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
 I5B  plan-1  C2   0.020
 I5B  plan-1  C12  0.020
 I5B  plan-1  C13  0.020
 I5B  plan-1  C14  0.020
 I5B  plan-1  C16  0.020
 I5B  plan-1  C17  0.020
 I5B  plan-1  N15  0.020
 I5B  plan-1  H5   0.020
 I5B  plan-1  H6   0.020
 I5B  plan-1  H7   0.020
 I5B  plan-1  H8   0.020
 I5B  plan-2  C1   0.020
 I5B  plan-2  C2   0.020
 I5B  plan-2  C3   0.020
 I5B  plan-2  C12  0.020
 I5B  plan-2  C4   0.020
 I5B  plan-2  C5   0.020
 I5B  plan-2  C6   0.020
 I5B  plan-2  N7   0.020
 I5B  plan-2  N8   0.020
 I5B  plan-2  C9   0.020
 I5B  plan-2  O10  0.020
 I5B  plan-2  H1   0.020
 I5B  plan-2  H20  0.020
 I5B  plan-2  H21  0.020
 I5B  plan-2  C18  0.020
 I5B  plan-3  C21  0.020
 I5B  plan-3  C25  0.020
 I5B  plan-3  C9   0.020
 I5B  plan-3  O19  0.020
 I5B  plan-3  N20  0.020
 I5B  plan-3  C18  0.020

