# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:23:11 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 1~{H}-indol-6-yl-(4-methylpiperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)c2ccc3cc[nH]c3c2
#
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
 B0M  B0M  1~{H}-indol-6-yl-(4-methylpiperazin-1-yl)methanone  ligand  35  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B0M
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
 B0M  N1   N  NT    0  -0.415  -3.9039   1.0003  -0.2629
 B0M  N3   N  NR15  0  -0.682   3.6565   1.2075   1.1510
 B0M  C4   C  CH2   0  -0.325  -2.9092  -0.6856   1.1894
 B0M  C5   C  CH2   0  -0.279  -3.9235  -0.4048   0.0936
 B0M  C7   C  CR6   0  -0.096   0.7079  -0.7244   0.0457
 B0M  C8   C  CR16  0  -0.288   1.2974  -1.2520  -1.1200
 B0M  C10  C  CR56  0   0.058   3.3311  -0.0746  -0.6553
 B0M  C13  C  CR56  0   0.365   2.7311   0.4265   0.5231
 B0M  C1   C  CH3   0  -0.516  -4.9019   1.3169  -1.2585
 B0M  C2   C  CH2   0  -0.267  -2.5804   1.4073  -0.6872
 B0M  C3   C  CH2   0  -0.326  -1.5465   1.1330   0.3942
 B0M  N2   N  NT    0  -0.452  -1.5802  -0.2706   0.7725
 B0M  O1   O  O     0  -0.492  -0.9025  -2.3976   0.4053
 B0M  C9   C  CR16  0  -0.337   2.5857  -0.9237  -1.4824
 B0M  C11  C  CR15  0  -0.415   4.6573   0.4511  -0.6984
 B0M  C12  C  CR15  0  -0.024   4.8073   1.2230   0.4185
 B0M  C14  C  CR16  0  -0.312   1.4228   0.1174   0.8817
 B0M  H3   H  HCH2  0   0.247  -3.1765  -0.1208   2.0871
 B0M  H4   H  HCH2  0   0.265  -2.9068  -1.7409   1.4461
 B0M  H5   H  HCH2  0   0.243  -4.9210  -0.6675   0.4542
 B0M  H6   H  HCH2  0   0.198  -3.7105  -1.0567  -0.7718
 B0M  H7   H  HCR6  0   0.250   0.7193  -1.9171  -1.7481
 B0M  H8   H  HCH3  0   0.234  -5.8914   1.0313  -0.8988
 B0M  H9   H  HCH3  0   0.234  -4.9116   2.3911  -1.4494
 B0M  H10  H  HCH3  0   0.193  -4.7343   0.8068  -2.2201
 B0M  H11  H  HCH2  0   0.194  -2.2691   0.8925  -1.6136
 B0M  H12  H  HCH2  0   0.245  -2.5858   2.4785  -0.9021
 B0M  H13  H  HCH2  0   0.275  -0.5636   1.4132   0.0285
 B0M  H14  H  HCH2  0   0.245  -1.7594   1.7432   1.2760
 B0M  H15  H  HCR6  0   0.249   3.0157  -1.3244  -2.3918
 B0M  H16  H  HCR5  0   0.251   5.4045   0.2780  -1.4561
 B0M  H17  H  HCR5  0   0.284   5.6589   1.7936   0.7521
 B0M  H18  H  HCR6  0   0.272   0.9855   0.5137   1.7904
 B0M  C6   C  C     0   0.512  -0.6624  -1.1958   0.4103
 B0M  H2   H  HNR5  0   0.412   3.5180   1.7025   2.0160

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
 B0M  C1   N1   single    1.445  0.020  1.445
 B0M  N1   C5   single    1.450  0.020  1.450
 B0M  N1   C2   single    1.448  0.020  1.448
 B0M  C5   C4   single    1.519  0.020  1.519
 B0M  C2   C3   single    1.521  0.020  1.521
 B0M  C4   N2   single    1.453  0.020  1.453
 B0M  C3   N2   single    1.454  0.020  1.454
 B0M  N2   C6   single    1.353  0.020  1.353
 B0M  C6   O1   double    1.226  0.020  1.226
 B0M  C6   C7   single    1.494  0.020  1.494
 B0M  C7   C8   aromatic  1.409  0.020  1.409
 B0M  C7   C14  aromatic  1.385  0.020  1.385
 B0M  C8   C9   aromatic  1.378  0.020  1.378
 B0M  C14  C13  aromatic  1.391  0.020  1.391
 B0M  C9   C10  aromatic  1.400  0.020  1.400
 B0M  C13  C10  aromatic  1.414  0.020  1.414
 B0M  C13  N3   aromatic  1.364  0.020  1.364
 B0M  C10  C11  aromatic  1.427  0.020  1.427
 B0M  N3   C12  aromatic  1.364  0.020  1.364
 B0M  C11  C12  aromatic  1.366  0.020  1.366
 B0M  N3   H2   single    0.860  0.020  1.020
 B0M  C4   H3   single    0.970  0.020  1.090
 B0M  C4   H4   single    0.970  0.020  1.090
 B0M  C5   H5   single    0.970  0.020  1.090
 B0M  C5   H6   single    0.970  0.020  1.090
 B0M  C8   H7   single    0.930  0.020  1.080
 B0M  C1   H8   single    0.970  0.020  1.090
 B0M  C1   H9   single    0.970  0.020  1.090
 B0M  C1   H10  single    0.970  0.020  1.090
 B0M  C2   H11  single    0.970  0.020  1.090
 B0M  C2   H12  single    0.970  0.020  1.090
 B0M  C3   H13  single    0.970  0.020  1.090
 B0M  C3   H14  single    0.970  0.020  1.090
 B0M  C9   H15  single    0.930  0.020  1.080
 B0M  C11  H16  single    0.930  0.020  1.080
 B0M  C12  H17  single    0.930  0.020  1.080
 B0M  C14  H18  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
 B0M  C2   N1   C1   111.58  3.000
 B0M  C2   N1   C5   110.90  3.000
 B0M  C1   N1   C5   111.87  3.000
 B0M  H2   N3   C12  124.90  3.000
 B0M  H2   N3   C13  125.74  3.000
 B0M  C12  N3   C13  109.36  3.000
 B0M  H4   C4   H3   107.96  3.000
 B0M  H4   C4   N2   110.08  3.000
 B0M  H3   C4   N2   108.15  3.000
 B0M  H4   C4   C5   110.58  3.000
 B0M  H3   C4   C5   109.47  3.000
 B0M  N2   C4   C5   110.54  3.000
 B0M  H6   C5   H5   107.03  3.000
 B0M  H6   C5   C4   109.10  3.000
 B0M  H5   C5   C4   109.08  3.000
 B0M  H6   C5   N1   112.14  3.000
 B0M  H5   C5   N1   109.06  3.000
 B0M  C4   C5   N1   110.33  3.000
 B0M  C14  C7   C8   120.73  3.000
 B0M  C14  C7   C6   121.18  3.000
 B0M  C8   C7   C6   117.87  3.000
 B0M  H7   C8   C9   119.55  3.000
 B0M  H7   C8   C7   119.14  3.000
 B0M  C9   C8   C7   121.31  3.000
 B0M  C11  C10  C9   134.43  3.000
 B0M  C11  C10  C13  106.79  3.000
 B0M  C9   C10  C13  118.77  3.000
 B0M  C14  C13  C10  122.35  3.000
 B0M  C10  C13  N3   107.38  3.000
 B0M  C14  C13  N3   130.28  3.000
 B0M  H10  C1   H9   107.73  3.000
 B0M  H10  C1   H8   107.74  3.000
 B0M  H9   C1   H8   107.90  3.000
 B0M  H10  C1   N1   113.27  3.000
 B0M  H9   C1   N1   110.02  3.000
 B0M  H8   C1   N1   110.00  3.000
 B0M  H12  C2   H11  107.06  3.000
 B0M  H12  C2   C3   108.67  3.000
 B0M  H11  C2   C3   108.70  3.000
 B0M  H12  C2   N1   109.19  3.000
 B0M  H11  C2   N1   111.85  3.000
 B0M  C3   C2   N1   111.23  3.000
 B0M  H14  C3   H13  107.70  3.000
 B0M  H14  C3   N2   108.93  3.000
 B0M  H13  C3   N2   110.97  3.000
 B0M  H14  C3   C2   109.90  3.000
 B0M  H13  C3   C2   109.23  3.000
 B0M  N2   C3   C2   110.08  3.000
 B0M  C3   N2   C6   125.09  3.000
 B0M  C6   N2   C4   120.13  3.000
 B0M  C3   N2   C4   111.81  3.000
 B0M  H15  C9   C10  120.61  3.000
 B0M  H15  C9   C8   120.26  3.000
 B0M  C10  C9   C8   119.13  3.000
 B0M  H16  C11  C12  126.11  3.000
 B0M  H16  C11  C10  127.31  3.000
 B0M  C12  C11  C10  106.58  3.000
 B0M  H17  C12  C11  129.71  3.000
 B0M  H17  C12  N3   120.41  3.000
 B0M  C11  C12  N3   109.88  3.000
 B0M  H18  C14  C13  120.96  3.000
 B0M  H18  C14  C7   121.34  3.000
 B0M  C13  C14  C7   117.70  3.000
 B0M  O1   C6   N2   122.61  3.000
 B0M  O1   C6   C7   119.21  3.000
 B0M  N2   C6   C7   118.15  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
 B0M  CONST_01  C7   C14  C13  N3    180.00   0.0  0
 B0M  CONST_02  C9   C10  C13  N3    180.00   0.0  0
 B0M  CONST_03  C11  C10  C13  N3      0.00   0.0  0
 B0M  CONST_04  C10  C11  C12  N3      0.00   0.0  0
 B0M  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 B0M  CONST_06  C10  C13  C14  C7      0.00   0.0  0
 B0M  CONST_07  C13  C14  C7   C8      0.00   0.0  0
 B0M  CONST_08  C13  C10  C9   C8      0.00   0.0  0
 B0M  CONST_09  C11  C10  C9   C8    180.00   0.0  0
 B0M  CONST_10  C12  N3   C13  C10     0.00   0.0  0
 B0M  CONST_11  C12  C11  C10  C13     0.00   0.0  0
 B0M  CONST_12  C11  C12  N3   C13     0.00   0.0  0
 B0M  CONST_13  C14  C7   C8   C9      0.00   0.0  0
 B0M  CONST_14  C14  C13  C10  C9      0.00   0.0  0
 B0M  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 B0M  CONST_16  C14  C13  C10  C11   180.00   0.0  0
 B0M  CONST_17  C14  C13  N3   C12   180.00   0.0  0
 B0M  CONST_18  C9   C8   C7   C6    180.00   0.0  0
 B0M  CONST_19  C13  C14  C7   C6    180.00   0.0  0
 B0M  CONST_20  C7   C6   N2   C4    180.00   0.0  0
 B0M  CONST_22  H18  C14  C13  N3      0.00   0.0  0
 B0M  CONST_23  H16  C11  C12  N3    180.00   0.0  0
 B0M  CONST_24  H15  C9   C8   C7    180.00   0.0  0
 B0M  CONST_25  H7   C8   C9   C10   180.00   0.0  0
 B0M  CONST_26  H2   N3   C13  C10   180.00   0.0  0
 B0M  CONST_27  H17  C12  C11  C10   180.00   0.0  0
 B0M  CONST_28  O1   C6   N2   C4      0.00   0.0  0
 B0M  Var_01    N2   C4   C5   N1    -56.74  30.0  1
 B0M  Var_02    N2   C3   C2   N1     55.73  30.0  1
 B0M  Var_03    C2   N1   C5   C4     57.49  30.0  1
 B0M  Var_04    C2   C3   N2   C4    -55.53  30.0  1
 B0M  Var_05    C3   C2   N1   C5    -57.36  30.0  1
 B0M  Var_06    C3   N2   C4   C5     56.43  30.0  1
 B0M  Var_07    N2   C6   C7   C8   -133.96  30.0  2
 B0M  Var_08    H8   C1   N1   C5     57.04  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
 B0M  plan-1  N3   0.020
 B0M  plan-1  C7   0.020
 B0M  plan-1  C8   0.020
 B0M  plan-1  C10  0.020
 B0M  plan-1  C13  0.020
 B0M  plan-1  C9   0.020
 B0M  plan-1  C11  0.020
 B0M  plan-1  C12  0.020
 B0M  plan-1  C14  0.020
 B0M  plan-1  H7   0.020
 B0M  plan-1  H15  0.020
 B0M  plan-1  H16  0.020
 B0M  plan-1  H17  0.020
 B0M  plan-1  H18  0.020
 B0M  plan-1  C6   0.020
 B0M  plan-1  H2   0.020
 B0M  plan-2  C4   0.020
 B0M  plan-2  C7   0.020
 B0M  plan-2  C3   0.020
 B0M  plan-2  N2   0.020
 B0M  plan-2  O1   0.020
 B0M  plan-2  C6   0.020

