# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:06:34 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-phenyl]-(4-methylpiperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)c2cc(I)c(n3cccc3)c(I)c2O
#
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
 9H5  9H5  '[3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-phenyl]-(4-methylpiperazin-1-yl)methanone'  ligand  40  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9H5
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
 9H5  N1   N  NR5   0  -0.505  -2.5306  -0.3572   0.2650
 9H5  N3   N  NT    0  -0.418   5.9083   0.2973   1.3049
 9H5  C4   C  CR6   0   0.409  -1.1785  -0.2934  -0.1114
 9H5  C5   C  CR6   0  -0.389  -0.4221   0.8414   0.1890
 9H5  C6   C  CR6   0   0.438   0.9164   0.9305  -0.1945
 9H5  C7   C  CR15  0  -0.067  -3.0021  -0.8636   1.4467
 9H5  C8   C  CR15  0  -0.352  -4.3662  -0.7632   1.4290
 9H5  C10  C  CR15  0  -0.066  -3.5802   0.0640  -0.5072
 9H5  C13  C  CH2   0  -0.277   6.0212   0.7357  -0.0713
 9H5  C15  C  CH2   0  -0.313   3.7557  -0.7407   0.8015
 9H5  C12  C  CH2   0  -0.317   5.2842  -0.2138  -0.9999
 9H5  C16  C  CH3   0  -0.516   6.6717   1.1372   2.1995
 9H5  C14  C  CH2   0  -0.272   4.5186   0.2132   1.7056
 9H5  N2   N  NT    0  -0.432   3.8976  -0.3378  -0.5854
 9H5  O2   O  O     0  -0.480   3.0411   0.3522  -2.5666
 9H5  C1   C  CR6   0  -0.195   1.4924  -0.1444  -0.8749
 9H5  I2   I  I     0   0.137  -1.3218   2.4324   1.2175
 9H5  O1   O  OH1   0  -0.596   1.7164   1.9725   0.0389
 9H5  C2   C  CR16  0  -0.240   0.7477  -1.2679  -1.1776
 9H5  C3   C  CR6   0  -0.271  -0.5826  -1.3481  -0.7922
 9H5  I1   I  I     0   0.106  -1.6873  -3.0654  -1.2599
 9H5  C9   C  CR15  0  -0.352  -4.7331  -0.1743   0.1889
 9H5  H2   H  HCR5  0   0.285  -2.3280  -1.2509   2.1934
 9H5  H3   H  HCR5  0   0.247  -5.0305  -1.0776   2.2184
 9H5  H4   H  HCR5  0   0.285  -3.4130   0.4960  -1.4807
 9H5  H5   H  HCH2  0   0.200   5.6280   1.7575  -0.2138
 9H5  H6   H  HCH2  0   0.246   7.0758   0.7544  -0.3566
 9H5  H7   H  HCH2  0   0.253   4.1548  -1.7530   0.9149
 9H5  H8   H  HCH2  0   0.272   2.7083  -0.7709   1.0915
 9H5  H9   H  HCH2  0   0.269   5.3325   0.1442  -2.0245
 9H5  H10  H  HCH2  0   0.249   5.7508  -1.2028  -0.9662
 9H5  H11  H  HCH3  0   0.235   6.6103   0.7502   3.2176
 9H5  H12  H  HCH3  0   0.235   7.7220   1.1384   1.9051
 9H5  H13  H  HCH3  0   0.195   6.3255   2.1820   2.2164
 9H5  H14  H  HCH2  0   0.246   4.4638  -0.1588   2.7312
 9H5  H15  H  HCH2  0   0.200   4.0223   1.1981   1.6887
 9H5  H16  H  HOH1  0   0.480   1.2867   2.6687   0.5532
 9H5  H17  H  HCR6  0   0.298   1.2162  -2.0853  -1.7091
 9H5  H18  H  HCR5  0   0.248  -5.7315   0.0472  -0.1532
 9H5  C11  C  C     0   0.526   2.8934  -0.0140  -1.4094

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
 9H5  I1   C3   single    2.095  0.020  2.095
 9H5  C12  N2   single    1.453  0.020  1.453
 9H5  C12  C13  single    1.519  0.020  1.519
 9H5  O2   C11  double    1.223  0.020  1.223
 9H5  C2   C3   aromatic  1.387  0.020  1.387
 9H5  C2   C1   aromatic  1.381  0.020  1.381
 9H5  N2   C11  single    1.339  0.020  1.339
 9H5  N2   C15  single    1.451  0.020  1.451
 9H5  C11  C1   single    1.505  0.020  1.505
 9H5  C15  C14  single    1.520  0.020  1.520
 9H5  C13  N3   single    1.449  0.020  1.449
 9H5  N3   C14  single    1.449  0.020  1.449
 9H5  N3   C16  single    1.445  0.020  1.445
 9H5  C3   C4   aromatic  1.390  0.020  1.390
 9H5  C1   C6   aromatic  1.397  0.020  1.397
 9H5  C4   N1   single    1.405  0.020  1.405
 9H5  C4   C5   aromatic  1.396  0.020  1.396
 9H5  C6   C5   aromatic  1.395  0.020  1.395
 9H5  C6   O1   single    1.334  0.020  1.334
 9H5  N1   C10  aromatic  1.369  0.020  1.369
 9H5  N1   C7   aromatic  1.369  0.020  1.369
 9H5  C5   I2   single    2.097  0.020  2.097
 9H5  C10  C9   aromatic  1.368  0.020  1.368
 9H5  C7   C8   aromatic  1.368  0.020  1.368
 9H5  C9   C8   aromatic  1.421  0.020  1.421
 9H5  C7   H2   single    0.930  0.020  1.080
 9H5  C8   H3   single    0.930  0.020  1.080
 9H5  C10  H4   single    0.930  0.020  1.080
 9H5  C13  H5   single    0.970  0.020  1.090
 9H5  C13  H6   single    0.970  0.020  1.090
 9H5  C15  H7   single    0.970  0.020  1.090
 9H5  C15  H8   single    0.970  0.020  1.090
 9H5  C12  H9   single    0.970  0.020  1.090
 9H5  C12  H10  single    0.970  0.020  1.090
 9H5  C16  H11  single    0.970  0.020  1.090
 9H5  C16  H12  single    0.970  0.020  1.090
 9H5  C16  H13  single    0.970  0.020  1.090
 9H5  C14  H14  single    0.970  0.020  1.090
 9H5  C14  H15  single    0.970  0.020  1.090
 9H5  O1   H16  single    0.850  0.020  0.980
 9H5  C2   H17  single    0.930  0.020  1.080
 9H5  C9   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
 9H5  C10  N1   C7   109.66  3.000
 9H5  C7   N1   C4   125.41  3.000
 9H5  C10  N1   C4   124.93  3.000
 9H5  C14  N3   C16  111.66  3.000
 9H5  C16  N3   C13  111.78  3.000
 9H5  C14  N3   C13  110.80  3.000
 9H5  C3   C4   C5   119.33  3.000
 9H5  C5   C4   N1   120.04  3.000
 9H5  C3   C4   N1   120.63  3.000
 9H5  I2   C5   C6   119.86  3.000
 9H5  I2   C5   C4   119.31  3.000
 9H5  C6   C5   C4   120.83  3.000
 9H5  O1   C6   C1   116.04  3.000
 9H5  O1   C6   C5   125.24  3.000
 9H5  C1   C6   C5   118.72  3.000
 9H5  H2   C7   C8   131.22  3.000
 9H5  H2   C7   N1   121.02  3.000
 9H5  C8   C7   N1   107.76  3.000
 9H5  H3   C8   C9   126.91  3.000
 9H5  H3   C8   C7   125.68  3.000
 9H5  C9   C8   C7   107.41  3.000
 9H5  H4   C10  C9   131.31  3.000
 9H5  H4   C10  N1   120.90  3.000
 9H5  C9   C10  N1   107.78  3.000
 9H5  H6   C13  H5   107.11  3.000
 9H5  H6   C13  C12  108.63  3.000
 9H5  H5   C13  C12  109.08  3.000
 9H5  H6   C13  N3   109.17  3.000
 9H5  H5   C13  N3   112.02  3.000
 9H5  C12  C13  N3   110.71  3.000
 9H5  H8   C15  H7   107.34  3.000
 9H5  H8   C15  N2   110.91  3.000
 9H5  H7   C15  N2   108.68  3.000
 9H5  H8   C15  C14  110.02  3.000
 9H5  H7   C15  C14  109.63  3.000
 9H5  N2   C15  C14  110.20  3.000
 9H5  H10  C12  H9   107.94  3.000
 9H5  H10  C12  N2   108.73  3.000
 9H5  H9   C12  N2   109.86  3.000
 9H5  H10  C12  C13  109.84  3.000
 9H5  H9   C12  C13  110.43  3.000
 9H5  N2   C12  C13  110.01  3.000
 9H5  H13  C16  H12  107.81  3.000
 9H5  H13  C16  H11  107.74  3.000
 9H5  H12  C16  H11  107.85  3.000
 9H5  H13  C16  N3   113.27  3.000
 9H5  H12  C16  N3   110.01  3.000
 9H5  H11  C16  N3   109.99  3.000
 9H5  H15  C14  H14  107.21  3.000
 9H5  H15  C14  C15  109.00  3.000
 9H5  H14  C14  C15  108.64  3.000
 9H5  H15  C14  N3   112.06  3.000
 9H5  H14  C14  N3   109.12  3.000
 9H5  C15  C14  N3   110.70  3.000
 9H5  C11  N2   C12  121.32  3.000
 9H5  C11  N2   C15  125.59  3.000
 9H5  C12  N2   C15  112.94  3.000
 9H5  C2   C1   C11  119.63  3.000
 9H5  C11  C1   C6   119.35  3.000
 9H5  C2   C1   C6   120.69  3.000
 9H5  H16  O1   C6   112.90  3.000
 9H5  H17  C2   C3   120.54  3.000
 9H5  H17  C2   C1   119.26  3.000
 9H5  C3   C2   C1   120.20  3.000
 9H5  I1   C3   C2   119.41  3.000
 9H5  C2   C3   C4   120.22  3.000
 9H5  I1   C3   C4   120.36  3.000
 9H5  H18  C9   C10  125.67  3.000
 9H5  H18  C9   C8   126.94  3.000
 9H5  C10  C9   C8   107.38  3.000
 9H5  C1   C11  O2   118.32  3.000
 9H5  C1   C11  N2   117.30  3.000
 9H5  O2   C11  N2   124.36  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
 9H5  CONST_01  C2   C3   C4   N1    180.00   0.0  0
 9H5  CONST_02  C6   C5   C4   N1    180.00   0.0  0
 9H5  CONST_03  C8   C9   C10  N1      0.00   0.0  0
 9H5  CONST_04  C9   C8   C7   N1      0.00   0.0  0
 9H5  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 9H5  CONST_06  C9   C10  N1   C4    180.00   0.0  0
 9H5  CONST_07  C8   C7   N1   C4    180.00   0.0  0
 9H5  CONST_08  C1   C6   C5   C4      0.00   0.0  0
 9H5  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 9H5  CONST_12  C2   C1   C6   C5      0.00   0.0  0
 9H5  CONST_13  C3   C2   C1   C6      0.00   0.0  0
 9H5  CONST_14  C3   C4   C5   C6      0.00   0.0  0
 9H5  CONST_16  C9   C10  N1   C7      0.00   0.0  0
 9H5  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 9H5  CONST_18  C10  N1   C7   C8      0.00   0.0  0
 9H5  CONST_20  I1   C3   C4   N1      0.00   0.0  0
 9H5  CONST_21  I2   C5   C4   N1      0.00   0.0  0
 9H5  CONST_22  O1   C6   C5   C4    180.00   0.0  0
 9H5  CONST_23  I1   C3   C4   C5    180.00   0.0  0
 9H5  CONST_24  C11  C1   C6   C5    180.00   0.0  0
 9H5  CONST_25  C3   C2   C1   C11   180.00   0.0  0
 9H5  CONST_26  I1   C3   C2   C1    180.00   0.0  0
 9H5  CONST_27  I2   C5   C6   C1    180.00   0.0  0
 9H5  CONST_28  C3   C4   C5   I2    180.00   0.0  0
 9H5  CONST_29  C2   C1   C6   O1    180.00   0.0  0
 9H5  CONST_30  C1   C11  N2   C15     0.00   0.0  0
 9H5  CONST_31  C1   C11  N2   C12   180.00   0.0  0
 9H5  CONST_32  H18  C9   C10  N1    180.00   0.0  0
 9H5  CONST_33  H3   C8   C7   N1    180.00   0.0  0
 9H5  CONST_34  H17  C2   C3   C4    180.00   0.0  0
 9H5  CONST_35  H4   C10  N1   C4      0.00   0.0  0
 9H5  CONST_36  H2   C7   N1   C4      0.00   0.0  0
 9H5  CONST_37  O2   C11  N2   C15   180.00   0.0  0
 9H5  CONST_38  O2   C11  N2   C12     0.00   0.0  0
 9H5  Var_01    N2   C12  C13  N3     55.93  30.0  1
 9H5  Var_02    N2   C15  C14  N3    -55.58  30.0  1
 9H5  Var_03    C15  N2   C12  C13   -54.98  30.0  1
 9H5  Var_04    C15  C14  N3   C13    58.15  30.0  1
 9H5  Var_05    C14  C15  N2   C12    54.85  30.0  1
 9H5  Var_06    C14  N3   C13  C12   -58.40  30.0  1
 9H5  Var_07    N2   C11  C1   C6     87.84  30.0  2
 9H5  Var_08    H11  C16  N3   C13  -176.94  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
 9H5  plan-1  N1   0.020
 9H5  plan-1  C4   0.020
 9H5  plan-1  C7   0.020
 9H5  plan-1  C8   0.020
 9H5  plan-1  C10  0.020
 9H5  plan-1  C9   0.020
 9H5  plan-1  H2   0.020
 9H5  plan-1  H3   0.020
 9H5  plan-1  H4   0.020
 9H5  plan-1  H18  0.020
 9H5  plan-2  N1   0.020
 9H5  plan-2  C4   0.020
 9H5  plan-2  C5   0.020
 9H5  plan-2  C6   0.020
 9H5  plan-2  C1   0.020
 9H5  plan-2  I2   0.020
 9H5  plan-2  O1   0.020
 9H5  plan-2  C2   0.020
 9H5  plan-2  C3   0.020
 9H5  plan-2  I1   0.020
 9H5  plan-2  H17  0.020
 9H5  plan-2  C11  0.020
 9H5  plan-3  C15  0.020
 9H5  plan-3  C12  0.020
 9H5  plan-3  N2   0.020
 9H5  plan-3  O2   0.020
 9H5  plan-3  C1   0.020
 9H5  plan-3  C11  0.020

