# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:29:02 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-(4-iodophenyl)-8~{H}-imidazo[1,2-c]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1ccc(cc1)c2cn3C(=O)N=CCc3n2
#
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
 T3W  T3W  2-(4-iodophenyl)-8~{H}-imidazo[1,2-c]pyrimidin-5-one  ligand  25  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T3W
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
 T3W  C1   C  CR16  0  -0.327  -32.1825   8.9920   -8.5433
 T3W  C2   C  CR16  0  -0.289  -33.4428   6.9688   -8.2909
 T3W  C3   C  CR16  0  -0.201  -32.7943   9.2311   -9.7624
 T3W  C7   C  C     0  -0.628  -31.3943   5.6492   -3.5230
 T3W  C8   C  CR15  0  -0.085  -30.8581   8.3094   -5.8910
 T3W  C9   C  CR16  0   0.021  -30.3544   6.0757   -2.5521
 T3W  C10  C  CR5   0   0.143  -31.8440   7.5979   -6.5080
 T3W  C11  C  CR56  0   0.526  -31.4470   6.5533   -4.6876
 T3W  C12  C  CR6   0   0.670  -29.6791   7.9563   -3.7260
 T3W  C4   C  CR16  0  -0.205  -34.0629   7.1958   -9.5101
 T3W  C5   C  CR6   0   0.037  -32.4930   7.8584   -7.7900
 T3W  C6   C  CR6   0  -0.239  -33.7333   8.3271  -10.2412
 T3W  N13  N  N     0  -0.425  -29.5936   7.0939   -2.6339
 T3W  N14  N  N     0  -0.464  -32.1955   6.5058   -5.7396
 T3W  N15  N  N     0  -0.563  -30.6065   7.6324   -4.7208
 T3W  O16  O  O     0  -0.393  -28.9911   8.9343   -3.8220
 T3W  I17  I  I     0   0.055  -34.6649   8.6790  -12.0913
 T3W  H1   H  HCR6  0   0.260  -31.4554   9.7089   -8.1835
 T3W  H2   H  HCR6  0   0.263  -33.7026   6.0830   -7.7270
 T3W  H3   H  HCR6  0   0.281  -32.5339  10.1190  -10.3223
 T3W  H5   H  H     0   0.332  -31.1908   4.6160   -3.8226
 T3W  H6   H  HCR5  0   0.313  -30.3242   9.2032   -6.1638
 T3W  H7   H  HCR6  0   0.306  -30.2355   5.4457   -1.6749
 T3W  H8   H  HCR6  0   0.279  -34.7942   6.4876   -9.8748
 T3W  H4   H  H     0   0.333  -32.3570   5.6132   -3.0010

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
 T3W  I17  C6   single    2.101  0.020  2.101
 T3W  C6   C3   aromatic  1.389  0.020  1.389
 T3W  C6   C4   aromatic  1.387  0.020  1.387
 T3W  C3   C1   aromatic  1.385  0.020  1.385
 T3W  C4   C2   aromatic  1.387  0.020  1.387
 T3W  C1   C5   aromatic  1.396  0.020  1.396
 T3W  C2   C5   aromatic  1.394  0.020  1.394
 T3W  C5   C10  single    1.460  0.020  1.460
 T3W  C10  C8   aromatic  1.363  0.020  1.363
 T3W  C10  N14  aromatic  1.381  0.020  1.381
 T3W  C8   N15  aromatic  1.375  0.020  1.375
 T3W  N14  C11  aromatic  1.292  0.020  1.292
 T3W  N15  C11  aromatic  1.368  0.020  1.368
 T3W  N15  C12  single    1.398  0.020  1.398
 T3W  C11  C7   single    1.475  0.020  1.475
 T3W  O16  C12  double    1.200  0.020  1.200
 T3W  C12  N13  single    1.394  0.020  1.394
 T3W  C7   C9   single    1.485  0.020  1.485
 T3W  N13  C9   double    1.274  0.020  1.274
 T3W  C1   H1   single    0.930  0.020  1.080
 T3W  C2   H2   single    0.930  0.020  1.080
 T3W  C3   H3   single    0.930  0.020  1.080
 T3W  C7   H4   single    0.970  0.020  1.090
 T3W  C7   H5   single    0.970  0.020  1.090
 T3W  C8   H6   single    0.930  0.020  1.080
 T3W  C9   H7   single    0.930  0.020  1.080
 T3W  C4   H8   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
 T3W  H1   C1   C5   120.51  3.000
 T3W  H1   C1   C3   118.35  3.000
 T3W  C5   C1   C3   121.13  3.000
 T3W  H2   C2   C5   119.92  3.000
 T3W  H2   C2   C4   119.01  3.000
 T3W  C5   C2   C4   121.06  3.000
 T3W  H3   C3   C6   121.26  3.000
 T3W  H3   C3   C1   119.41  3.000
 T3W  C6   C3   C1   119.33  3.000
 T3W  H5   C7   H4   105.23  3.000
 T3W  H5   C7   C11  111.65  3.000
 T3W  H4   C7   C11  111.39  3.000
 T3W  H5   C7   C9   108.65  3.000
 T3W  H4   C7   C9   108.26  3.000
 T3W  C11  C7   C9   111.41  3.000
 T3W  H6   C8   N15  122.26  3.000
 T3W  H6   C8   C10  132.64  3.000
 T3W  N15  C8   C10  105.10  3.000
 T3W  H7   C9   N13  116.74  3.000
 T3W  H7   C9   C7   115.97  3.000
 T3W  N13  C9   C7   127.29  3.000
 T3W  N14  C10  C5   121.10  3.000
 T3W  N14  C10  C8   110.18  3.000
 T3W  C5   C10  C8   128.72  3.000
 T3W  N15  C11  N14  111.42  3.000
 T3W  N15  C11  C7   118.72  3.000
 T3W  N14  C11  C7   129.86  3.000
 T3W  O16  C12  N15  120.82  3.000
 T3W  O16  C12  N13  122.12  3.000
 T3W  N15  C12  N13  117.05  3.000
 T3W  H8   C4   C6   121.15  3.000
 T3W  H8   C4   C2   119.46  3.000
 T3W  C6   C4   C2   119.39  3.000
 T3W  C10  C5   C2   120.28  3.000
 T3W  C10  C5   C1   121.32  3.000
 T3W  C2   C5   C1   118.41  3.000
 T3W  I17  C6   C4   119.70  3.000
 T3W  C4   C6   C3   120.67  3.000
 T3W  I17  C6   C3   119.63  3.000
 T3W  C12  N13  C9   120.54  3.000
 T3W  C11  N14  C10  106.06  3.000
 T3W  C12  N15  C11  124.96  3.000
 T3W  C12  N15  C8   127.80  3.000
 T3W  C11  N15  C8   107.25  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
 T3W  CONST_01  C4   C6   C3   C1      0.00   0.0  0
 T3W  CONST_02  C4   C2   C5   C1      0.00   0.0  0
 T3W  CONST_03  C8   C10  C5   C1      0.00   0.0  0
 T3W  CONST_04  N14  C10  C5   C1    180.00   0.0  0
 T3W  CONST_05  C3   C6   C4   C2      0.00   0.0  0
 T3W  CONST_06  C3   C1   C5   C2      0.00   0.0  0
 T3W  CONST_07  C8   C10  C5   C2    180.00   0.0  0
 T3W  CONST_08  N14  C10  C5   C2      0.00   0.0  0
 T3W  CONST_09  C10  C5   C1   C3    180.00   0.0  0
 T3W  CONST_10  C11  N14  C10  C8      0.00   0.0  0
 T3W  CONST_11  N14  C11  N15  C8      0.00   0.0  0
 T3W  CONST_12  C4   C2   C5   C10   180.00   0.0  0
 T3W  CONST_13  C11  N15  C8   C10     0.00   0.0  0
 T3W  CONST_14  N15  C11  N14  C10     0.00   0.0  0
 T3W  CONST_15  C5   C10  N14  C11   180.00   0.0  0
 T3W  CONST_16  C6   C3   C1   C5      0.00   0.0  0
 T3W  CONST_17  C6   C4   C2   C5      0.00   0.0  0
 T3W  CONST_18  N15  C8   C10  C5    180.00   0.0  0
 T3W  CONST_19  N15  C8   C10  N14     0.00   0.0  0
 T3W  CONST_20  N13  C12  N15  C8    180.00   0.0  0
 T3W  CONST_21  N15  C12  N13  C9      0.00   0.0  0
 T3W  CONST_22  N13  C12  N15  C11     0.00   0.0  0
 T3W  CONST_23  I17  C6   C3   C1    180.00   0.0  0
 T3W  CONST_24  I17  C6   C4   C2    180.00   0.0  0
 T3W  CONST_25  O16  C12  N15  C8      0.00   0.0  0
 T3W  CONST_26  O16  C12  N13  C9    180.00   0.0  0
 T3W  CONST_27  O16  C12  N15  C11   180.00   0.0  0
 T3W  CONST_28  H2   C2   C5   C1    180.00   0.0  0
 T3W  CONST_29  H1   C1   C5   C2    180.00   0.0  0
 T3W  CONST_30  H8   C4   C6   C3    180.00   0.0  0
 T3W  CONST_31  H6   C8   N15  C11   180.00   0.0  0
 T3W  CONST_32  H3   C3   C6   C4    180.00   0.0  0
 T3W  Var_01    H7   C9   C7   C11  -178.57  30.0  1

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
 T3W  plan-1  C1   0.020
 T3W  plan-1  C2   0.020
 T3W  plan-1  C3   0.020
 T3W  plan-1  C10  0.020
 T3W  plan-1  C4   0.020
 T3W  plan-1  C5   0.020
 T3W  plan-1  C6   0.020
 T3W  plan-1  I17  0.020
 T3W  plan-1  H1   0.020
 T3W  plan-1  H2   0.020
 T3W  plan-1  H3   0.020
 T3W  plan-1  H8   0.020
 T3W  plan-2  C7   0.020
 T3W  plan-2  C8   0.020
 T3W  plan-2  C9   0.020
 T3W  plan-2  C10  0.020
 T3W  plan-2  C11  0.020
 T3W  plan-2  C12  0.020
 T3W  plan-2  C5   0.020
 T3W  plan-2  N13  0.020
 T3W  plan-2  N14  0.020
 T3W  plan-2  N15  0.020
 T3W  plan-2  O16  0.020
 T3W  plan-2  H6   0.020

