# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 17:29:01 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 8-cyclohexyl-6~{H}-imidazo[1,2-c]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=C(C2CCCCC2)c3nccn13
#
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
 R7B  R7B  8-cyclohexyl-6~{H}-imidazo[1,2-c]pyrimidin-5-one  ligand  31  16  .  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_R7B
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
 R7B  C4   C  CR56  0   0.535  -12.7297   9.4810  33.8602
 R7B  C5   C  CR15  0  -0.202  -13.7188  10.4172  32.2179
 R7B  C6   C  CR15  0  -0.102  -13.9391  11.2478  33.2717
 R7B  C11  C  CH2   0  -0.432   -9.6849   5.5412  34.5695
 R7B  C7   C  CH1   0  -0.304  -11.3897   7.3657  34.2635
 R7B  C8   C  CH2   0  -0.416  -12.4716   6.2981  34.0449
 R7B  C9   C  CH2   0  -0.433  -11.8796   5.0222  33.4572
 R7B  C10  C  CH2   0  -0.428  -10.7528   4.4790  34.3284
 R7B  C12  C  CH2   0  -0.430  -10.2872   6.8103  35.1639
 R7B  N1   N  N     0  -0.576  -13.3011  10.6453  34.3318
 R7B  N2   N  NR16  0  -0.695  -12.5008  10.2765  36.4309
 R7B  C3   C  CR6   0  -0.022  -11.9907   8.6493  34.7623
 R7B  N3   N  N     0  -0.457  -12.9729   9.3301  32.5846
 R7B  C1   C  CR6   0   0.706  -13.2173  11.1116  35.6361
 R7B  C2   C  CR16  0  -0.026  -11.9096   9.0999  36.0285
 R7B  O1   O  O     0  -0.466  -13.7299  12.1487  35.9963
 R7B  H1   H  HCR5  0   0.260  -14.0625  10.5471  31.2034
 R7B  H2   H  HCR5  0   0.302  -14.4705  12.1783  33.3644
 R7B  H4   H  HCH2  0   0.212   -9.1933   5.7845  33.6216
 R7B  H5   H  HCH1  0   0.231  -10.9408   7.5833  33.2859
 R7B  H6   H  HCH2  0   0.236  -13.2560   6.6847  33.3915
 R7B  H7   H  HCH2  0   0.214  -12.9431   6.0759  35.0086
 R7B  H8   H  HCH2  0   0.228  -12.6635   4.2705  33.3374
 R7B  H9   H  HCH2  0   0.211  -11.4954   5.2316  32.4530
 R7B  H10  H  HCH2  0   0.209  -11.1652   4.1588  35.2914
 R7B  H11  H  HCH2  0   0.227  -10.3092   3.5927  33.8686
 R7B  H12  H  HCH2  0   0.235   -9.5099   7.5636  35.3169
 R7B  H13  H  HCH2  0   0.215  -10.6981   6.5747  36.1518
 R7B  H14  H  HNR6  0   0.434  -12.3949  10.5600  37.3946
 R7B  H15  H  HCR6  0   0.306  -11.3817   8.5799  36.8136
 R7B  H3   H  HCH2  0   0.229   -8.9075   5.1549  35.2327

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
 R7B  C5   N3   aromatic  1.368  0.020  1.368
 R7B  C5   C6   aromatic  1.360  0.020  1.360
 R7B  N3   C4   aromatic  1.307  0.020  1.307
 R7B  C6   N1   aromatic  1.376  0.020  1.376
 R7B  C9   C8   single    1.524  0.020  1.524
 R7B  C9   C10  single    1.524  0.020  1.524
 R7B  C4   N1   aromatic  1.380  0.020  1.380
 R7B  C4   C3   single    1.432  0.020  1.432
 R7B  C8   C7   single    1.536  0.020  1.536
 R7B  C7   C3   single    1.503  0.020  1.503
 R7B  C7   C12  single    1.528  0.020  1.528
 R7B  N1   C1   single    1.388  0.020  1.388
 R7B  C10  C11  single    1.525  0.020  1.525
 R7B  C11  C12  single    1.525  0.020  1.525
 R7B  C3   C2   double    1.346  0.020  1.346
 R7B  C1   O1   double    1.212  0.020  1.212
 R7B  C1   N2   single    1.357  0.020  1.357
 R7B  C2   N2   single    1.377  0.020  1.377
 R7B  C5   H1   single    0.930  0.020  1.080
 R7B  C6   H2   single    0.930  0.020  1.080
 R7B  C11  H3   single    0.970  0.020  1.090
 R7B  C11  H4   single    0.970  0.020  1.090
 R7B  C7   H5   single    0.970  0.020  1.090
 R7B  C8   H6   single    0.970  0.020  1.090
 R7B  C8   H7   single    0.970  0.020  1.090
 R7B  C9   H8   single    0.970  0.020  1.090
 R7B  C9   H9   single    0.970  0.020  1.090
 R7B  C10  H10  single    0.970  0.020  1.090
 R7B  C10  H11  single    0.970  0.020  1.090
 R7B  C12  H12  single    0.970  0.020  1.090
 R7B  C12  H13  single    0.970  0.020  1.090
 R7B  N2   H14  single    0.860  0.020  1.020
 R7B  C2   H15  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
 R7B  N3   C4   C3   130.06  3.000
 R7B  C3   C4   N1   119.23  3.000
 R7B  N3   C4   N1   110.72  3.000
 R7B  H1   C5   N3   121.41  3.000
 R7B  H1   C5   C6   127.13  3.000
 R7B  N3   C5   C6   111.46  3.000
 R7B  H2   C6   N1   122.78  3.000
 R7B  H2   C6   C5   132.48  3.000
 R7B  N1   C6   C5   104.74  3.000
 R7B  H4   C11  H3   106.54  3.000
 R7B  H4   C11  C12  109.25  3.000
 R7B  H3   C11  C12  109.79  3.000
 R7B  H4   C11  C10  109.40  3.000
 R7B  H3   C11  C10  110.36  3.000
 R7B  C12  C11  C10  111.38  3.000
 R7B  H5   C7   C3   106.86  3.000
 R7B  H5   C7   C12  107.57  3.000
 R7B  C3   C7   C12  113.80  3.000
 R7B  H5   C7   C8   107.41  3.000
 R7B  C12  C7   C8   109.84  3.000
 R7B  C3   C7   C8   111.06  3.000
 R7B  H7   C8   H6   106.80  3.000
 R7B  H7   C8   C9   109.66  3.000
 R7B  H6   C8   C9   110.16  3.000
 R7B  H7   C8   C7   108.60  3.000
 R7B  H6   C8   C7   110.20  3.000
 R7B  C9   C8   C7   111.29  3.000
 R7B  H9   C9   H8   106.42  3.000
 R7B  H9   C9   C10  109.44  3.000
 R7B  H8   C9   C10  110.36  3.000
 R7B  H9   C9   C8   109.24  3.000
 R7B  H8   C9   C8   109.84  3.000
 R7B  C10  C9   C8   111.40  3.000
 R7B  H11  C10  H10  106.60  3.000
 R7B  H11  C10  C9   110.40  3.000
 R7B  H10  C10  C9   109.16  3.000
 R7B  H11  C10  C11  110.31  3.000
 R7B  H10  C10  C11  109.16  3.000
 R7B  C9   C10  C11  111.08  3.000
 R7B  H13  C12  H12  106.77  3.000
 R7B  H13  C12  C7   109.81  3.000
 R7B  H12  C12  C7   110.18  3.000
 R7B  H13  C12  C11  108.70  3.000
 R7B  H12  C12  C11  110.31  3.000
 R7B  C7   C12  C11  110.96  3.000
 R7B  C1   N1   C6   127.23  3.000
 R7B  C1   N1   C4   125.43  3.000
 R7B  C6   N1   C4   107.34  3.000
 R7B  H14  N2   C2   118.27  3.000
 R7B  H14  N2   C1   116.19  3.000
 R7B  C2   N2   C1   125.54  3.000
 R7B  C2   C3   C7   125.03  3.000
 R7B  C2   C3   C4   115.41  3.000
 R7B  C7   C3   C4   119.56  3.000
 R7B  C5   N3   C4   105.74  3.000
 R7B  O1   C1   N2   125.16  3.000
 R7B  N2   C1   N1   112.06  3.000
 R7B  O1   C1   N1   122.79  3.000
 R7B  H15  C2   C3   123.52  3.000
 R7B  H15  C2   N2   114.14  3.000
 R7B  C3   C2   N2   122.34  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
 R7B  CONST_01  C6   C5   N3   C4     0.00   0.0  0
 R7B  CONST_02  C5   C6   N1   C4     0.00   0.0  0
 R7B  CONST_03  N1   C4   N3   C5     0.00   0.0  0
 R7B  CONST_04  N3   C4   N1   C6     0.00   0.0  0
 R7B  CONST_05  N3   C5   C6   N1     0.00   0.0  0
 R7B  CONST_06  N2   C1   N1   C4     0.00   0.0  0
 R7B  CONST_07  N2   C1   N1   C6   180.00   0.0  0
 R7B  CONST_08  C2   N2   C1   N1     0.00   0.0  0
 R7B  CONST_09  O1   C1   N1   C4   180.00   0.0  0
 R7B  CONST_10  O1   C1   N1   C6     0.00   0.0  0
 R7B  CONST_11  O1   C1   N2   C2   180.00   0.0  0
 R7B  CONST_12  H1   C5   N3   C4   180.00   0.0  0
 R7B  CONST_13  H2   C6   N1   C4   180.00   0.0  0
 R7B  CONST_14  H14  N2   C1   N1   180.00   0.0  0
 R7B  Var_01    C8   C9   C10  C11  -54.61  30.0  1
 R7B  Var_02    C10  C9   C8   C7    55.85  30.0  1
 R7B  Var_03    C10  C11  C12  C7   -56.85  30.0  1
 R7B  Var_04    C12  C11  C10  C9    55.13  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 R7B  chir_01  C7  C8  C3  C12  negativ

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
 R7B  plan-1  C4   0.020
 R7B  plan-1  C5   0.020
 R7B  plan-1  C6   0.020
 R7B  plan-1  C7   0.020
 R7B  plan-1  N1   0.020
 R7B  plan-1  N2   0.020
 R7B  plan-1  C3   0.020
 R7B  plan-1  N3   0.020
 R7B  plan-1  C1   0.020
 R7B  plan-1  C2   0.020
 R7B  plan-1  O1   0.020
 R7B  plan-1  H1   0.020
 R7B  plan-1  H2   0.020
 R7B  plan-1  H14  0.020
 R7B  plan-1  H15  0.020

