# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:57:48 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C1=C(C)N(c2cccc(c2)C(F)(F)F)c3[nH]cc[n+]3[C@@H]1c4ccc(cc4)C#N
#
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
 IUY  IUY  'ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate'  ligand  53  33  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IUY
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
 IUY  C1    C  CR6   0  -0.217  -1.1034   1.4776  -0.6130
 IUY  C2    C  CR16  0  -0.186  -1.8663   1.0355   0.6192
 IUY  C3    C  CR6   0   0.375   0.2485   1.4881  -0.6956
 IUY  N4    N  NR6   0  -0.678   1.0124   1.1174   0.4162
 IUY  C5    C  CH3   0  -0.742   1.0344   1.8759  -1.9078
 IUY  C6    C  CR6   0   0.184  -2.6051  -0.2739   0.4157
 IUY  C7    C  CR16  0  -0.289  -3.9477  -0.3726   0.7552
 IUY  C8    C  CR16  0  -0.224  -4.6252  -1.5691   0.5965
 IUY  C9    C  CR6   0  -0.004  -3.9459  -2.6770   0.0944
 IUY  C10   C  CR16  0  -0.218  -2.5964  -2.5876  -0.2465
 IUY  C11   C  CR16  0  -0.277  -1.9344  -1.3846  -0.0852
 IUY  C12   C  C     0   0.613  -1.9444   1.8661  -1.7613
 IUY  O13   O  O     0  -0.446  -1.5630   2.1034  -2.8832
 IUY  O14   O  O2    0  -0.466  -3.2198   1.9125  -1.4043
 IUY  C15   C  CH2   0  -0.177  -4.2024   2.2332  -2.4005
 IUY  C16   C  CH3   0  -0.688  -5.5616   2.1239  -1.7543
 IUY  C17   C  CSP   0   0.061  -4.6364  -3.9155  -0.0727
 IUY  N18   N  NS    0  -0.246  -5.1902  -4.9173  -0.2022
 IUY  N19   N  N     1  -0.502  -0.9300   0.8886   1.7254
 IUY  C20   C  CR56  0   0.968   0.3847   0.8819   1.5888
 IUY  N21   N  NR15  0  -0.655   0.9292   0.6326   2.7733
 IUY  C22   C  CR15  0  -0.069  -0.0791   0.4751   3.7015
 IUY  C23   C  CR15  0  -0.074  -1.2448   0.6329   3.0478
 IUY  C24   C  CR6   0   0.152   2.4385   1.0057   0.4102
 IUY  C25   C  CR16  0  -0.223   3.2122   2.0723   0.8476
 IUY  C26   C  CR16  0  -0.237   4.5905   1.9415   0.8629
 IUY  C27   C  CR16  0  -0.263   5.1873   0.7595   0.4457
 IUY  C28   C  CR6   0  -0.192   4.4002  -0.2997   0.0165
 IUY  C29   C  CR16  0  -0.237   3.0155  -0.1827   0.0006
 IUY  C30   C  CT    0   1.063   5.0090  -1.5841  -0.4597
 IUY  F31   F  F     0  -0.298   6.3186  -1.6511  -0.2174
 IUY  F32   F  F     0  -0.309   4.4399  -2.6431   0.1286
 IUY  F33   F  F     0  -0.310   4.8417  -1.7409  -1.7796
 IUY  H2    H  HCR6  0   0.333  -2.5796   1.8060   0.9160
 IUY  H5    H  HCH3  0   0.288   0.6711   2.8116  -2.3217
 IUY  H5A   H  HCH3  0   0.276   2.0899   1.9977  -1.6877
 IUY  H5B   H  HCH3  0   0.286   0.9404   1.1157  -2.6822
 IUY  H7    H  HCR6  0   0.279  -4.4732   0.4897   1.1454
 IUY  H8    H  HCR6  0   0.289  -5.6716  -1.6429   0.8583
 IUY  H10   H  HCR6  0   0.288  -2.0742  -3.4506  -0.6355
 IUY  H11   H  HCR6  0   0.270  -0.8885  -1.3231  -0.3608
 IUY  H15   H  HCH2  0   0.239  -4.0242   3.2431  -2.7748
 IUY  H15A  H  HCH2  0   0.238  -4.1133   1.5408  -3.2397
 IUY  H16   H  HCH3  0   0.236  -5.7602   1.1092  -1.4093
 IUY  H16A  H  HCH3  0   0.237  -5.6629   2.8059  -0.9102
 IUY  H16B  H  HCH3  0   0.243  -6.3246   2.3832  -2.4878
 IUY  HN21  H  HNR5  0   0.463   1.9188   0.5747   2.9712
 IUY  H22   H  HCR5  0   0.332   0.1312   0.2687   4.7350
 IUY  H23   H  HCR5  0   0.338  -2.2619   0.5864   3.3949
 IUY  H25   H  HCR6  0   0.300   2.7414   2.9943   1.1634
 IUY  H26   H  HCR6  0   0.290   5.2051   2.7650   1.1982
 IUY  H27   H  HCR6  0   0.289   6.2652   0.6807   0.4626
 IUY  H29   H  HCR6  0   0.297   2.3835  -0.9981  -0.3289

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
 IUY  C1   C2    single    1.515  0.020  1.515
 IUY  C1   C3    double    1.354  0.020  1.354
 IUY  C1   C12   single    1.475  0.020  1.475
 IUY  C2   C6    single    1.517  0.020  1.517
 IUY  C2   N19   single    1.457  0.020  1.457
 IUY  C3   N4    single    1.399  0.020  1.399
 IUY  C3   C5    single    1.496  0.020  1.496
 IUY  N4   C20   single    1.351  0.020  1.351
 IUY  N4   C24   single    1.431  0.020  1.431
 IUY  C6   C7    aromatic  1.388  0.020  1.388
 IUY  C6   C11   aromatic  1.391  0.020  1.391
 IUY  C7   C8    aromatic  1.384  0.020  1.384
 IUY  C8   C9    aromatic  1.393  0.020  1.393
 IUY  C9   C10   aromatic  1.395  0.020  1.395
 IUY  C9   C17   single    1.428  0.020  1.428
 IUY  C10  C11   aromatic  1.383  0.020  1.383
 IUY  C12  O13   double    1.209  0.020  1.209
 IUY  C12  O14   single    1.325  0.020  1.325
 IUY  O14  C15   single    1.436  0.020  1.436
 IUY  C15  C16   single    1.509  0.020  1.509
 IUY  C17  N18   triple    1.152  0.020  1.152
 IUY  N19  C20   aromatic  1.322  0.020  1.322
 IUY  N19  C23   aromatic  1.383  0.020  1.383
 IUY  C20  N21   aromatic  1.327  0.020  1.327
 IUY  N21  C22   aromatic  1.380  0.020  1.380
 IUY  C22  C23   aromatic  1.346  0.020  1.346
 IUY  C24  C25   aromatic  1.388  0.020  1.388
 IUY  C24  C29   aromatic  1.383  0.020  1.383
 IUY  C25  C26   aromatic  1.385  0.020  1.385
 IUY  C26  C27   aromatic  1.388  0.020  1.388
 IUY  C27  C28   aromatic  1.388  0.020  1.388
 IUY  C28  C29   aromatic  1.390  0.020  1.390
 IUY  C28  C30   single    1.499  0.020  1.499
 IUY  C30  F31   single    1.333  0.020  1.333
 IUY  C30  F32   single    1.338  0.020  1.338
 IUY  C30  F33   single    1.340  0.020  1.340
 IUY  C2   H2    single    0.970  0.020  1.090
 IUY  C5   H5    single    0.970  0.020  1.090
 IUY  C5   H5A   single    0.970  0.020  1.090
 IUY  C5   H5B   single    0.970  0.020  1.090
 IUY  C7   H7    single    0.930  0.020  1.080
 IUY  C8   H8    single    0.930  0.020  1.080
 IUY  C10  H10   single    0.930  0.020  1.080
 IUY  C11  H11   single    0.930  0.020  1.080
 IUY  C15  H15   single    0.970  0.020  1.090
 IUY  C15  H15A  single    0.970  0.020  1.090
 IUY  C16  H16   single    0.970  0.020  1.090
 IUY  C16  H16A  single    0.970  0.020  1.090
 IUY  C16  H16B  single    0.970  0.020  1.090
 IUY  N21  HN21  single    0.860  0.020  1.020
 IUY  C22  H22   single    0.930  0.020  1.080
 IUY  C23  H23   single    0.930  0.020  1.080
 IUY  C25  H25   single    0.930  0.020  1.080
 IUY  C26  H26   single    0.930  0.020  1.080
 IUY  C27  H27   single    0.930  0.020  1.080
 IUY  C29  H29   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
 IUY  C12   C1   C3    121.30  3.000
 IUY  C12   C1   C2    115.01  3.000
 IUY  C3    C1   C2    123.67  3.000
 IUY  H2    C2   N19   106.55  3.000
 IUY  H2    C2   C6    109.12  3.000
 IUY  N19   C2   C6    109.13  3.000
 IUY  H2    C2   C1    110.14  3.000
 IUY  N19   C2   C1    108.87  3.000
 IUY  C6    C2   C1    112.83  3.000
 IUY  C5    C3   N4    115.20  3.000
 IUY  C5    C3   C1    125.16  3.000
 IUY  N4    C3   C1    119.64  3.000
 IUY  C24   N4   C20   116.96  3.000
 IUY  C24   N4   C3    124.18  3.000
 IUY  C20   N4   C3    118.84  3.000
 IUY  H5B   C5   H5A   107.85  3.000
 IUY  H5B   C5   H5    107.55  3.000
 IUY  H5A   C5   H5    107.82  3.000
 IUY  H5B   C5   C3    110.48  3.000
 IUY  H5A   C5   C3    112.08  3.000
 IUY  H5    C5   C3    110.89  3.000
 IUY  C11   C6   C7    119.84  3.000
 IUY  C11   C6   C2    120.18  3.000
 IUY  C7    C6   C2    119.97  3.000
 IUY  H7    C7   C8    119.49  3.000
 IUY  H7    C7   C6    120.06  3.000
 IUY  C8    C7   C6    120.45  3.000
 IUY  H8    C8   C9    120.32  3.000
 IUY  H8    C8   C7    120.33  3.000
 IUY  C9    C8   C7    119.35  3.000
 IUY  C17   C9   C10   119.66  3.000
 IUY  C17   C9   C8    119.75  3.000
 IUY  C10   C9   C8    120.59  3.000
 IUY  H10   C10  C11   120.35  3.000
 IUY  H10   C10  C9    120.27  3.000
 IUY  C11   C10  C9    119.38  3.000
 IUY  H11   C11  C10   118.82  3.000
 IUY  H11   C11  C6    120.79  3.000
 IUY  C10   C11  C6    120.39  3.000
 IUY  O14   C12  O13   123.16  3.000
 IUY  O14   C12  C1    110.37  3.000
 IUY  O13   C12  C1    126.46  3.000
 IUY  C15   O14  C12   118.66  3.000
 IUY  H15A  C15  H15   108.05  3.000
 IUY  H15A  C15  C16   110.91  3.000
 IUY  H15   C15  C16   111.15  3.000
 IUY  H15A  C15  O14   109.63  3.000
 IUY  H15   C15  O14   109.44  3.000
 IUY  C16   C15  O14   107.65  3.000
 IUY  H16B  C16  H16A  107.90  3.000
 IUY  H16B  C16  H16   107.88  3.000
 IUY  H16A  C16  H16   108.69  3.000
 IUY  H16B  C16  C15   108.98  3.000
 IUY  H16A  C16  C15   111.72  3.000
 IUY  H16   C16  C15   111.53  3.000
 IUY  N18   C17  C9    180.00  3.000
 IUY  C23   N19  C20   108.92  3.000
 IUY  C23   N19  C2    126.75  3.000
 IUY  C20   N19  C2    124.15  3.000
 IUY  N21   C20  N19   108.46  3.000
 IUY  N21   C20  N4    128.09  3.000
 IUY  N19   C20  N4    123.44  3.000
 IUY  HN21  N21  C22   125.25  3.000
 IUY  HN21  N21  C20   125.95  3.000
 IUY  C22   N21  C20   108.79  3.000
 IUY  H22   C22  C23   131.24  3.000
 IUY  H22   C22  N21   121.73  3.000
 IUY  C23   C22  N21   107.03  3.000
 IUY  H23   C23  C22   131.09  3.000
 IUY  H23   C23  N19   122.12  3.000
 IUY  C22   C23  N19   106.79  3.000
 IUY  C29   C24  C25   121.40  3.000
 IUY  C29   C24  N4    118.96  3.000
 IUY  C25   C24  N4    119.62  3.000
 IUY  H25   C25  C26   120.68  3.000
 IUY  H25   C25  C24   120.26  3.000
 IUY  C26   C25  C24   119.05  3.000
 IUY  H26   C26  C27   119.83  3.000
 IUY  H26   C26  C25   119.83  3.000
 IUY  C27   C26  C25   120.34  3.000
 IUY  H27   C27  C28   120.99  3.000
 IUY  H27   C27  C26   119.08  3.000
 IUY  C28   C27  C26   119.93  3.000
 IUY  C30   C28  C29   118.24  3.000
 IUY  C30   C28  C27   121.46  3.000
 IUY  C29   C28  C27   120.30  3.000
 IUY  H29   C29  C28   121.44  3.000
 IUY  H29   C29  C24   119.58  3.000
 IUY  C28   C29  C24   118.98  3.000
 IUY  F33   C30  F32   106.70  3.000
 IUY  F33   C30  F31   107.21  3.000
 IUY  F32   C30  F31   107.34  3.000
 IUY  F33   C30  C28   111.25  3.000
 IUY  F32   C30  C28   111.45  3.000
 IUY  F31   C30  C28   112.60  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
 IUY  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 IUY  CONST_02  C9    C10  C11  C6      0.00   0.0  0
 IUY  CONST_03  C10   C11  C6   C7      0.00   0.0  0
 IUY  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 IUY  CONST_05  C11   C6   C7   C8      0.00   0.0  0
 IUY  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 IUY  CONST_07  C22   N21  C20  N19     0.00   0.0  0
 IUY  CONST_08  N21   C22  C23  N19     0.00   0.0  0
 IUY  CONST_09  C22   C23  N19  C20     0.00   0.0  0
 IUY  CONST_10  C23   C22  N21  C20     0.00   0.0  0
 IUY  CONST_11  C23   N19  C20  N21     0.00   0.0  0
 IUY  CONST_12  C27   C26  C25  C24     0.00   0.0  0
 IUY  CONST_13  C27   C28  C29  C24     0.00   0.0  0
 IUY  CONST_14  C28   C29  C24  C25     0.00   0.0  0
 IUY  CONST_15  C28   C27  C26  C25     0.00   0.0  0
 IUY  CONST_16  C29   C24  C25  C26     0.00   0.0  0
 IUY  CONST_17  C29   C28  C27  C26     0.00   0.0  0
 IUY  CONST_18  C8    C7   C6   C2    180.00   0.0  0
 IUY  CONST_19  C10   C11  C6   C2    180.00   0.0  0
 IUY  CONST_20  C26   C25  C24  N4    180.00   0.0  0
 IUY  CONST_21  C28   C29  C24  N4    180.00   0.0  0
 IUY  CONST_22  C17   C9   C8   C7    180.00   0.0  0
 IUY  CONST_23  C17   C9   C10  C11   180.00   0.0  0
 IUY  CONST_24  C30   C28  C29  C24   180.00   0.0  0
 IUY  CONST_25  C30   C28  C27  C26   180.00   0.0  0
 IUY  CONST_26  H7    C7   C6   C2      0.00   0.0  0
 IUY  CONST_27  H11   C11  C6   C2      0.00   0.0  0
 IUY  CONST_28  H23   C23  N19  C2      0.00   0.0  0
 IUY  CONST_29  HN21  N21  C20  N4      0.00   0.0  0
 IUY  CONST_30  H25   C25  C24  N4      0.00   0.0  0
 IUY  CONST_31  H29   C29  C24  N4      0.00   0.0  0
 IUY  CONST_32  H8    C8   C7   C6    180.00   0.0  0
 IUY  CONST_33  H10   C10  C11  C6    180.00   0.0  0
 IUY  CONST_34  H22   C22  C23  N19   180.00   0.0  0
 IUY  CONST_35  H26   C26  C25  C24   180.00   0.0  0
 IUY  CONST_36  H27   C27  C26  C25   180.00   0.0  0
 IUY  Var_01    C20   N4   C3   C1     -6.37  30.0  1
 IUY  Var_02    N4    C3   C1   C2     -2.20  30.0  1
 IUY  Var_03    N19   C20  N4   C3      5.03  30.0  1
 IUY  Var_04    C25   C24  N4   C3     95.86  30.0  2
 IUY  Var_05    O13   C12  C1   C2   -171.04  30.0  2
 IUY  Var_06    F31   C30  C28  C27    10.08  30.0  2
 IUY  Var_07    H5    C5   C3   C1     48.17  30.0  3
 IUY  Var_08    C16   C15  O14  C12   176.16  30.0  3
 IUY  Var_09    H16   C16  C15  O14   -62.15  30.0  3

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
 IUY  chir_01  C2  C1  C6  N19  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
 IUY  plan-1  C2    0.020
 IUY  plan-1  C6    0.020
 IUY  plan-1  C7    0.020
 IUY  plan-1  C8    0.020
 IUY  plan-1  C9    0.020
 IUY  plan-1  C10   0.020
 IUY  plan-1  C11   0.020
 IUY  plan-1  C17   0.020
 IUY  plan-1  N18   0.020
 IUY  plan-1  H7    0.020
 IUY  plan-1  H8    0.020
 IUY  plan-1  H10   0.020
 IUY  plan-1  H11   0.020
 IUY  plan-2  N4    0.020
 IUY  plan-2  C24   0.020
 IUY  plan-2  C25   0.020
 IUY  plan-2  C26   0.020
 IUY  plan-2  C27   0.020
 IUY  plan-2  C28   0.020
 IUY  plan-2  C29   0.020
 IUY  plan-2  C30   0.020
 IUY  plan-2  H25   0.020
 IUY  plan-2  H26   0.020
 IUY  plan-2  H27   0.020
 IUY  plan-2  H29   0.020
 IUY  plan-3  C2    0.020
 IUY  plan-3  N4    0.020
 IUY  plan-3  N19   0.020
 IUY  plan-3  C20   0.020
 IUY  plan-3  N21   0.020
 IUY  plan-3  C22   0.020
 IUY  plan-3  C23   0.020
 IUY  plan-3  HN21  0.020
 IUY  plan-3  H22   0.020
 IUY  plan-3  H23   0.020
 IUY  plan-4  C3    0.020
 IUY  plan-4  N4    0.020
 IUY  plan-4  C20   0.020
 IUY  plan-4  C24   0.020
 IUY  plan-5  C1    0.020
 IUY  plan-5  C12   0.020
 IUY  plan-5  O13   0.020
 IUY  plan-5  O14   0.020

