# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:36:02 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)c3c(Cl)cccc3Cl)C(=O)NCCc4ccccc4
#
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
 GY6  GY6  2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide  ligand  56  34  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GY6
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
 GY6  C01  C   CR6   0   0.510    0.4818  -1.0857  -0.4872
 GY6  C03  C   CR6   0  -0.004   -1.3696  -1.9748   0.5336
 GY6  C04  C   CR6   0   0.235   -0.6681  -3.0361   1.0212
 GY6  C07  C   CR6   0   0.481    0.7558  -3.1434   0.7139
 GY6  C11  C   C     0   0.550   -2.8357  -1.7909   0.7730
 GY6  C14  C   CH2   0  -0.228   -4.7480  -0.3523   0.2866
 GY6  C17  C   CH2   0  -0.566   -5.0223   0.9282  -0.4955
 GY6  C21  C   CH2   0  -0.479    2.4783   0.2445  -3.3245
 GY6  C24  C   CH2   0  -0.477    1.2592  -0.5209  -2.8255
 GY6  C27  C   CH1   0  -0.142    1.1304  -0.0574  -1.3673
 GY6  C30  C   CH2   0  -0.273    3.4248   0.2141  -2.1328
 GY6  C35  C   CR16  0  -0.274    6.8681   1.7014   1.0800
 GY6  C37  C   CR16  0  -0.192    6.4715   0.3764   1.1745
 GY6  C39  C   CR6   0  -0.085    5.1578   0.0494   0.8827
 GY6  C41  C   CR6   0   0.099    4.2339   1.0110   0.4983
 GY6  C42  C   CR6   0  -0.088    4.6654   2.3282   0.4100
 GY6  C44  C   CR16  0  -0.192    5.9720   2.6866   0.6943
 GY6  C46  C   CR16  0  -0.271   -9.2026   1.9192  -0.2689
 GY6  C48  C   CR16  0  -0.239   -8.3140   2.4180   0.6748
 GY6  C50  C   CR16  0  -0.306   -6.9627   2.1083   0.5921
 GY6  C52  C   CR6   0   0.125   -6.4774   1.2978  -0.4314
 GY6  C53  C   CR16  0  -0.305   -7.3780   0.8031  -1.3724
 GY6  C55  C   CR16  0  -0.240   -8.7298   1.1105  -1.2944
 GY6  N02  N   N     0  -0.474   -0.7665  -1.0001  -0.2157
 GY6  N09  N   NR16  0  -0.677    1.2393  -2.1294  -0.0620
 GY6  N13  N   NH1   0  -0.661   -3.3469  -0.6958   0.1994
 GY6  N29  N   NT    0  -0.483    2.5074   0.2356  -0.9900
 GY6  O05  O   OH1   0  -0.588   -1.1707  -4.0102   1.7706
 GY6  O08  O   O     0  -0.466    1.4441  -4.0679   1.1169
 GY6  O12  O   O     0  -0.483   -3.4996  -2.5812   1.4298
 GY6  O34  O   O     0  -0.438    1.9662   0.7474   1.1363
 GY6  CL   CL  CL    0  -0.094    3.5403   3.5349  -0.1073
 GY6  H15  H   HCH2  0   0.241   -5.0403  -0.2173   1.3318
 GY6  H16  H   HCH2  0   0.241   -5.3597  -1.1668  -0.1112
 GY6  H18  H   HCH2  0   0.259   -4.4115   1.7382  -0.0880
 GY6  H19  H   HCH2  0   0.258   -4.7183   0.7879  -1.5361
 GY6  H23  H   HCH2  0   0.270    2.9220  -0.2006  -4.2130
 GY6  H22  H   HCH2  0   0.254    2.2073   1.2752  -3.5592
 GY6  H26  H   HCH2  0   0.280    0.3515  -0.3094  -3.3868
 GY6  H25  H   HCH2  0   0.259    1.4404  -1.5974  -2.8758
 GY6  H28  H   HCH1  0   0.306    0.5146   0.8438  -1.3075
 GY6  H31  H   HCH2  0   0.256    4.0289  -0.6964  -2.1217
 GY6  H32  H   HCH2  0   0.271    4.0991   1.0682  -2.1168
 GY6  H36  H   HCR6  0   0.288    7.8909   1.9687   1.3067
 GY6  H38  H   HCR6  0   0.294    7.1739  -0.3902   1.4706
 GY6  H45  H   HCR6  0   0.294    6.2854   3.7181   0.6157
 GY6  H47  H   HCR6  0   0.255  -10.2554   2.1626  -0.2081
 GY6  H49  H   HCR6  0   0.254   -8.6724   3.0516   1.4762
 GY6  H51  H   HCR6  0   0.248   -6.2764   2.5079   1.3300
 GY6  H54  H   HCR6  0   0.248   -7.0173   0.1766  -2.1804
 GY6  H56  H   HCR6  0   0.254   -9.4136   0.7204  -2.0375
 GY6  H10  H   HNR6  0   0.414    2.2253  -2.1600  -0.2967
 GY6  H20  H   HNH1  0   0.409   -2.7212  -0.1053  -0.3279
 GY6  H06  H   HOH1  0   0.476   -0.4554  -4.6329   1.9766
 GY6  C33  C   C     0   0.493    2.7959   0.6604   0.2485
 GY6  CL2  CL  CL    0  -0.102    4.6566  -1.6053   0.9906

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
 GY6  CL   C42  single    1.729  0.020  1.729
 GY6  C44  C42  aromatic  1.384  0.020  1.384
 GY6  C44  C35  aromatic  1.387  0.020  1.387
 GY6  C42  C41  aromatic  1.389  0.020  1.389
 GY6  O34  C33  double    1.218  0.020  1.218
 GY6  C35  C37  aromatic  1.386  0.020  1.386
 GY6  C41  C33  single    1.501  0.020  1.501
 GY6  C41  C39  aromatic  1.388  0.020  1.388
 GY6  C33  N29  single    1.341  0.020  1.341
 GY6  C37  C39  aromatic  1.385  0.020  1.385
 GY6  N29  C27  single    1.458  0.020  1.458
 GY6  N29  C30  single    1.466  0.020  1.466
 GY6  C39  CL2  single    1.732  0.020  1.732
 GY6  C27  C24  single    1.535  0.020  1.535
 GY6  C27  C01  single    1.501  0.020  1.501
 GY6  C24  C21  single    1.523  0.020  1.523
 GY6  C30  C21  single    1.522  0.020  1.522
 GY6  N09  C01  single    1.358  0.020  1.358
 GY6  N09  C07  single    1.365  0.020  1.365
 GY6  C01  N02  double    1.280  0.020  1.280
 GY6  O08  C07  double    1.221  0.020  1.221
 GY6  C07  C04  single    1.461  0.020  1.461
 GY6  N02  C03  single    1.369  0.020  1.369
 GY6  C04  C03  double    1.362  0.020  1.362
 GY6  C04  O05  single    1.328  0.020  1.328
 GY6  C03  C11  single    1.497  0.020  1.497
 GY6  C55  C46  aromatic  1.389  0.020  1.389
 GY6  C55  C53  aromatic  1.389  0.020  1.389
 GY6  C46  C48  aromatic  1.389  0.020  1.389
 GY6  C53  C52  aromatic  1.393  0.020  1.393
 GY6  N13  C11  single    1.338  0.020  1.338
 GY6  N13  C14  single    1.445  0.020  1.445
 GY6  C11  O12  double    1.223  0.020  1.223
 GY6  C48  C50  aromatic  1.389  0.020  1.389
 GY6  C52  C50  aromatic  1.393  0.020  1.393
 GY6  C52  C17  single    1.503  0.020  1.503
 GY6  C14  C17  single    1.525  0.020  1.525
 GY6  C14  H15  single    0.970  0.020  1.090
 GY6  C14  H16  single    0.970  0.020  1.090
 GY6  C17  H18  single    0.970  0.020  1.090
 GY6  C17  H19  single    0.970  0.020  1.090
 GY6  C21  H23  single    0.970  0.020  1.090
 GY6  C21  H22  single    0.970  0.020  1.090
 GY6  C24  H26  single    0.970  0.020  1.090
 GY6  C24  H25  single    0.970  0.020  1.090
 GY6  C27  H28  single    0.970  0.020  1.090
 GY6  C30  H31  single    0.970  0.020  1.090
 GY6  C30  H32  single    0.970  0.020  1.090
 GY6  C35  H36  single    0.930  0.020  1.080
 GY6  C37  H38  single    0.930  0.020  1.080
 GY6  C44  H45  single    0.930  0.020  1.080
 GY6  C46  H47  single    0.930  0.020  1.080
 GY6  C48  H49  single    0.930  0.020  1.080
 GY6  C50  H51  single    0.930  0.020  1.080
 GY6  C53  H54  single    0.930  0.020  1.080
 GY6  C55  H56  single    0.930  0.020  1.080
 GY6  N09  H10  single    0.860  0.020  1.020
 GY6  N13  H20  single    0.860  0.020  1.020
 GY6  O05  H06  single    0.850  0.020  0.980

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
 GY6  N09  C01  N02  121.93  3.000
 GY6  N02  C01  C27  119.99  3.000
 GY6  N09  C01  C27  117.98  3.000
 GY6  N02  C03  C11  115.55  3.000
 GY6  C11  C03  C04  122.88  3.000
 GY6  N02  C03  C04  121.57  3.000
 GY6  O05  C04  C07  115.71  3.000
 GY6  O05  C04  C03  125.35  3.000
 GY6  C07  C04  C03  118.94  3.000
 GY6  O08  C07  N09  123.38  3.000
 GY6  O08  C07  C04  122.39  3.000
 GY6  N09  C07  C04  114.22  3.000
 GY6  O12  C11  N13  123.48  3.000
 GY6  O12  C11  C03  122.54  3.000
 GY6  N13  C11  C03  113.97  3.000
 GY6  H16  C14  H15  106.86  3.000
 GY6  H16  C14  N13  110.08  3.000
 GY6  H15  C14  N13  110.25  3.000
 GY6  H16  C14  C17  109.76  3.000
 GY6  H15  C14  C17  109.78  3.000
 GY6  N13  C14  C17  110.06  3.000
 GY6  H19  C17  H18  107.13  3.000
 GY6  H19  C17  C52  109.96  3.000
 GY6  H18  C17  C52  110.05  3.000
 GY6  H19  C17  C14  109.29  3.000
 GY6  H18  C17  C14  109.30  3.000
 GY6  C52  C17  C14  111.02  3.000
 GY6  H22  C21  H23  108.17  3.000
 GY6  H22  C21  C30  109.98  3.000
 GY6  H23  C21  C30  112.18  3.000
 GY6  H22  C21  C24  110.26  3.000
 GY6  H23  C21  C24  112.84  3.000
 GY6  C30  C21  C24  103.36  3.000
 GY6  H25  C24  H26  107.82  3.000
 GY6  H25  C24  C27  110.79  3.000
 GY6  H26  C24  C27  111.17  3.000
 GY6  H25  C24  C21  110.31  3.000
 GY6  H26  C24  C21  113.64  3.000
 GY6  C27  C24  C21  103.09  3.000
 GY6  H28  C27  N29  110.63  3.000
 GY6  H28  C27  C24  110.37  3.000
 GY6  N29  C27  C24  103.13  3.000
 GY6  H28  C27  C01  106.82  3.000
 GY6  C24  C27  C01  112.73  3.000
 GY6  N29  C27  C01  113.21  3.000
 GY6  H32  C30  H31  108.13  3.000
 GY6  H32  C30  N29  111.39  3.000
 GY6  H31  C30  N29  110.51  3.000
 GY6  H32  C30  C21  112.41  3.000
 GY6  H31  C30  C21  111.62  3.000
 GY6  N29  C30  C21  102.76  3.000
 GY6  H36  C35  C44  119.60  3.000
 GY6  H36  C35  C37  119.52  3.000
 GY6  C44  C35  C37  120.87  3.000
 GY6  H38  C37  C39  120.44  3.000
 GY6  H38  C37  C35  120.70  3.000
 GY6  C39  C37  C35  118.87  3.000
 GY6  CL2  C39  C41  119.11  3.000
 GY6  CL2  C39  C37  119.14  3.000
 GY6  C41  C39  C37  121.75  3.000
 GY6  C42  C41  C39  117.90  3.000
 GY6  C39  C41  C33  121.47  3.000
 GY6  C42  C41  C33  120.57  3.000
 GY6  CL   C42  C44  119.67  3.000
 GY6  C44  C42  C41  121.71  3.000
 GY6  CL   C42  C41  118.60  3.000
 GY6  H45  C44  C42  120.38  3.000
 GY6  H45  C44  C35  120.72  3.000
 GY6  C42  C44  C35  118.90  3.000
 GY6  H47  C46  C55  120.23  3.000
 GY6  H47  C46  C48  120.23  3.000
 GY6  C55  C46  C48  119.54  3.000
 GY6  H49  C48  C50  119.78  3.000
 GY6  H49  C48  C46  120.09  3.000
 GY6  C50  C48  C46  120.13  3.000
 GY6  H51  C50  C52  119.61  3.000
 GY6  H51  C50  C48  119.56  3.000
 GY6  C52  C50  C48  120.83  3.000
 GY6  C53  C52  C50  118.53  3.000
 GY6  C50  C52  C17  120.79  3.000
 GY6  C53  C52  C17  120.65  3.000
 GY6  H54  C53  C55  119.58  3.000
 GY6  H54  C53  C52  119.57  3.000
 GY6  C55  C53  C52  120.85  3.000
 GY6  H56  C55  C53  119.77  3.000
 GY6  H56  C55  C46  120.11  3.000
 GY6  C53  C55  C46  120.12  3.000
 GY6  C03  N02  C01  119.86  3.000
 GY6  H10  N09  C07  116.97  3.000
 GY6  H10  N09  C01  119.55  3.000
 GY6  C07  N09  C01  123.45  3.000
 GY6  H20  N13  C14  119.57  3.000
 GY6  H20  N13  C11  117.79  3.000
 GY6  C14  N13  C11  122.63  3.000
 GY6  C33  N29  C30  126.17  3.000
 GY6  C30  N29  C27  112.74  3.000
 GY6  C33  N29  C27  120.41  3.000
 GY6  H06  O05  C04  108.15  3.000
 GY6  O34  C33  N29  123.31  3.000
 GY6  N29  C33  C41  115.72  3.000
 GY6  O34  C33  C41  120.96  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
 GY6  CONST_01  C41  C42  C44  C35     0.00   0.0  0
 GY6  CONST_02  C41  C39  C37  C35     0.00   0.0  0
 GY6  CONST_03  C42  C44  C35  C37     0.00   0.0  0
 GY6  CONST_04  C42  C41  C39  C37     0.00   0.0  0
 GY6  CONST_05  C44  C42  C41  C39     0.00   0.0  0
 GY6  CONST_06  C44  C35  C37  C39     0.00   0.0  0
 GY6  CONST_07  C52  C53  C55  C46     0.00   0.0  0
 GY6  CONST_08  C52  C50  C48  C46     0.00   0.0  0
 GY6  CONST_09  C53  C55  C46  C48     0.00   0.0  0
 GY6  CONST_10  C53  C52  C50  C48     0.00   0.0  0
 GY6  CONST_11  C55  C46  C48  C50     0.00   0.0  0
 GY6  CONST_12  C55  C53  C52  C50     0.00   0.0  0
 GY6  CONST_13  C04  C07  N09  C01     0.00   0.0  0
 GY6  CONST_14  C27  C01  N02  C03   180.00   0.0  0
 GY6  CONST_15  N09  C01  N02  C03     0.00   0.0  0
 GY6  CONST_16  C27  C01  N09  C07   180.00   0.0  0
 GY6  CONST_17  N02  C01  N09  C07     0.00   0.0  0
 GY6  CONST_18  C55  C53  C52  C17   180.00   0.0  0
 GY6  CONST_19  C48  C50  C52  C17   180.00   0.0  0
 GY6  CONST_20  C44  C42  C41  C33   180.00   0.0  0
 GY6  CONST_21  C37  C39  C41  C33   180.00   0.0  0
 GY6  CONST_22  CL   C42  C44  C35   180.00   0.0  0
 GY6  CONST_23  CL2  C39  C37  C35   180.00   0.0  0
 GY6  CONST_24  CL   C42  C41  C39   180.00   0.0  0
 GY6  CONST_25  CL2  C39  C41  C42   180.00   0.0  0
 GY6  CONST_26  C41  C33  N29  C27   180.00   0.0  0
 GY6  CONST_27  C41  C33  N29  C30     0.00   0.0  0
 GY6  CONST_28  O08  C07  N09  C01   180.00   0.0  0
 GY6  CONST_29  H45  C44  C35  C37   180.00   0.0  0
 GY6  CONST_30  H36  C35  C37  C39   180.00   0.0  0
 GY6  CONST_31  H38  C37  C39  C41   180.00   0.0  0
 GY6  CONST_32  H54  C53  C55  C46   180.00   0.0  0
 GY6  CONST_33  H51  C50  C48  C46   180.00   0.0  0
 GY6  CONST_34  H56  C55  C46  C48   180.00   0.0  0
 GY6  CONST_35  H47  C46  C48  C50   180.00   0.0  0
 GY6  CONST_36  H49  C48  C50  C52   180.00   0.0  0
 GY6  CONST_37  H10  N09  C07  C04   180.00   0.0  0
 GY6  CONST_38  O34  C33  N29  C27     0.00   0.0  0
 GY6  CONST_39  O34  C33  N29  C30   180.00   0.0  0
 GY6  CONST_40  C14  N13  C11  C03   180.00   0.0  0
 GY6  CONST_41  H20  N13  C11  C03     0.00   0.0  0
 GY6  CONST_42  O12  C11  N13  C14     0.00   0.0  0
 GY6  Var_01    C27  N29  C30  C21    14.31  30.0  1
 GY6  Var_02    N29  C30  C21  C24   -32.54  30.0  1
 GY6  Var_03    C30  C21  C24  C27    38.89  30.0  1
 GY6  Var_04    N29  C33  C41  C39   -86.50  30.0  2
 GY6  Var_05    N13  C11  C03  C04  -179.25  30.0  2
 GY6  Var_06    C53  C52  C17  C14   -88.69  30.0  2
 GY6  Var_07    N13  C14  C17  C52   179.39  30.0  1
 GY6  Var_08    C17  C14  N13  C11  -178.60  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
 GY6  chir_01  C27  N29  C24  C01  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
 GY6  plan-1  C35  0.020
 GY6  plan-1  C37  0.020
 GY6  plan-1  C39  0.020
 GY6  plan-1  C41  0.020
 GY6  plan-1  C42  0.020
 GY6  plan-1  C44  0.020
 GY6  plan-1  CL   0.020
 GY6  plan-1  H36  0.020
 GY6  plan-1  H38  0.020
 GY6  plan-1  H45  0.020
 GY6  plan-1  C33  0.020
 GY6  plan-1  CL2  0.020
 GY6  plan-2  C17  0.020
 GY6  plan-2  C46  0.020
 GY6  plan-2  C48  0.020
 GY6  plan-2  C50  0.020
 GY6  plan-2  C52  0.020
 GY6  plan-2  C53  0.020
 GY6  plan-2  C55  0.020
 GY6  plan-2  H47  0.020
 GY6  plan-2  H49  0.020
 GY6  plan-2  H51  0.020
 GY6  plan-2  H54  0.020
 GY6  plan-2  H56  0.020
 GY6  plan-3  C01  0.020
 GY6  plan-3  C03  0.020
 GY6  plan-3  C04  0.020
 GY6  plan-3  C07  0.020
 GY6  plan-3  C11  0.020
 GY6  plan-3  C27  0.020
 GY6  plan-3  N02  0.020
 GY6  plan-3  N09  0.020
 GY6  plan-3  O05  0.020
 GY6  plan-3  O08  0.020
 GY6  plan-3  H10  0.020
 GY6  plan-4  C27  0.020
 GY6  plan-4  C30  0.020
 GY6  plan-4  C41  0.020
 GY6  plan-4  N29  0.020
 GY6  plan-4  O34  0.020
 GY6  plan-4  C33  0.020
 GY6  plan-5  C03  0.020
 GY6  plan-5  C11  0.020
 GY6  plan-5  C14  0.020
 GY6  plan-5  N13  0.020
 GY6  plan-5  O12  0.020
 GY6  plan-5  H20  0.020

