# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 15:01:55 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: N-({4-[(1R)-4-[(2R,4S,5S)-2,4-diamino-6-oxohexahydropyrimidin-5-yl]-1-(2,2,2-trifluoro-1,1-dihydroxyethyl)butyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1N[C@H](N)[C@H](CCC[C@H](c2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)(O)C(F)(F)F)C(=O)N1
#
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
 KEU  KEU  'N-({4-[(1R)-4-[(2R,4S,5S)-2,4-diamino-6-oxohexahydropyrimidin-5-yl]-1-(2,2,2-trifluoro-1,1-dihydroxyethyl)butyl]phenyl}carbonyl)-L-glutamic acid'  ligand  68  38  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KEU
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
 KEU  O4    O  OH1   0  -0.590  71.4434  18.3310  38.0638
 KEU  C21   C  C     0   0.572  72.7587  18.5349  38.0826
 KEU  O5    O  O     0  -0.435  73.4844  17.6547  38.4645
 KEU  C20   C  CH2   0  -0.639  73.2235  19.8877  37.6099
 KEU  C19   C  CH2   0  -0.457  74.7335  20.0484  37.6563
 KEU  C17   C  CH1   0  -0.210  75.1591  21.4391  37.1846
 KEU  N     N  NH1   0  -0.655  74.7838  21.6473  35.8134
 KEU  C     C  C     0   0.544  74.4147  22.8452  35.3195
 KEU  O     O  O     0  -0.481  74.3093  23.8428  36.0178
 KEU  C14   C  CR6   0  -0.054  74.0976  22.8761  33.8616
 KEU  C13   C  CR16  0  -0.260  73.1916  23.8274  33.4013
 KEU  C12   C  CR16  0  -0.284  72.8513  23.8805  32.0606
 KEU  C11   C  CR6   0   0.170  73.4129  23.0035  31.1348
 KEU  C16   C  CR16  0  -0.282  74.3526  22.0859  31.5960
 KEU  C15   C  CR16  0  -0.284  74.6879  22.0166  32.9387
 KEU  C10   C  CH1   0  -0.399  73.0215  23.1042  29.6754
 KEU  C1    C  CH2   0  -0.444  74.2067  22.9352  28.7178
 KEU  C2    C  CH2   0  -0.411  75.2055  24.0792  28.8627
 KEU  C3    C  CH2   0  -0.427  76.3283  23.9678  27.8386
 KEU  C4    C  CH1   0  -0.352  77.4458  25.0125  27.9865
 KEU  C9    C  C     0   0.532  76.8958  26.4087  27.7841
 KEU  O1    O  O     0  -0.498  76.3306  27.0220  28.6812
 KEU  N3    N  NH1   0  -0.638  77.0187  26.9269  26.5465
 KEU  C8    C  CH1   0   0.243  77.8582  26.4493  25.4615
 KEU  N2    N  NH2   0  -0.802  77.1916  26.7229  24.2226
 KEU  N1    N  NH1   0  -0.625  78.1326  25.0485  25.6801
 KEU  C7    C  CH1   0   0.045  78.6169  24.7710  27.0295
 KEU  N8    N  NH2   0  -0.805  79.1571  23.4460  27.1710
 KEU  C5    C  CT    0   0.321  71.7604  22.2719  29.3229
 KEU  OA2   O  OH1   0  -0.654  71.4273  22.6159  28.0186
 KEU  OA1   O  OH1   0  -0.648  70.7892  22.6277  30.2492
 KEU  C6    C  CT    0   0.976  71.9462  20.7378  29.3886
 KEU  F2    F  F     0  -0.293  72.2598  20.3093  30.6097
 KEU  F1    F  F     0  -0.296  72.8832  20.2933  28.5501
 KEU  F     F  F     0  -0.319  70.7987  20.1218  29.0456
 KEU  C18   C  C     0   0.563  76.6451  21.6614  37.4448
 KEU  O3    O  O     0  -0.442  77.1631  21.4116  38.5041
 KEU  O2    O  OH1   0  -0.575  77.2868  22.1774  36.4130
 KEU  HO4   H  HOH1  0   0.491  70.9633  19.1031  37.7370
 KEU  H201  H  HCH2  0   0.291  72.8387  20.0458  36.5973
 KEU  H202  H  HCH2  0   0.294  72.7417  20.6520  38.2299
 KEU  H191  H  HCH2  0   0.271  75.0880  19.9031  38.6755
 KEU  H192  H  HCH2  0   0.261  75.2191  19.2879  37.0392
 KEU  H17   H  HCH1  0   0.307  74.6431  22.1870  37.7959
 KEU  HN    H  HNH1  0   0.413  74.8317  20.8522  35.1965
 KEU  H13   H  HCR6  0   0.258  72.7386  24.5234  34.0949
 KEU  H12   H  HCR6  0   0.254  72.1399  24.6254  31.7277
 KEU  H16   H  HCR6  0   0.257  74.8512  21.4130  30.9110
 KEU  H15   H  HCR6  0   0.258  75.4383  21.2969  33.2424
 KEU  H10   H  HCH1  0   0.281  72.6616  24.1289  29.5257
 KEU  H11   H  HCH2  0   0.230  74.7231  21.9854  28.8674
 KEU  H12A  H  HCH2  0   0.248  73.8394  22.9230  27.6903
 KEU  H21   H  HCH2  0   0.227  74.6730  25.0266  28.7544
 KEU  H22   H  HCH2  0   0.221  75.6326  24.0827  29.8699
 KEU  H31   H  HCH2  0   0.229  76.7788  22.9770  27.9483
 KEU  H32   H  HCH2  0   0.229  75.9175  24.0096  26.8266
 KEU  H4    H  HCH1  0   0.260  77.8270  24.9679  29.0107
 KEU  HN3   H  HNH1  0   0.389  76.6717  27.8676  26.4204
 KEU  H8    H  HCH1  0   0.223  78.7828  27.0477  25.4583
 KEU  HN21  H  HNH2  0   0.344  76.4675  26.0320  24.0620
 KEU  HN22  H  HNH2  0   0.360  77.8446  26.6637  23.4525
 KEU  HN1   H  HNH1  0   0.356  78.8333  24.7609  25.0056
 KEU  H7    H  HCH1  0   0.226  79.4264  25.4635  27.3113
 KEU  HN61  H  HNH2  0   0.357  80.0349  23.3759  26.6721
 KEU  HN62  H  HNH2  0   0.347  78.5358  22.7631  26.7547
 KEU  HA2   H  HOH1  0   0.463  70.6298  22.1612  27.7189
 KEU  HA1   H  HOH1  0   0.462  69.9383  22.2198  30.0445
 KEU  HO2   H  HOH1  0   0.486  78.2163  22.3275  36.6448

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
 KEU  O4   C21   single    1.331  0.020  1.331
 KEU  O4   HO4   single    0.850  0.020  0.980
 KEU  C21  O5    double    1.203  0.020  1.203
 KEU  C21  C20   single    1.507  0.020  1.507
 KEU  C20  C19   single    1.519  0.020  1.519
 KEU  C20  H201  single    0.970  0.020  1.090
 KEU  C20  H202  single    0.970  0.020  1.090
 KEU  C19  C17   single    1.529  0.020  1.529
 KEU  C19  H191  single    0.970  0.020  1.090
 KEU  C19  H192  single    0.970  0.020  1.090
 KEU  C17  N     single    1.437  0.020  1.437
 KEU  C17  C18   single    1.525  0.020  1.525
 KEU  C17  H17   single    0.970  0.020  1.090
 KEU  N    C     single    1.347  0.020  1.347
 KEU  N    HN    single    0.860  0.020  1.020
 KEU  C    O     double    1.222  0.020  1.222
 KEU  C    C14   single    1.492  0.020  1.492
 KEU  C14  C13   aromatic  1.392  0.020  1.392
 KEU  C14  C15   aromatic  1.392  0.020  1.392
 KEU  C13  C12   aromatic  1.384  0.020  1.384
 KEU  C13  H13   single    0.930  0.020  1.080
 KEU  C12  C11   aromatic  1.393  0.020  1.393
 KEU  C12  H12   single    0.930  0.020  1.080
 KEU  C11  C16   aromatic  1.392  0.020  1.392
 KEU  C11  C10   single    1.514  0.020  1.514
 KEU  C16  C15   aromatic  1.386  0.020  1.386
 KEU  C16  H16   single    0.930  0.020  1.080
 KEU  C15  H15   single    0.930  0.020  1.080
 KEU  C10  C1    single    1.533  0.020  1.533
 KEU  C10  C5    single    1.552  0.020  1.552
 KEU  C10  H10   single    0.970  0.020  1.090
 KEU  C1   C2    single    1.526  0.020  1.526
 KEU  C1   H11   single    0.970  0.020  1.090
 KEU  C1   H12A  single    0.970  0.020  1.090
 KEU  C2   C3    single    1.524  0.020  1.524
 KEU  C2   H21   single    0.970  0.020  1.090
 KEU  C2   H22   single    0.970  0.020  1.090
 KEU  C3   C4    single    1.537  0.020  1.537
 KEU  C3   H31   single    0.970  0.020  1.090
 KEU  C3   H32   single    0.970  0.020  1.090
 KEU  C4   C9    single    1.514  0.020  1.514
 KEU  C4   C7    single    1.532  0.020  1.532
 KEU  C4   H4    single    0.970  0.020  1.090
 KEU  C9   O1    double    1.225  0.020  1.225
 KEU  C9   N3    single    1.347  0.020  1.347
 KEU  N3   C8    single    1.453  0.020  1.453
 KEU  N3   HN3   single    0.860  0.020  1.020
 KEU  C8   N2    single    1.433  0.020  1.433
 KEU  C8   N1    single    1.444  0.020  1.444
 KEU  C8   H8    single    0.970  0.020  1.090
 KEU  N2   HN21  single    0.890  0.020  1.040
 KEU  N2   HN22  single    0.890  0.020  1.040
 KEU  N1   C7    single    1.460  0.020  1.460
 KEU  N1   HN1   single    0.890  0.020  1.040
 KEU  C7   N8    single    1.438  0.020  1.438
 KEU  C7   H7    single    0.970  0.020  1.090
 KEU  N8   HN61  single    0.890  0.020  1.040
 KEU  N8   HN62  single    0.890  0.020  1.040
 KEU  C5   OA2   single    1.389  0.020  1.389
 KEU  C5   OA1   single    1.388  0.020  1.388
 KEU  C5   C6    single    1.547  0.020  1.547
 KEU  OA2  HA2   single    0.850  0.020  0.980
 KEU  OA1  HA1   single    0.850  0.020  0.980
 KEU  C6   F2    single    1.332  0.020  1.332
 KEU  C6   F1    single    1.334  0.020  1.334
 KEU  C6   F     single    1.347  0.020  1.347
 KEU  C18  O3    double    1.205  0.020  1.205
 KEU  C18  O2    single    1.320  0.020  1.320
 KEU  O2   HO2   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
 KEU  HO4   O4   C21   111.93  3.000
 KEU  C20   C21  O5    124.79  3.000
 KEU  C20   C21  O4    115.97  3.000
 KEU  O5    C21  O4    119.24  3.000
 KEU  H202  C20  H201  105.55  3.000
 KEU  H202  C20  C19   110.24  3.000
 KEU  H201  C20  C19   111.24  3.000
 KEU  H202  C20  C21   108.25  3.000
 KEU  H201  C20  C21   108.15  3.000
 KEU  C19   C20  C21   113.08  3.000
 KEU  H192  C19  H191  106.92  3.000
 KEU  H192  C19  C17   109.57  3.000
 KEU  H191  C19  C17   108.64  3.000
 KEU  H192  C19  C20   110.52  3.000
 KEU  H191  C19  C20   109.76  3.000
 KEU  C17   C19  C20   111.31  3.000
 KEU  H17   C17  C18   105.33  3.000
 KEU  H17   C17  N     108.10  3.000
 KEU  C18   C17  N     113.34  3.000
 KEU  H17   C17  C19   108.53  3.000
 KEU  C18   C17  C19   110.56  3.000
 KEU  N     C17  C19   110.70  3.000
 KEU  HN    N    C     119.35  3.000
 KEU  HN    N    C17   117.24  3.000
 KEU  C     N    C17   123.38  3.000
 KEU  C14   C    O     121.53  3.000
 KEU  C14   C    N     115.77  3.000
 KEU  O     C    N     122.68  3.000
 KEU  C15   C14  C13   118.59  3.000
 KEU  C15   C14  C     123.00  3.000
 KEU  C13   C14  C     118.39  3.000
 KEU  H13   C13  C12   119.56  3.000
 KEU  H13   C13  C14   120.01  3.000
 KEU  C12   C13  C14   120.43  3.000
 KEU  H12   C12  C11   119.57  3.000
 KEU  H12   C12  C13   119.07  3.000
 KEU  C11   C12  C13   121.35  3.000
 KEU  C10   C11  C16   122.52  3.000
 KEU  C10   C11  C12   119.63  3.000
 KEU  C16   C11  C12   117.82  3.000
 KEU  H16   C16  C15   118.09  3.000
 KEU  H16   C16  C11   120.75  3.000
 KEU  C15   C16  C11   121.16  3.000
 KEU  H15   C15  C16   118.20  3.000
 KEU  H15   C15  C14   121.19  3.000
 KEU  C16   C15  C14   120.58  3.000
 KEU  H10   C10  C5    101.74  3.000
 KEU  H10   C10  C1    105.75  3.000
 KEU  C5    C10  C1    115.30  3.000
 KEU  H10   C10  C11   106.18  3.000
 KEU  C5    C10  C11   113.17  3.000
 KEU  C1    C10  C11   113.26  3.000
 KEU  H12A  C1   H11   106.18  3.000
 KEU  H12A  C1   C2    108.55  3.000
 KEU  H11   C1   C2    109.26  3.000
 KEU  H12A  C1   C10   109.22  3.000
 KEU  H11   C1   C10   112.09  3.000
 KEU  C2    C1   C10   111.35  3.000
 KEU  H22   C2   H21   106.20  3.000
 KEU  H22   C2   C3    109.35  3.000
 KEU  H21   C2   C3    110.85  3.000
 KEU  H22   C2   C1    110.21  3.000
 KEU  H21   C2   C1    108.78  3.000
 KEU  C3    C2   C1    111.33  3.000
 KEU  H32   C3   H31   106.39  3.000
 KEU  H32   C3   C4    109.66  3.000
 KEU  H31   C3   C4    107.86  3.000
 KEU  H32   C3   C2    110.03  3.000
 KEU  H31   C3   C2    107.59  3.000
 KEU  C4    C3   C2    114.92  3.000
 KEU  H4    C4   C7    108.19  3.000
 KEU  H4    C4   C9    106.81  3.000
 KEU  C7    C4   C9    109.86  3.000
 KEU  H4    C4   C3    108.41  3.000
 KEU  C7    C4   C3    112.87  3.000
 KEU  C9    C4   C3    110.48  3.000
 KEU  N3    C9   O1    121.48  3.000
 KEU  N3    C9   C4    116.38  3.000
 KEU  O1    C9   C4    122.10  3.000
 KEU  HN3   N3   C8    114.28  3.000
 KEU  HN3   N3   C9    116.19  3.000
 KEU  C8    N3   C9    127.76  3.000
 KEU  H8    C8   N1    111.59  3.000
 KEU  H8    C8   N2    106.51  3.000
 KEU  N1    C8   N2    113.85  3.000
 KEU  H8    C8   N3    107.99  3.000
 KEU  N1    C8   N3    108.40  3.000
 KEU  N2    C8   N3    108.30  3.000
 KEU  HN22  N2   HN21  107.50  3.000
 KEU  HN22  N2   C8    110.29  3.000
 KEU  HN21  N2   C8    109.83  3.000
 KEU  HN1   N1   C7    109.36  3.000
 KEU  HN1   N1   C8    107.80  3.000
 KEU  C7    N1   C8    112.78  3.000
 KEU  H7    C7   N8    106.14  3.000
 KEU  H7    C7   N1    111.13  3.000
 KEU  N8    C7   N1    112.99  3.000
 KEU  H7    C7   C4    107.63  3.000
 KEU  N8    C7   C4    111.79  3.000
 KEU  N1    C7   C4    107.09  3.000
 KEU  HN62  N8   HN61  106.42  3.000
 KEU  HN62  N8   C7    110.51  3.000
 KEU  HN61  N8   C7    109.95  3.000
 KEU  C6    C5   OA1   108.05  3.000
 KEU  C6    C5   OA2   108.32  3.000
 KEU  OA1   C5   OA2   113.27  3.000
 KEU  C6    C5   C10   115.14  3.000
 KEU  OA1   C5   C10   106.23  3.000
 KEU  OA2   C5   C10   105.98  3.000
 KEU  HA2   OA2  C5    111.89  3.000
 KEU  HA1   OA1  C5    111.51  3.000
 KEU  F     C6   F1    106.62  3.000
 KEU  F     C6   F2    106.68  3.000
 KEU  F1    C6   F2    107.69  3.000
 KEU  F     C6   C5    109.91  3.000
 KEU  F1    C6   C5    112.84  3.000
 KEU  F2    C6   C5    112.73  3.000
 KEU  O2    C18  O3    123.99  3.000
 KEU  O2    C18  C17   113.41  3.000
 KEU  O3    C18  C17   122.59  3.000
 KEU  HO2   O2   C18   109.85  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
 KEU  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 KEU  CONST_02  C11  C16  C15  C14     0.00   0.0  0
 KEU  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 KEU  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 KEU  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 KEU  CONST_06  C15  C16  C11  C12     0.00   0.0  0
 KEU  CONST_07  C8   N3   C9   C4      0.00   0.0  0
 KEU  CONST_08  C12  C13  C14  C     180.00   0.0  0
 KEU  CONST_09  C16  C15  C14  C     180.00   0.0  0
 KEU  CONST_10  C10  C11  C12  C13   180.00   0.0  0
 KEU  CONST_11  C10  C11  C16  C15   180.00   0.0  0
 KEU  CONST_12  C8   N3   C9   O1    180.00   0.0  0
 KEU  CONST_13  H12  C12  C13  C14   180.00   0.0  0
 KEU  CONST_14  H16  C16  C15  C14   180.00   0.0  0
 KEU  CONST_15  H15  C15  C14  C13   180.00   0.0  0
 KEU  CONST_16  H13  C13  C12  C11   180.00   0.0  0
 KEU  CONST_17  HN3  N3   C9   C4    180.00   0.0  0
 KEU  CONST_18  C14  C    N    C17   180.00   0.0  0
 KEU  CONST_19  HN   N    C    C14     0.00   0.0  0
 KEU  CONST_20  O    C    N    C17     0.00   0.0  0
 KEU  CONST_21  HO4  O4   C21  O5    180.00   0.0  0
 KEU  CONST_22  HO2  O2   C18  C17   180.00   0.0  0
 KEU  Var_01    C13  C14  C    N     152.15  30.0  2
 KEU  Var_02    C4   C3   C2   C1   -175.08  30.0  3
 KEU  Var_03    C19  C20  C21  O4   -179.90  30.0  3
 KEU  Var_04    C17  C19  C20  C21  -179.33  30.0  3
 KEU  Var_05    C3   C2   C1   C10  -175.68  30.0  3
 KEU  Var_06    F2   C6   C5   C10    62.05  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
 KEU  chir_01  C17  C19  N   C18  positiv
 KEU  chir_02  C10  C11  C1  C5   negativ
 KEU  chir_03  C4   C3   C9  C7   positiv
 KEU  chir_04  C8   N1   N2  N3   negativ
 KEU  chir_05  C7   N1   N8  C4   positiv

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
 KEU  plan-1  C    0.020
 KEU  plan-1  C14  0.020
 KEU  plan-1  C13  0.020
 KEU  plan-1  C12  0.020
 KEU  plan-1  C11  0.020
 KEU  plan-1  C16  0.020
 KEU  plan-1  C15  0.020
 KEU  plan-1  C10  0.020
 KEU  plan-1  H13  0.020
 KEU  plan-1  H12  0.020
 KEU  plan-1  H16  0.020
 KEU  plan-1  H15  0.020
 KEU  plan-2  C17  0.020
 KEU  plan-2  N    0.020
 KEU  plan-2  C    0.020
 KEU  plan-2  O    0.020
 KEU  plan-2  C14  0.020
 KEU  plan-2  HN   0.020
 KEU  plan-3  C4   0.020
 KEU  plan-3  C9   0.020
 KEU  plan-3  O1   0.020
 KEU  plan-3  N3   0.020
 KEU  plan-3  C8   0.020
 KEU  plan-3  HN3  0.020
 KEU  plan-4  O4   0.020
 KEU  plan-4  C21  0.020
 KEU  plan-4  O5   0.020
 KEU  plan-4  C20  0.020
 KEU  plan-4  HO4  0.020
 KEU  plan-5  C17  0.020
 KEU  plan-5  C18  0.020
 KEU  plan-5  O3   0.020
 KEU  plan-5  O2   0.020
 KEU  plan-5  HO2  0.020

