# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:30:12 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-[(5-{2-[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}thiophen-2-yl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(C[C@@H](CCc3sc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)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
 4HF  4HF  'N-[(5-{2-[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}thiophen-2-yl)carbonyl]-L-glutamic acid'  ligand  54  31  .  2021-08-04  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4HF
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
 4HF  C5    C  CH2   0  -0.438   4.0056  -0.1403  -0.7608
 4HF  C4A   C  CR6   0  -0.272   5.4294   0.3298  -0.7967
 4HF  C4    C  CR6   0   0.498   6.0174   0.7546  -2.0083
 4HF  O4    O  OC    0  -0.519   5.4919   0.7704  -3.1223
 4HF  N3    N  NR16  0  -0.714   7.3406   1.1968  -1.8860
 4HF  C2    C  CR6   0   0.675   8.0086   1.2265  -0.7116
 4HF  N2    N  NH2   0  -0.828   9.2879   1.6417  -0.7331
 4HF  N1    N  N     0  -0.532   7.4723   0.8353   0.4118
 4HF  C8A   C  CR6   0   0.516   6.1952   0.3823   0.3605
 4HF  N8    N  NH1   0  -0.666   5.6836  -0.0122   1.5387
 4HF  C7    C  CH2   0  -0.242   4.3826  -0.6247   1.6573
 4HF  C6    C  CH1   0  -0.289   3.4129  -0.0249   0.6437
 4HF  C9    C  CH2   0  -0.415   2.0435  -0.6937   0.7039
 4HF  C10   C  CH2   0  -0.519   1.3185  -0.4889   2.0366
 4HF  C3'   C  CR5   0  -0.123  -0.0638  -1.0507   2.0374
 4HF  S2'   S  S2    0   0.233  -1.3253  -0.3020   1.1391
 4HF  C4'   C  CR15  0  -0.222  -0.5242  -2.1670   2.6771
 4HF  C5'   C  CR15  0  -0.166  -1.8965  -2.4193   2.4460
 4HF  C1'   C  CR5   0  -0.334  -2.4747  -1.4973   1.6202
 4HF  C11   C  C     0   0.565  -3.8903  -1.4924   1.2140
 4HF  O11   O  O     0  -0.475  -4.7162  -2.1795   1.7957
 4HF  N     N  NH1   0  -0.664  -4.2198  -0.6706   0.1920
 4HF  CA    C  CH1   0  -0.199  -5.5657  -0.6036  -0.3068
 4HF  C     C  C     0   0.551  -5.8955  -1.8416  -1.1311
 4HF  OX1   O  OH1   0  -0.590  -7.1963  -1.9298  -1.3641
 4HF  OX2   O  O     0  -0.428  -5.0811  -2.6301  -1.5326
 4HF  CB    C  CH2   0  -0.463  -5.7616   0.6678  -1.1376
 4HF  CG    C  CH2   0  -0.577  -5.5736   1.9169  -0.2920
 4HF  CD    C  C     0   0.555  -5.7729   3.1851  -1.0748
 4HF  OE1   O  O     0  -0.442  -6.0665   3.2401  -2.2428
 4HF  OE2   O  OH1   0  -0.595  -5.5861   4.2623  -0.3203
 4HF  H51   H  HCH2  0   0.240   3.4008   0.4470  -1.4565
 4HF  H52   H  HCH2  0   0.225   3.9209  -1.1814  -1.0971
 4HF  HN3   H  HNR6  0   0.413   7.8049   1.4845  -2.7367
 4HF  HN21  H  HNH2  0   0.406   9.7213   1.8279   0.1555
 4HF  HN22  H  HNH2  0   0.408   9.6298   2.1849  -1.5079
 4HF  HN8   H  HNH1  0   0.388   6.2964  -0.0014   2.3366
 4HF  H71   H  HCH2  0   0.254   4.0354  -0.4615   2.6774
 4HF  H72   H  HCH2  0   0.223   4.4403  -1.7112   1.5067
 4HF  H6    H  HCH1  0   0.240   3.2912   1.0383   0.8845
 4HF  H91   H  HCH2  0   0.238   1.4286  -0.2891  -0.1053
 4HF  H92   H  HCH2  0   0.234   2.1473  -1.7651   0.5053
 4HF  H101  H  HCH2  0   0.266   1.8662  -0.9722   2.8477
 4HF  H102  H  HCH2  0   0.260   1.2905   0.5789   2.2719
 4HF  H4'   H  HCR5  0   0.267   0.1077  -2.7837   3.3009
 4HF  H5'   H  HCR5  0   0.273  -2.4380  -3.2534   2.8685
 4HF  HN    H  HNH1  0   0.405  -3.4920  -0.3296  -0.4184
 4HF  HA    H  HCH1  0   0.298  -6.2552  -0.5777   0.5416
 4HF  HX1   H  HOH1  0   0.487  -7.3878  -2.7003  -1.9199
 4HF  HB1   H  HCH2  0   0.260  -5.0633   0.6645  -1.9788
 4HF  HB2   H  HCH2  0   0.274  -6.7649   0.6589  -1.5625
 4HF  HG1   H  HCH2  0   0.289  -6.2773   1.9193   0.5466
 4HF  HG2   H  HCH2  0   0.286  -4.5786   1.9479   0.1601
 4HF  HE2   H  HOH1  0   0.480  -5.7171   5.0635  -0.8490

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
 4HF  C5   C4A   single    1.500  0.020  1.500
 4HF  C5   C6    single    1.529  0.020  1.529
 4HF  C5   H51   single    0.970  0.020  1.090
 4HF  C5   H52   single    0.970  0.020  1.090
 4HF  C4A  C4    aromatic  1.412  0.020  1.412
 4HF  C4A  C8A   aromatic  1.389  0.020  1.389
 4HF  C4   O4    double    1.232  0.020  1.232
 4HF  C4   N3    aromatic  1.400  0.020  1.400
 4HF  N3   C2    aromatic  1.351  0.020  1.351
 4HF  N3   HN3   single    0.860  0.020  1.020
 4HF  C2   N2    single    1.345  0.020  1.345
 4HF  C2   N1    aromatic  1.305  0.020  1.305
 4HF  N2   HN21  single    0.890  0.020  1.040
 4HF  N2   HN22  single    0.890  0.020  1.040
 4HF  N1   C8A   aromatic  1.356  0.020  1.356
 4HF  C8A  N8    single    1.344  0.020  1.344
 4HF  N8   C7    single    1.443  0.020  1.443
 4HF  N8   HN8   single    0.860  0.020  1.020
 4HF  C7   C6    single    1.526  0.020  1.526
 4HF  C7   H71   single    0.970  0.020  1.090
 4HF  C7   H72   single    0.970  0.020  1.090
 4HF  C6   C9    single    1.525  0.020  1.525
 4HF  C6   H6    single    0.970  0.020  1.090
 4HF  C9   C10   single    1.531  0.020  1.531
 4HF  C9   H91   single    0.970  0.020  1.090
 4HF  C9   H92   single    0.970  0.020  1.090
 4HF  C10  C3'   single    1.492  0.020  1.492
 4HF  C10  H101  single    0.970  0.020  1.090
 4HF  C10  H102  single    0.970  0.020  1.090
 4HF  C3'  S2'   aromatic  1.720  0.020  1.720
 4HF  C3'  C4'   aromatic  1.366  0.020  1.366
 4HF  S2'  C1'   aromatic  1.727  0.020  1.727
 4HF  C4'  C5'   aromatic  1.414  0.020  1.414
 4HF  C4'  H4'   single    0.930  0.020  1.080
 4HF  C5'  C1'   aromatic  1.366  0.020  1.366
 4HF  C5'  H5'   single    0.930  0.020  1.080
 4HF  C1'  C11   single    1.473  0.020  1.473
 4HF  C11  O11   double    1.222  0.020  1.222
 4HF  C11  N     single    1.352  0.020  1.352
 4HF  N    CA    single    1.437  0.020  1.437
 4HF  N    HN    single    0.860  0.020  1.020
 4HF  CA   C     single    1.523  0.020  1.523
 4HF  CA   CB    single    1.531  0.020  1.531
 4HF  CA   HA    single    0.970  0.020  1.090
 4HF  C    OX1   single    1.324  0.020  1.324
 4HF  C    OX2   double    1.202  0.020  1.202
 4HF  OX1  HX1   single    0.850  0.020  0.980
 4HF  CB   CG    single    1.520  0.020  1.520
 4HF  CB   HB1   single    0.970  0.020  1.090
 4HF  CB   HB2   single    0.970  0.020  1.090
 4HF  CG   CD    single    1.504  0.020  1.504
 4HF  CG   HG1   single    0.970  0.020  1.090
 4HF  CG   HG2   single    0.970  0.020  1.090
 4HF  CD   OE1   double    1.206  0.020  1.206
 4HF  CD   OE2   single    1.328  0.020  1.328
 4HF  OE2  HE2   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
 4HF  H52   C5   H51   105.78  3.000
 4HF  H52   C5   C6    108.86  3.000
 4HF  H51   C5   C6    109.25  3.000
 4HF  H52   C5   C4A   111.30  3.000
 4HF  H51   C5   C4A   109.98  3.000
 4HF  C6    C5   C4A   111.49  3.000
 4HF  C8A   C4A  C4    118.30  3.000
 4HF  C8A   C4A  C5    121.02  3.000
 4HF  C4    C4A  C5    120.67  3.000
 4HF  N3    C4   O4    118.55  3.000
 4HF  N3    C4   C4A   114.43  3.000
 4HF  O4    C4   C4A   127.02  3.000
 4HF  HN3   N3   C2    119.86  3.000
 4HF  HN3   N3   C4    116.77  3.000
 4HF  C2    N3   C4    123.35  3.000
 4HF  N1    C2   N2    119.81  3.000
 4HF  N1    C2   N3    122.58  3.000
 4HF  N2    C2   N3    117.58  3.000
 4HF  HN22  N2   HN21  115.71  3.000
 4HF  HN22  N2   C2    120.14  3.000
 4HF  HN21  N2   C2    116.92  3.000
 4HF  C8A   N1   C2    117.04  3.000
 4HF  N8    C8A  N1    115.06  3.000
 4HF  N8    C8A  C4A   120.64  3.000
 4HF  N1    C8A  C4A   124.30  3.000
 4HF  HN8   N8   C7    119.25  3.000
 4HF  HN8   N8   C8A   117.41  3.000
 4HF  C7    N8   C8A   122.69  3.000
 4HF  H72   C7   H71   107.05  3.000
 4HF  H72   C7   C6    109.34  3.000
 4HF  H71   C7   C6    111.13  3.000
 4HF  H72   C7   N8    111.18  3.000
 4HF  H71   C7   N8    107.49  3.000
 4HF  C6    C7   N8    110.59  3.000
 4HF  H6    C6   C9    108.47  3.000
 4HF  H6    C6   C7    107.80  3.000
 4HF  C9    C6   C7    111.84  3.000
 4HF  H6    C6   C5    108.53  3.000
 4HF  C9    C6   C5    110.56  3.000
 4HF  C7    C6   C5    109.53  3.000
 4HF  H92   C9   H91   106.33  3.000
 4HF  H92   C9   C10   109.50  3.000
 4HF  H91   C9   C10   109.16  3.000
 4HF  H92   C9   C6    109.69  3.000
 4HF  H91   C9   C6    108.26  3.000
 4HF  C10   C9   C6    113.63  3.000
 4HF  H102  C10  H101  106.57  3.000
 4HF  H102  C10  C3'   110.11  3.000
 4HF  H101  C10  C3'   107.32  3.000
 4HF  H102  C10  C9    109.27  3.000
 4HF  H101  C10  C9    110.49  3.000
 4HF  C3'   C10  C9    112.88  3.000
 4HF  C4'   C3'  S2'   110.67  3.000
 4HF  C4'   C3'  C10   128.31  3.000
 4HF  S2'   C3'  C10   121.01  3.000
 4HF  C1'   S2'  C3'    92.37  3.000
 4HF  H4'   C4'  C5'   124.03  3.000
 4HF  H4'   C4'  C3'   122.63  3.000
 4HF  C5'   C4'  C3'   113.34  3.000
 4HF  H5'   C5'  C1'   123.04  3.000
 4HF  H5'   C5'  C4'   124.06  3.000
 4HF  C1'   C5'  C4'   112.90  3.000
 4HF  C11   C1'  C5'   125.16  3.000
 4HF  C11   C1'  S2'   124.10  3.000
 4HF  C5'   C1'  S2'   110.72  3.000
 4HF  N     C11  O11   122.48  3.000
 4HF  N     C11  C1'   116.40  3.000
 4HF  O11   C11  C1'   121.10  3.000
 4HF  HN    N    CA    116.73  3.000
 4HF  HN    N    C11   119.13  3.000
 4HF  CA    N    C11   121.26  3.000
 4HF  HA    CA   CB    108.69  3.000
 4HF  HA    CA   C     107.61  3.000
 4HF  CB    CA   C     110.70  3.000
 4HF  HA    CA   N     108.81  3.000
 4HF  CB    CA   N     110.30  3.000
 4HF  C     CA   N     110.65  3.000
 4HF  OX2   C    OX1   124.25  3.000
 4HF  OX2   C    CA    124.53  3.000
 4HF  OX1   C    CA    111.22  3.000
 4HF  HX1   OX1  C     110.36  3.000
 4HF  HB2   CB   HB1   106.74  3.000
 4HF  HB2   CB   CG    109.72  3.000
 4HF  HB1   CB   CG    110.58  3.000
 4HF  HB2   CB   CA    108.82  3.000
 4HF  HB1   CB   CA    109.46  3.000
 4HF  CG    CB   CA    111.39  3.000
 4HF  HG2   CG   HG1   105.55  3.000
 4HF  HG2   CG   CD    108.18  3.000
 4HF  HG1   CG   CD    108.17  3.000
 4HF  HG2   CG   CB    111.46  3.000
 4HF  HG1   CG   CB    110.39  3.000
 4HF  CD    CG   CB    112.77  3.000
 4HF  OE2   CD   OE1   123.20  3.000
 4HF  OE2   CD   CG    111.69  3.000
 4HF  OE1   CD   CG    125.11  3.000
 4HF  HE2   OE2  CD    109.98  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
 4HF  CONST_01  C2    N3   C4   C4A     0.00   0.0  0
 4HF  CONST_02  C2    N1   C8A  C4A     0.00   0.0  0
 4HF  CONST_03  N1    C8A  C4A  C4      0.00   0.0  0
 4HF  CONST_04  N1    C2   N3   C4      0.00   0.0  0
 4HF  CONST_05  C8A   C4A  C4   N3      0.00   0.0  0
 4HF  CONST_06  C8A   N1   C2   N3      0.00   0.0  0
 4HF  CONST_07  C5'   C1'  S2'  C3'     0.00   0.0  0
 4HF  CONST_08  C1'   C5'  C4'  C3'     0.00   0.0  0
 4HF  CONST_09  C5'   C4'  C3'  S2'     0.00   0.0  0
 4HF  CONST_10  C4'   C5'  C1'  S2'     0.00   0.0  0
 4HF  CONST_11  C1'   S2'  C3'  C4'     0.00   0.0  0
 4HF  CONST_12  O4    C4   C4A  C5      0.00   0.0  0
 4HF  CONST_13  N2    C2   N3   C4    180.00   0.0  0
 4HF  CONST_14  C8A   C4A  C4   O4    180.00   0.0  0
 4HF  CONST_15  C2    N3   C4   O4    180.00   0.0  0
 4HF  CONST_16  C8A   N1   C2   N2    180.00   0.0  0
 4HF  CONST_17  C1'   S2'  C3'  C10   180.00   0.0  0
 4HF  CONST_18  C5'   C4'  C3'  C10   180.00   0.0  0
 4HF  CONST_19  C11   C1'  S2'  C3'   180.00   0.0  0
 4HF  CONST_20  C11   C1'  C5'  C4'   180.00   0.0  0
 4HF  CONST_21  HN3   N3   C4   C4A   180.00   0.0  0
 4HF  CONST_22  H5'   C5'  C4'  C3'   180.00   0.0  0
 4HF  CONST_23  H4'   C4'  C3'  S2'   180.00   0.0  0
 4HF  CONST_24  HN21  N2   C2   N3    180.00   0.0  0
 4HF  CONST_26  CA    N    C11  C1'   180.00   0.0  0
 4HF  CONST_28  CA    N    C11  O11     0.00   0.0  0
 4HF  CONST_29  HX1   OX1  C    CA    180.00   0.0  0
 4HF  CONST_30  HE2   OE2  CD   CG    180.00   0.0  0
 4HF  Var_01    C7    N8   C8A  C4A     6.13  30.0  1
 4HF  Var_02    C6    C5   C4A  C4   -157.62  30.0  1
 4HF  Var_03    C6    C7   N8   C8A   -34.95  30.0  1
 4HF  Var_04    C3'   C10  C9   C6    175.17  30.0  3
 4HF  Var_05    S2'   C3'  C10  C9    -71.59  30.0  2
 4HF  Var_06    O11   C11  C1'  S2'  -164.25  30.0  2
 4HF  Var_07    CD    CG   CB   CA   -179.42  30.0  3
 4HF  Var_08    OE1   CD   CG   CB      0.87  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
 4HF  chir_01  C6  C5  C7  C9  positiv
 4HF  chir_02  CA  N   C   CB  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
 4HF  plan-1  C10   0.020
 4HF  plan-1  C3'   0.020
 4HF  plan-1  S2'   0.020
 4HF  plan-1  C4'   0.020
 4HF  plan-1  C5'   0.020
 4HF  plan-1  C1'   0.020
 4HF  plan-1  C11   0.020
 4HF  plan-1  H4'   0.020
 4HF  plan-1  H5'   0.020
 4HF  plan-2  CA    0.020
 4HF  plan-2  C     0.020
 4HF  plan-2  OX1   0.020
 4HF  plan-2  OX2   0.020
 4HF  plan-2  HX1   0.020
 4HF  plan-3  CG    0.020
 4HF  plan-3  CD    0.020
 4HF  plan-3  OE1   0.020
 4HF  plan-3  OE2   0.020
 4HF  plan-3  HE2   0.020
 4HF  plan-4  C1'   0.020
 4HF  plan-4  C11   0.020
 4HF  plan-4  O11   0.020
 4HF  plan-4  N     0.020
 4HF  plan-4  CA    0.020
 4HF  plan-4  HN    0.020
 4HF  plan-5  C2    0.020
 4HF  plan-5  N2    0.020
 4HF  plan-5  HN21  0.020
 4HF  plan-5  HN22  0.020
 4HF  plan-6  C5    0.020
 4HF  plan-6  C4A   0.020
 4HF  plan-6  C4    0.020
 4HF  plan-6  O4    0.020
 4HF  plan-6  N3    0.020
 4HF  plan-6  C2    0.020
 4HF  plan-6  N2    0.020
 4HF  plan-6  N1    0.020
 4HF  plan-6  C8A   0.020
 4HF  plan-6  N8    0.020
 4HF  plan-6  HN3   0.020

