# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:40:48 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-[8-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanoyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCCCCCC(=O)N[C@@H](CCC(O)=O)C(O)=O)cc2C(=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
 3YE  3YE  'N-[8-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanoyl]-L-glutamic acid'  ligand  57  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3YE
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
 3YE  N1   N  N     0  -0.508   -8.0483  -0.9442  -0.7147
 3YE  C2   C  CR6   0   0.669   -9.0822  -0.3454  -1.2392
 3YE  N3   N  NR16  0  -0.720   -9.2857   1.0016  -1.1520
 3YE  C4   C  CR6   0   0.496   -8.4416   1.9126  -0.5076
 3YE  N5   N  NR15  0  -0.704   -6.0583  -0.4932   0.5303
 3YE  C6   C  CR5   0   0.374   -5.4256   0.6058   1.0847
 3YE  C7   C  CR15  0  -0.469   -6.1770   1.7109   0.8091
 3YE  C8   C  CR56  0  -0.186   -7.3102   1.2683   0.0618
 3YE  C9   C  CR56  0   0.475   -7.1965  -0.1111  -0.0864
 3YE  O10  O  O     0  -0.488   -8.7262   3.1029  -0.4896
 3YE  N11  N  NH2   0  -0.834   -9.9886  -1.0518  -1.9449
 3YE  C12  C  CH2   0  -0.576    3.3462  -0.9054   1.2947
 3YE  C13  C  CH2   0  -0.417    2.0171  -0.8330   0.5490
 3YE  C14  C  CH2   0  -0.416    0.8574  -0.4673   1.4660
 3YE  C17  C  C     0   0.570    4.4828  -1.3327   0.3962
 3YE  O18  O  O     0  -0.499    4.4007  -2.2968  -0.3513
 3YE  N19  N  NH1   0  -0.640    5.5947  -0.5740   0.4608
 3YE  C20  C  CH1   0  -0.191    6.7845  -0.8999  -0.2734
 3YE  C21  C  CH2   0  -0.467    7.7171   0.3123  -0.3579
 3YE  C22  C  CH2   0  -0.579    7.0610   1.4631  -1.1048
 3YE  C23  C  C     0   0.555    7.9598   2.6613  -1.2363
 3YE  O24  O  O     0  -0.442    9.0851   2.7350  -0.8099
 3YE  O25  O  OH1   0  -0.595    7.3622   3.6528  -1.8879
 3YE  C26  C  C     0   0.549    7.5006  -2.0825   0.3658
 3YE  O27  O  OH1   0  -0.591    8.4356  -2.5677  -0.4385
 3YE  O28  O  O     0  -0.429    7.2631  -2.5147   1.4623
 3YE  C29  C  CH2   0  -0.519   -4.1272   0.4705   1.7995
 3YE  C30  C  CH2   0  -0.415   -2.9588   0.1072   0.8792
 3YE  C16  C  CH2   0  -0.418   -1.6399  -0.0116   1.6315
 3YE  C15  C  CH2   0  -0.414   -0.4682  -0.3608   0.7230
 3YE  H1   H  HNR6  0   0.419  -10.1080   1.3956  -1.5902
 3YE  H2   H  HNR5  0   0.406   -5.7379  -1.4466   0.5965
 3YE  H3   H  HCR5  0   0.249   -5.9402   2.7211   1.1039
 3YE  H4   H  HNH2  0   0.406   -9.9520  -2.0528  -1.8480
 3YE  H5   H  HNH2  0   0.408  -10.9057  -0.6693  -2.1032
 3YE  H6   H  HCH2  0   0.249    3.5641   0.0548   1.7683
 3YE  H7   H  HCH2  0   0.266    3.2742  -1.6411   2.1021
 3YE  H8   H  HCH2  0   0.225    2.0921  -0.0947  -0.2556
 3YE  H9   H  HCH2  0   0.226    1.8142  -1.7942   0.0713
 3YE  H10  H  HCH2  0   0.213    0.7721  -1.2169   2.2603
 3YE  H11  H  HCH2  0   0.212    1.0714   0.4835   1.9656
 3YE  H12  H  HNH1  0   0.405    5.6528   0.1443   1.1651
 3YE  H13  H  HCH1  0   0.293    6.5049  -1.1936  -1.2893
 3YE  H14  H  HCH2  0   0.260    8.0053   0.6237   0.6493
 3YE  H15  H  HCH2  0   0.274    8.6312   0.0163  -0.8717
 3YE  H16  H  HCH2  0   0.289    6.7630   1.1446  -2.1086
 3YE  H17  H  HCH2  0   0.287    6.1390   1.7830  -0.6124
 3YE  H18  H  HOH1  0   0.480    7.9605   4.4116  -1.9588
 3YE  H19  H  HOH1  0   0.486    8.9050  -3.2983  -0.0081
 3YE  H20  H  HCH2  0   0.248   -3.9138   1.4174   2.2997
 3YE  H21  H  HCH2  0   0.242   -4.2118  -0.2835   2.5898
 3YE  H22  H  HCH2  0   0.217   -3.1702  -0.8371   0.3677
 3YE  H23  H  HCH2  0   0.223   -2.8714   0.8670   0.0970
 3YE  H24  H  HCH2  0   0.212   -1.4305   0.9313   2.1482
 3YE  H25  H  HCH2  0   0.213   -1.7349  -0.7727   2.4137
 3YE  H26  H  HCH2  0   0.211   -0.3814   0.3958  -0.0645
 3YE  H27  H  HCH2  0   0.210   -0.6757  -1.3075   0.2126

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
 3YE  O24  C23  double    1.206  0.020  1.206
 3YE  O25  C23  single    1.328  0.020  1.328
 3YE  C23  C22  single    1.504  0.020  1.504
 3YE  O18  C17  double    1.223  0.020  1.223
 3YE  C22  C21  single    1.521  0.020  1.521
 3YE  C12  C17  single    1.511  0.020  1.511
 3YE  C12  C13  single    1.526  0.020  1.526
 3YE  C17  N19  single    1.348  0.020  1.348
 3YE  C21  C20  single    1.532  0.020  1.532
 3YE  O28  C26  double    1.202  0.020  1.202
 3YE  N19  C20  single    1.436  0.020  1.436
 3YE  C13  C14  single    1.523  0.020  1.523
 3YE  C20  C26  single    1.523  0.020  1.523
 3YE  C26  O27  single    1.325  0.020  1.325
 3YE  C14  C15  single    1.523  0.020  1.523
 3YE  C15  C16  single    1.523  0.020  1.523
 3YE  C16  C30  single    1.523  0.020  1.523
 3YE  C30  C29  single    1.531  0.020  1.531
 3YE  C29  C6   single    1.488  0.020  1.488
 3YE  C6   N5   aromatic  1.384  0.020  1.384
 3YE  C6   C7   aromatic  1.364  0.020  1.364
 3YE  N5   C9   aromatic  1.350  0.020  1.350
 3YE  C7   C8   aromatic  1.428  0.020  1.428
 3YE  C9   C8   aromatic  1.392  0.020  1.392
 3YE  C9   N1   single    1.347  0.020  1.347
 3YE  C8   C4   single    1.421  0.020  1.421
 3YE  N1   C2   double    1.305  0.020  1.305
 3YE  C4   O10  double    1.224  0.020  1.224
 3YE  C4   N3   single    1.399  0.020  1.399
 3YE  C2   N3   single    1.365  0.020  1.365
 3YE  C2   N11  single    1.349  0.020  1.349
 3YE  N3   H1   single    0.860  0.020  1.020
 3YE  N5   H2   single    0.860  0.020  1.020
 3YE  C7   H3   single    0.930  0.020  1.080
 3YE  N11  H4   single    0.890  0.020  1.040
 3YE  N11  H5   single    0.890  0.020  1.040
 3YE  C12  H6   single    0.970  0.020  1.090
 3YE  C12  H7   single    0.970  0.020  1.090
 3YE  C13  H8   single    0.970  0.020  1.090
 3YE  C13  H9   single    0.970  0.020  1.090
 3YE  C14  H10  single    0.970  0.020  1.090
 3YE  C14  H11  single    0.970  0.020  1.090
 3YE  N19  H12  single    0.860  0.020  1.020
 3YE  C20  H13  single    0.970  0.020  1.090
 3YE  C21  H14  single    0.970  0.020  1.090
 3YE  C21  H15  single    0.970  0.020  1.090
 3YE  C22  H16  single    0.970  0.020  1.090
 3YE  C22  H17  single    0.970  0.020  1.090
 3YE  O25  H18  single    0.850  0.020  0.980
 3YE  O27  H19  single    0.850  0.020  0.980
 3YE  C29  H20  single    0.970  0.020  1.090
 3YE  C29  H21  single    0.970  0.020  1.090
 3YE  C30  H22  single    0.970  0.020  1.090
 3YE  C30  H23  single    0.970  0.020  1.090
 3YE  C16  H24  single    0.970  0.020  1.090
 3YE  C16  H25  single    0.970  0.020  1.090
 3YE  C15  H26  single    0.970  0.020  1.090
 3YE  C15  H27  single    0.970  0.020  1.090

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
 3YE  C9   N1   C2   113.87  3.000
 3YE  N11  C2   N3   116.75  3.000
 3YE  N11  C2   N1   120.17  3.000
 3YE  N3   C2   N1   123.04  3.000
 3YE  H1   N3   C4   115.86  3.000
 3YE  H1   N3   C2   118.54  3.000
 3YE  C4   N3   C2   125.59  3.000
 3YE  O10  C4   C8   128.32  3.000
 3YE  O10  C4   N3   119.98  3.000
 3YE  C8   C4   N3   111.69  3.000
 3YE  H2   N5   C9   124.46  3.000
 3YE  H2   N5   C6   125.42  3.000
 3YE  C9   N5   C6   110.10  3.000
 3YE  C29  C6   C7   130.62  3.000
 3YE  C7   C6   N5   108.09  3.000
 3YE  C29  C6   N5   121.26  3.000
 3YE  H3   C7   C8   127.42  3.000
 3YE  H3   C7   C6   125.62  3.000
 3YE  C8   C7   C6   106.96  3.000
 3YE  C9   C8   C7   107.34  3.000
 3YE  C9   C8   C4   118.14  3.000
 3YE  C7   C8   C4   134.51  3.000
 3YE  C8   C9   N5   107.50  3.000
 3YE  C8   C9   N1   127.65  3.000
 3YE  N5   C9   N1   124.84  3.000
 3YE  H5   N11  H4   115.24  3.000
 3YE  H5   N11  C2   119.72  3.000
 3YE  H4   N11  C2   116.50  3.000
 3YE  H7   C12  H6   106.50  3.000
 3YE  H7   C12  C17  107.35  3.000
 3YE  H6   C12  C17  110.88  3.000
 3YE  H7   C12  C13  109.58  3.000
 3YE  H6   C12  C13  110.11  3.000
 3YE  C17  C12  C13  112.22  3.000
 3YE  H9   C13  H8   106.55  3.000
 3YE  H9   C13  C14  109.45  3.000
 3YE  H8   C13  C14  109.44  3.000
 3YE  H9   C13  C12  109.50  3.000
 3YE  H8   C13  C12  109.37  3.000
 3YE  C14  C13  C12  112.36  3.000
 3YE  H11  C14  H10  106.18  3.000
 3YE  H11  C14  C15  109.37  3.000
 3YE  H10  C14  C15  109.50  3.000
 3YE  H11  C14  C13  109.53  3.000
 3YE  H10  C14  C13  109.37  3.000
 3YE  C15  C14  C13  112.69  3.000
 3YE  N19  C17  O18  121.91  3.000
 3YE  N19  C17  C12  115.66  3.000
 3YE  O18  C17  C12  122.42  3.000
 3YE  H12  N19  C20  118.13  3.000
 3YE  H12  N19  C17  118.84  3.000
 3YE  C20  N19  C17  122.11  3.000
 3YE  H13  C20  C26  107.55  3.000
 3YE  H13  C20  C21  108.47  3.000
 3YE  C26  C20  C21  110.57  3.000
 3YE  H13  C20  N19  108.91  3.000
 3YE  C26  C20  N19  110.57  3.000
 3YE  C21  C20  N19  110.68  3.000
 3YE  H15  C21  H14  106.90  3.000
 3YE  H15  C21  C22  109.63  3.000
 3YE  H14  C21  C22  110.54  3.000
 3YE  H15  C21  C20  108.78  3.000
 3YE  H14  C21  C20  109.58  3.000
 3YE  C22  C21  C20  111.30  3.000
 3YE  H17  C22  H16  105.58  3.000
 3YE  H17  C22  C23  108.08  3.000
 3YE  H16  C22  C23  108.33  3.000
 3YE  H17  C22  C21  111.36  3.000
 3YE  H16  C22  C21  110.35  3.000
 3YE  C23  C22  C21  112.84  3.000
 3YE  O25  C23  O24  123.21  3.000
 3YE  O25  C23  C22  111.64  3.000
 3YE  O24  C23  C22  125.15  3.000
 3YE  H18  O25  C23  110.04  3.000
 3YE  O28  C26  O27  124.14  3.000
 3YE  O27  C26  C20  111.18  3.000
 3YE  O28  C26  C20  124.67  3.000
 3YE  H19  O27  C26  110.38  3.000
 3YE  H21  C29  H20  106.36  3.000
 3YE  H21  C29  C30  109.22  3.000
 3YE  H20  C29  C30  109.39  3.000
 3YE  H21  C29  C6   109.98  3.000
 3YE  H20  C29  C6   108.15  3.000
 3YE  C30  C29  C6   113.49  3.000
 3YE  H23  C30  H22  106.29  3.000
 3YE  H23  C30  C16  109.77  3.000
 3YE  H22  C30  C16  109.31  3.000
 3YE  H23  C30  C29  109.03  3.000
 3YE  H22  C30  C29  109.77  3.000
 3YE  C16  C30  C29  112.48  3.000
 3YE  H25  C16  H24  106.14  3.000
 3YE  H25  C16  C15  109.47  3.000
 3YE  H24  C16  C15  109.36  3.000
 3YE  H25  C16  C30  109.38  3.000
 3YE  H24  C16  C30  109.35  3.000
 3YE  C15  C16  C30  112.92  3.000
 3YE  H27  C15  H26  106.08  3.000
 3YE  H27  C15  C16  109.29  3.000
 3YE  H26  C15  C16  109.35  3.000
 3YE  H27  C15  C14  109.37  3.000
 3YE  H26  C15  C14  109.27  3.000
 3YE  C16  C15  C14  113.23  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
 3YE  CONST_01  C8   C7   C6   N5      0.00   0.0  0
 3YE  CONST_02  C7   C8   C9   N5      0.00   0.0  0
 3YE  CONST_03  C8   C9   N5   C6      0.00   0.0  0
 3YE  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 3YE  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YE  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 3YE  CONST_07  C8   C4   N3   C2      0.00   0.0  0
 3YE  CONST_08  C9   N1   C2   N3      0.00   0.0  0
 3YE  CONST_09  C29  C6   C7   C8    180.00   0.0  0
 3YE  CONST_10  C29  C6   N5   C9    180.00   0.0  0
 3YE  CONST_11  O10  C4   N3   C2    180.00   0.0  0
 3YE  CONST_12  N11  C2   N3   C4    180.00   0.0  0
 3YE  CONST_13  N11  C2   N1   C9    180.00   0.0  0
 3YE  CONST_14  H2   N5   C9   N1      0.00   0.0  0
 3YE  CONST_15  H3   C7   C8   C4      0.00   0.0  0
 3YE  CONST_16  H1   N3   C2   N1    180.00   0.0  0
 3YE  CONST_17  H4   N11  C2   N1      0.00   0.0  0
 3YE  CONST_19  C20  N19  C17  C12   180.00   0.0  0
 3YE  CONST_20  C20  N19  C17  O18     0.00   0.0  0
 3YE  CONST_21  H12  N19  C17  C12     0.00   0.0  0
 3YE  CONST_22  H19  O27  C26  C20   180.00   0.0  0
 3YE  CONST_23  H18  O25  C23  C22   180.00   0.0  0
 3YE  Var_01    C30  C29  C6   N5     68.51  30.0  2
 3YE  Var_02    C16  C30  C29  C6    179.42  30.0  1
 3YE  Var_03    C15  C14  C13  C12   178.65  30.0  3
 3YE  Var_04    O18  C17  C12  C13   -48.02  30.0  3
 3YE  Var_05    C16  C15  C14  C13   179.32  30.0  3
 3YE  Var_06    C17  C12  C13  C14   177.26  30.0  1
 3YE  Var_07    C30  C16  C15  C14   179.40  30.0  3
 3YE  Var_08    C23  C22  C21  C20  -178.65  30.0  1
 3YE  Var_09    O24  C23  C22  C21     0.12  30.0  2
 3YE  Var_10    C15  C16  C30  C29  -179.49  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
 3YE  chir_01  C20  C21  N19  C26  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
 3YE  plan-1  N1   0.020
 3YE  plan-1  C2   0.020
 3YE  plan-1  N3   0.020
 3YE  plan-1  C4   0.020
 3YE  plan-1  N5   0.020
 3YE  plan-1  C6   0.020
 3YE  plan-1  C7   0.020
 3YE  plan-1  C8   0.020
 3YE  plan-1  C9   0.020
 3YE  plan-1  O10  0.020
 3YE  plan-1  N11  0.020
 3YE  plan-1  C29  0.020
 3YE  plan-1  H1   0.020
 3YE  plan-1  H2   0.020
 3YE  plan-1  H3   0.020
 3YE  plan-1  H4   0.020
 3YE  plan-1  H5   0.020
 3YE  plan-2  C12  0.020
 3YE  plan-2  C17  0.020
 3YE  plan-2  O18  0.020
 3YE  plan-2  N19  0.020
 3YE  plan-2  C20  0.020
 3YE  plan-2  H12  0.020
 3YE  plan-3  C22  0.020
 3YE  plan-3  C23  0.020
 3YE  plan-3  O24  0.020
 3YE  plan-3  O25  0.020
 3YE  plan-3  H18  0.020
 3YE  plan-4  C20  0.020
 3YE  plan-4  C26  0.020
 3YE  plan-4  O27  0.020
 3YE  plan-4  O28  0.020
 3YE  plan-4  H19  0.020

