# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:03:42 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-({4-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-2-yl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCc3csc(c3)C(=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
 3YF  3YF  'N-({4-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-2-yl}carbonyl)-L-glutamic acid'  ligand  52  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3YF
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
 3YF  N1   N  N     0  -0.508   6.7250  -0.0425   1.7727
 3YF  C2   C  CR6   0   0.670   7.6113   0.9152   1.7597
 3YF  N3   N  NR16  0  -0.720   7.8788   1.6668   0.6519
 3YF  C4   C  CR6   0   0.496   7.2695   1.5199  -0.5987
 3YF  N5   N  NR15  0  -0.704   5.1567  -1.1588   0.3541
 3YF  C6   C  CR5   0   0.373   4.7364  -1.0844  -0.9622
 3YF  C7   C  CR15  0  -0.466   5.4306  -0.0813  -1.5735
 3YF  C8   C  CR56  0  -0.186   6.3070   0.4745  -0.5939
 3YF  C9   C  CR56  0   0.477   6.1055  -0.2281   0.5909
 3YF  O10  O  O     0  -0.487   7.5923   2.2499  -1.5265
 3YF  N11  N  NH2   0  -0.835   8.3467   1.1738   2.8593
 3YF  C12  C  CR15  0  -0.218  -0.9245  -1.1010  -1.4689
 3YF  C13  C  CR5   0  -0.318  -2.1189  -0.9528  -0.8239
 3YF  S14  S  S2    0   0.242  -2.3389  -2.1886   0.3582
 3YF  C15  C  CR15  0  -0.536  -0.8220  -2.8808  -0.0130
 3YF  C16  C  CR5   0   0.223  -0.1653  -2.2087  -1.0043
 3YF  O18  O  O     0  -0.472  -3.0876   0.7320  -2.1479
 3YF  N19  N  NH1   0  -0.664  -4.0625   0.2900  -0.1608
 3YF  C20  C  CH1   0  -0.197  -5.0679   1.3049  -0.3167
 3YF  C21  C  CH2   0  -0.465  -6.2096   1.0780   0.6789
 3YF  C22  C  CH2   0  -0.577  -6.9179  -0.2408   0.4137
 3YF  C23  C  C     0   0.555  -8.0688  -0.4836   1.3504
 3YF  O24  O  OH1   0  -0.595  -8.6838  -1.6306   1.0845
 3YF  O25  O  O     0  -0.442  -8.4074   0.2566   2.2399
 3YF  C26  C  C     0   0.551  -4.4663   2.6918  -0.1302
 3YF  O27  O  OH1   0  -0.590  -5.2847   3.6323  -0.5769
 3YF  O28  O  O     0  -0.429  -3.3984   2.9081   0.3782
 3YF  C29  C  CH2   0  -0.524   3.6659  -1.9752  -1.4859
 3YF  C30  C  CH2   0  -0.417   2.2773  -1.6364  -0.9384
 3YF  C31  C  CH2   0  -0.511   1.2001  -2.5589  -1.5091
 3YF  H1   H  HNR6  0   0.419   8.5896   2.3836   0.7156
 3YF  H2   H  HNR5  0   0.406   4.8208  -1.8189   1.0377
 3YF  H3   H  HCR5  0   0.250   5.3203   0.2225  -2.6027
 3YF  H4   H  HNH2  0   0.406   8.0414   0.7457   3.7171
 3YF  H5   H  HNH2  0   0.409   8.8064   2.0633   2.9596
 3YF  H6   H  HCR5  0   0.269  -0.5903  -0.4355  -2.2535
 3YF  H7   H  HCR5  0   0.300  -0.4891  -3.7638   0.5126
 3YF  H8   H  HNH1  0   0.406  -3.8962  -0.0455   0.7766
 3YF  H9   H  HCH1  0   0.298  -5.4728   1.2485  -1.3307
 3YF  H10  H  HCH2  0   0.261  -5.8141   1.1044   1.6977
 3YF  H11  H  HCH2  0   0.275  -6.9181   1.9012   0.5923
 3YF  H12  H  HCH2  0   0.289  -7.2971  -0.2700  -0.6124
 3YF  H13  H  HCH2  0   0.286  -6.2302  -1.0870   0.4957
 3YF  H14  H  HOH1  0   0.481  -9.4182  -1.7639   1.7020
 3YF  H15  H  HOH1  0   0.487  -4.9083   4.5112  -0.4185
 3YF  H16  H  HCH2  0   0.253   3.6559  -1.8909  -2.5746
 3YF  H17  H  HCH2  0   0.247   3.8993  -3.0206  -1.2583
 3YF  H18  H  HCH2  0   0.233   2.2720  -1.7132   0.1526
 3YF  H19  H  HCH2  0   0.237   2.0414  -0.5962  -1.1785
 3YF  H20  H  HCH2  0   0.248   1.4320  -3.5951  -1.2512
 3YF  H21  H  HCH2  0   0.247   1.2140  -2.4985  -2.6012
 3YF  C17  C  C     0   0.567  -3.1152   0.0971  -1.1055

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
 3YF  N11  C2   single    1.348  0.020  1.348
 3YF  N3   C2   single    1.365  0.020  1.365
 3YF  N3   C4   single    1.399  0.020  1.399
 3YF  C2   N1   double    1.305  0.020  1.305
 3YF  O10  C4   double    1.224  0.020  1.224
 3YF  C4   C8   single    1.421  0.020  1.421
 3YF  N1   C9   single    1.347  0.020  1.347
 3YF  C8   C9   aromatic  1.392  0.020  1.392
 3YF  C8   C7   aromatic  1.427  0.020  1.427
 3YF  C9   N5   aromatic  1.350  0.020  1.350
 3YF  C7   C6   aromatic  1.364  0.020  1.364
 3YF  N5   C6   aromatic  1.384  0.020  1.384
 3YF  C6   C29  single    1.488  0.020  1.488
 3YF  C29  C30  single    1.531  0.020  1.531
 3YF  C30  C31  single    1.529  0.020  1.529
 3YF  C31  C16  single    1.497  0.020  1.497
 3YF  C16  C12  aromatic  1.421  0.020  1.421
 3YF  C16  C15  aromatic  1.366  0.020  1.366
 3YF  O28  C26  double    1.202  0.020  1.202
 3YF  C12  C13  aromatic  1.365  0.020  1.365
 3YF  C15  S14  aromatic  1.708  0.020  1.708
 3YF  C13  S14  aromatic  1.724  0.020  1.724
 3YF  C13  C17  single    1.474  0.020  1.474
 3YF  C26  O27  single    1.324  0.020  1.324
 3YF  C26  C20  single    1.523  0.020  1.523
 3YF  N19  C17  single    1.352  0.020  1.352
 3YF  N19  C20  single    1.437  0.020  1.437
 3YF  C17  O18  double    1.221  0.020  1.221
 3YF  C20  C21  single    1.532  0.020  1.532
 3YF  C21  C22  single    1.520  0.020  1.520
 3YF  C22  C23  single    1.504  0.020  1.504
 3YF  O25  C23  double    1.206  0.020  1.206
 3YF  C23  O24  single    1.328  0.020  1.328
 3YF  N3   H1   single    0.860  0.020  1.020
 3YF  N5   H2   single    0.860  0.020  1.020
 3YF  C7   H3   single    0.930  0.020  1.080
 3YF  N11  H4   single    0.890  0.020  1.040
 3YF  N11  H5   single    0.890  0.020  1.040
 3YF  C12  H6   single    0.930  0.020  1.080
 3YF  C15  H7   single    0.930  0.020  1.080
 3YF  N19  H8   single    0.890  0.020  1.040
 3YF  C20  H9   single    0.970  0.020  1.090
 3YF  C21  H10  single    0.970  0.020  1.090
 3YF  C21  H11  single    0.970  0.020  1.090
 3YF  C22  H12  single    0.970  0.020  1.090
 3YF  C22  H13  single    0.970  0.020  1.090
 3YF  O24  H14  single    0.850  0.020  0.980
 3YF  O27  H15  single    0.850  0.020  0.980
 3YF  C29  H16  single    0.970  0.020  1.090
 3YF  C29  H17  single    0.970  0.020  1.090
 3YF  C30  H18  single    0.970  0.020  1.090
 3YF  C30  H19  single    0.970  0.020  1.090
 3YF  C31  H20  single    0.970  0.020  1.090
 3YF  C31  H21  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
 3YF  C9   N1   C2   113.87  3.000
 3YF  N11  C2   N3   116.71  3.000
 3YF  N3   C2   N1   123.04  3.000
 3YF  N11  C2   N1   120.21  3.000
 3YF  H1   N3   C4   115.90  3.000
 3YF  H1   N3   C2   118.47  3.000
 3YF  C4   N3   C2   125.61  3.000
 3YF  O10  C4   C8   128.32  3.000
 3YF  C8   C4   N3   111.67  3.000
 3YF  O10  C4   N3   120.01  3.000
 3YF  H2   N5   C9   124.52  3.000
 3YF  H2   N5   C6   125.39  3.000
 3YF  C9   N5   C6   110.07  3.000
 3YF  C29  C6   C7   130.43  3.000
 3YF  C29  C6   N5   121.41  3.000
 3YF  C7   C6   N5   108.13  3.000
 3YF  H3   C7   C8   127.44  3.000
 3YF  H3   C7   C6   125.62  3.000
 3YF  C8   C7   C6   106.93  3.000
 3YF  C9   C8   C7   107.38  3.000
 3YF  C7   C8   C4   134.44  3.000
 3YF  C9   C8   C4   118.18  3.000
 3YF  C8   C9   N5   107.48  3.000
 3YF  N5   C9   N1   124.89  3.000
 3YF  C8   C9   N1   127.63  3.000
 3YF  H5   N11  H4   115.45  3.000
 3YF  H5   N11  C2   120.01  3.000
 3YF  H4   N11  C2   116.64  3.000
 3YF  H6   C12  C16  123.48  3.000
 3YF  H6   C12  C13  123.10  3.000
 3YF  C16  C12  C13  113.43  3.000
 3YF  C17  C13  S14  123.72  3.000
 3YF  C17  C13  C12  125.32  3.000
 3YF  S14  C13  C12  110.95  3.000
 3YF  C15  S14  C13   91.62  3.000
 3YF  H7   C15  C16  127.39  3.000
 3YF  H7   C15  S14  119.95  3.000
 3YF  C16  C15  S14  112.66  3.000
 3YF  C31  C16  C15  124.61  3.000
 3YF  C15  C16  C12  111.34  3.000
 3YF  C31  C16  C12  124.01  3.000
 3YF  H8   N19  C20  116.79  3.000
 3YF  H8   N19  C17  119.09  3.000
 3YF  C20  N19  C17  121.01  3.000
 3YF  H9   C20  C26  107.87  3.000
 3YF  H9   C20  C21  108.61  3.000
 3YF  C26  C20  C21  110.47  3.000
 3YF  H9   C20  N19  108.86  3.000
 3YF  C21  C20  N19  110.26  3.000
 3YF  C26  C20  N19  110.70  3.000
 3YF  H11  C21  H10  106.92  3.000
 3YF  H11  C21  C22  109.79  3.000
 3YF  H10  C21  C22  110.62  3.000
 3YF  H11  C21  C20  108.73  3.000
 3YF  H10  C21  C20  109.43  3.000
 3YF  C22  C21  C20  111.25  3.000
 3YF  H13  C22  H12  105.52  3.000
 3YF  H13  C22  C23  108.04  3.000
 3YF  H12  C22  C23  108.34  3.000
 3YF  H13  C22  C21  111.42  3.000
 3YF  H12  C22  C21  110.37  3.000
 3YF  C23  C22  C21  112.83  3.000
 3YF  O25  C23  O24  123.21  3.000
 3YF  O24  C23  C22  111.66  3.000
 3YF  O25  C23  C22  125.13  3.000
 3YF  H14  O24  C23  110.01  3.000
 3YF  O28  C26  O27  124.31  3.000
 3YF  O27  C26  C20  111.17  3.000
 3YF  O28  C26  C20  124.50  3.000
 3YF  H15  O27  C26  110.42  3.000
 3YF  H17  C29  H16  106.43  3.000
 3YF  H17  C29  C30  109.29  3.000
 3YF  H16  C29  C30  109.35  3.000
 3YF  H17  C29  C6   110.19  3.000
 3YF  H16  C29  C6   108.14  3.000
 3YF  C30  C29  C6   113.22  3.000
 3YF  H19  C30  H18  106.56  3.000
 3YF  H19  C30  C31  109.88  3.000
 3YF  H18  C30  C31  109.06  3.000
 3YF  H19  C30  C29  109.13  3.000
 3YF  H18  C30  C29  110.22  3.000
 3YF  C31  C30  C29  111.84  3.000
 3YF  H21  C31  H20  106.58  3.000
 3YF  H21  C31  C30  109.29  3.000
 3YF  H20  C31  C30  109.55  3.000
 3YF  H21  C31  C16  109.59  3.000
 3YF  H20  C31  C16  109.62  3.000
 3YF  C30  C31  C16  112.06  3.000
 3YF  N19  C17  O18  122.57  3.000
 3YF  O18  C17  C13  121.20  3.000
 3YF  N19  C17  C13  116.21  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
 3YF  CONST_01  C7   C8   C9   N5      0.00   0.0  0
 3YF  CONST_02  C8   C7   C6   N5      0.00   0.0  0
 3YF  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 3YF  CONST_04  C8   C9   N5   C6      0.00   0.0  0
 3YF  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YF  CONST_06  S14  C15  C16  C12     0.00   0.0  0
 3YF  CONST_07  C15  S14  C13  C12     0.00   0.0  0
 3YF  CONST_08  C15  C16  C12  C13     0.00   0.0  0
 3YF  CONST_09  C16  C15  S14  C13     0.00   0.0  0
 3YF  CONST_10  C16  C12  C13  S14     0.00   0.0  0
 3YF  CONST_11  C4   N3   C2   N1      0.00   0.0  0
 3YF  CONST_12  C8   C4   N3   C2      0.00   0.0  0
 3YF  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 3YF  CONST_14  C29  C6   C7   C8    180.00   0.0  0
 3YF  CONST_15  C29  C6   N5   C9    180.00   0.0  0
 3YF  CONST_16  C31  C16  C12  C13   180.00   0.0  0
 3YF  CONST_17  C31  C16  C15  S14   180.00   0.0  0
 3YF  CONST_18  C17  C13  S14  C15   180.00   0.0  0
 3YF  CONST_19  C17  C13  C12  C16   180.00   0.0  0
 3YF  CONST_20  O10  C4   N3   C2    180.00   0.0  0
 3YF  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 3YF  CONST_22  N11  C2   N1   C9    180.00   0.0  0
 3YF  CONST_23  H2   N5   C9   N1      0.00   0.0  0
 3YF  CONST_24  H3   C7   C8   C4      0.00   0.0  0
 3YF  CONST_25  H7   C15  C16  C12   180.00   0.0  0
 3YF  CONST_26  H6   C12  C13  S14   180.00   0.0  0
 3YF  CONST_27  H1   N3   C2   N1    180.00   0.0  0
 3YF  CONST_28  H4   N11  C2   N1      0.00   0.0  0
 3YF  CONST_30  C20  N19  C17  C13   180.00   0.0  0
 3YF  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YF  CONST_33  H15  O27  C26  C20   180.00   0.0  0
 3YF  CONST_34  H14  O24  C23  C22   180.00   0.0  0
 3YF  Var_01    C30  C29  C6   N5     70.77  30.0  2
 3YF  Var_02    C30  C31  C16  C12    76.30  30.0  2
 3YF  Var_03    N19  C17  C13  C12  -163.89  30.0  2
 3YF  Var_04    C31  C30  C29  C6    179.31  30.0  3
 3YF  Var_05    C29  C30  C31  C16  -178.50  30.0  1
 3YF  Var_06    C23  C22  C21  C20  -178.55  30.0  3
 3YF  Var_07    O25  C23  C22  C21    -1.10  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
 3YF  chir_01  C20  C26  N19  C21  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
 3YF  plan-1  C12  0.020
 3YF  plan-1  C13  0.020
 3YF  plan-1  S14  0.020
 3YF  plan-1  C15  0.020
 3YF  plan-1  C16  0.020
 3YF  plan-1  C31  0.020
 3YF  plan-1  H6   0.020
 3YF  plan-1  H7   0.020
 3YF  plan-1  C17  0.020
 3YF  plan-2  N1   0.020
 3YF  plan-2  C2   0.020
 3YF  plan-2  N3   0.020
 3YF  plan-2  C4   0.020
 3YF  plan-2  N5   0.020
 3YF  plan-2  C6   0.020
 3YF  plan-2  C7   0.020
 3YF  plan-2  C8   0.020
 3YF  plan-2  C9   0.020
 3YF  plan-2  O10  0.020
 3YF  plan-2  N11  0.020
 3YF  plan-2  C29  0.020
 3YF  plan-2  H1   0.020
 3YF  plan-2  H2   0.020
 3YF  plan-2  H3   0.020
 3YF  plan-2  H4   0.020
 3YF  plan-2  H5   0.020
 3YF  plan-3  C13  0.020
 3YF  plan-3  O18  0.020
 3YF  plan-3  N19  0.020
 3YF  plan-3  C20  0.020
 3YF  plan-3  H8   0.020
 3YF  plan-3  C17  0.020
 3YF  plan-4  C22  0.020
 3YF  plan-4  C23  0.020
 3YF  plan-4  O24  0.020
 3YF  plan-4  O25  0.020
 3YF  plan-4  H14  0.020
 3YF  plan-5  C20  0.020
 3YF  plan-5  C26  0.020
 3YF  plan-5  O27  0.020
 3YF  plan-5  O28  0.020
 3YF  plan-5  H15  0.020

