# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 21:13:45 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-({5-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-3-yl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCc3scc(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
 3YG  3YG  'N-({5-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-3-yl}carbonyl)-L-glutamic acid'  ligand  50  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 PERFECT
;

data_comp_3YG
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
 3YG  N1   N  N      0  -0.507   7.0191  -0.4498   1.8179
 3YG  C2   C  CR6    0   0.669   8.0616   0.3287   1.9176
 3YG  N3   N  NR16   0  -0.720   8.4706   1.1573   0.9129
 3YG  C4   C  CR6    0   0.496   7.8509   1.2944  -0.3336
 3YG  C6   C  CR5    0   0.375   4.8934  -0.7427  -0.9944
 3YG  C8   C  CR56   0  -0.186   6.7113   0.4528  -0.4482
 3YG  N5   N  NR15   0  -0.705   5.2853  -1.0659   0.2927
 3YG  C7   C  CR15   0  -0.467   5.7561   0.1972  -1.4779
 3YG  C9   C  CR56   0   0.476   6.3808  -0.3563   0.6354
 3YG  O10  O  O      0  -0.487   8.3067   2.0711  -1.1624
 3YG  N11  N  NH2    0  -0.834   8.7662   0.3763   3.0662
 3YG  C12  C  CR15   0  -0.242  -1.2177  -0.8222  -1.6364
 3YG  C13  C  CR5    0   0.052  -2.3285  -0.6259  -0.7629
 3YG  C14  C  CR15   0  -0.547  -2.0512  -1.0193   0.5148
 3YG  S15  S  S2     0   0.234  -0.4567  -1.6146   0.6580
 3YG  C16  C  CR5    0  -0.135  -0.1264  -1.3475  -1.0183
 3YG  O18  O  O      0  -0.502  -3.8747  -0.1096  -2.4621
 3YG  N19  N  NH1    0  -0.638  -4.5060   0.2992  -0.3325
 3YG  C20  C  CH1    0  -0.188  -5.7771   0.8934  -0.6780
 3YG  C21  C  CH2    0  -0.446  -6.7185   0.8430   0.5260
 3YG  C22  C  CH2    0  -0.577  -7.0143  -0.5678   1.0099
 3YG  C23  C  C      0   0.412  -8.0273  -0.6749   2.1637
 3YG  O24  O  OC    -1  -0.634  -8.3425  -1.8343   2.5073
 3YG  O25  O  O      0  -0.609  -8.4479   0.3831   2.6721
 3YG  C26  C  C      0   0.411  -5.6362   2.3458  -1.2014
 3YG  O27  O  OC    -1  -0.619  -6.6631   2.8149  -1.7329
 3YG  O28  O  O      0  -0.600  -4.5479   2.9214  -1.0321
 3YG  C29  C  CH2    0  -0.524   3.7014  -1.3781  -1.6181
 3YG  C30  C  CH2    0  -0.426   2.3776  -0.9697  -0.9682
 3YG  C31  C  CH2    0  -0.503   1.1983  -1.7002  -1.6087
 3YG  H1   H  HNR6   0   0.419   9.2871   1.7347   1.0664
 3YG  H2   H  HNR5   0   0.407   4.8382  -1.7474   0.8858
 3YG  H3   H  HCR5   0   0.250   5.7099   0.6497  -2.4560
 3YG  H4   H  HNH2   0   0.406   8.5834  -0.3517   3.7364
 3YG  H5   H  HNH2   0   0.408   9.7090   0.7280   3.0592
 3YG  H6   H  HCR5   0   0.260  -1.2357  -0.5803  -2.6899
 3YG  H7   H  HCR5   0   0.295  -2.6989  -1.0171   1.3788
 3YG  H8   H  HNH1   0   0.390  -4.1658   0.4609   0.6023
 3YG  H9   H  HCH1   0   0.227  -6.2190   0.2915  -1.4774
 3YG  H10  H  HCH2   0   0.211  -6.3006   1.4414   1.3425
 3YG  H11  H  HCH2   0   0.227  -7.6462   1.3354   0.2344
 3YG  H12  H  HCH2   0   0.217  -7.3768  -1.1737   0.1714
 3YG  H13  H  HCH2   0   0.221  -6.0910  -1.0613   1.3328
 3YG  H16  H  HCH2   0   0.256   3.6847  -1.1116  -2.6768
 3YG  H17  H  HCH2   0   0.248   3.7972  -2.4687  -1.5765
 3YG  H18  H  HCH2   0   0.230   2.4075  -1.1896   0.1031
 3YG  H19  H  HCH2   0   0.245   2.2410   0.1104  -1.0604
 3YG  H20  H  HCH2   0   0.256   1.3606  -2.7799  -1.5299
 3YG  H21  H  HCH2   0   0.258   1.1610  -1.4729  -2.6768
 3YG  C17  C  C      0   0.539  -3.6307  -0.1086  -1.2602

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
 3YG  N11  C2   single    1.348  0.020  1.348
 3YG  N3   C2   single    1.365  0.020  1.365
 3YG  N3   C4   single    1.399  0.020  1.399
 3YG  C2   N1   double    1.305  0.020  1.305
 3YG  O10  C4   double    1.224  0.020  1.224
 3YG  C4   C8   single    1.421  0.020  1.421
 3YG  N1   C9   single    1.347  0.020  1.347
 3YG  C8   C9   aromatic  1.392  0.020  1.392
 3YG  C8   C7   aromatic  1.428  0.020  1.428
 3YG  C9   N5   aromatic  1.349  0.020  1.349
 3YG  C7   C6   aromatic  1.364  0.020  1.364
 3YG  N5   C6   aromatic  1.384  0.020  1.384
 3YG  C6   C29  single    1.488  0.020  1.488
 3YG  C29  C30  single    1.530  0.020  1.530
 3YG  C30  C31  single    1.528  0.020  1.528
 3YG  C31  C16  single    1.493  0.020  1.493
 3YG  C16  C12  aromatic  1.360  0.020  1.360
 3YG  C16  S15  aromatic  1.729  0.020  1.729
 3YG  O28  C26  deloc     1.243  0.020  1.243
 3YG  C12  C13  aromatic  1.427  0.020  1.427
 3YG  S15  C14  aromatic  1.708  0.020  1.708
 3YG  C26  O27  deloc     1.248  0.020  1.248
 3YG  C26  C20  single    1.550  0.020  1.550
 3YG  C13  C14  aromatic  1.365  0.020  1.365
 3YG  C13  C17  single    1.487  0.020  1.487
 3YG  N19  C17  single    1.339  0.020  1.339
 3YG  N19  C20  single    1.445  0.020  1.445
 3YG  C17  O18  double    1.226  0.020  1.226
 3YG  C20  C21  single    1.529  0.020  1.529
 3YG  C21  C22  single    1.520  0.020  1.520
 3YG  C22  C23  single    1.539  0.020  1.539
 3YG  C23  O25  deloc     1.247  0.020  1.247
 3YG  C23  O24  deloc     1.250  0.020  1.250
 3YG  N3   H1   single    0.860  0.020  1.020
 3YG  N5   H2   single    0.860  0.020  1.020
 3YG  C7   H3   single    0.930  0.020  1.080
 3YG  N11  H4   single    0.890  0.020  1.040
 3YG  N11  H5   single    0.890  0.020  1.040
 3YG  C12  H6   single    0.930  0.020  1.080
 3YG  C14  H7   single    0.930  0.020  1.080
 3YG  N19  H8   single    0.860  0.020  1.020
 3YG  C20  H9   single    0.970  0.020  1.090
 3YG  C21  H10  single    0.970  0.020  1.090
 3YG  C21  H11  single    0.970  0.020  1.090
 3YG  C22  H12  single    0.970  0.020  1.090
 3YG  C22  H13  single    0.970  0.020  1.090
 3YG  C29  H16  single    0.970  0.020  1.090
 3YG  C29  H17  single    0.970  0.020  1.090
 3YG  C30  H18  single    0.970  0.020  1.090
 3YG  C30  H19  single    0.970  0.020  1.090
 3YG  C31  H20  single    0.970  0.020  1.090
 3YG  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
 3YG  C9   N1   C2   113.85  3.000
 3YG  N11  C2   N3   116.68  3.000
 3YG  N3   C2   N1   123.04  3.000
 3YG  N11  C2   N1   120.24  3.000
 3YG  H1   N3   C4   115.90  3.000
 3YG  H1   N3   C2   118.47  3.000
 3YG  C4   N3   C2   125.63  3.000
 3YG  O10  C4   C8   128.30  3.000
 3YG  C8   C4   N3   111.66  3.000
 3YG  O10  C4   N3   120.04  3.000
 3YG  C29  C6   C7   130.72  3.000
 3YG  C29  C6   N5   121.14  3.000
 3YG  C7   C6   N5   108.14  3.000
 3YG  C9   C8   C7   107.37  3.000
 3YG  C7   C8   C4   134.48  3.000
 3YG  C9   C8   C4   118.14  3.000
 3YG  H2   N5   C9   124.49  3.000
 3YG  H2   N5   C6   125.42  3.000
 3YG  C9   N5   C6   110.08  3.000
 3YG  H3   C7   C8   127.41  3.000
 3YG  H3   C7   C6   125.68  3.000
 3YG  C8   C7   C6   106.91  3.000
 3YG  N5   C9   C8   107.50  3.000
 3YG  N5   C9   N1   124.83  3.000
 3YG  C8   C9   N1   127.67  3.000
 3YG  H5   N11  H4   115.32  3.000
 3YG  H5   N11  C2   119.73  3.000
 3YG  H4   N11  C2   116.54  3.000
 3YG  H6   C12  C16  122.88  3.000
 3YG  H6   C12  C13  123.56  3.000
 3YG  C16  C12  C13  113.56  3.000
 3YG  C17  C13  C14  126.24  3.000
 3YG  C17  C13  C12  121.67  3.000
 3YG  C14  C13  C12  112.03  3.000
 3YG  H7   C14  S15  119.58  3.000
 3YG  H7   C14  C13  128.78  3.000
 3YG  S15  C14  C13  111.63  3.000
 3YG  C16  S15  C14   92.47  3.000
 3YG  C31  C16  S15  121.10  3.000
 3YG  S15  C16  C12  110.31  3.000
 3YG  C31  C16  C12  128.59  3.000
 3YG  H8   N19  C20  116.92  3.000
 3YG  H8   N19  C17  118.09  3.000
 3YG  C20  N19  C17  122.31  3.000
 3YG  H9   C20  C26  107.79  3.000
 3YG  H9   C20  C21  107.97  3.000
 3YG  C26  C20  C21  110.65  3.000
 3YG  H9   C20  N19  107.69  3.000
 3YG  C21  C20  N19  109.86  3.000
 3YG  C26  C20  N19  112.71  3.000
 3YG  H11  C21  H10  106.10  3.000
 3YG  H11  C21  C22  109.80  3.000
 3YG  H10  C21  C22  110.12  3.000
 3YG  H11  C21  C20  107.36  3.000
 3YG  H10  C21  C20  109.52  3.000
 3YG  C22  C21  C20  113.64  3.000
 3YG  H13  C22  H12  104.78  3.000
 3YG  H13  C22  C23  107.60  3.000
 3YG  H12  C22  C23  108.50  3.000
 3YG  H13  C22  C21  110.35  3.000
 3YG  H12  C22  C21  109.49  3.000
 3YG  C23  C22  C21  115.54  3.000
 3YG  O25  C23  O24  126.16  3.000
 3YG  O24  C23  C22  115.89  3.000
 3YG  O25  C23  C22  117.94  3.000
 3YG  O28  C26  O27  127.21  3.000
 3YG  O27  C26  C20  114.91  3.000
 3YG  O28  C26  C20  117.87  3.000
 3YG  H17  C29  H16  106.33  3.000
 3YG  H17  C29  C30  108.98  3.000
 3YG  H16  C29  C30  109.48  3.000
 3YG  H17  C29  C6   109.82  3.000
 3YG  H16  C29  C6   108.33  3.000
 3YG  C30  C29  C6   113.64  3.000
 3YG  H19  C30  H18  106.55  3.000
 3YG  H19  C30  C31  109.93  3.000
 3YG  H18  C30  C31  109.60  3.000
 3YG  H19  C30  C29  109.64  3.000
 3YG  H18  C30  C29  109.79  3.000
 3YG  C31  C30  C29  111.22  3.000
 3YG  H21  C31  H20  106.29  3.000
 3YG  H21  C31  C30  109.68  3.000
 3YG  H20  C31  C30  109.08  3.000
 3YG  H21  C31  C16  107.89  3.000
 3YG  H20  C31  C16  109.64  3.000
 3YG  C30  C31  C16  113.97  3.000
 3YG  N19  C17  O18  123.31  3.000
 3YG  O18  C17  C13  120.12  3.000
 3YG  N19  C17  C13  116.53  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
 3YG  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 3YG  CONST_02  C8   C9   N5   C6      0.00   0.0  0
 3YG  CONST_03  N5   C6   C7   C8      0.00   0.0  0
 3YG  CONST_04  C7   C8   C9   N5      0.00   0.0  0
 3YG  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YG  CONST_06  C14  S15  C16  C12     0.00   0.0  0
 3YG  CONST_07  S15  C14  C13  C12     0.00   0.0  0
 3YG  CONST_08  S15  C16  C12  C13     0.00   0.0  0
 3YG  CONST_09  C16  S15  C14  C13     0.00   0.0  0
 3YG  CONST_10  C16  C12  C13  C14     0.00   0.0  0
 3YG  CONST_11  C4   N3   C2   N1      0.00   0.0  0
 3YG  CONST_12  C8   C4   N3   C2      0.00   0.0  0
 3YG  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 3YG  CONST_14  C29  C6   C7   C8    180.00   0.0  0
 3YG  CONST_15  C29  C6   N5   C9    180.00   0.0  0
 3YG  CONST_16  C31  C16  C12  C13   180.00   0.0  0
 3YG  CONST_17  C31  C16  S15  C14   180.00   0.0  0
 3YG  CONST_18  C17  C13  C14  S15   180.00   0.0  0
 3YG  CONST_19  C17  C13  C12  C16   180.00   0.0  0
 3YG  CONST_20  O10  C4   N3   C2    180.00   0.0  0
 3YG  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 3YG  CONST_22  N11  C2   N1   C9    180.00   0.0  0
 3YG  CONST_23  H2   N5   C9   N1      0.00   0.0  0
 3YG  CONST_24  H3   C7   C8   C4      0.00   0.0  0
 3YG  CONST_25  H7   C14  C13  C12   180.00   0.0  0
 3YG  CONST_26  H6   C12  C13  C14   180.00   0.0  0
 3YG  CONST_27  H1   N3   C2   N1    180.00   0.0  0
 3YG  CONST_28  H4   N11  C2   N1      0.00   0.0  0
 3YG  CONST_30  C20  N19  C17  C13   180.00   0.0  0
 3YG  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YG  Var_01    C30  C29  C6   N5     67.89  30.0  2
 3YG  Var_02    C30  C31  C16  C12   121.38  30.0  2
 3YG  Var_03    N19  C17  C13  C12  -166.52  30.0  2
 3YG  Var_04    C31  C30  C29  C6   -177.46  30.0  3
 3YG  Var_05    C29  C30  C31  C16   179.93  30.0  2
 3YG  Var_06    C23  C22  C21  C20  -176.29  30.0  3
 3YG  Var_07    O25  C23  C22  C21    -5.06  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
 3YG  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
 3YG  plan-1  C12  0.020
 3YG  plan-1  C13  0.020
 3YG  plan-1  C14  0.020
 3YG  plan-1  S15  0.020
 3YG  plan-1  C16  0.020
 3YG  plan-1  C31  0.020
 3YG  plan-1  H6   0.020
 3YG  plan-1  H7   0.020
 3YG  plan-1  C17  0.020
 3YG  plan-2  N1   0.020
 3YG  plan-2  C2   0.020
 3YG  plan-2  N3   0.020
 3YG  plan-2  C4   0.020
 3YG  plan-2  C6   0.020
 3YG  plan-2  C8   0.020
 3YG  plan-2  N5   0.020
 3YG  plan-2  C7   0.020
 3YG  plan-2  C9   0.020
 3YG  plan-2  O10  0.020
 3YG  plan-2  N11  0.020
 3YG  plan-2  C29  0.020
 3YG  plan-2  H1   0.020
 3YG  plan-2  H2   0.020
 3YG  plan-2  H3   0.020
 3YG  plan-2  H4   0.020
 3YG  plan-2  H5   0.020
 3YG  plan-3  C13  0.020
 3YG  plan-3  O18  0.020
 3YG  plan-3  N19  0.020
 3YG  plan-3  C20  0.020
 3YG  plan-3  H8   0.020
 3YG  plan-3  C17  0.020
 3YG  plan-4  C22  0.020
 3YG  plan-4  C23  0.020
 3YG  plan-4  O24  0.020
 3YG  plan-4  O25  0.020
 3YG  plan-5  C20  0.020
 3YG  plan-5  C26  0.020
 3YG  plan-5  O27  0.020
 3YG  plan-5  O28  0.020

