# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:17:28 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  55  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  -0.507   -8.0544  -1.0932  -0.6097
 3YE  C2   C  CR6    0   0.668   -9.1002  -0.5551  -1.1743
 3YE  N3   N  NR16   0  -0.720   -9.3293   0.7905  -1.1875
 3YE  C4   C  CR6    0   0.495   -8.5040   1.7631  -0.6127
 3YE  N5   N  NR15   0  -0.704   -6.0743  -0.5125   0.5975
 3YE  C6   C  CR5    0   0.373   -5.4639   0.6365   1.0690
 3YE  C7   C  CR15   0  -0.468   -6.2365   1.7034   0.7128
 3YE  C8   C  CR56   0  -0.185   -7.3597   1.1848   0.0002
 3YE  C9   C  CR56   0   0.475   -7.2188  -0.1994  -0.0459
 3YE  O10  O  O      0  -0.488   -8.8130   2.9455  -0.6802
 3YE  N11  N  NH2    0  -0.834   -9.9944  -1.3287  -1.8236
 3YE  C12  C  CH2    0  -0.573    3.3283  -0.7786   1.2965
 3YE  C13  C  CH2    0  -0.415    1.9920  -0.7137   0.5640
 3YE  C14  C  CH2    0  -0.415    0.8385  -0.3179   1.4765
 3YE  C17  C  C      0   0.556    4.4504  -1.2507   0.3956
 3YE  O18  O  O      0  -0.525    4.3330  -2.2579  -0.2962
 3YE  N19  N  NH1    0  -0.621    5.5485  -0.4874   0.3869
 3YE  C20  C  CH1    0  -0.185    6.7649  -0.8615  -0.2966
 3YE  C21  C  CH2    0  -0.449    7.6641   0.3659  -0.4542
 3YE  C22  C  CH2    0  -0.579    7.0221   1.4801  -1.2660
 3YE  C23  C  C      0   0.412    7.8900   2.7297  -1.4959
 3YE  O24  O  O      0  -0.609    9.0552   2.7238  -1.0522
 3YE  O25  O  OC    -1  -0.634    7.3434   3.6627  -2.1224
 3YE  C26  C  C      0   0.409    7.5199  -2.0136   0.4142
 3YE  O27  O  OC    -1  -0.621    8.4621  -2.5055  -0.2402
 3YE  O28  O  O      0  -0.599    7.1509  -2.3362   1.5563
 3YE  C29  C  CH2    0  -0.519   -4.1614   0.5786   1.7870
 3YE  C30  C  CH2    0  -0.415   -2.9854   0.2017   0.8818
 3YE  C16  C  CH2    0  -0.418   -1.6637   0.1332   1.6356
 3YE  C15  C  CH2    0  -0.413   -0.4904  -0.2337   0.7360
 3YE  H1   H  HNR6   0   0.419  -10.1617   1.1334  -1.6488
 3YE  H2   H  HNR5   0   0.406   -5.7318  -1.4514   0.7285
 3YE  H3   H  HCR5   0   0.249   -6.0192   2.7369   0.9323
 3YE  H4   H  HNH2   0   0.405   -9.9391  -2.3187  -1.6508
 3YE  H5   H  HNH2   0   0.407  -10.9207  -0.9771  -1.9998
 3YE  H6   H  HCH2   0   0.240    3.5612   0.1938   1.7378
 3YE  H7   H  HCH2   0   0.253    3.2553  -1.4870   2.1282
 3YE  H8   H  HCH2   0   0.221    2.0647   0.0029  -0.2605
 3YE  H9   H  HCH2   0   0.222    1.7788  -1.6853   0.1122
 3YE  H10  H  HCH2   0   0.211    0.7567  -1.0440   2.2928
 3YE  H11  H  HCH2   0   0.211    1.0563   0.6468   1.9470
 3YE  H12  H  HNH1   0   0.385    5.6030   0.2673   1.0518
 3YE  H13  H  HCH1   0   0.225    6.4939  -1.2108  -1.2979
 3YE  H14  H  HCH2   0   0.210    7.9482   0.7364   0.5367
 3YE  H15  H  HCH2   0   0.227    8.5879   0.0438  -0.9344
 3YE  H16  H  HCH2   0   0.220    6.7241   1.0866  -2.2457
 3YE  H17  H  HCH2   0   0.220    6.0856   1.7998  -0.7977
 3YE  H20  H  HCH2   0   0.248   -3.9752   1.5561   2.2364
 3YE  H21  H  HCH2   0   0.241   -4.2221  -0.1359   2.6153
 3YE  H22  H  HCH2   0   0.217   -3.1801  -0.7650   0.4065
 3YE  H23  H  HCH2   0   0.223   -2.9127   0.9328   0.0712
 3YE  H24  H  HCH2   0   0.212   -1.4671   1.0976   2.1165
 3YE  H25  H  HCH2   0   0.212   -1.7451  -0.6003   2.4452
 3YE  H26  H  HCH2   0   0.210   -0.4090   0.5022  -0.0713
 3YE  H27  H  HCH2   0   0.209   -0.6956  -1.1943   0.2509

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  deloc     1.247  0.020  1.247
 3YE  O25  C23  deloc     1.250  0.020  1.250
 3YE  C23  C22  single    1.539  0.020  1.539
 3YE  O18  C17  double    1.228  0.020  1.228
 3YE  C22  C21  single    1.521  0.020  1.521
 3YE  C12  C17  single    1.514  0.020  1.514
 3YE  C12  C13  single    1.525  0.020  1.525
 3YE  C17  N19  single    1.337  0.020  1.337
 3YE  C21  C20  single    1.530  0.020  1.530
 3YE  O28  C26  deloc     1.243  0.020  1.243
 3YE  N19  C20  single    1.445  0.020  1.445
 3YE  C13  C14  single    1.523  0.020  1.523
 3YE  C20  C26  single    1.550  0.020  1.550
 3YE  C26  O27  deloc     1.248  0.020  1.248
 3YE  C14  C15  single    1.524  0.020  1.524
 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  1.365  0.020  1.365
 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  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   116.71  3.000
 3YE  N11  C2   N1   120.20  3.000
 3YE  N3   C2   N1   123.05  3.000
 3YE  H1   N3   C4   115.92  3.000
 3YE  H1   N3   C2   118.47  3.000
 3YE  C4   N3   C2   125.61  3.000
 3YE  O10  C4   C8   128.34  3.000
 3YE  O10  C4   N3   120.00  3.000
 3YE  C8   C4   N3   111.67  3.000
 3YE  H2   N5   C9   124.48  3.000
 3YE  H2   N5   C6   125.40  3.000
 3YE  C9   N5   C6   110.11  3.000
 3YE  C29  C6   C7   130.68  3.000
 3YE  C7   C6   N5   108.09  3.000
 3YE  C29  C6   N5   121.20  3.000
 3YE  H3   C7   C8   127.45  3.000
 3YE  H3   C7   C6   125.59  3.000
 3YE  C8   C7   C6   106.96  3.000
 3YE  C9   C8   C7   107.34  3.000
 3YE  C9   C8   C4   118.16  3.000
 3YE  C7   C8   C4   134.50  3.000
 3YE  C8   C9   N5   107.50  3.000
 3YE  C8   C9   N1   127.64  3.000
 3YE  N5   C9   N1   124.85  3.000
 3YE  H5   N11  H4   115.11  3.000
 3YE  H5   N11  C2   119.61  3.000
 3YE  H4   N11  C2   116.42  3.000
 3YE  H7   C12  H6   106.44  3.000
 3YE  H7   C12  C17  107.43  3.000
 3YE  H6   C12  C17  111.08  3.000
 3YE  H7   C12  C13  109.51  3.000
 3YE  H6   C12  C13  110.05  3.000
 3YE  C17  C12  C13  112.13  3.000
 3YE  H9   C13  H8   106.48  3.000
 3YE  H9   C13  C14  109.33  3.000
 3YE  H8   C13  C14  109.35  3.000
 3YE  H9   C13  C12  109.38  3.000
 3YE  H8   C13  C12  109.35  3.000
 3YE  C14  C13  C12  112.76  3.000
 3YE  H11  C14  H10  106.17  3.000
 3YE  H11  C14  C15  109.48  3.000
 3YE  H10  C14  C15  109.49  3.000
 3YE  H11  C14  C13  109.61  3.000
 3YE  H10  C14  C13  109.31  3.000
 3YE  C15  C14  C13  112.57  3.000
 3YE  N19  C17  O18  122.90  3.000
 3YE  N19  C17  C12  115.74  3.000
 3YE  O18  C17  C12  121.34  3.000
 3YE  H12  N19  C20  117.44  3.000
 3YE  H12  N19  C17  117.89  3.000
 3YE  C20  N19  C17  123.14  3.000
 3YE  H13  C20  C26  107.63  3.000
 3YE  H13  C20  C21  107.90  3.000
 3YE  C26  C20  C21  110.93  3.000
 3YE  H13  C20  N19  107.88  3.000
 3YE  C26  C20  N19  112.68  3.000
 3YE  C21  C20  N19  109.63  3.000
 3YE  H15  C21  H14  106.18  3.000
 3YE  H15  C21  C22  109.83  3.000
 3YE  H14  C21  C22  110.16  3.000
 3YE  H15  C21  C20  107.85  3.000
 3YE  H14  C21  C20  109.31  3.000
 3YE  C22  C21  C20  113.25  3.000
 3YE  H17  C22  H16  104.74  3.000
 3YE  H17  C22  C23  108.02  3.000
 3YE  H16  C22  C23  108.12  3.000
 3YE  H17  C22  C21  110.29  3.000
 3YE  H16  C22  C21  109.18  3.000
 3YE  C23  C22  C21  115.89  3.000
 3YE  O25  C23  O24  126.20  3.000
 3YE  O25  C23  C22  115.75  3.000
 3YE  O24  C23  C22  118.04  3.000
 3YE  O28  C26  O27  127.13  3.000
 3YE  O27  C26  C20  114.85  3.000
 3YE  O28  C26  C20  118.01  3.000
 3YE  H21  C29  H20  106.38  3.000
 3YE  H21  C29  C30  109.21  3.000
 3YE  H20  C29  C30  109.43  3.000
 3YE  H21  C29  C6   109.98  3.000
 3YE  H20  C29  C6   108.24  3.000
 3YE  C30  C29  C6   113.36  3.000
 3YE  H23  C30  H22  106.28  3.000
 3YE  H23  C30  C16  109.82  3.000
 3YE  H22  C30  C16  109.24  3.000
 3YE  H23  C30  C29  108.94  3.000
 3YE  H22  C30  C29  109.72  3.000
 3YE  C16  C30  C29  112.64  3.000
 3YE  H25  C16  H24  106.16  3.000
 3YE  H25  C16  C15  109.41  3.000
 3YE  H24  C16  C15  109.46  3.000
 3YE  H25  C16  C30  109.35  3.000
 3YE  H24  C16  C30  109.48  3.000
 3YE  C15  C16  C30  112.76  3.000
 3YE  H27  C15  H26  106.06  3.000
 3YE  H27  C15  C16  109.18  3.000
 3YE  H26  C15  C16  109.31  3.000
 3YE  H27  C15  C14  109.27  3.000
 3YE  H26  C15  C14  109.30  3.000
 3YE  C16  C15  C14  113.46  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  Var_01    C30  C29  C6   N5     69.70  30.0  1
 3YE  Var_02    C16  C30  C29  C6   -179.41  30.0  2
 3YE  Var_03    C15  C14  C13  C12   179.12  30.0  3
 3YE  Var_04    O18  C17  C12  C13   -49.33  30.0  3
 3YE  Var_05    C16  C15  C14  C13   178.82  30.0  3
 3YE  Var_06    C17  C12  C13  C14   176.68  30.0  2
 3YE  Var_07    C30  C16  C15  C14  -179.52  30.0  3
 3YE  Var_08    C23  C22  C21  C20  -178.35  30.0  1
 3YE  Var_09    O24  C23  C22  C21     2.56  30.0  2
 3YE  Var_10    C15  C16  C30  C29  -179.67  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-4  C20  0.020
 3YE  plan-4  C26  0.020
 3YE  plan-4  O27  0.020
 3YE  plan-4  O28  0.020

