# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:37:03 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-(4-{[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)ethyl]amino}benzene-1-carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCNc3ccc(cc3)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
 83A  83A  'N-(4-{[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)ethyl]amino}benzene-1-carbonyl)-L-glutamic acid'  ligand  52  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_83A
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
 83A  C1   C  CR56   0  -0.185   6.7317   0.3617   0.4990
 83A  N1   N  NR16   0  -0.720   8.3443  -1.2837   0.8679
 83A  O1   O  O      0  -0.486   8.5647   0.6836   1.9855
 83A  C2   C  CR6    0   0.498   7.9221   0.0099   1.1917
 83A  N2   N  N      0  -0.508   6.6318  -1.8091  -0.6497
 83A  O2   O  O      0  -0.514  -4.9914   2.4346  -0.5152
 83A  C3   C  CR6    0   0.671   7.7208  -2.1282  -0.0048
 83A  N3   N  NH2    0  -0.834   8.2590  -3.3550  -0.1501
 83A  O3   O  O      0  -0.602  -5.7318   0.9972   2.4234
 83A  C4   C  CR56   0   0.479   6.1757  -0.5731  -0.3700
 83A  N4   N  NR15   0  -0.705   5.0732  -0.0165  -0.9145
 83A  O4   O  OC    -1  -0.621  -7.8205   0.7004   1.6985
 83A  C5   C  CR5    0   0.368   4.8995   1.2655  -0.4229
 83A  N5   N  NH1    0  -0.700   1.3516   2.4474  -0.8282
 83A  O5   O  OC    -1  -0.634  -6.0544  -4.2150  -2.2497
 83A  C6   C  CR15   0  -0.459   5.9088   1.5261   0.4568
 83A  N6   N  NH1    0  -0.659  -4.6755   0.2743   0.0132
 83A  O6   O  O      0  -0.608  -6.8756  -4.2098  -0.1807
 83A  C7   C  CH2    0  -0.564   3.7545   2.1110  -0.8537
 83A  C8   C  CH2    0  -0.246   2.4096   1.5981  -0.3418
 83A  C9   C  CR6    0   0.392   0.0286   2.1919  -0.6404
 83A  C10  C  CR16   0  -0.339  -0.9261   3.1644  -0.9905
 83A  C11  C  CR16   0  -0.260  -2.2726   2.9153  -0.8555
 83A  C12  C  CR6    0  -0.081  -2.7499   1.6933  -0.3703
 83A  C13  C  CR16   0  -0.291  -1.8008   0.7397  -0.0050
 83A  C14  C  CR16   0  -0.342  -0.4421   0.9734  -0.1269
 83A  C15  C  C      0   0.549  -4.2248   1.5029  -0.2797
 83A  C16  C  CH1    0  -0.172  -6.0735   0.0104   0.2640
 83A  C17  C  C      0   0.408  -6.5787   0.6404   1.5867
 83A  C18  C  CH2    0  -0.456  -6.3189  -1.4992   0.2634
 83A  C19  C  CH2    0  -0.579  -6.0173  -2.1617  -1.0722
 83A  C20  C  C      0   0.412  -6.3462  -3.6621  -1.1676
 83A  H1   H  HNR6   0   0.420   9.1835  -1.6040   1.3334
 83A  H2   H  HNH2   0   0.409   9.2201  -3.5161   0.1006
 83A  H3   H  HNH2   0   0.406   7.9124  -3.9116  -0.9133
 83A  H4   H  HNR5   0   0.408   4.4860  -0.4669  -1.5993
 83A  H6   H  HNH1   0   0.388   1.5965   3.4110  -0.9922
 83A  H8   H  HCR5   0   0.252   6.0430   2.4449   1.0058
 83A  H9   H  HNH1   0   0.392  -4.0211  -0.4339   0.2995
 83A  H10  H  HCH2   0   0.266   3.9219   3.1257  -0.4861
 83A  H11  H  HCH2   0   0.261   3.7161   2.1712  -1.9457
 83A  H12  H  HCH2   0   0.232   2.4282   1.5490   0.7544
 83A  H13  H  HCH2   0   0.232   2.2483   0.5785  -0.7016
 83A  H14  H  HCR6   0   0.258  -0.5930   4.1197  -1.3790
 83A  H15  H  HCR6   0   0.249  -2.9778   3.6854  -1.1382
 83A  H16  H  HCR6   0   0.246  -2.0940  -0.2197   0.4035
 83A  H17  H  HCR6   0   0.267   0.2479   0.1994   0.1806
 83A  H18  H  HCH1   0   0.222  -6.6535   0.4448  -0.5560
 83A  H19  H  HCH2   0   0.211  -5.7268  -1.9627   1.0603
 83A  H20  H  HCH2   0   0.228  -7.3636  -1.6632   0.5279
 83A  H21  H  HCH2   0   0.220  -6.5695  -1.6421  -1.8646
 83A  H22  H  HCH2   0   0.220  -4.9631  -2.0317  -1.3383

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
 83A  N3   C3   single    1.348  0.020  1.348
 83A  N1   C3   single    1.365  0.020  1.365
 83A  N1   C2   single    1.399  0.020  1.399
 83A  C3   N2   double    1.305  0.020  1.305
 83A  O1   C2   double    1.224  0.020  1.224
 83A  C2   C1   single    1.422  0.020  1.422
 83A  N2   C4   single    1.347  0.020  1.347
 83A  C1   C4   aromatic  1.392  0.020  1.392
 83A  C1   C6   aromatic  1.426  0.020  1.426
 83A  C4   N4   aromatic  1.350  0.020  1.350
 83A  C6   C5   aromatic  1.364  0.020  1.364
 83A  N4   C5   aromatic  1.384  0.020  1.384
 83A  C5   C7   single    1.487  0.020  1.487
 83A  C7   C8   single    1.528  0.020  1.528
 83A  C8   N5   single    1.441  0.020  1.441
 83A  O6   C20  deloc     1.247  0.020  1.247
 83A  N5   C9   single    1.360  0.020  1.360
 83A  C20  O5   deloc     1.250  0.020  1.250
 83A  C20  C19  single    1.539  0.020  1.539
 83A  C9   C10  aromatic  1.407  0.020  1.407
 83A  C9   C14  aromatic  1.404  0.020  1.404
 83A  C10  C11  aromatic  1.376  0.020  1.376
 83A  C19  C18  single    1.521  0.020  1.521
 83A  C14  C13  aromatic  1.384  0.020  1.384
 83A  C11  C12  aromatic  1.399  0.020  1.399
 83A  C13  C12  aromatic  1.394  0.020  1.394
 83A  C18  C16  single    1.529  0.020  1.529
 83A  C12  C15  single    1.490  0.020  1.490
 83A  N6   C15  single    1.341  0.020  1.341
 83A  N6   C16  single    1.445  0.020  1.445
 83A  C15  O2   double    1.229  0.020  1.229
 83A  C16  C17  single    1.550  0.020  1.550
 83A  C17  O3   deloc     1.243  0.020  1.243
 83A  C17  O4   deloc     1.248  0.020  1.248
 83A  N1   H1   single    0.860  0.020  1.020
 83A  N3   H2   single    0.890  0.020  1.040
 83A  N3   H3   single    0.890  0.020  1.040
 83A  N4   H4   single    0.860  0.020  1.020
 83A  N5   H6   single    0.890  0.020  1.040
 83A  C6   H8   single    0.930  0.020  1.080
 83A  N6   H9   single    0.860  0.020  1.020
 83A  C7   H10  single    0.970  0.020  1.090
 83A  C7   H11  single    0.970  0.020  1.090
 83A  C8   H12  single    0.970  0.020  1.090
 83A  C8   H13  single    0.970  0.020  1.090
 83A  C10  H14  single    0.930  0.020  1.080
 83A  C11  H15  single    0.930  0.020  1.080
 83A  C13  H16  single    0.930  0.020  1.080
 83A  C14  H17  single    0.930  0.020  1.080
 83A  C16  H18  single    0.970  0.020  1.090
 83A  C18  H19  single    0.970  0.020  1.090
 83A  C18  H20  single    0.970  0.020  1.090
 83A  C19  H21  single    0.970  0.020  1.090
 83A  C19  H22  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
 83A  C6   C1   C4   107.41  3.000
 83A  C6   C1   C2   134.39  3.000
 83A  C4   C1   C2   118.19  3.000
 83A  H1   N1   C3   118.50  3.000
 83A  H1   N1   C2   115.89  3.000
 83A  C3   N1   C2   125.61  3.000
 83A  O1   C2   N1   120.06  3.000
 83A  O1   C2   C1   128.30  3.000
 83A  N1   C2   C1   111.65  3.000
 83A  C4   N2   C3   113.85  3.000
 83A  N3   C3   N2   120.17  3.000
 83A  N2   C3   N1   123.07  3.000
 83A  N3   C3   N1   116.72  3.000
 83A  H3   N3   H2   115.43  3.000
 83A  H3   N3   C3   116.60  3.000
 83A  H2   N3   C3   120.03  3.000
 83A  N4   C4   N2   124.84  3.000
 83A  N4   C4   C1   107.52  3.000
 83A  N2   C4   C1   127.63  3.000
 83A  H4   N4   C5   125.59  3.000
 83A  H4   N4   C4   124.43  3.000
 83A  C5   N4   C4   109.95  3.000
 83A  C7   C5   C6   130.39  3.000
 83A  C7   C5   N4   121.36  3.000
 83A  C6   C5   N4   108.25  3.000
 83A  H6   N5   C9   116.00  3.000
 83A  H6   N5   C8   116.11  3.000
 83A  C9   N5   C8   123.82  3.000
 83A  H8   C6   C5   125.66  3.000
 83A  H8   C6   C1   127.48  3.000
 83A  C5   C6   C1   106.86  3.000
 83A  H9   N6   C16  116.84  3.000
 83A  H9   N6   C15  119.25  3.000
 83A  C16  N6   C15  122.04  3.000
 83A  H11  C7   H10  106.86  3.000
 83A  H11  C7   C8   108.78  3.000
 83A  H10  C7   C8   109.52  3.000
 83A  H11  C7   C5   110.33  3.000
 83A  H10  C7   C5   108.22  3.000
 83A  C8   C7   C5   112.94  3.000
 83A  H13  C8   H12  106.83  3.000
 83A  H13  C8   C7   109.44  3.000
 83A  H12  C8   C7   109.56  3.000
 83A  H13  C8   N5   109.28  3.000
 83A  H12  C8   N5   112.08  3.000
 83A  C7   C8   N5   109.59  3.000
 83A  C14  C9   C10  117.61  3.000
 83A  C14  C9   N5   122.66  3.000
 83A  C10  C9   N5   119.72  3.000
 83A  H14  C10  C11  119.71  3.000
 83A  H14  C10  C9   119.33  3.000
 83A  C11  C10  C9   120.96  3.000
 83A  H15  C11  C12  119.35  3.000
 83A  H15  C11  C10  118.90  3.000
 83A  C12  C11  C10  121.74  3.000
 83A  C15  C12  C13  124.79  3.000
 83A  C15  C12  C11  118.07  3.000
 83A  C13  C12  C11  117.14  3.000
 83A  H16  C13  C14  116.65  3.000
 83A  H16  C13  C12  121.36  3.000
 83A  C14  C13  C12  121.99  3.000
 83A  H17  C14  C13  118.72  3.000
 83A  H17  C14  C9   120.75  3.000
 83A  C13  C14  C9   120.53  3.000
 83A  C12  C15  N6   117.58  3.000
 83A  N6   C15  O2   121.78  3.000
 83A  C12  C15  O2   120.59  3.000
 83A  H18  C16  C18  107.85  3.000
 83A  H18  C16  C17  107.78  3.000
 83A  C18  C16  C17  110.45  3.000
 83A  H18  C16  N6   108.08  3.000
 83A  C17  C16  N6   112.92  3.000
 83A  C18  C16  N6   109.61  3.000
 83A  C16  C17  O4   114.85  3.000
 83A  O4   C17  O3   127.14  3.000
 83A  C16  C17  O3   117.98  3.000
 83A  H20  C18  H19  106.13  3.000
 83A  H20  C18  C19  109.73  3.000
 83A  H19  C18  C19  110.32  3.000
 83A  H20  C18  C16  107.59  3.000
 83A  H19  C18  C16  109.30  3.000
 83A  C19  C18  C16  113.48  3.000
 83A  H22  C19  H21  104.65  3.000
 83A  H22  C19  C20  107.85  3.000
 83A  H21  C19  C20  108.03  3.000
 83A  H22  C19  C18  110.64  3.000
 83A  H21  C19  C18  109.16  3.000
 83A  C20  C19  C18  115.89  3.000
 83A  C19  C20  O6   118.04  3.000
 83A  C19  C20  O5   115.79  3.000
 83A  O6   C20  O5   126.17  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
 83A  CONST_01  C5   N4   C4   C1      0.00   0.0  0
 83A  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 83A  CONST_03  C5   C6   C1   C4      0.00   0.0  0
 83A  CONST_04  C6   C5   N4   C4      0.00   0.0  0
 83A  CONST_05  C6   C1   C4   N4      0.00   0.0  0
 83A  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 83A  CONST_07  C12  C13  C14  C9      0.00   0.0  0
 83A  CONST_08  C13  C14  C9   C10     0.00   0.0  0
 83A  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 83A  CONST_10  C14  C9   C10  C11     0.00   0.0  0
 83A  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 83A  CONST_12  C3   N1   C2   C1      0.00   0.0  0
 83A  CONST_13  C4   N2   C3   N1      0.00   0.0  0
 83A  CONST_14  N2   C3   N1   C2      0.00   0.0  0
 83A  CONST_15  C7   C5   C6   C1    180.00   0.0  0
 83A  CONST_16  C7   C5   N4   C4    180.00   0.0  0
 83A  CONST_17  C11  C10  C9   N5    180.00   0.0  0
 83A  CONST_18  C13  C14  C9   N5    180.00   0.0  0
 83A  CONST_19  C15  C12  C11  C10   180.00   0.0  0
 83A  CONST_20  C15  C12  C13  C14   180.00   0.0  0
 83A  CONST_21  C3   N1   C2   O1    180.00   0.0  0
 83A  CONST_22  N3   C3   N1   C2    180.00   0.0  0
 83A  CONST_23  C4   N2   C3   N3    180.00   0.0  0
 83A  CONST_24  H4   N4   C4   C1    180.00   0.0  0
 83A  CONST_25  H8   C6   C1   C2      0.00   0.0  0
 83A  CONST_26  H15  C11  C10  C9    180.00   0.0  0
 83A  CONST_27  H16  C13  C14  C9    180.00   0.0  0
 83A  CONST_28  H17  C14  C9   C10   180.00   0.0  0
 83A  CONST_29  H14  C10  C11  C12   180.00   0.0  0
 83A  CONST_30  H1   N1   C2   C1    180.00   0.0  0
 83A  CONST_31  C10  C9   N5   C8    180.00   0.0  0
 83A  CONST_32  C14  C9   N5   C8      0.00   0.0  0
 83A  CONST_35  H3   N3   C3   N1    180.00   0.0  0
 83A  CONST_36  C16  N6   C15  C12   180.00   0.0  0
 83A  CONST_37  H9   N6   C15  C12     0.00   0.0  0
 83A  CONST_38  C16  N6   C15  O2      0.00   0.0  0
 83A  Var_01    C11  C12  C15  O2     -6.18  30.0  3
 83A  Var_02    C8   C7   C5   N4     68.80  30.0  2
 83A  Var_03    N5   C8   C7   C5   -178.53  30.0  3
 83A  Var_04    C9   N5   C8   C7    174.27  30.0  3
 83A  Var_05    C18  C19  C20  O5   -177.59  30.0  3
 83A  Var_06    C20  C19  C18  C16  -175.54  30.0  2

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
 83A  chir_01  C16  C18  N6  C17  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
 83A  plan-1  N5   0.020
 83A  plan-1  C9   0.020
 83A  plan-1  C10  0.020
 83A  plan-1  C11  0.020
 83A  plan-1  C12  0.020
 83A  plan-1  C13  0.020
 83A  plan-1  C14  0.020
 83A  plan-1  C15  0.020
 83A  plan-1  H14  0.020
 83A  plan-1  H15  0.020
 83A  plan-1  H16  0.020
 83A  plan-1  H17  0.020
 83A  plan-2  C1   0.020
 83A  plan-2  N1   0.020
 83A  plan-2  O1   0.020
 83A  plan-2  C2   0.020
 83A  plan-2  N2   0.020
 83A  plan-2  C3   0.020
 83A  plan-2  N3   0.020
 83A  plan-2  C4   0.020
 83A  plan-2  N4   0.020
 83A  plan-2  C5   0.020
 83A  plan-2  C6   0.020
 83A  plan-2  C7   0.020
 83A  plan-2  H1   0.020
 83A  plan-2  H2   0.020
 83A  plan-2  H3   0.020
 83A  plan-2  H4   0.020
 83A  plan-2  H8   0.020
 83A  plan-3  O2   0.020
 83A  plan-3  N6   0.020
 83A  plan-3  C12  0.020
 83A  plan-3  C15  0.020
 83A  plan-3  C16  0.020
 83A  plan-3  H9   0.020
 83A  plan-4  N5   0.020
 83A  plan-4  C8   0.020
 83A  plan-4  C9   0.020
 83A  plan-4  H6   0.020
 83A  plan-5  O3   0.020
 83A  plan-5  O4   0.020
 83A  plan-5  C16  0.020
 83A  plan-5  C17  0.020
 83A  plan-6  O5   0.020
 83A  plan-6  O6   0.020
 83A  plan-6  C19  0.020
 83A  plan-6  C20  0.020

