# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:18:02 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  54  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  -0.186   6.6364   0.2131   0.6406
 83A  N1   N  NR16  0  -0.721   8.2342  -1.4796   0.8034
 83A  O1   O  O     0  -0.486   8.2582   0.1552   2.3834
 83A  C2   C  CR6   0   0.498   7.7395  -0.3022   1.3740
 83A  N2   N  N     0  -0.508   6.7288  -1.6211  -0.9928
 83A  O2   O  O     0  -0.492  -4.9864   2.2666  -0.8940
 83A  C3   C  CR6   0   0.673   7.7435  -2.0873  -0.3163
 83A  N3   N  NH2   0  -0.834   8.3855  -3.1938  -0.7376
 83A  O3   O  O     0  -0.431  -5.9762   1.3365   2.1700
 83A  C4   C  CR56  0   0.479   6.2142  -0.4837  -0.4883
 83A  N4   N  NR15  0  -0.706   5.1686   0.1890  -1.0139
 83A  O4   O  OH1   0  -0.591  -7.9302   0.8551   1.1991
 83A  C5   C  CR5   0   0.368   4.8998   1.3133  -0.2531
 83A  N5   N  NH1   0  -0.695   1.3701   2.5228  -0.7349
 83A  O5   O  OH1   0  -0.595  -5.6767  -4.5491  -1.5841
 83A  C6   C  CR15  0  -0.459   5.7903   1.3533   0.7793
 83A  N6   N  NH1   0  -0.662  -4.6030   0.2537   0.0279
 83A  O6   O  O     0  -0.442  -6.4899  -4.3244   0.4800
 83A  C7   C  CH2   0  -0.564   3.7801   2.2321  -0.5913
 83A  C8   C  CH2   0  -0.250   2.4114   1.5822  -0.3996
 83A  C9   C  CR6   0   0.393   0.0461   2.2251  -0.6548
 83A  C10  C  CR16  0  -0.338  -0.9111   3.2498  -0.7848
 83A  C11  C  CR16  0  -0.255  -2.2566   2.9699  -0.7319
 83A  C12  C  CR6   0  -0.082  -2.7230   1.6661  -0.5327
 83A  C13  C  CR16  0  -0.279  -1.7754   0.6504  -0.4123
 83A  C14  C  CR16  0  -0.343  -0.4189   0.9130  -0.4687
 83A  C15  C  C     0   0.554  -4.1845   1.4371  -0.4825
 83A  C16  C  CH1   0  -0.192  -6.0038  -0.0256   0.1730
 83A  C17  C  C     0   0.547  -6.6090   0.8094   1.2937
 83A  C18  C  CH2   0  -0.463  -6.2283  -1.5156   0.4463
 83A  C19  C  CH2   0  -0.577  -5.7938  -2.3658  -0.7369
 83A  C20  C  C     0   0.554  -6.0336  -3.8343  -0.5226
 83A  H1   H  HNR6  0   0.420   9.0260  -1.8985   1.2739
 83A  H2   H  HNH2  0   0.409   8.9912  -3.6971  -0.1115
 83A  H3   H  HNH2  0   0.407   7.9183  -3.7530  -1.4314
 83A  H4   H  HNR5  0   0.408   4.6825  -0.0825  -1.8544
 83A  H5   H  HOH1  0   0.485  -8.3058   1.3445   1.9466
 83A  H6   H  HNH1  0   0.390   1.6079   3.4981  -0.6446
 83A  H7   H  HOH1  0   0.480  -5.8359  -5.4904  -1.4189
 83A  H8   H  HCR5  0   0.254   5.8300   2.1094   1.5473
 83A  H9   H  HNH1  0   0.405  -3.9670  -0.2858   0.5936
 83A  H10  H  HCH2  0   0.266   3.8571   3.1111   0.0522
 83A  H11  H  HCH2  0   0.262   3.8686   2.5837  -1.6239
 83A  H12  H  HCH2  0   0.234   2.3195   1.2240   0.6337
 83A  H13  H  HCH2  0   0.233   2.3291   0.7050  -1.0476
 83A  H14  H  HCR6  0   0.261  -0.5806   4.2713  -0.9319
 83A  H15  H  HCR6  0   0.254  -2.9648   3.7812  -0.8365
 83A  H16  H  HCR6  0   0.249  -2.0783  -0.3822  -0.2879
 83A  H17  H  HCR6  0   0.271   0.2762   0.0900  -0.3738
 83A  H18  H  HCH1  0   0.290  -6.5164   0.2395  -0.7552
 83A  H19  H  HCH2  0   0.258  -5.6859  -1.8078   1.3495
 83A  H20  H  HCH2  0   0.272  -7.2870  -1.6790   0.6485
 83A  H21  H  HCH2  0   0.287  -6.3255  -2.0571  -1.6424
 83A  H22  H  HCH2  0   0.287  -4.7323  -2.2262  -0.9596

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    1.347  0.020  1.347
 83A  N1   C3   single    1.365  0.020  1.365
 83A  N1   C2   single    1.399  0.020  1.399
 83A  C3   N2   double    1.306  0.020  1.306
 83A  O1   C2   double    1.224  0.020  1.224
 83A  C2   C1   single    1.421  0.020  1.421
 83A  N2   C4   single    1.346  0.020  1.346
 83A  C1   C4   aromatic  1.392  0.020  1.392
 83A  C1   C6   aromatic  1.427  0.020  1.427
 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    1.527  0.020  1.527
 83A  C8   N5   single    1.443  0.020  1.443
 83A  O6   C20  double    1.206  0.020  1.206
 83A  N5   C9   single    1.359  0.020  1.359
 83A  C20  O5   single    1.329  0.020  1.329
 83A  C20  C19  single    1.503  0.020  1.503
 83A  C9   C10  aromatic  1.408  0.020  1.408
 83A  C9   C14  aromatic  1.404  0.020  1.404
 83A  C10  C11  aromatic  1.375  0.020  1.375
 83A  C19  C18  single    1.520  0.020  1.520
 83A  C14  C13  aromatic  1.383  0.020  1.383
 83A  C11  C12  aromatic  1.399  0.020  1.399
 83A  C13  C12  aromatic  1.394  0.020  1.394
 83A  C18  C16  single    1.531  0.020  1.531
 83A  C12  C15  single    1.480  0.020  1.480
 83A  N6   C15  single    1.355  0.020  1.355
 83A  N6   C16  single    1.436  0.020  1.436
 83A  C15  O2   double    1.225  0.020  1.225
 83A  C16  C17  single    1.523  0.020  1.523
 83A  C17  O3   double    1.203  0.020  1.203
 83A  C17  O4   single    1.325  0.020  1.325
 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  O4   H5   single    0.850  0.020  0.980
 83A  N5   H6   single    0.890  0.020  1.040
 83A  O5   H7   single    0.850  0.020  0.980
 83A  C6   H8   single    0.930  0.020  1.080
 83A  N6   H9   single    0.890  0.020  1.040
 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   107.40  3.000
 83A  C6   C1   C2   134.42  3.000
 83A  C4   C1   C2   118.18  3.000
 83A  H1   N1   C3   118.57  3.000
 83A  H1   N1   C2   115.83  3.000
 83A  C3   N1   C2   125.60  3.000
 83A  O1   C2   N1   120.09  3.000
 83A  O1   C2   C1   128.25  3.000
 83A  N1   C2   C1   111.67  3.000
 83A  C4   N2   C3   113.86  3.000
 83A  N3   C3   N2   120.12  3.000
 83A  N2   C3   N1   123.05  3.000
 83A  N3   C3   N1   116.80  3.000
 83A  H3   N3   H2   115.51  3.000
 83A  H3   N3   C3   116.81  3.000
 83A  H2   N3   C3   120.22  3.000
 83A  N4   C4   N2   124.83  3.000
 83A  N4   C4   C1   107.53  3.000
 83A  N2   C4   C1   127.64  3.000
 83A  H4   N4   C5   125.69  3.000
 83A  H4   N4   C4   124.33  3.000
 83A  C5   N4   C4   109.95  3.000
 83A  H5   O4   C17  110.41  3.000
 83A  C7   C5   C6   130.21  3.000
 83A  C7   C5   N4   121.54  3.000
 83A  C6   C5   N4   108.25  3.000
 83A  H6   N5   C9   115.87  3.000
 83A  H6   N5   C8   116.09  3.000
 83A  C9   N5   C8   123.13  3.000
 83A  H7   O5   C20  110.02  3.000
 83A  H8   C6   C5   125.70  3.000
 83A  H8   C6   C1   127.42  3.000
 83A  C5   C6   C1   106.87  3.000
 83A  H9   N6   C16  117.06  3.000
 83A  H9   N6   C15  118.95  3.000
 83A  C16  N6   C15  120.62  3.000
 83A  H11  C7   H10  106.96  3.000
 83A  H11  C7   C8   109.12  3.000
 83A  H10  C7   C8   109.37  3.000
 83A  H11  C7   C5   110.62  3.000
 83A  H10  C7   C5   108.07  3.000
 83A  C8   C7   C5   112.54  3.000
 83A  H13  C8   H12  106.85  3.000
 83A  H13  C8   C7   109.53  3.000
 83A  H12  C8   C7   109.40  3.000
 83A  H13  C8   N5   109.32  3.000
 83A  H12  C8   N5   111.79  3.000
 83A  C7   C8   N5   109.89  3.000
 83A  C14  C9   C10  117.84  3.000
 83A  C14  C9   N5   122.33  3.000
 83A  C10  C9   N5   119.82  3.000
 83A  H14  C10  C11  119.70  3.000
 83A  H14  C10  C9   119.41  3.000
 83A  C11  C10  C9   120.89  3.000
 83A  H15  C11  C12  119.62  3.000
 83A  H15  C11  C10  118.95  3.000
 83A  C12  C11  C10  121.43  3.000
 83A  C15  C12  C13  123.74  3.000
 83A  C15  C12  C11  118.57  3.000
 83A  C13  C12  C11  117.68  3.000
 83A  H16  C13  C14  117.39  3.000
 83A  H16  C13  C12  120.95  3.000
 83A  C14  C13  C12  121.66  3.000
 83A  H17  C14  C13  118.84  3.000
 83A  H17  C14  C9   120.65  3.000
 83A  C13  C14  C9   120.50  3.000
 83A  C12  C15  N6   116.93  3.000
 83A  N6   C15  O2   121.05  3.000
 83A  C12  C15  O2   122.02  3.000
 83A  H18  C16  C18  108.59  3.000
 83A  H18  C16  C17  107.79  3.000
 83A  C18  C16  C17  110.11  3.000
 83A  H18  C16  N6   108.94  3.000
 83A  C17  C16  N6   110.81  3.000
 83A  C18  C16  N6   110.51  3.000
 83A  C16  C17  O4   111.25  3.000
 83A  O4   C17  O3   124.15  3.000
 83A  C16  C17  O3   124.57  3.000
 83A  H20  C18  H19  106.77  3.000
 83A  H20  C18  C19  109.76  3.000
 83A  H19  C18  C19  110.59  3.000
 83A  H20  C18  C16  108.74  3.000
 83A  H19  C18  C16  109.56  3.000
 83A  C19  C18  C16  111.30  3.000
 83A  H22  C19  H21  105.49  3.000
 83A  H22  C19  C20  107.97  3.000
 83A  H21  C19  C20  108.42  3.000
 83A  H22  C19  C18  111.38  3.000
 83A  H21  C19  C18  110.32  3.000
 83A  C20  C19  C18  112.94  3.000
 83A  C19  C20  O6   125.17  3.000
 83A  C19  C20  O5   111.64  3.000
 83A  O6   C20  O5   123.19  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_38  C16  N6   C15  O2      0.00   0.0  0
 83A  CONST_39  H5   O4   C17  O3      0.00   0.0  0
 83A  CONST_40  H7   O5   C20  O6      0.00   0.0  0
 83A  Var_01    C11  C12  C15  O2     16.42  30.0  2
 83A  Var_02    C8   C7   C5   N4     67.36  30.0  2
 83A  Var_03    N5   C8   C7   C5    179.66  30.0  3
 83A  Var_04    C9   N5   C8   C7   -179.73  30.0  3
 83A  Var_05    C18  C19  C20  O5    178.41  30.0  3
 83A  Var_06    C20  C19  C18  C16  -178.42  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-5  H5   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
 83A  plan-6  H7   0.020

