# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:42:59 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-{4-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]benzoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCCc3ccc(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
 3Y9  3Y9  'N-{4-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]benzoyl}-L-glutamic acid'  ligand  58  33  .  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_3Y9
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
 3Y9  C13  C  CR16  0  -0.250    2.4340   1.8353   1.6581
 3Y9  C15  C  CR16  0  -0.300    1.0823   1.5892   1.8292
 3Y9  C17  C  C     0   0.553    4.7134   1.1808   0.9470
 3Y9  C20  C  CH1   0  -0.202    6.7783   0.6861  -0.2300
 3Y9  C21  C  CH2   0  -0.459    7.4331  -0.5314  -0.8890
 3Y9  N1   N  N     0  -0.508   -8.1319  -1.8633  -0.4350
 3Y9  C6   C  CR5   0   0.374   -5.4298   0.4033  -0.7146
 3Y9  C7   C  CR15  0  -0.468   -6.4545   1.3014  -0.6453
 3Y9  C8   C  CR56  0  -0.186   -7.6606   0.5474  -0.5225
 3Y9  C9   C  CR56  0   0.476   -7.3102  -0.7997  -0.5225
 3Y9  C14  C  CR16  0  -0.275    2.7204  -0.3750   0.7739
 3Y9  C16  C  CR16  0  -0.295    1.3682  -0.6173   0.9552
 3Y9  C2   C  CR6   0   0.670   -9.3939  -1.5484  -0.3288
 3Y9  N3   N  NR16  0  -0.720   -9.8412  -0.2586  -0.3173
 3Y9  C4   C  CR6   0   0.496   -9.0373   0.8826  -0.4143
 3Y9  N5   N  NR15  0  -0.704   -5.9669  -0.8696  -0.6366
 3Y9  O10  O  O     0  -0.488   -9.5483   1.9946  -0.3981
 3Y9  N11  N  NH2   0  -0.835  -10.3216  -2.5146  -0.1772
 3Y9  C12  C  CR6   0  -0.061    3.2677   0.8607   1.1144
 3Y9  O18  O  O     0  -0.480    5.2527   2.0716   1.5868
 3Y9  N19  N  NH1   0  -0.654    5.3960   0.4249   0.0592
 3Y9  C22  C  CH2   0  -0.577    7.4581  -1.7195   0.0590
 3Y9  C23  C  C     0   0.554    8.1480  -2.9205  -0.5261
 3Y9  O24  O  OH1   0  -0.595    8.1919  -3.9288   0.3380
 3Y9  O25  O  O     0  -0.442    8.6097  -2.9824  -1.6380
 3Y9  C26  C  C     0   0.551    6.9180   1.9188  -1.1138
 3Y9  O27  O  O     0  -0.428    6.0139   2.4296  -1.7199
 3Y9  O28  O  OH1   0  -0.590    8.1712   2.3477  -1.1434
 3Y9  C29  C  CH2   0  -0.521   -3.9603   0.6168  -0.8116
 3Y9  C30  C  CH2   0  -0.421   -3.2046   0.2357   0.4639
 3Y9  C31  C  CH2   0  -0.418   -1.7071   0.4794   0.3387
 3Y9  C32  C  CH2   0  -0.510   -0.9480   0.1121   1.6153
 3Y9  C33  C  CR6   0   0.140    0.5256   0.3608   1.4786
 3Y9  H1   H  HCR6  0   0.258    2.8431   2.7949   1.9453
 3Y9  H2   H  HCR6  0   0.252    0.4512   2.3644   2.2475
 3Y9  H3   H  HCH1  0   0.295    7.2991   0.8933   0.7087
 3Y9  H4   H  HCH2  0   0.259    6.8998  -0.7847  -1.8090
 3Y9  H5   H  HCH2  0   0.273    8.4511  -0.2686  -1.1759
 3Y9  H6   H  HCR5  0   0.249   -6.3521   2.3748  -0.6742
 3Y9  H7   H  HCR6  0   0.255    3.3406  -1.1747   0.3875
 3Y9  H8   H  HCR6  0   0.255    0.9638  -1.5869   0.6900
 3Y9  H9   H  HNR6  0   0.419  -10.8349  -0.0937  -0.2225
 3Y9  H10  H  HNR5  0   0.406   -5.4409  -1.7283  -0.6819
 3Y9  H11  H  HNH2  0   0.406  -10.0242  -3.4578  -0.3617
 3Y9  H12  H  HNH2  0   0.408  -11.2889  -2.3209  -0.3741
 3Y9  H13  H  HNH1  0   0.409    4.8791  -0.1198  -0.6137
 3Y9  H14  H  HCH2  0   0.287    7.9650  -1.4508   0.9909
 3Y9  H15  H  HCH2  0   0.288    6.4473  -2.0181   0.3499
 3Y9  H16  H  HOH1  0   0.480    8.6444  -4.6880  -0.0592
 3Y9  H17  H  HOH1  0   0.486    8.2526   3.1131  -1.7324
 3Y9  H18  H  HCH2  0   0.244   -3.5522   0.0490  -1.6548
 3Y9  H19  H  HCH2  0   0.250   -3.7844   1.6707  -1.0376
 3Y9  H20  H  HCH2  0   0.228   -3.6045   0.8115   1.3039
 3Y9  H21  H  HCH2  0   0.223   -3.3802  -0.8179   0.7025
 3Y9  H22  H  HCH2  0   0.228   -1.3083  -0.1000  -0.5003
 3Y9  H23  H  HCH2  0   0.228   -1.5258   1.5316   0.0982
 3Y9  H24  H  HCH2  0   0.244   -1.3476   0.6920   2.4514
 3Y9  H25  H  HCH2  0   0.244   -1.1253  -0.9412   1.8491

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
 3Y9  N11  C2   single    1.348  0.020  1.348
 3Y9  N3   C2   single    1.365  0.020  1.365
 3Y9  N3   C4   single    1.399  0.020  1.399
 3Y9  C2   N1   double    1.305  0.020  1.305
 3Y9  O10  C4   double    1.224  0.020  1.224
 3Y9  C4   C8   single    1.421  0.020  1.421
 3Y9  N1   C9   single    1.347  0.020  1.347
 3Y9  C8   C9   aromatic  1.392  0.020  1.392
 3Y9  C8   C7   aromatic  1.428  0.020  1.428
 3Y9  C9   N5   aromatic  1.350  0.020  1.350
 3Y9  C7   C6   aromatic  1.364  0.020  1.364
 3Y9  N5   C6   aromatic  1.384  0.020  1.384
 3Y9  C6   C29  single    1.488  0.020  1.488
 3Y9  C29  C30  single    1.531  0.020  1.531
 3Y9  C30  C31  single    1.522  0.020  1.522
 3Y9  C31  C32  single    1.530  0.020  1.530
 3Y9  O27  C26  double    1.202  0.020  1.202
 3Y9  C32  C33  single    1.501  0.020  1.501
 3Y9  O28  C26  single    1.325  0.020  1.325
 3Y9  C15  C33  aromatic  1.393  0.020  1.393
 3Y9  C15  C13  aromatic  1.385  0.020  1.385
 3Y9  C33  C16  aromatic  1.393  0.020  1.393
 3Y9  C26  C20  single    1.523  0.020  1.523
 3Y9  C13  C12  aromatic  1.393  0.020  1.393
 3Y9  C16  C14  aromatic  1.386  0.020  1.386
 3Y9  C14  C12  aromatic  1.394  0.020  1.394
 3Y9  C12  C17  single    1.490  0.020  1.490
 3Y9  N19  C17  single    1.351  0.020  1.351
 3Y9  N19  C20  single    1.436  0.020  1.436
 3Y9  C17  O18  double    1.222  0.020  1.222
 3Y9  C20  C21  single    1.531  0.020  1.531
 3Y9  C21  C22  single    1.520  0.020  1.520
 3Y9  O25  C23  double    1.206  0.020  1.206
 3Y9  C22  C23  single    1.504  0.020  1.504
 3Y9  C23  O24  single    1.329  0.020  1.329
 3Y9  C13  H1   single    0.930  0.020  1.080
 3Y9  C15  H2   single    0.930  0.020  1.080
 3Y9  C20  H3   single    0.970  0.020  1.090
 3Y9  C21  H4   single    0.970  0.020  1.090
 3Y9  C21  H5   single    0.970  0.020  1.090
 3Y9  C7   H6   single    0.930  0.020  1.080
 3Y9  C14  H7   single    0.930  0.020  1.080
 3Y9  C16  H8   single    0.930  0.020  1.080
 3Y9  N3   H9   single    0.860  0.020  1.020
 3Y9  N5   H10  single    0.860  0.020  1.020
 3Y9  N11  H11  single    0.890  0.020  1.040
 3Y9  N11  H12  single    0.890  0.020  1.040
 3Y9  N19  H13  single    0.860  0.020  1.020
 3Y9  C22  H14  single    0.970  0.020  1.090
 3Y9  C22  H15  single    0.970  0.020  1.090
 3Y9  O24  H16  single    0.850  0.020  0.980
 3Y9  O28  H17  single    0.850  0.020  0.980
 3Y9  C29  H18  single    0.970  0.020  1.090
 3Y9  C29  H19  single    0.970  0.020  1.090
 3Y9  C30  H20  single    0.970  0.020  1.090
 3Y9  C30  H21  single    0.970  0.020  1.090
 3Y9  C31  H22  single    0.970  0.020  1.090
 3Y9  C31  H23  single    0.970  0.020  1.090
 3Y9  C32  H24  single    0.970  0.020  1.090
 3Y9  C32  H25  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
 3Y9  H1   C13  C12  119.85  3.000
 3Y9  H1   C13  C15  119.60  3.000
 3Y9  C12  C13  C15  120.54  3.000
 3Y9  H2   C15  C33  119.68  3.000
 3Y9  H2   C15  C13  119.28  3.000
 3Y9  C33  C15  C13  121.04  3.000
 3Y9  N19  C17  O18  121.93  3.000
 3Y9  O18  C17  C12  121.73  3.000
 3Y9  N19  C17  C12  116.34  3.000
 3Y9  H3   C20  C26  107.52  3.000
 3Y9  H3   C20  N19  108.67  3.000
 3Y9  C26  C20  N19  110.62  3.000
 3Y9  H3   C20  C21  108.45  3.000
 3Y9  N19  C20  C21  110.71  3.000
 3Y9  C26  C20  C21  110.77  3.000
 3Y9  H5   C21  H4   106.86  3.000
 3Y9  H5   C21  C22  109.71  3.000
 3Y9  H4   C21  C22  110.60  3.000
 3Y9  H5   C21  C20  108.72  3.000
 3Y9  H4   C21  C20  109.74  3.000
 3Y9  C22  C21  C20  111.10  3.000
 3Y9  C2   N1   C9   113.87  3.000
 3Y9  C29  C6   N5   121.26  3.000
 3Y9  C29  C6   C7   130.59  3.000
 3Y9  N5   C6   C7   108.13  3.000
 3Y9  H6   C7   C8   127.45  3.000
 3Y9  H6   C7   C6   125.62  3.000
 3Y9  C8   C7   C6   106.93  3.000
 3Y9  C4   C8   C9   118.17  3.000
 3Y9  C9   C8   C7   107.37  3.000
 3Y9  C4   C8   C7   134.46  3.000
 3Y9  N5   C9   C8   107.49  3.000
 3Y9  N5   C9   N1   124.87  3.000
 3Y9  C8   C9   N1   127.64  3.000
 3Y9  H7   C14  C12  121.12  3.000
 3Y9  H7   C14  C16  118.44  3.000
 3Y9  C12  C14  C16  120.42  3.000
 3Y9  H8   C16  C33  119.64  3.000
 3Y9  H8   C16  C14  119.25  3.000
 3Y9  C33  C16  C14  121.11  3.000
 3Y9  N11  C2   N3   116.79  3.000
 3Y9  N3   C2   N1   123.06  3.000
 3Y9  N11  C2   N1   120.11  3.000
 3Y9  H9   N3   C4   115.96  3.000
 3Y9  H9   N3   C2   118.46  3.000
 3Y9  C4   N3   C2   125.57  3.000
 3Y9  O10  C4   N3   120.02  3.000
 3Y9  O10  C4   C8   128.30  3.000
 3Y9  N3   C4   C8   111.68  3.000
 3Y9  H10  N5   C9   124.55  3.000
 3Y9  H10  N5   C6   125.35  3.000
 3Y9  C9   N5   C6   110.08  3.000
 3Y9  H12  N11  H11  115.40  3.000
 3Y9  H12  N11  C2   120.12  3.000
 3Y9  H11  N11  C2   116.61  3.000
 3Y9  C14  C12  C17  122.95  3.000
 3Y9  C17  C12  C13  118.31  3.000
 3Y9  C14  C12  C13  118.73  3.000
 3Y9  H13  N19  C20  117.21  3.000
 3Y9  H13  N19  C17  118.81  3.000
 3Y9  C20  N19  C17  121.12  3.000
 3Y9  H15  C22  H14  105.59  3.000
 3Y9  H15  C22  C23  108.03  3.000
 3Y9  H14  C22  C23  108.36  3.000
 3Y9  H15  C22  C21  111.35  3.000
 3Y9  H14  C22  C21  110.29  3.000
 3Y9  C23  C22  C21  112.91  3.000
 3Y9  O25  C23  O24  123.24  3.000
 3Y9  O24  C23  C22  111.61  3.000
 3Y9  O25  C23  C22  125.15  3.000
 3Y9  H16  O24  C23  110.09  3.000
 3Y9  O28  C26  O27  124.23  3.000
 3Y9  O28  C26  C20  111.20  3.000
 3Y9  O27  C26  C20  124.56  3.000
 3Y9  H17  O28  C26  110.41  3.000
 3Y9  H19  C29  H18  106.31  3.000
 3Y9  H19  C29  C30  109.46  3.000
 3Y9  H18  C29  C30  109.18  3.000
 3Y9  H19  C29  C6   108.12  3.000
 3Y9  H18  C29  C6   110.10  3.000
 3Y9  C30  C29  C6   113.42  3.000
 3Y9  H21  C30  H20  106.30  3.000
 3Y9  H21  C30  C31  109.26  3.000
 3Y9  H20  C30  C31  109.78  3.000
 3Y9  H21  C30  C29  110.01  3.000
 3Y9  H20  C30  C29  109.17  3.000
 3Y9  C31  C30  C29  112.17  3.000
 3Y9  H23  C31  H22  106.26  3.000
 3Y9  H23  C31  C32  109.39  3.000
 3Y9  H22  C31  C32  109.37  3.000
 3Y9  H23  C31  C30  109.56  3.000
 3Y9  H22  C31  C30  109.66  3.000
 3Y9  C32  C31  C30  112.40  3.000
 3Y9  H25  C32  H24  106.75  3.000
 3Y9  H25  C32  C33  109.77  3.000
 3Y9  H24  C32  C33  109.92  3.000
 3Y9  H25  C32  C31  109.22  3.000
 3Y9  H24  C32  C31  109.23  3.000
 3Y9  C33  C32  C31  111.80  3.000
 3Y9  C32  C33  C16  120.78  3.000
 3Y9  C16  C33  C15  118.16  3.000
 3Y9  C32  C33  C15  121.03  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
 3Y9  CONST_01  C16  C33  C15  C13     0.00   0.0  0
 3Y9  CONST_02  C16  C14  C12  C13     0.00   0.0  0
 3Y9  CONST_03  C14  C16  C33  C15     0.00   0.0  0
 3Y9  CONST_04  C14  C12  C13  C15     0.00   0.0  0
 3Y9  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 3Y9  CONST_06  C8   C9   N5   C6      0.00   0.0  0
 3Y9  CONST_07  N5   C9   C8   C7      0.00   0.0  0
 3Y9  CONST_08  C9   N5   C6   C7      0.00   0.0  0
 3Y9  CONST_09  N5   C6   C7   C8      0.00   0.0  0
 3Y9  CONST_10  C33  C15  C13  C12     0.00   0.0  0
 3Y9  CONST_11  C33  C16  C14  C12     0.00   0.0  0
 3Y9  CONST_12  C4   N3   C2   N1      0.00   0.0  0
 3Y9  CONST_13  C2   N3   C4   C8      0.00   0.0  0
 3Y9  CONST_14  N3   C2   N1   C9      0.00   0.0  0
 3Y9  CONST_15  C32  C33  C15  C13   180.00   0.0  0
 3Y9  CONST_16  C17  C12  C13  C15   180.00   0.0  0
 3Y9  CONST_17  C16  C14  C12  C17   180.00   0.0  0
 3Y9  CONST_18  C29  C6   C7   C8    180.00   0.0  0
 3Y9  CONST_19  C29  C6   N5   C9    180.00   0.0  0
 3Y9  CONST_20  C32  C33  C16  C14   180.00   0.0  0
 3Y9  CONST_21  N11  C2   N1   C9    180.00   0.0  0
 3Y9  CONST_22  O10  C4   N3   C2    180.00   0.0  0
 3Y9  CONST_23  N11  C2   N3   C4    180.00   0.0  0
 3Y9  CONST_24  H7   C14  C12  C13   180.00   0.0  0
 3Y9  CONST_25  H8   C16  C33  C15   180.00   0.0  0
 3Y9  CONST_26  H10  N5   C9   N1      0.00   0.0  0
 3Y9  CONST_27  H6   C7   C8   C9    180.00   0.0  0
 3Y9  CONST_28  H1   C13  C12  C14   180.00   0.0  0
 3Y9  CONST_29  H2   C15  C33  C16   180.00   0.0  0
 3Y9  CONST_30  H9   N3   C2   N1    180.00   0.0  0
 3Y9  CONST_31  H11  N11  C2   N1      0.00   0.0  0
 3Y9  CONST_33  C12  C17  N19  C20   180.00   0.0  0
 3Y9  CONST_35  O18  C17  N19  C20     0.00   0.0  0
 3Y9  CONST_36  H17  O28  C26  C20   180.00   0.0  0
 3Y9  CONST_37  H16  O24  C23  C22   180.00   0.0  0
 3Y9  Var_01    N19  C17  C12  C13  -159.66  30.0  2
 3Y9  Var_02    C31  C32  C33  C15    90.36  30.0  2
 3Y9  Var_03    C30  C29  C6   C7    109.60  30.0  2
 3Y9  Var_04    C31  C30  C29  C6   -179.38  30.0  3
 3Y9  Var_05    C33  C32  C31  C30  -179.85  30.0  3
 3Y9  Var_06    C23  C22  C21  C20  -177.45  30.0  3
 3Y9  Var_07    O25  C23  C22  C21    -2.00  30.0  3
 3Y9  Var_08    C32  C31  C30  C29   179.49  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
 3Y9  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
 3Y9  plan-1  C13  0.020
 3Y9  plan-1  C15  0.020
 3Y9  plan-1  C17  0.020
 3Y9  plan-1  C14  0.020
 3Y9  plan-1  C16  0.020
 3Y9  plan-1  C12  0.020
 3Y9  plan-1  C32  0.020
 3Y9  plan-1  C33  0.020
 3Y9  plan-1  H1   0.020
 3Y9  plan-1  H2   0.020
 3Y9  plan-1  H7   0.020
 3Y9  plan-1  H8   0.020
 3Y9  plan-2  N1   0.020
 3Y9  plan-2  C6   0.020
 3Y9  plan-2  C7   0.020
 3Y9  plan-2  C8   0.020
 3Y9  plan-2  C9   0.020
 3Y9  plan-2  C2   0.020
 3Y9  plan-2  N3   0.020
 3Y9  plan-2  C4   0.020
 3Y9  plan-2  N5   0.020
 3Y9  plan-2  O10  0.020
 3Y9  plan-2  N11  0.020
 3Y9  plan-2  C29  0.020
 3Y9  plan-2  H6   0.020
 3Y9  plan-2  H9   0.020
 3Y9  plan-2  H10  0.020
 3Y9  plan-2  H11  0.020
 3Y9  plan-2  H12  0.020
 3Y9  plan-3  C17  0.020
 3Y9  plan-3  C20  0.020
 3Y9  plan-3  C12  0.020
 3Y9  plan-3  O18  0.020
 3Y9  plan-3  N19  0.020
 3Y9  plan-3  H13  0.020
 3Y9  plan-4  C22  0.020
 3Y9  plan-4  C23  0.020
 3Y9  plan-4  O24  0.020
 3Y9  plan-4  O25  0.020
 3Y9  plan-4  H16  0.020
 3Y9  plan-5  C20  0.020
 3Y9  plan-5  C26  0.020
 3Y9  plan-5  O27  0.020
 3Y9  plan-5  O28  0.020
 3Y9  plan-5  H17  0.020

