# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:54:58 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)N[C@H](CCC(O)=O)C(O)=O)c2C(=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
 D96  D96  'N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid'  ligand  49  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D96
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
 D96  N1   N  N     0  -0.507   5.9636   0.4453  -1.7670
 D96  C1   C  CR56  0   0.501   5.0604  -0.4680  -1.3615
 D96  C2   C  CR56  0  -0.244   4.5216  -0.6285  -0.0839
 D96  C3   C  CR6   0   0.505   4.9844   0.2384   0.9453
 D96  N2   N  NR16  0  -0.721   5.9139   1.1660   0.4645
 D96  C4   C  CR6   0   0.674   6.3681   1.2467  -0.8202
 D96  C5   C  CR5   0   0.037   3.6200  -1.7397  -0.1310
 D96  C6   C  CR15  0  -0.088   3.6533  -2.1923  -1.4169
 D96  N3   N  NR15  0  -0.662   4.5223  -1.4153  -2.1530
 D96  O1   O  O     0  -0.483   4.6805   0.2494   2.1312
 D96  N4   N  NH2   0  -0.834   7.3068   2.1773  -1.0750
 D96  C7   C  CH2   0  -0.632   2.7639  -2.2799   0.9739
 D96  C8   C  CR6   0   0.149   1.4490  -1.5473   1.0757
 D96  C9   C  CR16  0  -0.298   0.3545  -1.9662   0.3239
 D96  C10  C  CR16  0  -0.276  -0.8520  -1.2885   0.3806
 D96  C11  C  CR6   0  -0.059  -0.9937  -0.1675   1.1973
 D96  C12  C  CR16  0  -0.251   0.0945   0.2446   1.9628
 D96  C13  C  CR16  0  -0.302   1.3008  -0.4328   1.8972
 D96  C14  C  C     0   0.553  -2.2712   0.5898   1.3168
 D96  O2   O  O     0  -0.481  -2.5151   1.2882   2.2900
 D96  N5   N  NH1   0  -0.655  -3.1515   0.4472   0.3022
 D96  C15  C  CH1   0  -0.198  -4.3966   1.1624   0.2903
 D96  C16  C  CH2   0  -0.462  -5.3756   0.5234  -0.6993
 D96  C17  C  C     0   0.550  -4.1710   2.6303  -0.0486
 D96  O3   O  OH1   0  -0.590  -5.2470   3.3547   0.2208
 D96  O4   O  O     0  -0.429  -3.1563   3.0753  -0.5158
 D96  C18  C  CH2   0  -0.576  -5.7411  -0.8898  -0.2745
 D96  C19  C  C     0   0.554  -6.7665  -1.5243  -1.1726
 D96  O5   O  O     0  -0.442  -7.2574  -1.0029  -2.1425
 D96  O6   O  OH1   0  -0.595  -7.0799  -2.7505  -0.7689
 D96  H1   H  HNR6  0   0.419   6.2846   1.8108   1.1498
 D96  H2   H  HCR5  0   0.281   3.1226  -3.0096  -1.8775
 D96  H3   H  HNR5  0   0.410   4.7401  -1.5469  -3.1274
 D96  H4   H  HNH2  0   0.409   7.4434   2.9490  -0.4441
 D96  H5   H  HNH2  0   0.407   7.5164   2.3605  -2.0418
 D96  H6   H  HCH2  0   0.266   2.5679  -3.3381   0.7891
 D96  H7   H  HCH2  0   0.265   3.2968  -2.2165   1.9234
 D96  H8   H  HCR6  0   0.254   0.4430  -2.8400  -0.3108
 D96  H9   H  HCR6  0   0.254  -1.6849  -1.6652  -0.1999
 D96  H10  H  HCR6  0   0.257   0.0008   1.1048   2.6123
 D96  H11  H  HCR6  0   0.260   2.1400  -0.0908   2.4888
 D96  H12  H  HNH1  0   0.409  -2.8278   0.0715  -0.5757
 D96  H13  H  HCH1  0   0.295  -4.8377   1.1192   1.2896
 D96  H14  H  HCH2  0   0.273  -6.2749   1.1371  -0.7455
 D96  H15  H  HCH2  0   0.260  -4.9395   0.5240  -1.7016
 D96  H16  H  HOH1  0   0.486  -5.1018   4.2800  -0.0282
 D96  H17  H  HCH2  0   0.287  -4.8627  -1.5402  -0.2507
 D96  H18  H  HCH2  0   0.288  -6.1340  -0.8889   0.7471
 D96  H19  H  HOH1  0   0.481  -7.7475  -3.1340  -1.3571

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
 D96  O5   C19  double    1.206  0.020  1.206
 D96  O4   C17  double    1.202  0.020  1.202
 D96  C19  O6   single    1.329  0.020  1.329
 D96  C19  C18  single    1.504  0.020  1.504
 D96  C17  C15  single    1.523  0.020  1.523
 D96  C17  O3   single    1.325  0.020  1.325
 D96  C15  C16  single    1.532  0.020  1.532
 D96  C15  N5   single    1.436  0.020  1.436
 D96  C16  C18  single    1.520  0.020  1.520
 D96  O2   C14  double    1.222  0.020  1.222
 D96  N5   C14  single    1.351  0.020  1.351
 D96  C14  C11  single    1.490  0.020  1.490
 D96  C11  C12  aromatic  1.393  0.020  1.393
 D96  C11  C10  aromatic  1.394  0.020  1.394
 D96  C12  C13  aromatic  1.385  0.020  1.385
 D96  N4   C4   single    1.346  0.020  1.346
 D96  C10  C9   aromatic  1.385  0.020  1.385
 D96  N2   C4   single    1.365  0.020  1.365
 D96  N2   C3   single    1.398  0.020  1.398
 D96  O1   C3   double    1.224  0.020  1.224
 D96  C4   N1   double    1.305  0.020  1.305
 D96  C3   C2   single    1.423  0.020  1.423
 D96  C13  C8   aromatic  1.392  0.020  1.392
 D96  C9   C8   aromatic  1.392  0.020  1.392
 D96  C8   C7   single    1.509  0.020  1.509
 D96  N1   C1   single    1.347  0.020  1.347
 D96  C2   C1   aromatic  1.396  0.020  1.396
 D96  C2   C5   aromatic  1.432  0.020  1.432
 D96  C1   N3   aromatic  1.347  0.020  1.347
 D96  C5   C7   single    1.498  0.020  1.498
 D96  C5   C6   aromatic  1.364  0.020  1.364
 D96  N3   C6   aromatic  1.379  0.020  1.379
 D96  N2   H1   single    0.860  0.020  1.020
 D96  C6   H2   single    0.930  0.020  1.080
 D96  N3   H3   single    0.860  0.020  1.020
 D96  N4   H4   single    0.890  0.020  1.040
 D96  N4   H5   single    0.890  0.020  1.040
 D96  C7   H6   single    0.970  0.020  1.090
 D96  C7   H7   single    0.970  0.020  1.090
 D96  C9   H8   single    0.930  0.020  1.080
 D96  C10  H9   single    0.930  0.020  1.080
 D96  C12  H10  single    0.930  0.020  1.080
 D96  C13  H11  single    0.930  0.020  1.080
 D96  N5   H12  single    0.860  0.020  1.020
 D96  C15  H13  single    0.970  0.020  1.090
 D96  C16  H14  single    0.970  0.020  1.090
 D96  C16  H15  single    0.970  0.020  1.090
 D96  O3   H16  single    0.850  0.020  0.980
 D96  C18  H17  single    0.970  0.020  1.090
 D96  C18  H18  single    0.970  0.020  1.090
 D96  O6   H19  single    0.850  0.020  0.980

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
 D96  C4   N1   C1   113.94  3.000
 D96  N3   C1   C2   107.63  3.000
 D96  N3   C1   N1   124.61  3.000
 D96  C2   C1   N1   127.76  3.000
 D96  C5   C2   C3   134.54  3.000
 D96  C5   C2   C1   107.59  3.000
 D96  C3   C2   C1   117.80  3.000
 D96  O1   C3   N2   119.48  3.000
 D96  O1   C3   C2   128.71  3.000
 D96  N2   C3   C2   111.81  3.000
 D96  H1   N2   C4   118.56  3.000
 D96  H1   N2   C3   115.69  3.000
 D96  C4   N2   C3   125.73  3.000
 D96  N4   C4   N2   116.81  3.000
 D96  N2   C4   N1   122.92  3.000
 D96  N4   C4   N1   120.23  3.000
 D96  C7   C5   C6   126.13  3.000
 D96  C6   C5   C2   105.86  3.000
 D96  C7   C5   C2   127.97  3.000
 D96  H2   C6   N3   120.64  3.000
 D96  H2   C6   C5   129.99  3.000
 D96  N3   C6   C5   109.38  3.000
 D96  H3   N3   C6   125.40  3.000
 D96  H3   N3   C1   125.04  3.000
 D96  C6   N3   C1   109.54  3.000
 D96  H5   N4   H4   115.76  3.000
 D96  H5   N4   C4   116.93  3.000
 D96  H4   N4   C4   120.41  3.000
 D96  H7   C7   H6   106.94  3.000
 D96  H7   C7   C8   109.81  3.000
 D96  H6   C7   C8   108.99  3.000
 D96  H7   C7   C5   109.99  3.000
 D96  H6   C7   C5   109.09  3.000
 D96  C8   C7   C5   111.88  3.000
 D96  C13  C8   C9   118.40  3.000
 D96  C9   C8   C7   120.17  3.000
 D96  C13  C8   C7   121.41  3.000
 D96  H8   C9   C10  119.33  3.000
 D96  H8   C9   C8   119.65  3.000
 D96  C10  C9   C8   121.03  3.000
 D96  H9   C10  C11  121.04  3.000
 D96  H9   C10  C9   118.54  3.000
 D96  C11  C10  C9   120.40  3.000
 D96  C14  C11  C12  118.39  3.000
 D96  C12  C11  C10  118.71  3.000
 D96  C14  C11  C10  122.88  3.000
 D96  H10  C12  C13  119.51  3.000
 D96  H10  C12  C11  119.84  3.000
 D96  C13  C12  C11  120.65  3.000
 D96  H11  C13  C12  119.67  3.000
 D96  H11  C13  C8   119.53  3.000
 D96  C12  C13  C8   120.80  3.000
 D96  N5   C14  O2   121.89  3.000
 D96  N5   C14  C11  116.41  3.000
 D96  O2   C14  C11  121.69  3.000
 D96  H12  N5   C15  117.18  3.000
 D96  H12  N5   C14  118.96  3.000
 D96  C15  N5   C14  121.24  3.000
 D96  H13  C15  C17  107.53  3.000
 D96  H13  C15  C16  108.43  3.000
 D96  C17  C15  C16  110.67  3.000
 D96  H13  C15  N5   108.82  3.000
 D96  C16  C15  N5   110.60  3.000
 D96  C17  C15  N5   110.70  3.000
 D96  H15  C16  H14  106.86  3.000
 D96  H15  C16  C18  110.65  3.000
 D96  H14  C16  C18  109.70  3.000
 D96  H15  C16  C15  109.71  3.000
 D96  H14  C16  C15  108.66  3.000
 D96  C18  C16  C15  111.16  3.000
 D96  O4   C17  O3   124.20  3.000
 D96  O3   C17  C15  111.19  3.000
 D96  O4   C17  C15  124.61  3.000
 D96  H16  O3   C17  110.38  3.000
 D96  H18  C18  H17  105.59  3.000
 D96  H18  C18  C19  108.24  3.000
 D96  H17  C18  C19  108.06  3.000
 D96  H18  C18  C16  110.26  3.000
 D96  H17  C18  C16  111.47  3.000
 D96  C19  C18  C16  112.91  3.000
 D96  O6   C19  O5   123.20  3.000
 D96  O6   C19  C18  111.64  3.000
 D96  O5   C19  C18  125.15  3.000
 D96  H19  O6   C19  110.08  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
 D96  CONST_01  C6   C5   C2   C1     0.00   0.0  0
 D96  CONST_02  C5   C6   N3   C1     0.00   0.0  0
 D96  CONST_03  C6   N3   C1   C2     0.00   0.0  0
 D96  CONST_04  N3   C6   C5   C2     0.00   0.0  0
 D96  CONST_05  N3   C1   C2   C5     0.00   0.0  0
 D96  CONST_06  C11  C12  C13  C8     0.00   0.0  0
 D96  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 D96  CONST_08  C12  C11  C10  C9     0.00   0.0  0
 D96  CONST_09  C12  C13  C8   C9     0.00   0.0  0
 D96  CONST_10  C13  C12  C11  C10    0.00   0.0  0
 D96  CONST_11  C13  C8   C9   C10    0.00   0.0  0
 D96  CONST_12  C3   N2   C4   N1     0.00   0.0  0
 D96  CONST_13  N2   C4   N1   C1     0.00   0.0  0
 D96  CONST_14  C4   N2   C3   C2     0.00   0.0  0
 D96  CONST_15  C7   C5   C2   C1   180.00   0.0  0
 D96  CONST_16  C7   C5   C2   C3     0.00   0.0  0
 D96  CONST_17  C7   C5   C6   N3   180.00   0.0  0
 D96  CONST_18  C12  C13  C8   C7   180.00   0.0  0
 D96  CONST_19  C10  C9   C8   C7   180.00   0.0  0
 D96  CONST_20  C14  C11  C10  C9   180.00   0.0  0
 D96  CONST_21  C14  C11  C12  C13  180.00   0.0  0
 D96  CONST_22  N4   C4   N1   C1   180.00   0.0  0
 D96  CONST_23  N4   C4   N2   C3   180.00   0.0  0
 D96  CONST_24  O1   C3   N2   C4   180.00   0.0  0
 D96  CONST_25  H3   N3   C1   N1     0.00   0.0  0
 D96  CONST_26  H2   C6   N3   C1   180.00   0.0  0
 D96  CONST_27  H10  C12  C13  C8   180.00   0.0  0
 D96  CONST_28  H9   C10  C9   C8   180.00   0.0  0
 D96  CONST_29  H11  C13  C8   C9   180.00   0.0  0
 D96  CONST_30  H8   C9   C10  C11  180.00   0.0  0
 D96  CONST_31  H1   N2   C4   N1   180.00   0.0  0
 D96  CONST_33  H5   N4   C4   N1     0.00   0.0  0
 D96  CONST_34  C15  N5   C14  C11  180.00   0.0  0
 D96  CONST_36  C15  N5   C14  O2     0.00   0.0  0
 D96  CONST_37  H16  O3   C17  C15  180.00   0.0  0
 D96  CONST_38  H19  O6   C19  C18  180.00   0.0  0
 D96  Var_01    C8   C7   C5   C2    85.34  30.0  2
 D96  Var_02    C13  C8   C7   C5   -90.94  30.0  2
 D96  Var_03    O2   C14  C11  C10  157.63  30.0  2
 D96  Var_04    C19  C18  C16  C15  176.45  30.0  3
 D96  Var_05    O5   C19  C18  C16    0.75  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
 D96  chir_01  C15  C17  C16  N5  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
 D96  plan-1  C7   0.020
 D96  plan-1  C8   0.020
 D96  plan-1  C9   0.020
 D96  plan-1  C10  0.020
 D96  plan-1  C11  0.020
 D96  plan-1  C12  0.020
 D96  plan-1  C13  0.020
 D96  plan-1  C14  0.020
 D96  plan-1  H8   0.020
 D96  plan-1  H9   0.020
 D96  plan-1  H10  0.020
 D96  plan-1  H11  0.020
 D96  plan-2  N1   0.020
 D96  plan-2  C1   0.020
 D96  plan-2  C2   0.020
 D96  plan-2  C3   0.020
 D96  plan-2  N2   0.020
 D96  plan-2  C4   0.020
 D96  plan-2  C5   0.020
 D96  plan-2  C6   0.020
 D96  plan-2  N3   0.020
 D96  plan-2  O1   0.020
 D96  plan-2  N4   0.020
 D96  plan-2  C7   0.020
 D96  plan-2  H1   0.020
 D96  plan-2  H2   0.020
 D96  plan-2  H3   0.020
 D96  plan-2  H4   0.020
 D96  plan-2  H5   0.020
 D96  plan-3  C11  0.020
 D96  plan-3  C14  0.020
 D96  plan-3  O2   0.020
 D96  plan-3  N5   0.020
 D96  plan-3  C15  0.020
 D96  plan-3  H12  0.020
 D96  plan-4  C15  0.020
 D96  plan-4  C17  0.020
 D96  plan-4  O3   0.020
 D96  plan-4  O4   0.020
 D96  plan-4  H16  0.020
 D96  plan-5  C18  0.020
 D96  plan-5  C19  0.020
 D96  plan-5  O5   0.020
 D96  plan-5  O6   0.020
 D96  plan-5  H19  0.020

