# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 23:45:57 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[7-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanoyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCCCCC(=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
 3YD  3YD  'N-[7-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanoyl]-L-glutamic acid'  ligand  52  29  .  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_3YD
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
 3YD  N1   N  N      0  -0.508   -7.4544  -1.6582   0.5981
 3YD  C2   C  CR6    0   0.670   -8.5861  -1.6435  -0.0518
 3YD  N3   N  NR16   0  -0.720   -8.9716  -0.6061  -0.8510
 3YD  C4   C  CR6    0   0.495   -8.2360   0.5616  -1.0822
 3YD  N5   N  NR15   0  -0.703   -5.4996  -0.3374   0.9788
 3YD  C6   C  CR5    0   0.373   -5.0028   0.8923   0.5843
 3YD  C7   C  CR15   0  -0.468   -5.9127   1.4682  -0.2539
 3YD  C8   C  CR56   0  -0.186   -7.0043   0.5553  -0.3735
 3YD  C9   C  CR56   0   0.476   -6.7052  -0.5544   0.4125
 3YD  O10  O  O      0  -0.488   -8.6816   1.4287  -1.8225
 3YD  N11  N  NH2    0  -0.835   -9.4572  -2.6627   0.0824
 3YD  C12  C  CH2    0  -0.583    2.5252  -0.0208   0.2008
 3YD  C13  C  CH2    0  -0.412    1.3703   0.7601   0.8101
 3YD  C14  C  CH2    0  -0.416    0.0183   0.3106   0.2713
 3YD  C15  C  CH2    0  -0.419   -1.1467   1.0626   0.9013
 3YD  C16  C  CH2    0  -0.416   -2.5039   0.5911   0.3975
 3YD  C17  C  C      0   0.563    3.8763   0.3359   0.7909
 3YD  O18  O  O      0  -0.520    3.9943   0.7436   1.9414
 3YD  N19  N  NH1    0  -0.619    4.9241   0.1061  -0.0097
 3YD  C20  C  CH1    0  -0.188    6.2840   0.4339   0.3500
 3YD  C21  C  CH2    0  -0.443    7.2588  -0.3976  -0.4860
 3YD  C22  C  CH2    0  -0.577    7.1148  -1.8960  -0.2709
 3YD  C23  C  C      0   0.412    8.1211  -2.7793  -1.0298
 3YD  O24  O  O      0  -0.609    9.0548  -2.2157  -1.6341
 3YD  O25  O  OC    -1  -0.634    7.9225  -4.0114  -0.9651
 3YD  C26  C  C      0   0.409    6.5903   1.9469   0.2100
 3YD  O27  O  O      0  -0.599    5.7698   2.6521  -0.4010
 3YD  O28  O  OC    -1  -0.622    7.6696   2.3156   0.7179
 3YD  C29  C  CH2    0  -0.520   -3.6639   1.3606   1.0353
 3YD  H1   H  HNR6   0   0.419   -9.8665  -0.6643  -1.3192
 3YD  H2   H  HNR5   0   0.406   -5.0431  -0.9741   1.6130
 3YD  H3   H  HCR5   0   0.248   -5.8068   2.4300  -0.7304
 3YD  H4   H  HNH2   0   0.406   -9.1125  -3.4984   0.5243
 3YD  H5   H  HNH2   0   0.408  -10.1829  -2.8011  -0.6006
 3YD  H6   H  HCH2   0   0.260    2.3698  -1.0924   0.3716
 3YD  H7   H  HCH2   0   0.244    2.5378   0.1072  -0.8853
 3YD  H8   H  HCH2   0   0.219    1.3821   0.6406   1.8960
 3YD  H9   H  HCH2   0   0.219    1.5018   1.8291   0.6172
 3YD  H10  H  HCH2   0   0.212   -0.0098   0.4400  -0.8161
 3YD  H11  H  HCH2   0   0.211   -0.1026  -0.7634   0.4513
 3YD  H12  H  HCH2   0   0.213   -1.1050   0.9470   1.9900
 3YD  H13  H  HCH2   0   0.214   -1.0379   2.1349   0.7062
 3YD  H14  H  HCH2   0   0.223   -2.5572   0.7030  -0.6896
 3YD  H15  H  HCH2   0   0.218   -2.6121  -0.4788   0.6011
 3YD  H16  H  HNH1   0   0.382    4.7385  -0.1055  -0.9770
 3YD  H17  H  HCH1   0   0.223    6.4247   0.1602   1.4002
 3YD  H18  H  HCH2   0   0.208    7.1267  -0.1537  -1.5465
 3YD  H19  H  HCH2   0   0.226    8.2696  -0.0842  -0.2266
 3YD  H20  H  HCH2   0   0.220    7.2149  -2.1167   0.7995
 3YD  H21  H  HCH2   0   0.218    6.1050  -2.2272  -0.5318
 3YD  H24  H  HCH2   0   0.249   -3.5719   2.4217   0.7944
 3YD  H25  H  HCH2   0   0.242   -3.5894   1.2843   2.1256

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
 3YD  O24  C23  deloc     1.247  0.020  1.247
 3YD  C23  C22  single    1.539  0.020  1.539
 3YD  C23  O25  deloc     1.250  0.020  1.250
 3YD  C22  C21  single    1.521  0.020  1.521
 3YD  O18  C17  double    1.226  0.020  1.226
 3YD  N19  C20  single    1.444  0.020  1.444
 3YD  N19  C17  single    1.339  0.020  1.339
 3YD  C21  C20  single    1.530  0.020  1.530
 3YD  C20  C26  single    1.550  0.020  1.550
 3YD  C17  C12  single    1.517  0.020  1.517
 3YD  C12  C13  single    1.521  0.020  1.521
 3YD  C13  C14  single    1.523  0.020  1.523
 3YD  C26  O27  deloc     1.243  0.020  1.243
 3YD  C26  O28  deloc     1.249  0.020  1.249
 3YD  C14  C15  single    1.523  0.020  1.523
 3YD  C15  C16  single    1.523  0.020  1.523
 3YD  C16  C29  single    1.531  0.020  1.531
 3YD  C29  C6   single    1.488  0.020  1.488
 3YD  C6   N5   aromatic  1.384  0.020  1.384
 3YD  C6   C7   aromatic  1.365  0.020  1.365
 3YD  N5   C9   aromatic  1.350  0.020  1.350
 3YD  C7   C8   aromatic  1.428  0.020  1.428
 3YD  C9   C8   aromatic  1.392  0.020  1.392
 3YD  C9   N1   single    1.347  0.020  1.347
 3YD  C8   C4   single    1.421  0.020  1.421
 3YD  N1   C2   double    1.305  0.020  1.305
 3YD  C4   O10  double    1.224  0.020  1.224
 3YD  C4   N3   single    1.399  0.020  1.399
 3YD  C2   N3   single    1.365  0.020  1.365
 3YD  C2   N11  single    1.347  0.020  1.347
 3YD  N3   H1   single    0.860  0.020  1.020
 3YD  N5   H2   single    0.860  0.020  1.020
 3YD  C7   H3   single    0.930  0.020  1.080
 3YD  N11  H4   single    0.890  0.020  1.040
 3YD  N11  H5   single    0.890  0.020  1.040
 3YD  C12  H6   single    0.970  0.020  1.090
 3YD  C12  H7   single    0.970  0.020  1.090
 3YD  C13  H8   single    0.970  0.020  1.090
 3YD  C13  H9   single    0.970  0.020  1.090
 3YD  C14  H10  single    0.970  0.020  1.090
 3YD  C14  H11  single    0.970  0.020  1.090
 3YD  C15  H12  single    0.970  0.020  1.090
 3YD  C15  H13  single    0.970  0.020  1.090
 3YD  C16  H14  single    0.970  0.020  1.090
 3YD  C16  H15  single    0.970  0.020  1.090
 3YD  N19  H16  single    0.860  0.020  1.020
 3YD  C20  H17  single    0.970  0.020  1.090
 3YD  C21  H18  single    0.970  0.020  1.090
 3YD  C21  H19  single    0.970  0.020  1.090
 3YD  C22  H20  single    0.970  0.020  1.090
 3YD  C22  H21  single    0.970  0.020  1.090
 3YD  C29  H24  single    0.970  0.020  1.090
 3YD  C29  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
 3YD  C9   N1   C2   113.86  3.000
 3YD  N11  C2   N3   116.78  3.000
 3YD  N11  C2   N1   120.16  3.000
 3YD  N3   C2   N1   123.02  3.000
 3YD  H1   N3   C4   115.88  3.000
 3YD  H1   N3   C2   118.49  3.000
 3YD  C4   N3   C2   125.62  3.000
 3YD  O10  C4   C8   128.34  3.000
 3YD  O10  C4   N3   119.98  3.000
 3YD  C8   C4   N3   111.68  3.000
 3YD  H2   N5   C9   124.54  3.000
 3YD  H2   N5   C6   125.32  3.000
 3YD  C9   N5   C6   110.12  3.000
 3YD  C29  C6   C7   130.78  3.000
 3YD  C7   C6   N5   108.11  3.000
 3YD  C29  C6   N5   121.07  3.000
 3YD  H3   C7   C8   127.45  3.000
 3YD  H3   C7   C6   125.61  3.000
 3YD  C8   C7   C6   106.94  3.000
 3YD  C9   C8   C7   107.34  3.000
 3YD  C9   C8   C4   118.12  3.000
 3YD  C7   C8   C4   134.54  3.000
 3YD  C8   C9   N5   107.49  3.000
 3YD  C8   C9   N1   127.69  3.000
 3YD  N5   C9   N1   124.81  3.000
 3YD  H5   N11  H4   115.53  3.000
 3YD  H5   N11  C2   120.18  3.000
 3YD  H4   N11  C2   116.77  3.000
 3YD  H7   C12  H6   105.71  3.000
 3YD  H7   C12  C17  110.39  3.000
 3YD  H6   C12  C17  107.19  3.000
 3YD  H7   C12  C13  110.27  3.000
 3YD  H6   C12  C13  109.38  3.000
 3YD  C17  C12  C13  113.56  3.000
 3YD  H9   C13  H8   106.31  3.000
 3YD  H9   C13  C14  109.43  3.000
 3YD  H8   C13  C14  109.20  3.000
 3YD  H9   C13  C12  109.86  3.000
 3YD  H8   C13  C12  109.50  3.000
 3YD  C14  C13  C12  112.37  3.000
 3YD  H11  C14  H10  106.02  3.000
 3YD  H11  C14  C15  109.37  3.000
 3YD  H10  C14  C15  109.43  3.000
 3YD  H11  C14  C13  109.22  3.000
 3YD  H10  C14  C13  109.82  3.000
 3YD  C15  C14  C13  112.76  3.000
 3YD  H13  C15  H12  106.05  3.000
 3YD  H13  C15  C16  109.44  3.000
 3YD  H12  C15  C16  109.27  3.000
 3YD  H13  C15  C14  109.49  3.000
 3YD  H12  C15  C14  109.26  3.000
 3YD  C16  C15  C14  113.09  3.000
 3YD  H15  C16  H14  106.26  3.000
 3YD  H15  C16  C29  109.81  3.000
 3YD  H14  C16  C29  109.00  3.000
 3YD  H15  C16  C15  109.22  3.000
 3YD  H14  C16  C15  109.90  3.000
 3YD  C29  C16  C15  112.45  3.000
 3YD  N19  C17  O18  122.88  3.000
 3YD  N19  C17  C12  115.10  3.000
 3YD  O18  C17  C12  121.93  3.000
 3YD  H16  N19  C20  117.41  3.000
 3YD  H16  N19  C17  117.79  3.000
 3YD  C20  N19  C17  123.30  3.000
 3YD  H17  C20  C26  107.78  3.000
 3YD  H17  C20  C21  107.85  3.000
 3YD  C26  C20  C21  110.81  3.000
 3YD  H17  C20  N19  107.66  3.000
 3YD  C26  C20  N19  112.65  3.000
 3YD  C21  C20  N19  109.90  3.000
 3YD  H19  C21  H18  106.14  3.000
 3YD  H19  C21  C22  109.73  3.000
 3YD  H18  C21  C22  110.16  3.000
 3YD  H19  C21  C20  107.74  3.000
 3YD  H18  C21  C20  109.33  3.000
 3YD  C22  C21  C20  113.45  3.000
 3YD  H21  C22  H20  104.83  3.000
 3YD  H21  C22  C23  108.18  3.000
 3YD  H20  C22  C23  107.81  3.000
 3YD  H21  C22  C21  110.60  3.000
 3YD  H20  C22  C21  109.12  3.000
 3YD  C23  C22  C21  115.72  3.000
 3YD  O25  C23  O24  126.14  3.000
 3YD  O25  C23  C22  115.88  3.000
 3YD  O24  C23  C22  117.98  3.000
 3YD  O28  C26  O27  127.10  3.000
 3YD  O28  C26  C20  114.98  3.000
 3YD  O27  C26  C20  117.90  3.000
 3YD  H25  C29  H24  106.35  3.000
 3YD  H25  C29  C16  109.15  3.000
 3YD  H24  C29  C16  109.43  3.000
 3YD  H25  C29  C6   109.93  3.000
 3YD  H24  C29  C6   108.34  3.000
 3YD  C16  C29  C6   113.40  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
 3YD  CONST_01  C8   C7   C6   N5      0.00   0.0  0
 3YD  CONST_02  C7   C8   C9   N5      0.00   0.0  0
 3YD  CONST_03  C8   C9   N5   C6      0.00   0.0  0
 3YD  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 3YD  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YD  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 3YD  CONST_07  C8   C4   N3   C2      0.00   0.0  0
 3YD  CONST_08  C9   N1   C2   N3      0.00   0.0  0
 3YD  CONST_09  C29  C6   C7   C8    180.00   0.0  0
 3YD  CONST_10  C29  C6   N5   C9    180.00   0.0  0
 3YD  CONST_11  O10  C4   N3   C2    180.00   0.0  0
 3YD  CONST_12  N11  C2   N3   C4    180.00   0.0  0
 3YD  CONST_13  N11  C2   N1   C9    180.00   0.0  0
 3YD  CONST_14  H2   N5   C9   N1      0.00   0.0  0
 3YD  CONST_15  H3   C7   C8   C4      0.00   0.0  0
 3YD  CONST_16  H1   N3   C2   N1    180.00   0.0  0
 3YD  CONST_17  H4   N11  C2   N1      0.00   0.0  0
 3YD  CONST_19  C20  N19  C17  C12   180.00   0.0  0
 3YD  CONST_20  C20  N19  C17  O18     0.00   0.0  0
 3YD  CONST_21  H16  N19  C17  C12     0.00   0.0  0
 3YD  Var_01    C16  C29  C6   N5     70.62  30.0  2
 3YD  Var_02    C15  C16  C29  C6   -178.49  30.0  1
 3YD  Var_03    C15  C14  C13  C12   178.56  30.0  3
 3YD  Var_04    O18  C17  C12  C13    28.35  30.0  2
 3YD  Var_05    C16  C15  C14  C13  -178.34  30.0  3
 3YD  Var_06    C17  C12  C13  C14  -175.86  30.0  1
 3YD  Var_07    C29  C16  C15  C14  -179.75  30.0  3
 3YD  Var_08    C23  C22  C21  C20  -176.86  30.0  1
 3YD  Var_09    O24  C23  C22  C21     7.71  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
 3YD  chir_01  C20  N19  C21  C26  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
 3YD  plan-1  N1   0.020
 3YD  plan-1  C2   0.020
 3YD  plan-1  N3   0.020
 3YD  plan-1  C4   0.020
 3YD  plan-1  N5   0.020
 3YD  plan-1  C6   0.020
 3YD  plan-1  C7   0.020
 3YD  plan-1  C8   0.020
 3YD  plan-1  C9   0.020
 3YD  plan-1  O10  0.020
 3YD  plan-1  N11  0.020
 3YD  plan-1  C29  0.020
 3YD  plan-1  H1   0.020
 3YD  plan-1  H2   0.020
 3YD  plan-1  H3   0.020
 3YD  plan-1  H4   0.020
 3YD  plan-1  H5   0.020
 3YD  plan-2  C12  0.020
 3YD  plan-2  C17  0.020
 3YD  plan-2  O18  0.020
 3YD  plan-2  N19  0.020
 3YD  plan-2  C20  0.020
 3YD  plan-2  H16  0.020
 3YD  plan-3  C22  0.020
 3YD  plan-3  C23  0.020
 3YD  plan-3  O24  0.020
 3YD  plan-3  O25  0.020
 3YD  plan-4  C20  0.020
 3YD  plan-4  C26  0.020
 3YD  plan-4  O27  0.020
 3YD  plan-4  O28  0.020

