# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:16:40 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-{4-[4-(2-amino-4-oxo-1,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]benzoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2cc(CCCCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)sc2N1
#
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
 3YA  3YA  'N-{4-[4-(2-amino-4-oxo-1,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]benzoyl}-L-glutamic acid'  ligand  55  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_3YA
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
 3YA  C13  C  C1     0  -0.280    3.0344   0.4699  -0.7765
 3YA  C14  C  C1     0  -0.256    2.6418  -1.6893  -1.7355
 3YA  C16  C  C1     0  -0.301    1.3002  -1.3788  -1.8822
 3YA  N1   N  NR16   0  -0.719   -8.5866   1.5036   0.2066
 3YA  C2   C  CR6    0   0.676   -9.7596   0.8121   0.1570
 3YA  N3   N  N      0  -0.531   -9.8368  -0.4885   0.2623
 3YA  C4   C  CR6    0   0.436   -8.7207  -1.2604   0.4314
 3YA  S5   S  S2     0   0.240   -5.8548   1.4585   0.4702
 3YA  C6   C  CR5    0  -0.143   -5.1661  -0.1375   0.6780
 3YA  C7   C  CR15   0  -0.244   -6.1285  -1.0901   0.6657
 3YA  C8   C  CR56   0  -0.087   -7.4438  -0.5632   0.4936
 3YA  C9   C  CR56   0   0.107   -7.4347   0.7980   0.3766
 3YA  C12  C  C      0  -0.060    3.5254  -0.7745  -1.1679
 3YA  C17  C  C      0   0.537    4.9650  -1.1618  -1.0433
 3YA  O18  O  O      0  -0.505    5.4414  -2.0356  -1.7605
 3YA  N19  N  NH1    0  -0.632    5.6859  -0.4872  -0.1382
 3YA  C20  C  CH1    0  -0.193    7.0547  -0.8320   0.1724
 3YA  C21  C  CH2    0  -0.444    7.7406   0.3466   0.8639
 3YA  C22  C  CH2    0  -0.578    7.8466   1.5824  -0.0155
 3YA  C23  C  C      0   0.412    8.5749   2.7847   0.6097
 3YA  O24  O  OC    -1  -0.634    8.7661   3.7609  -0.1465
 3YA  O25  O  O      0  -0.609    8.9100   2.7058   1.8081
 3YA  C26  C  C      0   0.411    7.1658  -2.1222   1.0260
 3YA  O27  O  OC    -1  -0.618    8.3232  -2.5718   1.1475
 3YA  O28  O  O      0  -0.599    6.1238  -2.5848   1.5205
 3YA  C29  C  CH2    0  -0.503   -3.6886  -0.2974   0.8047
 3YA  C30  C  CH2    0  -0.422   -2.9235   0.0756  -0.4657
 3YA  C31  C  CH2    0  -0.418   -1.4304  -0.1905  -0.3344
 3YA  C33  C  C      0   0.137    0.8015  -0.1400  -1.4845
 3YA  C15  C  C1     0  -0.297    1.6920   0.7790  -0.9344
 3YA  H1   H  H      0   0.252    3.6948   1.2263  -0.3697
 3YA  H2   H  H      0   0.254    3.0058  -2.6541  -2.0634
 3YA  H3   H  H      0   0.249    0.6310  -2.1096  -2.3214
 3YA  H5   H  HCR5   0   0.265   -5.9133  -2.1437   0.7769
 3YA  H6   H  HNH2   0   0.415  -10.8708   2.5353   0.0374
 3YA  H7   H  HNH2   0   0.413  -11.7564   1.0653   0.0453
 3YA  H8   H  HNH1   0   0.390    5.1899   0.0539   0.5520
 3YA  H9   H  HCH1   0   0.229    7.5723  -1.0169  -0.7736
 3YA  H10  H  HCH2   0   0.211    7.2096   0.5874   1.7906
 3YA  H11  H  HCH2   0   0.226    8.7368   0.0190   1.1620
 3YA  H12  H  HCH2   0   0.217    8.3511   1.3184  -0.9522
 3YA  H13  H  HCH2   0   0.223    6.8495   1.9187  -0.3206
 3YA  H16  H  HCH2   0   0.254   -3.3117   0.2942   1.6445
 3YA  H17  H  HCH2   0   0.257   -3.4947  -1.3437   1.0540
 3YA  H18  H  HCH2   0   0.232   -3.3267  -0.4932  -1.3088
 3YA  H19  H  HCH2   0   0.225   -3.0858   1.1323  -0.7011
 3YA  H20  H  HCH2   0   0.229   -1.0256   0.3733   0.5122
 3YA  H21  H  HCH2   0   0.229   -1.2676  -1.2481  -0.1048
 3YA  H24  H  H      0   0.252    1.3341   1.7558  -0.6313
 3YA  H25  H  HNR6   0   0.436   -8.5777   2.5098   0.1225
 3YA  C32  C  CH2    0  -0.510   -0.6607   0.1775  -1.6041
 3YA  O10  O  O      0  -0.490   -8.8007  -2.4810   0.5267
 3YA  H22  H  HCH2   0   0.242   -1.0886  -0.3632  -2.4525
 3YA  H23  H  HCH2   0   0.243   -0.7945   1.2430  -1.8102
 3YA  N11  N  NH2    0  -0.825  -10.8701   1.5326  -0.0378

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
 3YA  O18  C17  double    1.227  0.020  1.227
 3YA  O28  C26  deloc     1.243  0.020  1.243
 3YA  O25  C23  deloc     1.247  0.020  1.247
 3YA  O24  C23  deloc     1.250  0.020  1.250
 3YA  C17  C12  single    1.496  0.020  1.496
 3YA  C17  N19  single    1.339  0.020  1.339
 3YA  C23  C22  single    1.538  0.020  1.538
 3YA  C26  C20  single    1.551  0.020  1.551
 3YA  C26  O27  deloc     1.248  0.020  1.248
 3YA  C20  N19  single    1.445  0.020  1.445
 3YA  C20  C21  single    1.529  0.020  1.529
 3YA  C12  C14  aromatic  1.393  0.020  1.393
 3YA  C12  C13  aromatic  1.394  0.020  1.394
 3YA  C14  C16  aromatic  1.385  0.020  1.385
 3YA  C13  C15  aromatic  1.387  0.020  1.387
 3YA  C16  C33  aromatic  1.393  0.020  1.393
 3YA  C21  C22  single    1.520  0.020  1.520
 3YA  C15  C33  aromatic  1.393  0.020  1.393
 3YA  C33  C32  single    1.501  0.020  1.501
 3YA  C32  C31  single    1.530  0.020  1.530
 3YA  C31  C30  single    1.522  0.020  1.522
 3YA  C30  C29  single    1.529  0.020  1.529
 3YA  C29  C6   single    1.491  0.020  1.491
 3YA  C6   S5   aromatic  1.751  0.020  1.751
 3YA  C6   C7   aromatic  1.354  0.020  1.354
 3YA  S5   C9   aromatic  1.715  0.020  1.715
 3YA  C7   C8   aromatic  1.427  0.020  1.427
 3YA  C8   C9   aromatic  1.366  0.020  1.366
 3YA  C8   C4   single    1.456  0.020  1.456
 3YA  C9   N1   single    1.362  0.020  1.362
 3YA  N1   C2   single    1.363  0.020  1.363
 3YA  C4   O10  double    1.227  0.020  1.227
 3YA  C4   N3   single    1.368  0.020  1.368
 3YA  C2   N3   double    1.307  0.020  1.307
 3YA  C2   N11  single    1.338  0.020  1.338
 3YA  C13  H1   single    0.930  0.020  1.080
 3YA  C14  H2   single    0.930  0.020  1.080
 3YA  C16  H3   single    0.930  0.020  1.080
 3YA  C7   H5   single    0.930  0.020  1.080
 3YA  N11  H6   single    0.890  0.020  1.040
 3YA  N11  H7   single    0.890  0.020  1.040
 3YA  N19  H8   single    0.890  0.020  1.040
 3YA  C20  H9   single    0.970  0.020  1.090
 3YA  C21  H10  single    0.970  0.020  1.090
 3YA  C21  H11  single    0.970  0.020  1.090
 3YA  C22  H12  single    0.970  0.020  1.090
 3YA  C22  H13  single    0.970  0.020  1.090
 3YA  C29  H16  single    0.970  0.020  1.090
 3YA  C29  H17  single    0.970  0.020  1.090
 3YA  C30  H18  single    0.970  0.020  1.090
 3YA  C30  H19  single    0.970  0.020  1.090
 3YA  C31  H20  single    0.970  0.020  1.090
 3YA  C31  H21  single    0.970  0.020  1.090
 3YA  C32  H22  single    0.970  0.020  1.090
 3YA  C32  H23  single    0.970  0.020  1.090
 3YA  C15  H24  single    0.930  0.020  1.080
 3YA  N1   H25  single    0.860  0.020  1.020

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
 3YA  H1   C13  C15  118.51  3.000
 3YA  H1   C13  C12  120.93  3.000
 3YA  C15  C13  C12  120.54  3.000
 3YA  H2   C14  C12  119.72  3.000
 3YA  H2   C14  C16  119.58  3.000
 3YA  C12  C14  C16  120.70  3.000
 3YA  H3   C16  C33  119.61  3.000
 3YA  H3   C16  C14  119.33  3.000
 3YA  C33  C16  C14  121.05  3.000
 3YA  H25  N1   C9   121.29  3.000
 3YA  H25  N1   C2   120.68  3.000
 3YA  C9   N1   C2   118.02  3.000
 3YA  N11  C2   N3   119.90  3.000
 3YA  N11  C2   N1   116.52  3.000
 3YA  N3   C2   N1   123.57  3.000
 3YA  C4   N3   C2   121.55  3.000
 3YA  O10  C4   C8   122.02  3.000
 3YA  O10  C4   N3   121.19  3.000
 3YA  C8   C4   N3   116.79  3.000
 3YA  C9   S5   C6    91.02  3.000
 3YA  C29  C6   C7   129.00  3.000
 3YA  C7   C6   S5   111.14  3.000
 3YA  C29  C6   S5   119.84  3.000
 3YA  H5   C7   C8   123.76  3.000
 3YA  H5   C7   C6   122.89  3.000
 3YA  C8   C7   C6   113.35  3.000
 3YA  C9   C8   C7   111.84  3.000
 3YA  C9   C8   C4   118.63  3.000
 3YA  C7   C8   C4   129.53  3.000
 3YA  C8   C9   S5   112.65  3.000
 3YA  C8   C9   N1   121.43  3.000
 3YA  S5   C9   N1   125.92  3.000
 3YA  C17  C12  C14  118.32  3.000
 3YA  C14  C12  C13  118.51  3.000
 3YA  C17  C12  C13  123.15  3.000
 3YA  N19  C17  O18  123.02  3.000
 3YA  N19  C17  C12  116.35  3.000
 3YA  O18  C17  C12  120.62  3.000
 3YA  H8   N19  C20  116.55  3.000
 3YA  H8   N19  C17  117.94  3.000
 3YA  C20  N19  C17  122.33  3.000
 3YA  H9   C20  C26  107.54  3.000
 3YA  H9   C20  C21  108.00  3.000
 3YA  C26  C20  C21  111.11  3.000
 3YA  H9   C20  N19  107.61  3.000
 3YA  C21  C20  N19  109.77  3.000
 3YA  C26  C20  N19  112.62  3.000
 3YA  H11  C21  H10  106.13  3.000
 3YA  H11  C21  C22  109.80  3.000
 3YA  H10  C21  C22  110.15  3.000
 3YA  H11  C21  C20  107.58  3.000
 3YA  H10  C21  C20  109.56  3.000
 3YA  C22  C21  C20  113.34  3.000
 3YA  H13  C22  H12  104.76  3.000
 3YA  H13  C22  C23  107.70  3.000
 3YA  H12  C22  C23  108.52  3.000
 3YA  H13  C22  C21  110.31  3.000
 3YA  H12  C22  C21  109.30  3.000
 3YA  C23  C22  C21  115.67  3.000
 3YA  O25  C23  O24  126.15  3.000
 3YA  O24  C23  C22  115.92  3.000
 3YA  O25  C23  C22  117.93  3.000
 3YA  O28  C26  O27  127.23  3.000
 3YA  O27  C26  C20  114.82  3.000
 3YA  O28  C26  C20  117.94  3.000
 3YA  H17  C29  H16  106.34  3.000
 3YA  H17  C29  C30  109.53  3.000
 3YA  H16  C29  C30  109.47  3.000
 3YA  H17  C29  C6   107.33  3.000
 3YA  H16  C29  C6   110.39  3.000
 3YA  C30  C29  C6   113.51  3.000
 3YA  H19  C30  H18  106.35  3.000
 3YA  H19  C30  C31  109.43  3.000
 3YA  H18  C30  C31  109.69  3.000
 3YA  H19  C30  C29  109.88  3.000
 3YA  H18  C30  C29  109.20  3.000
 3YA  C31  C30  C29  112.11  3.000
 3YA  H21  C31  H20  106.29  3.000
 3YA  H21  C31  C32  109.38  3.000
 3YA  H20  C31  C32  109.39  3.000
 3YA  H21  C31  C30  109.45  3.000
 3YA  H20  C31  C30  109.83  3.000
 3YA  C32  C31  C30  112.32  3.000
 3YA  C15  C33  C32  120.97  3.000
 3YA  C32  C33  C16  120.93  3.000
 3YA  C15  C33  C16  118.07  3.000
 3YA  H24  C15  C33  119.61  3.000
 3YA  H24  C15  C13  119.27  3.000
 3YA  C33  C15  C13  121.12  3.000
 3YA  H23  C32  H22  106.73  3.000
 3YA  H23  C32  C33  109.89  3.000
 3YA  H22  C32  C33  109.78  3.000
 3YA  H23  C32  C31  109.23  3.000
 3YA  H22  C32  C31  109.16  3.000
 3YA  C33  C32  C31  111.91  3.000
 3YA  H7   N11  H6   117.17  3.000
 3YA  H7   N11  C2   117.99  3.000
 3YA  H6   N11  C2   121.79  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
 3YA  CONST_01  C16  C14  C12  C13     0.00   0.0  0
 3YA  CONST_02  C16  C33  C15  C13     0.00   0.0  0
 3YA  CONST_03  C15  C13  C12  C14     0.00   0.0  0
 3YA  CONST_04  C15  C33  C16  C14     0.00   0.0  0
 3YA  CONST_05  C8   C7   C6   S5      0.00   0.0  0
 3YA  CONST_06  C7   C8   C9   S5      0.00   0.0  0
 3YA  CONST_07  C8   C9   S5   C6      0.00   0.0  0
 3YA  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 3YA  CONST_09  C9   S5   C6   C7      0.00   0.0  0
 3YA  CONST_10  C33  C16  C14  C12     0.00   0.0  0
 3YA  CONST_11  C33  C15  C13  C12     0.00   0.0  0
 3YA  CONST_12  C4   N3   C2   N1      0.00   0.0  0
 3YA  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 3YA  CONST_14  C32  C33  C15  C13   180.00   0.0  0
 3YA  CONST_15  C32  C33  C16  C14   180.00   0.0  0
 3YA  CONST_16  C17  C12  C14  C16   180.00   0.0  0
 3YA  CONST_17  C29  C6   C7   C8    180.00   0.0  0
 3YA  CONST_18  C29  C6   S5   C9    180.00   0.0  0
 3YA  CONST_19  C15  C13  C12  C17   180.00   0.0  0
 3YA  CONST_20  N11  C2   N3   C4    180.00   0.0  0
 3YA  CONST_21  N11  C2   N1   C9    180.00   0.0  0
 3YA  CONST_22  H2   C14  C12  C13   180.00   0.0  0
 3YA  CONST_23  H1   C13  C12  C14   180.00   0.0  0
 3YA  CONST_24  H24  C15  C33  C16   180.00   0.0  0
 3YA  CONST_25  H5   C7   C8   C4      0.00   0.0  0
 3YA  CONST_26  H3   C16  C14  C12   180.00   0.0  0
 3YA  CONST_27  H25  N1   C2   N3    180.00   0.0  0
 3YA  CONST_28  H6   N11  C2   N1      0.00   0.0  0
 3YA  CONST_29  H7   N11  C2   N1    180.00   0.0  0
 3YA  CONST_30  C20  N19  C17  C12   180.00   0.0  0
 3YA  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YA  Var_01    O18  C17  C12  C13  -156.04  30.0  2
 3YA  Var_02    C31  C32  C33  C16    90.82  30.0  2
 3YA  Var_03    C30  C29  C6   S5    -66.07  30.0  2
 3YA  Var_04    C31  C30  C29  C6   -176.03  30.0  1
 3YA  Var_05    C33  C32  C31  C30  -177.70  30.0  1
 3YA  Var_06    C23  C22  C21  C20  -177.84  30.0  3
 3YA  Var_07    O25  C23  C22  C21    -6.35  30.0  3
 3YA  Var_08    C32  C31  C30  C29   179.84  30.0  1

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
 3YA  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
 3YA  plan-1  C13  0.020
 3YA  plan-1  C14  0.020
 3YA  plan-1  C16  0.020
 3YA  plan-1  C12  0.020
 3YA  plan-1  C17  0.020
 3YA  plan-1  C33  0.020
 3YA  plan-1  C15  0.020
 3YA  plan-1  H1   0.020
 3YA  plan-1  H2   0.020
 3YA  plan-1  H3   0.020
 3YA  plan-1  H24  0.020
 3YA  plan-1  C32  0.020
 3YA  plan-2  N1   0.020
 3YA  plan-2  C2   0.020
 3YA  plan-2  N3   0.020
 3YA  plan-2  C4   0.020
 3YA  plan-2  S5   0.020
 3YA  plan-2  C6   0.020
 3YA  plan-2  C7   0.020
 3YA  plan-2  C8   0.020
 3YA  plan-2  C9   0.020
 3YA  plan-2  C29  0.020
 3YA  plan-2  H5   0.020
 3YA  plan-2  H6   0.020
 3YA  plan-2  H7   0.020
 3YA  plan-2  H25  0.020
 3YA  plan-2  O10  0.020
 3YA  plan-2  N11  0.020
 3YA  plan-3  C12  0.020
 3YA  plan-3  C17  0.020
 3YA  plan-3  O18  0.020
 3YA  plan-3  N19  0.020
 3YA  plan-3  C20  0.020
 3YA  plan-3  H8   0.020
 3YA  plan-4  C22  0.020
 3YA  plan-4  C23  0.020
 3YA  plan-4  O24  0.020
 3YA  plan-4  O25  0.020
 3YA  plan-5  C20  0.020
 3YA  plan-5  C26  0.020
 3YA  plan-5  O27  0.020
 3YA  plan-5  O28  0.020

