# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 02:15:03 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: N-{5-[3-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)propyl]thiophene-2-carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2sc(CCCc3sc(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
 V9V  V9V  'N-{5-[3-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)propyl]thiophene-2-carbonyl}-L-glutamic acid'  ligand  49  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V9V
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
 V9V  C8   C  CR56   0  -0.067  -25.1446  13.5211  26.3608
 V9V  C6   C  CR5    0  -0.148  -26.6833  12.4957  27.7592
 V9V  N1   N  N      0  -0.494  -23.9858  11.7379  25.1649
 V9V  C2   C  CR6    0   0.688  -23.2894  12.6621  24.5518
 V9V  N3   N  NR16   0  -0.716  -23.4651  13.9934  24.7906
 V9V  C4   C  CR6    0   0.528  -24.3845  14.5321  25.6890
 V9V  C7   C  CR15   0  -0.232  -26.1708  13.6761  27.3397
 V9V  C13  C  CR5    0  -0.318  -25.5910  10.0321  34.0552
 V9V  C14  C  CR15   0  -0.179  -24.3713  10.2644  33.4888
 V9V  C15  C  CR15   0  -0.226  -24.4502  11.0199  32.2925
 V9V  C16  C  CR5    0  -0.122  -25.7261  11.3715  31.9574
 V9V  C20  C  CH1    0  -0.177  -27.5471   8.0201  36.5849
 V9V  C21  C  CH2    0  -0.410  -27.8480   8.8712  37.8285
 V9V  C22  C  CH2    0  -0.580  -28.1409   8.0738  39.0888
 V9V  C23  C  C      0   0.406  -28.2961   8.9064  40.3772
 V9V  C26  C  C      0   0.416  -28.7963   7.2407  36.0992
 V9V  C29  C  CH2    0  -0.512  -27.7549  12.2477  28.7662
 V9V  C30  C  CH2    0  -0.445  -27.2899  11.4449  29.9814
 V9V  C31  C  CH2    0  -0.486  -26.1983  12.1567  30.7792
 V9V  C9   C  CR56   0  -0.014  -24.8840  12.2002  26.0476
 V9V  N11  N  NH2    0  -0.829  -22.3416  12.3077  23.6744
 V9V  N19  N  NH1    0  -0.665  -27.0994   8.8582  35.4909
 V9V  O10  O  O      0  -0.459  -24.4749  15.7396  25.8339
 V9V  O18  O  O      0  -0.496  -24.8993   8.9530  36.0251
 V9V  O24  O  O      0  -0.625  -28.8494   8.3255  41.3349
 V9V  O25  O  OC    -1  -0.607  -27.8448  10.0697  40.3776
 V9V  O27  O  O      0  -0.598  -29.4384   7.7630  35.1627
 V9V  O28  O  OC    -1  -0.588  -29.0590   6.1823  36.6939
 V9V  S12  S  S2     0   0.214  -26.8420  10.7674  33.1206
 V9V  S5   S  S2     0   0.192  -25.9047  11.1472  26.9624
 V9V  H2   H  HCR5   0   0.264  -26.5134  14.6310  27.7141
 V9V  H3   H  HCR5   0   0.264  -23.4473   9.8906  33.9063
 V9V  H4   H  HCR5   0   0.261  -23.5927  11.2963  31.6944
 V9V  H5   H  HCH1   0   0.221  -26.7561   7.3054  36.8296
 V9V  H6   H  HCH2   0   0.215  -26.9874   9.5178  38.0115
 V9V  H7   H  HCH2   0   0.200  -28.6840   9.5409  37.5998
 V9V  H8   H  HCH2   0   0.215  -29.0335   7.4611  38.9584
 V9V  H9   H  HCH2   0   0.211  -27.3259   7.3568  39.2549
 V9V  H10  H  HCH2   0   0.258  -28.1387  13.2175  29.0929
 V9V  H11  H  HCH2   0   0.265  -28.5933  11.7236  28.2993
 V9V  H12  H  HCH2   0   0.245  -28.1595  11.2666  30.6190
 V9V  H13  H  HCH2   0   0.240  -26.9329  10.4594  29.6689
 V9V  H14  H  HCH2   0   0.256  -26.5707  13.1338  31.1032
 V9V  H15  H  HCH2   0   0.260  -25.3333  12.3533  30.1418
 V9V  H16  H  HNH2   0   0.412  -22.2963  11.3403  23.4023
 V9V  H17  H  HNH2   0   0.416  -21.9271  12.9744  23.0447
 V9V  H18  H  HNH1   0   0.384  -27.8204   9.0074  34.7956
 V9V  H1   H  HNR6   0   0.425  -22.8878  14.6626  24.2956
 V9V  C17  C  C      0   0.535  -25.8347   9.2374  35.2829

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
 V9V  C8   C4   single    1.432  0.020  1.432
 V9V  C8   C7   aromatic  1.427  0.020  1.427
 V9V  C8   C9   aromatic  1.382  0.020  1.382
 V9V  C6   C7   aromatic  1.353  0.020  1.353
 V9V  C6   C29  single    1.491  0.020  1.491
 V9V  C6   S5   aromatic  1.749  0.020  1.749
 V9V  N1   C2   double    1.310  0.020  1.310
 V9V  N1   C9   single    1.341  0.020  1.341
 V9V  C2   N3   single    1.364  0.020  1.364
 V9V  C2   N11  single    1.339  0.020  1.339
 V9V  N3   C4   single    1.394  0.020  1.394
 V9V  C4   O10  double    1.219  0.020  1.219
 V9V  C13  C14  aromatic  1.365  0.020  1.365
 V9V  C13  C17  single    1.483  0.020  1.483
 V9V  C13  S12  aromatic  1.726  0.020  1.726
 V9V  C14  C15  aromatic  1.417  0.020  1.417
 V9V  C15  C16  aromatic  1.365  0.020  1.365
 V9V  C16  C31  single    1.493  0.020  1.493
 V9V  C16  S12  aromatic  1.721  0.020  1.721
 V9V  C17  N19  single    1.337  0.020  1.337
 V9V  C17  O18  double    1.227  0.020  1.227
 V9V  C20  C21  single    1.537  0.020  1.537
 V9V  C20  C26  single    1.550  0.020  1.550
 V9V  C20  N19  single    1.449  0.020  1.449
 V9V  C21  C22  single    1.520  0.020  1.520
 V9V  C22  C23  single    1.542  0.020  1.542
 V9V  C23  O24  deloc     1.249  0.020  1.249
 V9V  C23  O25  deloc     1.248  0.020  1.248
 V9V  C26  O27  deloc     1.250  0.020  1.250
 V9V  C26  O28  deloc     1.242  0.020  1.242
 V9V  C29  C30  single    1.529  0.020  1.529
 V9V  C30  C31  single    1.528  0.020  1.528
 V9V  C9   S5   aromatic  1.728  0.020  1.728
 V9V  C7   H2   single    0.930  0.020  1.080
 V9V  C14  H3   single    0.930  0.020  1.080
 V9V  C15  H4   single    0.930  0.020  1.080
 V9V  C20  H5   single    0.970  0.020  1.090
 V9V  C21  H6   single    0.970  0.020  1.090
 V9V  C21  H7   single    0.970  0.020  1.090
 V9V  C22  H8   single    0.970  0.020  1.090
 V9V  C22  H9   single    0.970  0.020  1.090
 V9V  C29  H10  single    0.970  0.020  1.090
 V9V  C29  H11  single    0.970  0.020  1.090
 V9V  C30  H12  single    0.970  0.020  1.090
 V9V  C30  H13  single    0.970  0.020  1.090
 V9V  C31  H14  single    0.970  0.020  1.090
 V9V  C31  H15  single    0.970  0.020  1.090
 V9V  N11  H16  single    0.890  0.020  1.040
 V9V  N11  H17  single    0.890  0.020  1.040
 V9V  N19  H18  single    0.860  0.020  1.020
 V9V  N3   H1   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
 V9V  C9   C8   C7   113.26  3.000
 V9V  C9   C8   C4   117.92  3.000
 V9V  C7   C8   C4   128.82  3.000
 V9V  S5   C6   C29  119.95  3.000
 V9V  S5   C6   C7   111.26  3.000
 V9V  C29  C6   C7   128.78  3.000
 V9V  C9   N1   C2   114.89  3.000
 V9V  N11  C2   N3   117.65  3.000
 V9V  N11  C2   N1   119.76  3.000
 V9V  N3   C2   N1   122.57  3.000
 V9V  H1   N3   C4   115.82  3.000
 V9V  H1   N3   C2   119.07  3.000
 V9V  C4   N3   C2   125.11  3.000
 V9V  O10  C4   N3   120.54  3.000
 V9V  O10  C4   C8   127.15  3.000
 V9V  N3   C4   C8   112.31  3.000
 V9V  H2   C7   C6   122.88  3.000
 V9V  H2   C7   C8   124.15  3.000
 V9V  C6   C7   C8   112.97  3.000
 V9V  S12  C13  C17  123.89  3.000
 V9V  S12  C13  C14  110.52  3.000
 V9V  C17  C13  C14  125.58  3.000
 V9V  H3   C14  C15  123.93  3.000
 V9V  H3   C14  C13  123.03  3.000
 V9V  C15  C14  C13  113.04  3.000
 V9V  H4   C15  C16  122.65  3.000
 V9V  H4   C15  C14  123.99  3.000
 V9V  C16  C15  C14  113.37  3.000
 V9V  S12  C16  C31  120.86  3.000
 V9V  S12  C16  C15  110.46  3.000
 V9V  C31  C16  C15  128.68  3.000
 V9V  H5   C20  N19  108.87  3.000
 V9V  H5   C20  C26  108.92  3.000
 V9V  N19  C20  C26  107.65  3.000
 V9V  H5   C20  C21  108.81  3.000
 V9V  N19  C20  C21  110.56  3.000
 V9V  C26  C20  C21  111.97  3.000
 V9V  H7   C21  H6   105.94  3.000
 V9V  H7   C21  C22  110.30  3.000
 V9V  H6   C21  C22  108.88  3.000
 V9V  H7   C21  C20  108.61  3.000
 V9V  H6   C21  C20  108.01  3.000
 V9V  C22  C21  C20  114.72  3.000
 V9V  H9   C22  H8   104.99  3.000
 V9V  H9   C22  C23  107.52  3.000
 V9V  H8   C22  C23  108.72  3.000
 V9V  H9   C22  C21  108.96  3.000
 V9V  H8   C22  C21  110.69  3.000
 V9V  C23  C22  C21  115.40  3.000
 V9V  O25  C23  O24  126.40  3.000
 V9V  O25  C23  C22  117.86  3.000
 V9V  O24  C23  C22  115.72  3.000
 V9V  O28  C26  O27  127.31  3.000
 V9V  O28  C26  C20  116.67  3.000
 V9V  O27  C26  C20  116.01  3.000
 V9V  H11  C29  H10  106.48  3.000
 V9V  H11  C29  C30  108.72  3.000
 V9V  H10  C29  C30  109.59  3.000
 V9V  H11  C29  C6   110.02  3.000
 V9V  H10  C29  C6   107.85  3.000
 V9V  C30  C29  C6   113.92  3.000
 V9V  H13  C30  H12  106.22  3.000
 V9V  H13  C30  C31  109.62  3.000
 V9V  H12  C30  C31  109.87  3.000
 V9V  H13  C30  C29  110.20  3.000
 V9V  H12  C30  C29  107.90  3.000
 V9V  C31  C30  C29  112.81  3.000
 V9V  H15  C31  H14  106.35  3.000
 V9V  H15  C31  C30  110.18  3.000
 V9V  H14  C31  C30  109.10  3.000
 V9V  H15  C31  C16  107.75  3.000
 V9V  H14  C31  C16  110.09  3.000
 V9V  C30  C31  C16  113.15  3.000
 V9V  S5   C9   N1   122.25  3.000
 V9V  S5   C9   C8   110.54  3.000
 V9V  N1   C9   C8   127.20  3.000
 V9V  H17  N11  H16  116.70  3.000
 V9V  H17  N11  C2   121.74  3.000
 V9V  H16  N11  C2   117.61  3.000
 V9V  H18  N19  C20  112.56  3.000
 V9V  H18  N19  C17  121.67  3.000
 V9V  C20  N19  C17  125.02  3.000
 V9V  C16  S12  C13   92.61  3.000
 V9V  C9   S5   C6    91.96  3.000
 V9V  O18  C17  N19  124.14  3.000
 V9V  O18  C17  C13  119.97  3.000
 V9V  N19  C17  C13  115.88  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
 V9V  CONST_01  S5   C6   C7   C8      0.00   0.0  0
 V9V  CONST_02  C6   S5   C9   C8      0.00   0.0  0
 V9V  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 V9V  CONST_04  S5   C9   C8   C7      0.00   0.0  0
 V9V  CONST_05  C9   S5   C6   C7      0.00   0.0  0
 V9V  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 V9V  CONST_07  C15  C16  S12  C13     0.00   0.0  0
 V9V  CONST_08  C16  S12  C13  C14     0.00   0.0  0
 V9V  CONST_09  S12  C16  C15  C14     0.00   0.0  0
 V9V  CONST_10  S12  C13  C14  C15     0.00   0.0  0
 V9V  CONST_11  C2   N3   C4   C8      0.00   0.0  0
 V9V  CONST_12  C4   N3   C2   N1      0.00   0.0  0
 V9V  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 V9V  CONST_14  C29  C6   C7   C8    180.00   0.0  0
 V9V  CONST_15  C31  C16  S12  C13   180.00   0.0  0
 V9V  CONST_16  C31  C16  C15  C14   180.00   0.0  0
 V9V  CONST_17  C17  C13  C14  C15   180.00   0.0  0
 V9V  CONST_18  C17  C13  S12  C16   180.00   0.0  0
 V9V  CONST_19  C9   S5   C6   C29   180.00   0.0  0
 V9V  CONST_20  O10  C4   N3   C2    180.00   0.0  0
 V9V  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 V9V  CONST_22  N11  C2   N1   C9    180.00   0.0  0
 V9V  CONST_23  H2   C7   C8   C4      0.00   0.0  0
 V9V  CONST_24  H4   C15  C14  C13   180.00   0.0  0
 V9V  CONST_25  H3   C14  C15  C16   180.00   0.0  0
 V9V  CONST_26  H1   N3   C4   C8    180.00   0.0  0
 V9V  CONST_27  H16  N11  C2   N1      0.00   0.0  0
 V9V  CONST_28  H17  N11  C2   N1    180.00   0.0  0
 V9V  CONST_29  C20  N19  C17  C13   180.00   0.0  0
 V9V  CONST_30  H18  N19  C17  C13     0.00   0.0  0
 V9V  CONST_31  O18  C17  N19  C20     0.00   0.0  0
 V9V  Var_01    C30  C29  C6   C7   -118.05  30.0  2
 V9V  Var_02    N19  C17  C13  C14  -164.33  30.0  2
 V9V  Var_03    C30  C31  C16  C15   126.82  30.0  2
 V9V  Var_04    C31  C30  C29  C6     62.01  30.0  3
 V9V  Var_05    C29  C30  C31  C16  -179.25  30.0  1
 V9V  Var_06    C23  C22  C21  C20   173.74  30.0  3
 V9V  Var_07    O24  C23  C22  C21   163.13  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
 V9V  chir_01  C20  C21  C26  N19  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
 V9V  plan-1  C13  0.020
 V9V  plan-1  C14  0.020
 V9V  plan-1  C15  0.020
 V9V  plan-1  C16  0.020
 V9V  plan-1  C31  0.020
 V9V  plan-1  S12  0.020
 V9V  plan-1  H3   0.020
 V9V  plan-1  H4   0.020
 V9V  plan-1  C17  0.020
 V9V  plan-2  C8   0.020
 V9V  plan-2  C6   0.020
 V9V  plan-2  N1   0.020
 V9V  plan-2  C2   0.020
 V9V  plan-2  N3   0.020
 V9V  plan-2  C4   0.020
 V9V  plan-2  C7   0.020
 V9V  plan-2  C29  0.020
 V9V  plan-2  C9   0.020
 V9V  plan-2  N11  0.020
 V9V  plan-2  O10  0.020
 V9V  plan-2  S5   0.020
 V9V  plan-2  H2   0.020
 V9V  plan-2  H16  0.020
 V9V  plan-2  H17  0.020
 V9V  plan-2  H1   0.020
 V9V  plan-3  C13  0.020
 V9V  plan-3  C20  0.020
 V9V  plan-3  N19  0.020
 V9V  plan-3  O18  0.020
 V9V  plan-3  H18  0.020
 V9V  plan-3  C17  0.020
 V9V  plan-4  C22  0.020
 V9V  plan-4  C23  0.020
 V9V  plan-4  O24  0.020
 V9V  plan-4  O25  0.020
 V9V  plan-5  C20  0.020
 V9V  plan-5  C26  0.020
 V9V  plan-5  O27  0.020
 V9V  plan-5  O28  0.020

