# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 07:55:15 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{5-[4-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]furan-2-carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2sc(CCCCc3oc(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
 V9A  V9A  'N-{5-[4-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]furan-2-carbonyl}-L-glutamic acid'  ligand  52  32  .  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_V9A
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
 V9A  O25  O  OC    -1  -0.624  -30.9092   9.9182  37.9316
 V9A  C26  C  C      0   0.409  -27.0947   6.2314  34.6633
 V9A  C30  C  CH2    0  -0.508  -28.2611  13.0417  29.1485
 V9A  C32  C  CH2    0  -0.424  -26.8151  12.4821  31.1865
 V9A  C31  C  CH2    0  -0.419  -27.6614  13.5250  30.4715
 V9A  C20  C  CH1    0  -0.186  -27.3580   7.4488  35.5970
 V9A  C16  C  CR5    0   0.399  -25.4228  12.0444  33.2431
 V9A  C22  C  CH2    0  -0.574  -29.1574   8.6996  36.9048
 V9A  C21  C  CH2    0  -0.444  -28.8526   7.6273  35.8697
 V9A  C13  C  CR5    0   0.204  -25.1130  10.2091  34.3950
 V9A  C8   C  CR56   0  -0.063  -25.6215  12.9848  26.4527
 V9A  C9   C  CR56   0  -0.019  -25.5930  11.6090  26.5918
 V9A  C4   C  CR6    0   0.527  -24.7446  13.5789  25.4869
 V9A  C14  C  CR15   0  -0.313  -23.8885  10.7777  34.2518
 V9A  C15  C  CR15   0  -0.384  -24.0901  11.9690  33.5025
 V9A  C2   C  CR6    0   0.688  -24.0301  11.2836  25.0281
 V9A  C23  C  C      0   0.408  -30.6484   8.9104  37.2412
 V9A  C6   C  CR5    0  -0.159  -27.2344  12.7429  28.1018
 V9A  C7   C  CR15   0  -0.226  -26.5609  13.6189  27.3175
 V9A  N1   N  N      0  -0.495  -24.8250  10.7407  25.9150
 V9A  N19  N  NH1    0  -0.634  -26.8202   8.6839  35.0724
 V9A  N3   N  NR16   0  -0.716  -23.9795  12.6299  24.8129
 V9A  O12  O  O      0  -0.439  -26.0453  10.9769  33.7821
 V9A  O18  O  O      0  -0.499  -24.6621   8.2993  35.6574
 V9A  O24  O  O      0  -0.605  -31.4658   8.0681  36.8189
 V9A  O28  O  O      0  -0.593  -26.6390   6.4578  33.5295
 V9A  S5   S  S2     0   0.198  -26.7246  11.1019  27.7938
 V9A  H2   H  HCH2   0   0.262  -28.9267  13.8160  28.7611
 V9A  H3   H  HCH2   0   0.249  -28.8882  12.1647  29.3298
 V9A  H4   H  HCH2   0   0.228  -27.4203  11.5917  31.3802
 V9A  H5   H  HCH2   0   0.232  -25.9852  12.1632  30.5501
 V9A  H6   H  HCH2   0   0.226  -27.0629  14.4210  30.2835
 V9A  H7   H  HCH2   0   0.232  -28.4821  13.8335  31.1261
 V9A  H10  H  HCH1   0   0.225  -26.8620   7.2464  36.5512
 V9A  H11  H  HCH2   0   0.216  -28.6347   8.4527  37.8379
 V9A  H12  H  HCH2   0   0.212  -28.7392   9.6620  36.5958
 V9A  H13  H  HCH2   0   0.207  -29.3632   7.8563  34.9272
 V9A  H14  H  HCH2   0   0.223  -29.2484   6.6693  36.2040
 V9A  H15  H  HCR5   0   0.264  -22.9569  10.3946  34.6353
 V9A  H16  H  HCR5   0   0.261  -23.3444  12.6843  33.1949
 V9A  H17  H  HCR5   0   0.261  -26.7277  14.6872  27.3490
 V9A  H20  H  HNH1   0   0.390  -27.4303   9.2366  34.4901
 V9A  H21  H  HNR6   0   0.425  -23.3464  12.9917  24.1099
 V9A  C17  C  C      0   0.479  -25.5143   8.9727  35.0859
 V9A  N11  N  NH2    0  -0.831  -23.2474  10.5066  24.2690
 V9A  O27  O  OC    -1  -0.610  -27.3880   5.1247  35.1583
 V9A  C33  C  CH2    0  -0.541  -26.2515  13.0251  32.5018
 V9A  O10  O  O      0  -0.460  -24.6278  14.7655  25.2301
 V9A  H8   H  HCH2   0   0.257  -25.6304  13.9000  32.2985
 V9A  H18  H  HNH2   0   0.413  -23.1864   9.5300  24.5021
 V9A  H19  H  HNH2   0   0.416  -22.5088  10.8879  23.7025
 V9A  H9   H  HCH2   0   0.254  -27.0741  13.3682  33.1377

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
 V9A  N11  C2   single    1.339  0.020  1.339
 V9A  N3   C2   single    1.364  0.020  1.364
 V9A  N3   C4   single    1.393  0.020  1.393
 V9A  C2   N1   double    1.309  0.020  1.309
 V9A  O10  C4   double    1.220  0.020  1.220
 V9A  C4   C8   single    1.433  0.020  1.433
 V9A  N1   C9   single    1.342  0.020  1.342
 V9A  C8   C9   aromatic  1.383  0.020  1.383
 V9A  C8   C7   aromatic  1.426  0.020  1.426
 V9A  C9   S5   aromatic  1.727  0.020  1.727
 V9A  C7   C6   aromatic  1.355  0.020  1.355
 V9A  S5   C6   aromatic  1.746  0.020  1.746
 V9A  C6   C30  single    1.496  0.020  1.496
 V9A  C30  C31  single    1.531  0.020  1.531
 V9A  C31  C32  single    1.522  0.020  1.522
 V9A  C32  C33  single    1.531  0.020  1.531
 V9A  C33  C16  single    1.483  0.020  1.483
 V9A  O28  C26  deloc     1.243  0.020  1.243
 V9A  C16  C15  aromatic  1.360  0.020  1.360
 V9A  C16  O12  aromatic  1.348  0.020  1.348
 V9A  C15  C14  aromatic  1.422  0.020  1.422
 V9A  O12  C13  aromatic  1.354  0.020  1.354
 V9A  C14  C13  aromatic  1.358  0.020  1.358
 V9A  C26  O27  deloc     1.247  0.020  1.247
 V9A  C26  C20  single    1.557  0.020  1.557
 V9A  C13  C17  single    1.472  0.020  1.472
 V9A  N19  C17  single    1.337  0.020  1.337
 V9A  N19  C20  single    1.446  0.020  1.446
 V9A  C17  O18  double    1.227  0.020  1.227
 V9A  C20  C21  single    1.530  0.020  1.530
 V9A  C21  C22  single    1.521  0.020  1.521
 V9A  C22  C23  single    1.543  0.020  1.543
 V9A  O24  C23  deloc     1.247  0.020  1.247
 V9A  C23  O25  deloc     1.249  0.020  1.249
 V9A  C30  H2   single    0.970  0.020  1.090
 V9A  C30  H3   single    0.970  0.020  1.090
 V9A  C32  H4   single    0.970  0.020  1.090
 V9A  C32  H5   single    0.970  0.020  1.090
 V9A  C31  H6   single    0.970  0.020  1.090
 V9A  C31  H7   single    0.970  0.020  1.090
 V9A  C33  H8   single    0.970  0.020  1.090
 V9A  C33  H9   single    0.970  0.020  1.090
 V9A  C20  H10  single    0.970  0.020  1.090
 V9A  C22  H11  single    0.970  0.020  1.090
 V9A  C22  H12  single    0.970  0.020  1.090
 V9A  C21  H13  single    0.970  0.020  1.090
 V9A  C21  H14  single    0.970  0.020  1.090
 V9A  C14  H15  single    0.930  0.020  1.080
 V9A  C15  H16  single    0.930  0.020  1.080
 V9A  C7   H17  single    0.930  0.020  1.080
 V9A  N11  H18  single    0.890  0.020  1.040
 V9A  N11  H19  single    0.890  0.020  1.040
 V9A  N19  H20  single    0.860  0.020  1.020
 V9A  N3   H21  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
 V9A  O28  C26  O27  127.58  3.000
 V9A  O27  C26  C20  114.59  3.000
 V9A  O28  C26  C20  117.83  3.000
 V9A  H3   C30  H2   106.14  3.000
 V9A  H3   C30  C6   110.45  3.000
 V9A  H2   C30  C6   108.15  3.000
 V9A  H3   C30  C31  109.55  3.000
 V9A  H2   C30  C31  108.75  3.000
 V9A  C6   C30  C31  113.51  3.000
 V9A  H5   C32  H4   106.60  3.000
 V9A  H5   C32  C33  108.92  3.000
 V9A  H4   C32  C33  109.89  3.000
 V9A  H5   C32  C31  110.40  3.000
 V9A  H4   C32  C31  109.47  3.000
 V9A  C33  C32  C31  111.43  3.000
 V9A  H7   C31  H6   106.39  3.000
 V9A  H7   C31  C32  109.23  3.000
 V9A  H6   C31  C32  109.75  3.000
 V9A  H7   C31  C30  108.20  3.000
 V9A  H6   C31  C30  108.93  3.000
 V9A  C32  C31  C30  114.05  3.000
 V9A  H10  C20  N19  107.81  3.000
 V9A  H10  C20  C21  108.00  3.000
 V9A  N19  C20  C21  109.18  3.000
 V9A  H10  C20  C26  107.56  3.000
 V9A  C21  C20  C26  111.31  3.000
 V9A  N19  C20  C26  112.80  3.000
 V9A  O12  C16  C15  109.41  3.000
 V9A  O12  C16  C33  117.75  3.000
 V9A  C15  C16  C33  132.84  3.000
 V9A  H12  C22  H11  104.83  3.000
 V9A  H12  C22  C23  108.11  3.000
 V9A  H11  C22  C23  107.79  3.000
 V9A  H12  C22  C21  110.57  3.000
 V9A  H11  C22  C21  108.93  3.000
 V9A  C23  C22  C21  116.00  3.000
 V9A  H14  C21  H13  106.16  3.000
 V9A  H14  C21  C22  109.78  3.000
 V9A  H13  C21  C22  110.15  3.000
 V9A  H14  C21  C20  107.89  3.000
 V9A  H13  C21  C20  109.04  3.000
 V9A  C22  C21  C20  113.54  3.000
 V9A  O12  C13  C14  109.62  3.000
 V9A  C14  C13  C17  130.33  3.000
 V9A  O12  C13  C17  120.05  3.000
 V9A  C7   C8   C4   128.86  3.000
 V9A  C7   C8   C9   113.27  3.000
 V9A  C4   C8   C9   117.87  3.000
 V9A  S5   C9   N1   122.40  3.000
 V9A  S5   C9   C8   110.40  3.000
 V9A  N1   C9   C8   127.20  3.000
 V9A  O10  C4   N3   120.56  3.000
 V9A  O10  C4   C8   127.13  3.000
 V9A  N3   C4   C8   112.31  3.000
 V9A  H15  C14  C15  127.44  3.000
 V9A  H15  C14  C13  126.38  3.000
 V9A  C15  C14  C13  106.18  3.000
 V9A  H16  C15  C14  127.46  3.000
 V9A  H16  C15  C16  125.92  3.000
 V9A  C14  C15  C16  106.62  3.000
 V9A  N3   C2   N11  117.49  3.000
 V9A  N3   C2   N1   122.60  3.000
 V9A  N11  C2   N1   119.90  3.000
 V9A  O24  C23  C22  117.85  3.000
 V9A  O24  C23  O25  126.52  3.000
 V9A  C22  C23  O25  115.63  3.000
 V9A  S5   C6   C7   111.13  3.000
 V9A  S5   C6   C30  120.76  3.000
 V9A  C7   C6   C30  128.09  3.000
 V9A  H17  C7   C6   123.02  3.000
 V9A  H17  C7   C8   123.96  3.000
 V9A  C6   C7   C8   113.02  3.000
 V9A  C2   N1   C9   114.89  3.000
 V9A  H20  N19  C17  118.57  3.000
 V9A  H20  N19  C20  116.92  3.000
 V9A  C17  N19  C20  122.96  3.000
 V9A  H21  N3   C2   119.02  3.000
 V9A  H21  N3   C4   115.84  3.000
 V9A  C2   N3   C4   125.14  3.000
 V9A  C13  O12  C16  108.18  3.000
 V9A  C6   S5   C9    92.18  3.000
 V9A  O18  C17  N19  124.35  3.000
 V9A  O18  C17  C13  119.34  3.000
 V9A  N19  C17  C13  116.28  3.000
 V9A  H19  N11  H18  117.00  3.000
 V9A  H19  N11  C2   121.91  3.000
 V9A  H18  N11  C2   117.87  3.000
 V9A  H9   C33  H8   106.52  3.000
 V9A  H9   C33  C16  109.69  3.000
 V9A  H8   C33  C16  107.76  3.000
 V9A  H9   C33  C32  109.49  3.000
 V9A  H8   C33  C32  109.49  3.000
 V9A  C16  C33  C32  113.63  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
 V9A  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 V9A  CONST_02  C14  C13  O12  C16     0.00   0.0  0
 V9A  CONST_03  C15  C16  O12  C13     0.00   0.0  0
 V9A  CONST_04  C6   S5   C9   C8      0.00   0.0  0
 V9A  CONST_05  S5   C6   C7   C8      0.00   0.0  0
 V9A  CONST_06  C6   C7   C8   C9      0.00   0.0  0
 V9A  CONST_07  C7   C6   S5   C9      0.00   0.0  0
 V9A  CONST_08  O12  C16  C15  C14     0.00   0.0  0
 V9A  CONST_09  O12  C13  C14  C15     0.00   0.0  0
 V9A  CONST_10  S5   C9   C8   C7      0.00   0.0  0
 V9A  CONST_11  C2   N3   C4   C8      0.00   0.0  0
 V9A  CONST_12  N3   C2   N1   C9      0.00   0.0  0
 V9A  CONST_13  N1   C2   N3   C4      0.00   0.0  0
 V9A  CONST_14  C8   C7   C6   C30   180.00   0.0  0
 V9A  CONST_15  C9   S5   C6   C30   180.00   0.0  0
 V9A  CONST_16  C14  C15  C16  C33   180.00   0.0  0
 V9A  CONST_17  C13  O12  C16  C33   180.00   0.0  0
 V9A  CONST_18  C17  C13  O12  C16   180.00   0.0  0
 V9A  CONST_19  C15  C14  C13  C17   180.00   0.0  0
 V9A  CONST_20  N11  C2   N1   C9    180.00   0.0  0
 V9A  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 V9A  CONST_22  O10  C4   N3   C2    180.00   0.0  0
 V9A  CONST_23  H15  C14  C15  C16   180.00   0.0  0
 V9A  CONST_24  H16  C15  C14  C13   180.00   0.0  0
 V9A  CONST_25  H17  C7   C8   C9    180.00   0.0  0
 V9A  CONST_26  H21  N3   C4   C8    180.00   0.0  0
 V9A  CONST_27  H18  N11  C2   N1      0.00   0.0  0
 V9A  CONST_28  H19  N11  C2   N1    180.00   0.0  0
 V9A  CONST_29  C13  C17  N19  C20   180.00   0.0  0
 V9A  CONST_30  H20  N19  C17  C13     0.00   0.0  0
 V9A  CONST_31  O18  C17  N19  C20     0.00   0.0  0
 V9A  Var_01    C15  C16  C33  C32   110.26  30.0  2
 V9A  Var_02    C7   C6   C30  C31   -78.44  30.0  1
 V9A  Var_03    N19  C17  C13  C14   178.85  30.0  2
 V9A  Var_04    C6   C30  C31  C32   -65.12  30.0  2
 V9A  Var_05    C16  C33  C32  C31   179.72  30.0  3
 V9A  Var_06    C21  C22  C23  O25  -169.58  30.0  2
 V9A  Var_07    C33  C32  C31  C30  -179.75  30.0  3
 V9A  Var_08    C23  C22  C21  C20  -179.00  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
 V9A  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
 V9A  plan-1  C16  0.020
 V9A  plan-1  C13  0.020
 V9A  plan-1  C14  0.020
 V9A  plan-1  C15  0.020
 V9A  plan-1  O12  0.020
 V9A  plan-1  H15  0.020
 V9A  plan-1  H16  0.020
 V9A  plan-1  C17  0.020
 V9A  plan-1  C33  0.020
 V9A  plan-2  C30  0.020
 V9A  plan-2  C8   0.020
 V9A  plan-2  C9   0.020
 V9A  plan-2  C4   0.020
 V9A  plan-2  C2   0.020
 V9A  plan-2  C6   0.020
 V9A  plan-2  C7   0.020
 V9A  plan-2  N1   0.020
 V9A  plan-2  N3   0.020
 V9A  plan-2  S5   0.020
 V9A  plan-2  H17  0.020
 V9A  plan-2  H21  0.020
 V9A  plan-2  N11  0.020
 V9A  plan-2  O10  0.020
 V9A  plan-2  H18  0.020
 V9A  plan-2  H19  0.020
 V9A  plan-3  C20  0.020
 V9A  plan-3  C13  0.020
 V9A  plan-3  N19  0.020
 V9A  plan-3  O18  0.020
 V9A  plan-3  H20  0.020
 V9A  plan-3  C17  0.020
 V9A  plan-4  C26  0.020
 V9A  plan-4  C20  0.020
 V9A  plan-4  O28  0.020
 V9A  plan-4  O27  0.020
 V9A  plan-5  O25  0.020
 V9A  plan-5  C22  0.020
 V9A  plan-5  C23  0.020
 V9A  plan-5  O24  0.020

