# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 08:53:53 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]thiophene-2-carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2sc(CCCCc3sc(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
 V97  V97  'N-{5-[4-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]thiophene-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_V97
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
 V97  C9   C  CR56   0  -0.019  26.0251  -11.9645  -23.1084
 V97  C8   C  CR56   0  -0.064  25.4267  -13.2045  -23.2390
 V97  C13  C  CR5    0  -0.331  26.0515  -10.0677  -15.3550
 V97  C6   C  CR5    0  -0.157  27.0629  -13.7421  -21.6861
 V97  C4   C  CR6    0   0.527  24.3224  -13.3236  -24.1447
 V97  C2   C  CR6    0   0.687  24.6778  -10.9396  -24.5672
 V97  C14  C  CR15   0  -0.172  24.7941  -10.5535  -15.5724
 V97  C15  C  CR15   0  -0.221  24.7885  -11.8073  -16.2296
 V97  C16  C  CR5    0  -0.129  26.0396  -12.2793  -16.5070
 V97  C20  C  CH1    0  -0.136  28.0731   -7.1381  -14.0998
 V97  C21  C  CH2    0  -0.463  29.6035   -7.1453  -14.0858
 V97  C22  C  CH2    0  -0.575  30.2432   -5.9660  -13.3739
 V97  C23  C  C      0   0.407  31.7654   -6.0931  -13.1489
 V97  C26  C  C      0   0.402  27.5204   -5.9235  -14.8909
 V97  C30  C  CH2    0  -0.510  27.9030  -14.4851  -20.6963
 V97  C31  C  CH2    0  -0.416  27.2472  -14.6357  -19.3216
 V97  C32  C  CH2    0  -0.421  26.9869  -13.3177  -18.6063
 V97  C33  C  CH2    0  -0.496  26.4163  -13.5434  -17.2048
 V97  C7   C  CR15   0  -0.226  26.0283  -14.2095  -22.4259
 V97  N1   N  N      0  -0.494  25.6906  -10.8311  -23.7450
 V97  N11  N  NH2    0  -0.831  24.2341   -9.8630  -25.2279
 V97  N19  N  NH1    0  -0.665  27.6418   -8.4037  -14.6630
 V97  N3   N  NR16   0  -0.716  24.0179  -12.1163  -24.7690
 V97  O10  O  O      0  -0.460  23.6766  -14.3286  -24.3899
 V97  O18  O  O      0  -0.492  25.4598   -8.1486  -14.1411
 V97  O24  O  OC    -1  -0.606  32.2680   -7.2339  -13.2037
 V97  O25  O  O      0  -0.622  32.3685   -5.0290  -12.8984
 V97  O27  O  OC    -1  -0.605  27.2708   -4.9043  -14.2184
 V97  O28  O  O      0  -0.604  27.4179   -6.0624  -16.1236
 V97  S12  S  S2     0   0.215  27.2361  -11.1723  -15.9568
 V97  S5   S  S2     0   0.198  27.3276  -12.0405  -21.9769
 V97  H1   H  HCR5   0   0.264  23.9005  -10.0262  -15.2707
 V97  H2   H  HCR5   0   0.261  23.8899  -12.3506  -16.4878
 V97  H3   H  HCH1   0   0.214  27.7174   -7.0791  -13.0668
 V97  H4   H  HCH2   0   0.222  29.9363   -8.0678  -13.6049
 V97  H5   H  HCH2   0   0.209  29.9618   -7.1946  -15.1205
 V97  H6   H  HCH2   0   0.214  30.0411   -5.0332  -13.9036
 V97  H7   H  HCH2   0   0.215  29.7750   -5.8422  -12.3889
 V97  H8   H  HCH2   0   0.262  28.1049  -15.4799  -21.0992
 V97  H9   H  HCH2   0   0.249  28.8757  -13.9988  -20.5847
 V97  H10  H  HCH2   0   0.226  26.3062  -15.1824  -19.4319
 V97  H11  H  HCH2   0   0.232  27.8965  -15.2612  -18.7017
 V97  H12  H  HCH2   0   0.224  27.9175  -12.7449  -18.5399
 V97  H13  H  HCH2   0   0.235  26.2865  -12.7063  -19.1810
 V97  H14  H  HCH2   0   0.255  25.5182  -14.1622  -17.2717
 V97  H15  H  HCH2   0   0.255  27.1363  -14.1070  -16.6047
 V97  H16  H  HCR5   0   0.261  25.7019  -15.2404  -22.3983
 V97  H17  H  HNH2   0   0.413  24.7849   -9.0225  -25.1842
 V97  H18  H  HNH2   0   0.416  23.5748   -9.9393  -25.9838
 V97  H19  H  HNH1   0   0.391  28.3091   -8.8919  -15.2403
 V97  H20  H  HNR6   0   0.425  23.2402  -12.1379  -25.4173
 V97  C17  C  C      0   0.551  26.3588   -8.7872  -14.6773

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
 V97  N11  C2   single    1.339  0.020  1.339
 V97  N3   C2   single    1.364  0.020  1.364
 V97  N3   C4   single    1.393  0.020  1.393
 V97  C2   N1   double    1.309  0.020  1.309
 V97  O10  C4   double    1.219  0.020  1.219
 V97  C4   C8   single    1.433  0.020  1.433
 V97  N1   C9   single    1.342  0.020  1.342
 V97  C8   C9   aromatic  1.383  0.020  1.383
 V97  C8   C7   aromatic  1.426  0.020  1.426
 V97  C9   S5   aromatic  1.727  0.020  1.727
 V97  C7   C6   aromatic  1.355  0.020  1.355
 V97  S5   C6   aromatic  1.746  0.020  1.746
 V97  C6   C30  single    1.496  0.020  1.496
 V97  C30  C31  single    1.531  0.020  1.531
 V97  C31  C32  single    1.522  0.020  1.522
 V97  C32  C33  single    1.530  0.020  1.530
 V97  C33  C16  single    1.492  0.020  1.492
 V97  O28  C26  deloc     1.245  0.020  1.245
 V97  C16  C15  aromatic  1.366  0.020  1.366
 V97  C16  S12  aromatic  1.720  0.020  1.720
 V97  C15  C14  aromatic  1.416  0.020  1.416
 V97  S12  C13  aromatic  1.728  0.020  1.728
 V97  C26  O27  deloc     1.246  0.020  1.246
 V97  C26  C20  single    1.551  0.020  1.551
 V97  C14  C13  aromatic  1.365  0.020  1.365
 V97  C13  C17  single    1.481  0.020  1.481
 V97  N19  C17  single    1.339  0.020  1.339
 V97  N19  C20  single    1.451  0.020  1.451
 V97  C17  O18  double    1.226  0.020  1.226
 V97  C20  C21  single    1.531  0.020  1.531
 V97  C22  C21  single    1.519  0.020  1.519
 V97  C22  C23  single    1.544  0.020  1.544
 V97  O25  C23  deloc     1.248  0.020  1.248
 V97  C23  O24  deloc     1.248  0.020  1.248
 V97  C14  H1   single    0.930  0.020  1.080
 V97  C15  H2   single    0.930  0.020  1.080
 V97  C20  H3   single    0.970  0.020  1.090
 V97  C21  H4   single    0.970  0.020  1.090
 V97  C21  H5   single    0.970  0.020  1.090
 V97  C22  H6   single    0.970  0.020  1.090
 V97  C22  H7   single    0.970  0.020  1.090
 V97  C30  H8   single    0.970  0.020  1.090
 V97  C30  H9   single    0.970  0.020  1.090
 V97  C31  H10  single    0.970  0.020  1.090
 V97  C31  H11  single    0.970  0.020  1.090
 V97  C32  H12  single    0.970  0.020  1.090
 V97  C32  H13  single    0.970  0.020  1.090
 V97  C33  H14  single    0.970  0.020  1.090
 V97  C33  H15  single    0.970  0.020  1.090
 V97  C7   H16  single    0.930  0.020  1.080
 V97  N11  H17  single    0.890  0.020  1.040
 V97  N11  H18  single    0.890  0.020  1.040
 V97  N19  H19  single    0.860  0.020  1.020
 V97  N3   H20  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
 V97  S5   C9   N1   122.40  3.000
 V97  S5   C9   C8   110.41  3.000
 V97  N1   C9   C8   127.19  3.000
 V97  C7   C8   C4   128.83  3.000
 V97  C7   C8   C9   113.30  3.000
 V97  C4   C8   C9   117.88  3.000
 V97  S12  C13  C17  124.74  3.000
 V97  C17  C13  C14  124.86  3.000
 V97  S12  C13  C14  110.39  3.000
 V97  S5   C6   C7   111.16  3.000
 V97  S5   C6   C30  120.60  3.000
 V97  C7   C6   C30  128.22  3.000
 V97  O10  C4   N3   120.56  3.000
 V97  O10  C4   C8   127.12  3.000
 V97  N3   C4   C8   112.31  3.000
 V97  N3   C2   N11  117.41  3.000
 V97  N3   C2   N1   122.60  3.000
 V97  N11  C2   N1   119.98  3.000
 V97  H1   C14  C15  123.96  3.000
 V97  H1   C14  C13  122.92  3.000
 V97  C15  C14  C13  113.12  3.000
 V97  H2   C15  C16  122.62  3.000
 V97  H2   C15  C14  124.00  3.000
 V97  C16  C15  C14  113.38  3.000
 V97  S12  C16  C33  121.27  3.000
 V97  S12  C16  C15  110.48  3.000
 V97  C33  C16  C15  128.24  3.000
 V97  H3   C20  N19  108.47  3.000
 V97  H3   C20  C26  108.87  3.000
 V97  N19  C20  C26  112.28  3.000
 V97  H3   C20  C21  108.46  3.000
 V97  N19  C20  C21  107.26  3.000
 V97  C26  C20  C21  111.39  3.000
 V97  H5   C21  H4   106.13  3.000
 V97  H5   C21  C22  109.86  3.000
 V97  H4   C21  C22  108.73  3.000
 V97  H5   C21  C20  108.56  3.000
 V97  H4   C21  C20  108.22  3.000
 V97  C22  C21  C20  114.95  3.000
 V97  H7   C22  H6   105.08  3.000
 V97  H7   C22  C23  107.40  3.000
 V97  H6   C22  C23  108.88  3.000
 V97  H7   C22  C21  109.18  3.000
 V97  H6   C22  C21  110.99  3.000
 V97  C23  C22  C21  114.81  3.000
 V97  O25  C23  O24  126.40  3.000
 V97  O24  C23  C22  117.77  3.000
 V97  O25  C23  C22  115.81  3.000
 V97  O28  C26  O27  127.53  3.000
 V97  O27  C26  C20  115.88  3.000
 V97  O28  C26  C20  116.55  3.000
 V97  H9   C30  H8   106.16  3.000
 V97  H9   C30  C31  109.47  3.000
 V97  H8   C30  C31  108.72  3.000
 V97  H9   C30  C6   110.26  3.000
 V97  H8   C30  C6   108.19  3.000
 V97  C31  C30  C6   113.74  3.000
 V97  H11  C31  H10  106.38  3.000
 V97  H11  C31  C32  109.29  3.000
 V97  H10  C31  C32  109.45  3.000
 V97  H11  C31  C30  108.11  3.000
 V97  H10  C31  C30  109.10  3.000
 V97  C32  C31  C30  114.21  3.000
 V97  H13  C32  H12  106.50  3.000
 V97  H13  C32  C33  108.98  3.000
 V97  H12  C32  C33  109.79  3.000
 V97  H13  C32  C31  110.30  3.000
 V97  H12  C32  C31  109.65  3.000
 V97  C33  C32  C31  111.50  3.000
 V97  H15  C33  H14  106.43  3.000
 V97  H15  C33  C32  109.46  3.000
 V97  H14  C33  C32  109.51  3.000
 V97  H15  C33  C16  110.25  3.000
 V97  H14  C33  C16  107.52  3.000
 V97  C32  C33  C16  113.42  3.000
 V97  H16  C7   C6   123.04  3.000
 V97  H16  C7   C8   123.98  3.000
 V97  C6   C7   C8   112.98  3.000
 V97  C2   N1   C9   114.88  3.000
 V97  H18  N11  H17  117.06  3.000
 V97  H18  N11  C2   121.80  3.000
 V97  H17  N11  C2   117.98  3.000
 V97  H19  N19  C20  116.60  3.000
 V97  H19  N19  C17  119.29  3.000
 V97  C20  N19  C17  122.60  3.000
 V97  H20  N3   C2   118.99  3.000
 V97  H20  N3   C4   115.87  3.000
 V97  C2   N3   C4   125.14  3.000
 V97  C16  S12  C13   92.63  3.000
 V97  C6   S5   C9    92.16  3.000
 V97  O18  C17  N19  123.27  3.000
 V97  O18  C17  C13  119.89  3.000
 V97  N19  C17  C13  116.83  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
 V97  CONST_01  C6   C7   C8   C9      0.00   0.0  0
 V97  CONST_02  C7   C6   S5   C9      0.00   0.0  0
 V97  CONST_03  C6   S5   C9   C8      0.00   0.0  0
 V97  CONST_04  S5   C6   C7   C8      0.00   0.0  0
 V97  CONST_05  C15  C16  S12  C13     0.00   0.0  0
 V97  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 V97  CONST_07  S12  C16  C15  C14     0.00   0.0  0
 V97  CONST_08  C16  S12  C13  C14     0.00   0.0  0
 V97  CONST_09  S12  C13  C14  C15     0.00   0.0  0
 V97  CONST_10  S5   C9   C8   C7      0.00   0.0  0
 V97  CONST_11  N3   C2   N1   C9      0.00   0.0  0
 V97  CONST_12  C2   N3   C4   C8      0.00   0.0  0
 V97  CONST_13  N1   C2   N3   C4      0.00   0.0  0
 V97  CONST_14  C30  C6   S5   C9    180.00   0.0  0
 V97  CONST_15  C30  C6   C7   C8    180.00   0.0  0
 V97  CONST_16  C33  C16  S12  C13   180.00   0.0  0
 V97  CONST_17  C33  C16  C15  C14   180.00   0.0  0
 V97  CONST_18  C17  C13  C14  C15   180.00   0.0  0
 V97  CONST_19  C17  C13  S12  C16   180.00   0.0  0
 V97  CONST_20  N11  C2   N1   C9    180.00   0.0  0
 V97  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 V97  CONST_22  O10  C4   N3   C2    180.00   0.0  0
 V97  CONST_23  H16  C7   C8   C9    180.00   0.0  0
 V97  CONST_24  H2   C15  C14  C13   180.00   0.0  0
 V97  CONST_25  H1   C14  C15  C16   180.00   0.0  0
 V97  CONST_26  H20  N3   C4   C8    180.00   0.0  0
 V97  CONST_27  H17  N11  C2   N1      0.00   0.0  0
 V97  CONST_28  H18  N11  C2   N1    180.00   0.0  0
 V97  CONST_29  C20  N19  C17  C13   180.00   0.0  0
 V97  CONST_30  H19  N19  C17  C13     0.00   0.0  0
 V97  CONST_31  O18  C17  N19  C20     0.00   0.0  0
 V97  Var_01    N19  C17  C13  C14  -173.77  30.0  2
 V97  Var_02    C32  C33  C16  C15   108.67  30.0  3
 V97  Var_03    C7   C6   C30  C31   -80.41  30.0  1
 V97  Var_04    C32  C31  C30  C6    -62.90  30.0  3
 V97  Var_05    C31  C32  C33  C16  -175.25  30.0  1
 V97  Var_06    C23  C22  C21  C20   170.03  30.0  3
 V97  Var_07    O25  C23  C22  C21   161.87  30.0  3
 V97  Var_08    C33  C32  C31  C30  -176.28  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
 V97  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
 V97  plan-1  C13  0.020
 V97  plan-1  C14  0.020
 V97  plan-1  C15  0.020
 V97  plan-1  C16  0.020
 V97  plan-1  C33  0.020
 V97  plan-1  S12  0.020
 V97  plan-1  H1   0.020
 V97  plan-1  H2   0.020
 V97  plan-1  C17  0.020
 V97  plan-2  C9   0.020
 V97  plan-2  C8   0.020
 V97  plan-2  C6   0.020
 V97  plan-2  C4   0.020
 V97  plan-2  C2   0.020
 V97  plan-2  C30  0.020
 V97  plan-2  C7   0.020
 V97  plan-2  N1   0.020
 V97  plan-2  N11  0.020
 V97  plan-2  N3   0.020
 V97  plan-2  O10  0.020
 V97  plan-2  S5   0.020
 V97  plan-2  H16  0.020
 V97  plan-2  H17  0.020
 V97  plan-2  H18  0.020
 V97  plan-2  H20  0.020
 V97  plan-3  C13  0.020
 V97  plan-3  C20  0.020
 V97  plan-3  N19  0.020
 V97  plan-3  O18  0.020
 V97  plan-3  H19  0.020
 V97  plan-3  C17  0.020
 V97  plan-4  C22  0.020
 V97  plan-4  C23  0.020
 V97  plan-4  O24  0.020
 V97  plan-4  O25  0.020
 V97  plan-5  C20  0.020
 V97  plan-5  C26  0.020
 V97  plan-5  O27  0.020
 V97  plan-5  O28  0.020

