# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 23:52:40 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: (4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)S\C2=C(\O)CCC(O)=O)C)c(N)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
 TD7  TD7  '(4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid'  ligand  57  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TD7
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
 TD7  O1B   O  OH1   0  -0.731  19.3259  11.6234  -66.5266
 TD7  PB    P  P     0   1.476  19.9243  12.6328  -65.4556
 TD7  O3B   O  OH1   0  -0.737  21.3811  12.1456  -65.0650
 TD7  O2B   O  O     0  -0.672  19.0424  12.8243  -64.3003
 TD7  O3A   O  O2    0  -0.692  20.1188  14.0344  -66.2518
 TD7  PA    P  P     0   1.490  20.8613  14.4705  -67.6177
 TD7  O1A   O  O     0  -0.669  20.6486  15.8958  -67.8989
 TD7  O2A   O  OH1   0  -0.737  22.3271  13.9500  -67.3001
 TD7  O7    O  O2    0  -0.589  20.3659  13.4394  -68.7171
 TD7  C7    C  CH2   0  -0.153  19.0894  13.6029  -69.3638
 TD7  C6    C  CH2   0  -0.557  18.8992  12.4357  -70.3162
 TD7  C5    C  CR5   0  -0.319  17.5643  12.5258  -70.9762
 TD7  S1    S  S2    0   0.116  16.1610  11.7796  -70.2051
 TD7  C4    C  CR5   0   0.467  17.2266  13.1627  -72.1042
 TD7  CM4   C  CH3   0  -0.752  18.1632  13.8796  -73.0146
 TD7  N3    N  NR5   0  -0.508  15.8695  13.0855  -72.4379
 TD7  C2    C  CR5   0  -0.001  15.1616  12.2070  -71.6054
 TD7  OL1   O  OH1   0  -0.636  13.3456  11.8680  -73.0464
 TD7  CLB   C  CH2   0  -0.551  13.2779  10.7141  -70.9017
 TD7  CLC   C  C     0   0.525  12.6524   9.0022  -72.6986
 TD7  OL2   O  O     0  -0.447  13.1615   8.4702  -73.6538
 TD7  OL3   O  OH1   0  -0.594  11.3810   9.3953  -72.6829
 TD7  C7'   C  CH2   0  -0.439  15.2163  14.2497  -73.0412
 TD7  C5'   C  CR6   0  -0.039  15.3381  15.5308  -72.2621
 TD7  C6'   C  CR16  0  -0.093  16.0104  16.6075  -72.7891
 TD7  N1'   N  N     0  -0.448  16.1566  17.7887  -72.1841
 TD7  C2'   C  CR6   0   0.353  15.5969  17.8902  -70.9871
 TD7  CM2   C  CH3   0  -0.729  15.7372  19.1876  -70.2542
 TD7  N3'   N  N     0  -0.470  14.9077  16.9372  -70.3759
 TD7  C4'   C  CR6   0   0.464  14.7573  15.7608  -70.9897
 TD7  C13   C  CH2   0  -0.541  13.3437   9.2591  -71.3878
 TD7  N4'   N  NH2   0  -0.831  14.0170  14.8464  -70.3510
 TD7  C11   C  C     0   0.240  13.9567  11.6587  -71.8400
 TD7  H1B   H  HOH1  0   0.503  19.9452  11.1024  -67.0542
 TD7  H2A   H  HOH1  0   0.518  23.0098  14.1799  -67.9474
 TD7  H71C  H  HCH2  0   0.246  18.2918  13.6252  -68.6172
 TD7  H72C  H  HCH2  0   0.255  19.0740  14.5458  -69.9124
 TD7  H61C  H  HCH2  0   0.276  19.6904  12.4445  -71.0684
 TD7  H62C  H  HCH2  0   0.267  18.9951  11.4924  -69.7732
 TD7  HM41  H  HCH3  0   0.260  18.0882  14.9628  -72.9169
 TD7  HM42  H  HCH3  0   0.267  19.1943  13.6092  -72.7959
 TD7  HM43  H  HCH3  0   0.261  17.9677  13.6265  -74.0570
 TD7  H7'1  H  HCH2  0   0.279  15.6418  14.4118  -74.0338
 TD7  H7'2  H  HCH2  0   0.298  14.1737  13.9924  -73.2130
 TD7  HL1   H  HOH1  0   0.467  12.4034  12.0280  -72.9135
 TD7  HLB1  H  HCH2  0   0.270  12.2363  11.0149  -70.7504
 TD7  HLB2  H  HCH2  0   0.265  13.7326  10.7544  -69.9115
 TD7  H131  H  HCH2  0   0.269  14.3829   8.9462  -71.4803
 TD7  H132  H  HCH2  0   0.290  12.8766   8.6176  -70.6346
 TD7  HL3   H  HOH1  0   0.481  10.9657   9.1996  -73.5359
 TD7  H6'   H  HCR6  0   0.263  16.4618  16.5165  -73.7741
 TD7  HM21  H  HCH3  0   0.252  16.1762  19.0272  -69.2690
 TD7  HM22  H  HCH3  0   0.244  16.3608  19.8855  -70.8072
 TD7  HM23  H  HCH3  0   0.253  14.7587  19.6443  -70.0969
 TD7  H4'1  H  HNH2  0   0.418  13.9206  13.8997  -70.6763
 TD7  H4'2  H  HNH2  0   0.397  13.6803  15.0548  -69.4265
 TD7  H3B   H  HOH1  0   0.503  22.1078  12.2846  -65.6897

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
 TD7  O1B  PB    single    1.589  0.020  1.589
 TD7  PB   O2B   double    1.466  0.020  1.466
 TD7  PB   O3B   single    1.585  0.020  1.585
 TD7  PB   O3A   single    1.624  0.020  1.624
 TD7  O3A  PA    single    1.615  0.020  1.615
 TD7  PA   O1A   double    1.468  0.020  1.468
 TD7  PA   O2A   single    1.588  0.020  1.588
 TD7  PA   O7    single    1.587  0.020  1.587
 TD7  O7   C7    single    1.440  0.020  1.440
 TD7  C7   C6    single    1.518  0.020  1.518
 TD7  C6   C5    single    1.492  0.020  1.492
 TD7  C5   S1    single    1.767  0.020  1.767
 TD7  C5   C4    double    1.339  0.020  1.339
 TD7  S1   C2    single    1.773  0.020  1.773
 TD7  C4   CM4   single    1.490  0.020  1.490
 TD7  C4   N3    single    1.400  0.020  1.400
 TD7  N3   C2    single    1.402  0.020  1.402
 TD7  N3   C7'   single    1.465  0.020  1.465
 TD7  C2   C11   double    1.344  0.020  1.344
 TD7  OL1  C11   single    1.369  0.020  1.369
 TD7  CLB  C13   single    1.535  0.020  1.535
 TD7  CLB  C11   single    1.495  0.020  1.495
 TD7  CLC  OL2   double    1.206  0.020  1.206
 TD7  CLC  OL3   single    1.331  0.020  1.331
 TD7  CLC  C13   single    1.504  0.020  1.504
 TD7  C7'  C5'   single    1.504  0.020  1.504
 TD7  C5'  C6'   aromatic  1.374  0.020  1.374
 TD7  C5'  C4'   aromatic  1.417  0.020  1.417
 TD7  C6'  N1'   aromatic  1.335  0.020  1.335
 TD7  N1'  C2'   aromatic  1.325  0.020  1.325
 TD7  C2'  CM2   single    1.497  0.020  1.497
 TD7  C2'  N3'   aromatic  1.325  0.020  1.325
 TD7  N3'  C4'   aromatic  1.335  0.020  1.335
 TD7  C4'  N4'   single    1.339  0.020  1.339
 TD7  O1B  H1B   single    0.850  0.020  0.980
 TD7  O2A  H2A   single    0.850  0.020  0.980
 TD7  C7   H71C  single    0.970  0.020  1.090
 TD7  C7   H72C  single    0.970  0.020  1.090
 TD7  C6   H61C  single    0.970  0.020  1.090
 TD7  C6   H62C  single    0.970  0.020  1.090
 TD7  CM4  HM41  single    0.970  0.020  1.090
 TD7  CM4  HM42  single    0.970  0.020  1.090
 TD7  CM4  HM43  single    0.970  0.020  1.090
 TD7  C7'  H7'1  single    0.970  0.020  1.090
 TD7  C7'  H7'2  single    0.970  0.020  1.090
 TD7  OL1  HL1   single    0.850  0.020  0.980
 TD7  CLB  HLB1  single    0.970  0.020  1.090
 TD7  CLB  HLB2  single    0.970  0.020  1.090
 TD7  C13  H131  single    0.970  0.020  1.090
 TD7  C13  H132  single    0.970  0.020  1.090
 TD7  OL3  HL3   single    0.850  0.020  0.980
 TD7  C6'  H6'   single    0.930  0.020  1.080
 TD7  CM2  HM21  single    0.970  0.020  1.090
 TD7  CM2  HM22  single    0.970  0.020  1.090
 TD7  CM2  HM23  single    0.970  0.020  1.090
 TD7  N4'  H4'1  single    0.860  0.020  1.020
 TD7  N4'  H4'2  single    0.860  0.020  1.020
 TD7  O3B  H3B   single    0.850  0.020  0.980

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
 TD7  H1B   O1B  PB    117.99  3.000
 TD7  O3A   PB   O2B   110.23  3.000
 TD7  O3A   PB   O3B   106.03  3.000
 TD7  O2B   PB   O3B   113.51  3.000
 TD7  O3A   PB   O1B   105.25  3.000
 TD7  O3B   PB   O1B   108.48  3.000
 TD7  O2B   PB   O1B   112.81  3.000
 TD7  H3B   O3B  PB    119.12  3.000
 TD7  PA    O3A  PB    134.67  3.000
 TD7  O7    PA   O2A   102.35  3.000
 TD7  O7    PA   O1A   116.93  3.000
 TD7  O2A   PA   O1A   119.36  3.000
 TD7  O7    PA   O3A   105.49  3.000
 TD7  O2A   PA   O3A    99.60  3.000
 TD7  O1A   PA   O3A   110.95  3.000
 TD7  H2A   O2A  PA    116.06  3.000
 TD7  C7    O7   PA    120.94  3.000
 TD7  H72C  C7   H71C  108.40  3.000
 TD7  H72C  C7   C6    110.32  3.000
 TD7  H71C  C7   C6    110.65  3.000
 TD7  H72C  C7   O7    109.66  3.000
 TD7  H71C  C7   O7    110.03  3.000
 TD7  C6    C7   O7    107.78  3.000
 TD7  H62C  C6   H61C  106.60  3.000
 TD7  H62C  C6   C5    110.53  3.000
 TD7  H61C  C6   C5    110.07  3.000
 TD7  H62C  C6   C7    109.94  3.000
 TD7  H61C  C6   C7    109.58  3.000
 TD7  C5    C6   C7    110.07  3.000
 TD7  C4    C5   S1    111.61  3.000
 TD7  C4    C5   C6    128.85  3.000
 TD7  S1    C5   C6    119.48  3.000
 TD7  C2    S1   C5     90.07  3.000
 TD7  N3    C4   CM4   119.36  3.000
 TD7  N3    C4   C5    114.79  3.000
 TD7  CM4   C4   C5    125.82  3.000
 TD7  HM43  CM4  HM42  107.71  3.000
 TD7  HM43  CM4  HM41  107.69  3.000
 TD7  HM42  CM4  HM41  107.10  3.000
 TD7  HM43  CM4  C4    111.09  3.000
 TD7  HM42  CM4  C4    110.69  3.000
 TD7  HM41  CM4  C4    112.34  3.000
 TD7  C7'   N3   C2    121.16  3.000
 TD7  C7'   N3   C4    119.12  3.000
 TD7  C2    N3   C4    112.49  3.000
 TD7  C11   C2   N3    127.19  3.000
 TD7  C11   C2   S1    123.01  3.000
 TD7  N3    C2   S1    109.60  3.000
 TD7  HL1   OL1  C11   109.87  3.000
 TD7  HLB2  CLB  HLB1  105.13  3.000
 TD7  HLB2  CLB  C11   110.93  3.000
 TD7  HLB1  CLB  C11   110.20  3.000
 TD7  HLB2  CLB  C13   107.74  3.000
 TD7  HLB1  CLB  C13   110.18  3.000
 TD7  C11   CLB  C13   112.38  3.000
 TD7  C13   CLC  OL3   112.23  3.000
 TD7  C13   CLC  OL2   124.86  3.000
 TD7  OL3   CLC  OL2   122.88  3.000
 TD7  HL3   OL3  CLC   109.84  3.000
 TD7  H7'2  C7'  H7'1  105.37  3.000
 TD7  H7'2  C7'  C5'   111.15  3.000
 TD7  H7'1  C7'  C5'   108.22  3.000
 TD7  H7'2  C7'  N3    107.73  3.000
 TD7  H7'1  C7'  N3    108.58  3.000
 TD7  C5'   C7'  N3    115.30  3.000
 TD7  C4'   C5'  C6'   114.68  3.000
 TD7  C4'   C5'  C7'   124.75  3.000
 TD7  C6'   C5'  C7'   120.54  3.000
 TD7  H6'   C6'  N1'   116.04  3.000
 TD7  H6'   C6'  C5'   119.00  3.000
 TD7  N1'   C6'  C5'   124.95  3.000
 TD7  C2'   N1'  C6'   115.52  3.000
 TD7  N3'   C2'  CM2   116.50  3.000
 TD7  N3'   C2'  N1'   125.52  3.000
 TD7  CM2   C2'  N1'   117.98  3.000
 TD7  HM23  CM2  HM22  108.61  3.000
 TD7  HM23  CM2  HM21  107.00  3.000
 TD7  HM22  CM2  HM21  108.85  3.000
 TD7  HM23  CM2  C2'   110.45  3.000
 TD7  HM22  CM2  C2'   111.17  3.000
 TD7  HM21  CM2  C2'   110.64  3.000
 TD7  C4'   N3'  C2'   118.69  3.000
 TD7  N4'   C4'  N3'   116.41  3.000
 TD7  N4'   C4'  C5'   122.96  3.000
 TD7  N3'   C4'  C5'   120.62  3.000
 TD7  H132  C13  H131  107.29  3.000
 TD7  H132  C13  CLC   107.67  3.000
 TD7  H131  C13  CLC   108.39  3.000
 TD7  H132  C13  CLB   108.63  3.000
 TD7  H131  C13  CLB   109.88  3.000
 TD7  CLC   C13  CLB   114.71  3.000
 TD7  H4'2  N4'  H4'1  117.42  3.000
 TD7  H4'2  N4'  C4'   118.82  3.000
 TD7  H4'1  N4'  C4'   122.79  3.000
 TD7  CLB   C11  OL1   116.57  3.000
 TD7  CLB   C11  C2    123.74  3.000
 TD7  OL1   C11  C2    119.45  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
 TD7  CONST_01  C2'   N1'  C6'  C5'     0.00   0.0  0
 TD7  CONST_02  C2'   N3'  C4'  C5'     0.00   0.0  0
 TD7  CONST_03  N3'   C4'  C5'  C6'     0.00   0.0  0
 TD7  CONST_04  N3'   C2'  N1'  C6'     0.00   0.0  0
 TD7  CONST_05  C4'   C5'  C6'  N1'     0.00   0.0  0
 TD7  CONST_06  C4'   N3'  C2'  N1'     0.00   0.0  0
 TD7  CONST_07  N1'   C6'  C5'  C7'   180.00   0.0  0
 TD7  CONST_08  N3'   C4'  C5'  C7'   180.00   0.0  0
 TD7  CONST_09  N4'   C4'  C5'  C6'   180.00   0.0  0
 TD7  CONST_10  CM2   C2'  N1'  C6'   180.00   0.0  0
 TD7  CONST_11  N4'   C4'  N3'  C2'   180.00   0.0  0
 TD7  CONST_12  C4'   N3'  C2'  CM2   180.00   0.0  0
 TD7  CONST_13  H6'   C6'  N1'  C2'   180.00   0.0  0
 TD7  CONST_14  H4'1  N4'  C4'  C5'     0.00   0.0  0
 TD7  CONST_15  H4'2  N4'  C4'  C5'   180.00   0.0  0
 TD7  CONST_16  HL3   OL3  CLC  OL2     0.00   0.0  0
 TD7  Var_01    C5'   C7'  N3   C4    -54.65  30.0  3
 TD7  Var_02    C6'   C5'  C7'  N3    116.32  30.0  2
 TD7  Var_03    OL1   C11  C2   S1   -169.16   0.0  2
 TD7  Var_04    S1    C5   C6   C7    -88.71  30.0  3
 TD7  Var_05    HM41  CM4  C4   C5   -104.85  30.0  3
 TD7  Var_06    HM21  CM2  C2'  N1'  -124.61  30.0  2
 TD7  Var_07    C5    C6   C7   O7    177.78  30.0  3
 TD7  Var_08    C13   CLB  C11  C2   -104.44  30.0  1
 TD7  Var_09    O1A   PA   O3A  PB    176.90  30.0  3
 TD7  Var_10    C6    C7   O7   PA   -178.09  30.0  3
 TD7  Var_11    OL2   CLC  C13  CLB   126.92  30.0  2
 TD7  Var_12    C11   CLB  C13  CLC   -62.37  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
 TD7  chir_01  PA  O1A  O2A  O7  both

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
 TD7  plan-1  C6    0.020
 TD7  plan-1  C5    0.020
 TD7  plan-1  S1    0.020
 TD7  plan-1  C4    0.020
 TD7  plan-1  CM4   0.020
 TD7  plan-1  N3    0.020
 TD7  plan-1  C2    0.020
 TD7  plan-1  OL1   0.020
 TD7  plan-1  CLB   0.020
 TD7  plan-1  C7'   0.020
 TD7  plan-1  C11   0.020
 TD7  plan-2  C7'   0.020
 TD7  plan-2  C5'   0.020
 TD7  plan-2  C6'   0.020
 TD7  plan-2  N1'   0.020
 TD7  plan-2  C2'   0.020
 TD7  plan-2  CM2   0.020
 TD7  plan-2  N3'   0.020
 TD7  plan-2  C4'   0.020
 TD7  plan-2  N4'   0.020
 TD7  plan-2  H6'   0.020
 TD7  plan-3  C4'   0.020
 TD7  plan-3  N4'   0.020
 TD7  plan-3  H4'1  0.020
 TD7  plan-3  H4'2  0.020
 TD7  plan-4  CLC   0.020
 TD7  plan-4  OL2   0.020
 TD7  plan-4  OL3   0.020
 TD7  plan-4  C13   0.020
 TD7  plan-4  HL3   0.020

