# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 06:13:38 2021
#   Inital geometry file: a 155 line input string
#   Ligand name: (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN2[C@H](SC(=C2C)CCO[P](O)(=O)O[P](O)(O)=O)[C@](O)(CCC(O)=O)[P](O)(O)=O)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
 QSP  QSP  '(4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid'  ligand  64  37  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QSP
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
 QSP  N1'  N  N     0  -0.440  40.0677  23.8053  25.0374
 QSP  C2'  C  CR6   0   0.358  39.2863  24.5965  24.3096
 QSP  CM2  C  CH3   0  -0.704  37.9823  24.0302  23.8418
 QSP  N3'  N  N     0  -0.461  39.5532  25.8511  23.9834
 QSP  C4'  C  CR6   0   0.451  40.6959  26.3939  24.4152
 QSP  N4'  N  NH2   0  -0.822  40.9112  27.6852  24.0852
 QSP  C5'  C  CR6   0  -0.039  41.5923  25.6486  25.2099
 QSP  C6'  C  CR16  0  -0.044  41.1995  24.3551  25.4716
 QSP  C7'  C  CH2   0  -0.408  42.8980  26.1816  25.7433
 QSP  N3   N  NR5   0  -0.478  44.0624  25.6618  25.0595
 QSP  C2   C  CR15  0  -0.233  44.2468  25.9360  23.6573
 QSP  S1   S  S2    0   0.070  45.1017  24.4674  22.9942
 QSP  C5   C  CR5   0  -0.271  45.5243  23.9379  24.6364
 QSP  C4   C  CR5   0   0.457  44.8562  24.6401  25.5607
 QSP  CM4  C  CH3   0  -0.727  44.9440  24.4381  27.0343
 QSP  C6   C  CH2   0  -0.525  46.5794  22.9006  24.7902
 QSP  C7   C  CH2   0  -0.148  46.1018  21.5427  24.3068
 QSP  O7   O  O2    0  -0.579  47.2287  20.6459  24.3411
 QSP  PA   P  P     0   1.500  47.2768  19.3499  23.4357
 QSP  O1A  O  OH1   0  -0.696  48.6586  18.7646  23.9458
 QSP  O2A  O  O     0  -0.672  46.1028  18.4640  23.4178
 QSP  O3A  O  O2    0  -0.704  47.5573  19.8817  21.9274
 QSP  PB   P  P     0   1.461  48.5345  21.0222  21.3079
 QSP  O1B  O  O     0  -0.715  48.9218  20.6423  19.9414
 QSP  O2B  O  OH1   0  -0.695  49.6720  21.2588  22.3859
 QSP  O3B  O  OH1   0  -0.694  47.7488  22.3858  21.5139
 QSP  C11  C  CT    0   0.018  44.9811  27.2633  23.3412
 QSP  P4   P  P     0   1.370  46.4750  27.6605  24.3613
 QSP  O5   O  O     0  -0.664  46.9905  29.0014  23.9738
 QSP  O6   O  OH1   0  -0.713  46.1093  27.5506  25.9193
 QSP  O8   O  OH1   0  -0.710  47.4426  26.4144  24.1371
 QSP  C12  C  CH2   0  -0.500  45.3682  27.3666  21.8601
 QSP  O11  O  OH1   0  -0.667  44.0520  28.2803  23.6914
 QSP  C13  C  CH2   0  -0.568  44.2208  27.1380  20.8737
 QSP  C14  C  C     0   0.530  43.0858  28.1236  20.9425
 QSP  O15  O  OH1   0  -0.587  43.5079  29.3844  20.8913
 QSP  O16  O  O     0  -0.403  41.9190  27.8227  20.9833
 QSP  H1   H  HCH3  0   0.239  37.5971  24.5832  22.9884
 QSP  H2   H  HCH3  0   0.240  38.0843  22.9792  23.5768
 QSP  H3   H  HCH3  0   0.246  37.2416  24.0926  24.6420
 QSP  H4   H  HNH2  0   0.373  40.3287  28.0595  23.3542
 QSP  H5   H  HNH2  0   0.390  41.8489  28.0540  24.1001
 QSP  H6   H  HCR6  0   0.236  41.8384  23.7169  26.0768
 QSP  H7   H  HCH2  0   0.284  42.9828  25.9196  26.7970
 QSP  H8   H  HCH2  0   0.241  42.9124  27.2709  25.7276
 QSP  H9   H  HCR5  0   0.296  43.2730  26.0085  23.1592
 QSP  H10  H  HCH3  0   0.250  45.1828  25.3717  27.5446
 QSP  H11  H  HCH3  0   0.237  44.0078  24.0629  27.4526
 QSP  H12  H  HCH3  0   0.250  45.7127  23.7097  27.2809
 QSP  H13  H  HCH2  0   0.253  46.8853  22.8254  25.8348
 QSP  H14  H  HCH2  0   0.258  47.4659  23.1948  24.2216
 QSP  H15  H  HCH2  0   0.220  45.6942  21.6123  23.2950
 QSP  H16  H  HCH2  0   0.258  45.3162  21.1543  24.9565
 QSP  H17  H  HOH1  0   0.483  48.7950  17.8291  23.7418
 QSP  H18  H  HOH1  0   0.483  50.4299  20.6628  22.3112
 QSP  H19  H  HOH1  0   0.487  47.0696  22.5640  20.8487
 QSP  H20  H  HOH1  0   0.465  45.7829  28.3764  26.2990
 QSP  H21  H  HOH1  0   0.466  48.2625  26.4399  24.6505
 QSP  H22  H  HCH2  0   0.274  46.1482  26.6381  21.6373
 QSP  H23  H  HCH2  0   0.275  45.8129  28.3468  21.6784
 QSP  H24  H  HOH1  0   0.447  44.3822  29.1417  23.4059
 QSP  H25  H  HCH2  0   0.273  43.8056  26.1335  20.9520
 QSP  H26  H  HCH2  0   0.279  44.6439  27.2090  19.8670
 QSP  H27  H  HOH1  0   0.451  42.7498  29.9876  20.9087

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
 QSP  O16  C14  double    1.206  0.020  1.206
 QSP  O1B  PB   double    1.470  0.020  1.470
 QSP  C14  C13  single    1.505  0.020  1.505
 QSP  C14  O15  single    1.331  0.020  1.331
 QSP  C13  C12  single    1.530  0.020  1.530
 QSP  PB   O3A  single    1.625  0.020  1.625
 QSP  PB   O3B  single    1.587  0.020  1.587
 QSP  PB   O2B  single    1.585  0.020  1.585
 QSP  O3A  PA   single    1.624  0.020  1.624
 QSP  C12  C11  single    1.534  0.020  1.534
 QSP  O2A  PA   double    1.471  0.020  1.471
 QSP  PA   O1A  single    1.585  0.020  1.585
 QSP  PA   O7   single    1.582  0.020  1.582
 QSP  N4'  C4'  single    1.350  0.020  1.350
 QSP  S1   C2   single    1.824  0.020  1.824
 QSP  S1   C5   single    1.776  0.020  1.776
 QSP  O11  C11  single    1.421  0.020  1.421
 QSP  C11  C2   single    1.550  0.020  1.550
 QSP  C11  P4   single    1.852  0.020  1.852
 QSP  C2   N3   single    1.441  0.020  1.441
 QSP  C7   O7   single    1.441  0.020  1.441
 QSP  C7   C6   single    1.518  0.020  1.518
 QSP  N3'  C4'  aromatic  1.337  0.020  1.337
 QSP  N3'  C2'  aromatic  1.323  0.020  1.323
 QSP  O5   P4   double    1.488  0.020  1.488
 QSP  C4'  C5'  aromatic  1.411  0.020  1.411
 QSP  O8   P4   single    1.593  0.020  1.593
 QSP  P4   O6   single    1.604  0.020  1.604
 QSP  C5   C6   single    1.488  0.020  1.488
 QSP  C5   C4   double    1.339  0.020  1.339
 QSP  CM2  C2'  single    1.497  0.020  1.497
 QSP  C2'  N1'  aromatic  1.329  0.020  1.329
 QSP  N3   C4   single    1.387  0.020  1.387
 QSP  N3   C7'  single    1.447  0.020  1.447
 QSP  C5'  C7'  single    1.508  0.020  1.508
 QSP  C5'  C6'  aromatic  1.377  0.020  1.377
 QSP  C4   CM4  single    1.490  0.020  1.490
 QSP  N1'  C6'  aromatic  1.331  0.020  1.331
 QSP  CM2  H1   single    0.970  0.020  1.090
 QSP  CM2  H2   single    0.970  0.020  1.090
 QSP  CM2  H3   single    0.970  0.020  1.090
 QSP  N4'  H4   single    0.890  0.020  1.040
 QSP  N4'  H5   single    0.890  0.020  1.040
 QSP  C6'  H6   single    0.930  0.020  1.080
 QSP  C7'  H7   single    0.970  0.020  1.090
 QSP  C7'  H8   single    0.970  0.020  1.090
 QSP  C2   H9   single    0.970  0.020  1.090
 QSP  CM4  H10  single    0.970  0.020  1.090
 QSP  CM4  H11  single    0.970  0.020  1.090
 QSP  CM4  H12  single    0.970  0.020  1.090
 QSP  C6   H13  single    0.970  0.020  1.090
 QSP  C6   H14  single    0.970  0.020  1.090
 QSP  C7   H15  single    0.970  0.020  1.090
 QSP  C7   H16  single    0.970  0.020  1.090
 QSP  O1A  H17  single    0.850  0.020  0.980
 QSP  O2B  H18  single    0.850  0.020  0.980
 QSP  O3B  H19  single    0.850  0.020  0.980
 QSP  O6   H20  single    0.850  0.020  0.980
 QSP  O8   H21  single    0.850  0.020  0.980
 QSP  C12  H22  single    0.970  0.020  1.090
 QSP  C12  H23  single    0.970  0.020  1.090
 QSP  O11  H24  single    0.850  0.020  0.980
 QSP  C13  H25  single    0.970  0.020  1.090
 QSP  C13  H26  single    0.970  0.020  1.090
 QSP  O15  H27  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
 QSP  C6'  N1'  C2'  115.64  3.000
 QSP  N3'  C2'  CM2  117.22  3.000
 QSP  CM2  C2'  N1'  117.27  3.000
 QSP  N3'  C2'  N1'  125.50  3.000
 QSP  H3   CM2  H2   107.28  3.000
 QSP  H3   CM2  H1   107.80  3.000
 QSP  H2   CM2  H1   109.46  3.000
 QSP  H3   CM2  C2'  109.89  3.000
 QSP  H2   CM2  C2'  111.08  3.000
 QSP  H1   CM2  C2'  111.19  3.000
 QSP  C4'  N3'  C2'  118.54  3.000
 QSP  C5'  C4'  N4'  122.79  3.000
 QSP  C5'  C4'  N3'  120.70  3.000
 QSP  N4'  C4'  N3'  116.47  3.000
 QSP  H5   N4'  H4   114.40  3.000
 QSP  H5   N4'  C4'  119.66  3.000
 QSP  H4   N4'  C4'  116.15  3.000
 QSP  C7'  C5'  C6'  120.78  3.000
 QSP  C6'  C5'  C4'  114.97  3.000
 QSP  C7'  C5'  C4'  124.25  3.000
 QSP  H6   C6'  C5'  119.32  3.000
 QSP  H6   C6'  N1'  116.03  3.000
 QSP  C5'  C6'  N1'  124.65  3.000
 QSP  H8   C7'  H7   104.68  3.000
 QSP  H8   C7'  N3   109.98  3.000
 QSP  H7   C7'  N3   107.94  3.000
 QSP  H8   C7'  C5'  111.08  3.000
 QSP  H7   C7'  C5'  108.95  3.000
 QSP  N3   C7'  C5'  113.75  3.000
 QSP  C4   N3   C2   114.74  3.000
 QSP  C4   N3   C7'  123.66  3.000
 QSP  C2   N3   C7'  119.64  3.000
 QSP  H9   C2   C11  105.76  3.000
 QSP  H9   C2   S1   107.72  3.000
 QSP  C11  C2   S1   113.17  3.000
 QSP  H9   C2   N3   109.95  3.000
 QSP  C11  C2   N3   114.98  3.000
 QSP  S1   C2   N3   105.10  3.000
 QSP  C5   S1   C2    90.88  3.000
 QSP  C6   C5   C4   130.40  3.000
 QSP  C4   C5   S1   111.28  3.000
 QSP  C6   C5   S1   118.18  3.000
 QSP  CM4  C4   C5   125.59  3.000
 QSP  CM4  C4   N3   119.39  3.000
 QSP  C5   C4   N3   114.97  3.000
 QSP  H12  CM4  H11  106.81  3.000
 QSP  H12  CM4  H10  108.22  3.000
 QSP  H11  CM4  H10  107.62  3.000
 QSP  H12  CM4  C4   110.90  3.000
 QSP  H11  CM4  C4   112.02  3.000
 QSP  H10  CM4  C4   111.08  3.000
 QSP  H14  C6   H13  106.80  3.000
 QSP  H14  C6   C7   109.27  3.000
 QSP  H13  C6   C7   109.35  3.000
 QSP  H14  C6   C5   109.49  3.000
 QSP  H13  C6   C5   110.24  3.000
 QSP  C7   C6   C5   111.57  3.000
 QSP  H16  C7   H15  107.79  3.000
 QSP  H16  C7   O7   109.11  3.000
 QSP  H15  C7   O7   110.70  3.000
 QSP  H16  C7   C6   110.81  3.000
 QSP  H15  C7   C6   110.80  3.000
 QSP  O7   C7   C6   107.65  3.000
 QSP  PA   O7   C7   121.35  3.000
 QSP  O3A  PA   O2A  108.89  3.000
 QSP  O2A  PA   O1A  118.51  3.000
 QSP  O3A  PA   O1A  105.62  3.000
 QSP  O1A  PA   O7    98.33  3.000
 QSP  O2A  PA   O7   118.44  3.000
 QSP  O3A  PA   O7   105.59  3.000
 QSP  H17  O1A  PA   114.35  3.000
 QSP  PB   O3A  PA   133.47  3.000
 QSP  O3B  PB   O2B   97.97  3.000
 QSP  O2B  PB   O1B  118.79  3.000
 QSP  O3B  PB   O1B  118.23  3.000
 QSP  O2B  PB   O3A  106.09  3.000
 QSP  O3B  PB   O3A  104.83  3.000
 QSP  O1B  PB   O3A  109.36  3.000
 QSP  H18  O2B  PB   114.71  3.000
 QSP  H19  O3B  PB   114.62  3.000
 QSP  O11  C11  C12  110.77  3.000
 QSP  O11  C11  P4   103.78  3.000
 QSP  C12  C11  P4   108.29  3.000
 QSP  P4   C11  C2   116.97  3.000
 QSP  O11  C11  C2   104.65  3.000
 QSP  C12  C11  C2   111.97  3.000
 QSP  O8   P4   O6   102.80  3.000
 QSP  O6   P4   O5   113.18  3.000
 QSP  O8   P4   O5   117.24  3.000
 QSP  O6   P4   C11  109.66  3.000
 QSP  O8   P4   C11  104.16  3.000
 QSP  O5   P4   C11  109.22  3.000
 QSP  H20  O6   P4   113.60  3.000
 QSP  H21  O8   P4   114.78  3.000
 QSP  H23  C12  H22  105.93  3.000
 QSP  H23  C12  C13  109.41  3.000
 QSP  H22  C12  C13  107.75  3.000
 QSP  H23  C12  C11  108.90  3.000
 QSP  H22  C12  C11  109.44  3.000
 QSP  C13  C12  C11  115.03  3.000
 QSP  H24  O11  C11  109.99  3.000
 QSP  H26  C13  H25  105.86  3.000
 QSP  H26  C13  C14  106.93  3.000
 QSP  H25  C13  C14  108.25  3.000
 QSP  H26  C13  C12  107.06  3.000
 QSP  H25  C13  C12  112.15  3.000
 QSP  C14  C13  C12  115.99  3.000
 QSP  O16  C14  O15  123.01  3.000
 QSP  O15  C14  C13  112.31  3.000
 QSP  O16  C14  C13  124.62  3.000
 QSP  H27  O15  C14  109.93  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
 QSP  CONST_01  C4'  N3'  C2'  N1'     0.00   0.0  0
 QSP  CONST_02  C4'  C5'  C6'  N1'     0.00   0.0  0
 QSP  CONST_03  C5'  C4'  N3'  C2'     0.00   0.0  0
 QSP  CONST_04  C5'  C6'  N1'  C2'     0.00   0.0  0
 QSP  CONST_05  C6'  C5'  C4'  N3'     0.00   0.0  0
 QSP  CONST_06  C6'  N1'  C2'  N3'     0.00   0.0  0
 QSP  CONST_07  C7'  C5'  C6'  N1'   180.00   0.0  0
 QSP  CONST_08  N4'  C4'  N3'  C2'   180.00   0.0  0
 QSP  CONST_09  C4'  N3'  C2'  CM2   180.00   0.0  0
 QSP  CONST_10  C6'  N1'  C2'  CM2   180.00   0.0  0
 QSP  CONST_11  C7'  C5'  C4'  N3'   180.00   0.0  0
 QSP  CONST_12  C6'  C5'  C4'  N4'   180.00   0.0  0
 QSP  CONST_13  H6   C6'  N1'  C2'   180.00   0.0  0
 QSP  CONST_16  H27  O15  C14  C13   180.00   0.0  0
 QSP  Var_01    S1   C5   C4   N3     -3.87  30.0  1
 QSP  Var_02    C4   C5   S1   C2     11.69  30.0  1
 QSP  Var_03    C5   C4   N3   C2     -9.30  30.0  1
 QSP  Var_04    N3   C7'  C5'  C4'  -105.98  30.0  2
 QSP  Var_05    C2   N3   C7'  C5'    62.66  30.0  2
 QSP  Var_06    C7   C6   C5   S1    -70.31  30.0  3
 QSP  Var_07    H1   CM2  C2'  N1'  -159.29  30.0  2
 QSP  Var_08    H10  CM4  C4   N3    -50.90  30.0  3
 QSP  Var_09    O7   C7   C6   C5    173.18  30.0  1
 QSP  Var_10    O3A  PA   O7   C7     73.71  30.0  1
 QSP  Var_11    O1B  PB   O3A  PA    150.55  30.0  1
 QSP  Var_12    C14  C13  C12  C11    62.53  30.0  2
 QSP  Var_13    O16  C14  C13  C12  -131.70  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
 QSP  chir_01  C2   S1   C11  N3  positiv
 QSP  chir_03  C11  O11  C2   P4  positiv
 QSP  chir_04  PA   O2A  O1A  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
 QSP  plan-1  N1'  0.020
 QSP  plan-1  C2'  0.020
 QSP  plan-1  CM2  0.020
 QSP  plan-1  N3'  0.020
 QSP  plan-1  C4'  0.020
 QSP  plan-1  N4'  0.020
 QSP  plan-1  C5'  0.020
 QSP  plan-1  C6'  0.020
 QSP  plan-1  C7'  0.020
 QSP  plan-1  H6   0.020
 QSP  plan-2  C4'  0.020
 QSP  plan-2  N4'  0.020
 QSP  plan-2  H4   0.020
 QSP  plan-2  H5   0.020
 QSP  plan-3  C7'  0.020
 QSP  plan-3  N3   0.020
 QSP  plan-3  C2   0.020
 QSP  plan-3  C4   0.020
 QSP  plan-4  C13  0.020
 QSP  plan-4  C14  0.020
 QSP  plan-4  O15  0.020
 QSP  plan-4  O16  0.020
 QSP  plan-4  H27  0.020

