# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:21:58 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)CO)[C@@H](O)[C@H]2O)C1=O
#
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
 FZT  FZT  '[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'  ligand  48  28  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FZT
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
 FZT  C3U  C  CH3   0  -0.531   5.1207  -2.2212   1.0947
 FZT  N3   N  NR6   0  -0.597   3.8135  -1.7622   0.6387
 FZT  C4   C  CR6   0   0.596   2.8347  -2.7051   0.3134
 FZT  O4   O  O     0  -0.467   3.0585  -3.8987   0.3992
 FZT  C5   C  CR16  0  -0.529   1.5769  -2.1483  -0.1163
 FZT  C6   C  CR16  0   0.104   1.4243  -0.8214  -0.1803
 FZT  N1   N  NR6   0  -0.578   2.4179   0.0546   0.1476
 FZT  C1'  C  CH1   0   0.190   2.1678   1.4820   0.0706
 FZT  O4'  O  O2    0  -0.486   1.0033   1.7805   0.7969
 FZT  C4'  C  CH1   0  -0.037   0.2616   2.8107   0.1475
 FZT  C5'  C  CH2   0  -0.203  -1.0884   2.2978  -0.3079
 FZT  O5'  O  OC2   0  -0.565  -1.7482   1.7766   0.8597
 FZT  S    S  S     0   1.633  -3.2424   1.2659   0.7390
 FZT  O1S  O  OS    0  -0.605  -3.6043   0.8891   2.0751
 FZT  O2S  O  OS    0  -0.629  -4.0352   2.1949  -0.0251
 FZT  N3S  N  NC1   0  -0.838  -3.1180  -0.0810  -0.2305
 FZT  C    C  C     0   0.586  -2.4628  -1.2423   0.1334
 FZT  O    O  O     0  -0.401  -1.8040  -1.3182   1.1385
 FZT  CA   C  CH1   0  -0.267  -2.6907  -2.3927  -0.8293
 FZT  N    N  NH2   0  -0.764  -1.5981  -3.3303  -0.7246
 FZT  CB   C  CH2   0  -0.134  -4.0811  -2.9823  -0.5485
 FZT  OG   O  OH1   0  -0.662  -4.3089  -3.9895  -1.5007
 FZT  C3'  C  CH1   0  -0.041   1.1075   3.2707  -1.0372
 FZT  O3'  O  OH1   0  -0.663   1.9526   4.2999  -0.6002
 FZT  C2'  C  CH1   0  -0.038   1.9043   1.9974  -1.3420
 FZT  O2'  O  OH1   0  -0.649   3.1115   2.2030  -2.0073
 FZT  C2   C  CR6   0   0.789   3.6458  -0.3951   0.5961
 FZT  O2   O  O     0  -0.482   4.5324   0.3634   0.9294
 FZT  H1   H  HCH3  0   0.268   5.1723  -3.2968   0.9805
 FZT  H2   H  HCH3  0   0.258   5.9102  -1.7653   0.5028
 FZT  H3   H  HCH3  0   0.258   5.2729  -1.9698   2.1427
 FZT  H4   H  HCR6  0   0.315   0.7515  -2.7987  -0.3725
 FZT  H5   H  HCR6  0   0.298   0.4873  -0.3870  -0.4928
 FZT  H6   H  HCH1  0   0.281   3.0410   1.9809   0.4940
 FZT  H7   H  HCH1  0   0.284   0.1053   3.6322   0.8527
 FZT  H8   H  HCH2  0   0.285  -1.6608   3.1246  -0.7317
 FZT  H9   H  HCH2  0   0.252  -0.9982   1.5118  -1.0639
 FZT  H10  H  HNC1  0   0.458  -3.6035  -0.0250  -1.1186
 FZT  H11  H  HCH1  0   0.283  -2.6975  -1.9886  -1.8479
 FZT  H12  H  HNH2  0   0.352  -1.5866  -3.7577   0.1939
 FZT  H13  H  HNH2  0   0.364  -1.7450  -4.0809  -1.3867
 FZT  H15  H  HCH2  0   0.211  -4.0939  -3.3760   0.4765
 FZT  H16  H  HCH2  0   0.203  -4.8439  -2.1952  -0.6033
 FZT  H17  H  HOH1  0   0.462  -5.1210  -4.4471  -1.2653
 FZT  H18  H  HCH1  0   0.262   0.4906   3.5848  -1.8899
 FZT  H19  H  HOH1  0   0.453   2.6835   4.3731  -1.2252
 FZT  H20  H  HCH1  0   0.251   1.2589   1.2937  -1.8844
 FZT  H21  H  HOH1  0   0.471   2.9474   2.2185  -2.9555

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
 FZT  OG   CB   single  1.405  0.020  1.405
 FZT  CB   CA   single  1.536  0.020  1.536
 FZT  N    CA   single  1.444  0.020  1.444
 FZT  CA   C    single  1.517  0.020  1.517
 FZT  C    O    double  1.204  0.020  1.204
 FZT  C    N3S  single  1.382  0.020  1.382
 FZT  C5'  C4'  single  1.514  0.020  1.514
 FZT  C5'  O5'  single  1.439  0.020  1.439
 FZT  N3S  S    single  1.664  0.020  1.664
 FZT  C4'  O4'  single  1.426  0.020  1.426
 FZT  C4'  C3'  single  1.527  0.020  1.527
 FZT  O3'  C3'  single  1.402  0.020  1.402
 FZT  O5'  S    single  1.584  0.020  1.584
 FZT  O4'  C1'  single  1.404  0.020  1.404
 FZT  O2'  C2'  single  1.394  0.020  1.394
 FZT  C3'  C2'  single  1.533  0.020  1.533
 FZT  S    O2S  deloc   1.441  0.020  1.441
 FZT  S    O1S  deloc   1.435  0.020  1.435
 FZT  C1'  C2'  single  1.527  0.020  1.527
 FZT  C1'  N1   single  1.451  0.020  1.451
 FZT  O2   C2   double  1.213  0.020  1.213
 FZT  N1   C2   single  1.382  0.020  1.382
 FZT  N1   C6   single  1.365  0.020  1.365
 FZT  C2   N3   single  1.378  0.020  1.378
 FZT  C6   C5   double  1.337  0.020  1.337
 FZT  N3   C3U  single  1.459  0.020  1.459
 FZT  N3   C4   single  1.397  0.020  1.397
 FZT  C5   C4   single  1.441  0.020  1.441
 FZT  C4   O4   double  1.217  0.020  1.217
 FZT  C3U  H1   single  0.970  0.020  1.090
 FZT  C3U  H2   single  0.970  0.020  1.090
 FZT  C3U  H3   single  0.970  0.020  1.090
 FZT  C5   H4   single  0.930  0.020  1.080
 FZT  C6   H5   single  0.930  0.020  1.080
 FZT  C1'  H6   single  0.970  0.020  1.090
 FZT  C4'  H7   single  0.970  0.020  1.090
 FZT  C5'  H8   single  0.970  0.020  1.090
 FZT  C5'  H9   single  0.970  0.020  1.090
 FZT  N3S  H10  single  0.860  0.020  1.020
 FZT  CA   H11  single  0.970  0.020  1.090
 FZT  N    H12  single  0.890  0.020  1.040
 FZT  N    H13  single  0.890  0.020  1.040
 FZT  CB   H15  single  0.970  0.020  1.090
 FZT  CB   H16  single  0.970  0.020  1.090
 FZT  OG   H17  single  0.850  0.020  0.980
 FZT  C3'  H18  single  0.970  0.020  1.090
 FZT  O3'  H19  single  0.850  0.020  0.980
 FZT  C2'  H20  single  0.970  0.020  1.090
 FZT  O2'  H21  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
 FZT  H3   C3U  H2   109.01  3.000
 FZT  H3   C3U  H1   108.93  3.000
 FZT  H2   C3U  H1   108.94  3.000
 FZT  H3   C3U  N3   110.71  3.000
 FZT  H2   C3U  N3   110.41  3.000
 FZT  H1   C3U  N3   108.80  3.000
 FZT  C2   N3   C4   125.24  3.000
 FZT  C4   N3   C3U  119.22  3.000
 FZT  C2   N3   C3U  115.53  3.000
 FZT  C5   C4   O4   124.07  3.000
 FZT  O4   C4   N3   121.09  3.000
 FZT  C5   C4   N3   114.84  3.000
 FZT  H4   C5   C6   119.88  3.000
 FZT  H4   C5   C4   120.29  3.000
 FZT  C6   C5   C4   119.82  3.000
 FZT  H5   C6   N1   116.32  3.000
 FZT  H5   C6   C5   120.83  3.000
 FZT  N1   C6   C5   122.84  3.000
 FZT  C2   N1   C1'  119.36  3.000
 FZT  C2   N1   C6   121.05  3.000
 FZT  C1'  N1   C6   119.55  3.000
 FZT  H6   C1'  C2'  110.05  3.000
 FZT  H6   C1'  O4'  111.46  3.000
 FZT  C2'  C1'  O4'  105.29  3.000
 FZT  H6   C1'  N1   106.93  3.000
 FZT  C2'  C1'  N1   114.26  3.000
 FZT  O4'  C1'  N1   108.93  3.000
 FZT  C4'  O4'  C1'  110.45  3.000
 FZT  H7   C4'  C3'  110.68  3.000
 FZT  H7   C4'  C5'  108.71  3.000
 FZT  C3'  C4'  C5'  111.27  3.000
 FZT  H7   C4'  O4'  108.86  3.000
 FZT  C3'  C4'  O4'  106.43  3.000
 FZT  C5'  C4'  O4'  110.86  3.000
 FZT  H9   C5'  H8   108.61  3.000
 FZT  H9   C5'  O5'  109.77  3.000
 FZT  H8   C5'  O5'  110.43  3.000
 FZT  H9   C5'  C4'  112.18  3.000
 FZT  H8   C5'  C4'  109.14  3.000
 FZT  O5'  C5'  C4'  106.71  3.000
 FZT  S    O5'  C5'  119.18  3.000
 FZT  N3S  S    O2S  104.72  3.000
 FZT  O2S  S    O1S  121.64  3.000
 FZT  N3S  S    O1S  110.41  3.000
 FZT  O1S  S    O5'  104.58  3.000
 FZT  O2S  S    O5'  110.59  3.000
 FZT  N3S  S    O5'  103.58  3.000
 FZT  H10  N3S  C    120.27  3.000
 FZT  H10  N3S  S    115.46  3.000
 FZT  C    N3S  S    124.20  3.000
 FZT  CA   C    O    124.33  3.000
 FZT  O    C    N3S  122.14  3.000
 FZT  CA   C    N3S  113.51  3.000
 FZT  H11  CA   CB   107.81  3.000
 FZT  H11  CA   N    108.15  3.000
 FZT  CB   CA   N    114.99  3.000
 FZT  H11  CA   C    108.13  3.000
 FZT  N    CA   C    109.44  3.000
 FZT  CB   CA   C    108.12  3.000
 FZT  H13  N    H12  106.38  3.000
 FZT  H13  N    CA   108.94  3.000
 FZT  H12  N    CA   110.39  3.000
 FZT  H16  CB   H15  107.19  3.000
 FZT  H16  CB   OG   111.58  3.000
 FZT  H15  CB   OG   111.95  3.000
 FZT  H16  CB   CA   110.16  3.000
 FZT  H15  CB   CA   108.59  3.000
 FZT  OG   CB   CA   107.35  3.000
 FZT  H17  OG   CB   108.20  3.000
 FZT  H18  C3'  C2'  112.04  3.000
 FZT  H18  C3'  O3'  111.76  3.000
 FZT  C2'  C3'  O3'  111.01  3.000
 FZT  H18  C3'  C4'  112.18  3.000
 FZT  C2'  C3'  C4'  101.08  3.000
 FZT  O3'  C3'  C4'  108.27  3.000
 FZT  H19  O3'  C3'  108.10  3.000
 FZT  H20  C2'  O2'  111.58  3.000
 FZT  H20  C2'  C3'  108.96  3.000
 FZT  O2'  C2'  C3'  115.01  3.000
 FZT  H20  C2'  C1'  110.01  3.000
 FZT  C3'  C2'  C1'  100.73  3.000
 FZT  O2'  C2'  C1'  110.00  3.000
 FZT  H21  O2'  C2'  108.97  3.000
 FZT  O2   C2   N1   122.33  3.000
 FZT  N1   C2   N3   116.16  3.000
 FZT  O2   C2   N3   121.51  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
 FZT  CONST_01  C1'  N1   C2   N3   180.00   0.0  0
 FZT  CONST_02  C6   N1   C2   N3     0.00   0.0  0
 FZT  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 FZT  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 FZT  CONST_05  N1   C2   N3   C3U  180.00   0.0  0
 FZT  CONST_06  C5   C4   N3   C3U  180.00   0.0  0
 FZT  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 FZT  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 FZT  CONST_09  O2   C2   N1   C6   180.00   0.0  0
 FZT  CONST_10  O2   C2   N1   C1'    0.00   0.0  0
 FZT  CONST_11  O2   C2   N3   C3U    0.00   0.0  0
 FZT  CONST_12  O4   C4   N3   C3U    0.00   0.0  0
 FZT  CONST_13  CA   C    N3S  S    180.00   0.0  0
 FZT  CONST_14  O    C    N3S  S      0.00   0.0  0
 FZT  CONST_15  H10  N3S  C    O    180.00   0.0  0
 FZT  Var_01    H1   C3U  N3   C4     7.71  30.0  3
 FZT  Var_02    N3S  S    O5'  C5'   67.24  30.0  3
 FZT  Var_03    C    N3S  S    O5'   65.88  30.0  1
 FZT  Var_04    H8   C5'  O5'  S     56.60  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
 FZT  chir_01  C1'  O4'  C2'  N1   positiv
 FZT  chir_02  C4'  O4'  C5'  C3'  positiv
 FZT  chir_03  CA   N    CB   C    negativ
 FZT  chir_04  C3'  O3'  C4'  C2'  positiv
 FZT  chir_05  C2'  O2'  C3'  C1'  positiv

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
 FZT  plan-1  C3U  0.020
 FZT  plan-1  N3   0.020
 FZT  plan-1  C4   0.020
 FZT  plan-1  O4   0.020
 FZT  plan-1  C5   0.020
 FZT  plan-1  C6   0.020
 FZT  plan-1  N1   0.020
 FZT  plan-1  C1'  0.020
 FZT  plan-1  C2   0.020
 FZT  plan-1  O2   0.020
 FZT  plan-1  H4   0.020
 FZT  plan-1  H5   0.020
 FZT  plan-2  S    0.020
 FZT  plan-2  N3S  0.020
 FZT  plan-2  C    0.020
 FZT  plan-2  O    0.020
 FZT  plan-2  CA   0.020
 FZT  plan-2  H10  0.020

