# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 22:18:03 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl)methyl](hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)C[S](=O)(=O)NCCNC(=O)CCl)[C@@H](O)[C@H]3O)c2N1
#
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
 6ZD  6ZD  5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl)methyl](hydroxy)phosphoryl]guanosine  ligand  57  35  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6ZD
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
 6ZD  C10  C   CH1    0   0.092   3.7491  -1.1260  -1.2143
 6ZD  C17  C   CR56   0   0.034   0.7939   1.9724  -0.6522
 6ZD  C20  C   CR6    0   0.612   3.1537   3.2007  -0.1755
 6ZD  C28  C   CH2    0  -0.290  -2.8087   0.2142   1.1686
 6ZD  O01  O   OS     0  -0.639  -3.8010  -2.6593   0.8501
 6ZD  S02  S   S      0   1.388  -2.6432  -2.3880   1.6863
 6ZD  C03  C   CH2    0  -0.916  -1.1825  -2.4408   0.6683
 6ZD  P04  P   P      0   1.236  -0.6562  -4.1629   0.2125
 6ZD  C06  C   CH2    0  -0.177   1.7577  -3.4088  -0.5830
 6ZD  C07  C   CH1    0   0.031   2.5235  -3.0317  -1.8368
 6ZD  C08  C   CH1    0  -0.084   3.9545  -2.6062  -1.5505
 6ZD  O09  O   OH1    0  -0.650   4.7017  -2.7644  -2.7253
 6ZD  O11  O   OH1    0  -0.672   4.8730  -0.3107  -1.4205
 6ZD  C12  C   CH1    0   0.149   2.6322  -0.7394  -2.1961
 6ZD  N13  N   NR5    0  -0.572   1.6917   0.2202  -1.6137
 6ZD  C14  C   CR15   0   0.101   0.3182   0.1325  -1.5958
 6ZD  N15  N   N      0  -0.471  -0.2406   1.1571  -1.0273
 6ZD  C16  C   CR56   0   0.586   1.9823   1.4022  -1.0260
 6ZD  C18  C   CR6    0   0.361   0.8176   3.2257   0.0602
 6ZD  N19  N   N      0  -0.440   2.0543   3.7833   0.2305
 6ZD  N22  N   NR16   0  -0.660   3.1844   1.9917  -0.8072
 6ZD  O23  O   O      0  -0.633  -0.1877   3.7852   0.5069
 6ZD  O24  O   O2     0  -0.504   1.9427  -1.9034  -2.5026
 6ZD  O25  O   O      0  -0.729   0.0469  -4.7853   1.3769
 6ZD  O26  O   OP    -1  -0.962  -1.7903  -4.8286  -0.4960
 6ZD  N27  N   NC1    0  -0.733  -2.7834  -0.8179   2.2030
 6ZD  C29  C   CH2    0  -0.302  -3.0470   1.5859   1.7935
 6ZD  N30  N   NH1    0  -0.536  -2.8233   2.6279   0.8195
 6ZD  C31  C   C      0   0.550  -3.7062   2.9082  -0.1480
 6ZD  C32  C   CH2    0  -0.537  -3.1153   3.8107  -1.2225
 6ZD  O34  O   O      0  -0.508  -4.8458   2.4807  -0.1952
 6ZD  O35  O   OS     0  -0.650  -2.4249  -3.1893   2.8806
 6ZD  H1   H   HCH1   0   0.278   3.3867  -1.0423  -0.1826
 6ZD  H2   H   HCH2   0   0.158  -1.8741   0.2584   0.6032
 6ZD  H3   H   HCH2   0   0.251  -3.6136  -0.0079   0.4686
 6ZD  H4   H   HCH2   0   0.328  -1.4131  -1.8755  -0.2351
 6ZD  H5   H   HCH2   0   0.373  -0.3917  -1.9198   1.2126
 6ZD  H6   H   HCH2   0   0.269   1.7604  -2.5795   0.1364
 6ZD  H7   H   HCH2   0   0.255   2.2781  -4.2447  -0.1052
 6ZD  H8   H   HCH1   0   0.287   2.4936  -3.8719  -2.5353
 6ZD  H9   H   HCH1   0   0.223   4.3915  -3.1536  -0.7059
 6ZD  H10  H   HOH1   0   0.435   5.5059  -2.2381  -2.6523
 6ZD  H11  H   HOH1   0   0.466   5.4735  -0.4128  -0.6725
 6ZD  H12  H   HCH1   0   0.261   3.0486  -0.2889  -3.1040
 6ZD  H13  H   HCR5   0   0.346  -0.1953  -0.7130  -2.0226
 6ZD  H14  H   HNH2   0   0.334   4.3326   4.7197   0.4177
 6ZD  H15  H   HNH2   0   0.399   5.1695   3.4904  -0.4302
 6ZD  H16  H   HNR6   0   0.457   4.0538   1.5209  -1.0440
 6ZD  H18  H   HNC1   0   0.406  -2.0971  -0.6246   2.9269
 6ZD  H19  H   HCH2   0   0.256  -4.0538   1.6555   2.2046
 6ZD  H20  H   HCH2   0   0.187  -2.3477   1.7507   2.6145
 6ZD  H21  H   HNH1   0   0.410  -1.8648   2.9632   0.7059
 6ZD  H22  H   HCH2   0   0.336  -2.5690   4.6448  -0.7864
 6ZD  H23  H   HCH2   0   0.328  -2.4177   3.2301  -1.8272
 6ZD  CL1  CL  CL     0  -0.184  -4.3738   4.4605  -2.2927
 6ZD  O05  O   O2     0  -0.568   0.4455  -3.7673  -0.9537
 6ZD  N21  N   NH2    0  -0.763   4.3379   3.7817   0.0554

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
 6ZD  O01  S02  double    1.454  0.020  1.454
 6ZD  C28  C29  single    1.526  0.020  1.526
 6ZD  C28  N27  single    1.461  0.020  1.461
 6ZD  C29  N30  single    1.444  0.020  1.444
 6ZD  S02  C03  single    1.781  0.020  1.781
 6ZD  S02  N27  single    1.659  0.020  1.659
 6ZD  S02  O35  double    1.455  0.020  1.455
 6ZD  O34  C31  double    1.218  0.020  1.218
 6ZD  C03  P04  single    1.858  0.020  1.858
 6ZD  N30  C31  single    1.339  0.020  1.339
 6ZD  O25  P04  deloc     1.496  0.020  1.496
 6ZD  C31  C32  single    1.523  0.020  1.523
 6ZD  P04  O26  deloc     1.494  0.020  1.494
 6ZD  P04  O05  single    1.652  0.020  1.652
 6ZD  O05  C06  single    1.410  0.020  1.410
 6ZD  N15  C14  aromatic  1.298  0.020  1.298
 6ZD  N15  C17  aromatic  1.369  0.020  1.369
 6ZD  C14  N13  aromatic  1.376  0.020  1.376
 6ZD  O23  C18  double    1.234  0.020  1.234
 6ZD  O11  C10  single    1.404  0.020  1.404
 6ZD  C10  C08  single    1.532  0.020  1.532
 6ZD  C10  C12  single    1.537  0.020  1.537
 6ZD  C06  C07  single    1.517  0.020  1.517
 6ZD  C17  C18  single    1.442  0.020  1.442
 6ZD  C17  C16  aromatic  1.370  0.020  1.370
 6ZD  C08  C07  single    1.520  0.020  1.520
 6ZD  C08  O09  single    1.401  0.020  1.401
 6ZD  C18  N19  single    1.367  0.020  1.367
 6ZD  N13  C16  aromatic  1.352  0.020  1.352
 6ZD  N13  C12  single    1.464  0.020  1.464
 6ZD  C16  N22  single    1.357  0.020  1.357
 6ZD  C07  O24  single    1.433  0.020  1.433
 6ZD  C12  O24  single    1.387  0.020  1.387
 6ZD  N19  C20  double    1.309  0.020  1.309
 6ZD  N22  C20  single    1.364  0.020  1.364
 6ZD  C20  N21  single    1.339  0.020  1.339
 6ZD  C10  H1   single    0.970  0.020  1.090
 6ZD  C28  H2   single    0.970  0.020  1.090
 6ZD  C28  H3   single    0.970  0.020  1.090
 6ZD  C03  H4   single    0.970  0.020  1.090
 6ZD  C03  H5   single    0.970  0.020  1.090
 6ZD  C06  H6   single    0.970  0.020  1.090
 6ZD  C06  H7   single    0.970  0.020  1.090
 6ZD  C07  H8   single    0.970  0.020  1.090
 6ZD  C08  H9   single    0.970  0.020  1.090
 6ZD  O09  H10  single    0.850  0.020  0.980
 6ZD  O11  H11  single    0.850  0.020  0.980
 6ZD  C12  H12  single    0.970  0.020  1.090
 6ZD  C14  H13  single    0.930  0.020  1.080
 6ZD  N21  H14  single    0.890  0.020  1.040
 6ZD  N21  H15  single    0.890  0.020  1.040
 6ZD  N22  H16  single    0.860  0.020  1.020
 6ZD  N27  H18  single    0.890  0.020  1.040
 6ZD  C29  H19  single    0.970  0.020  1.090
 6ZD  C29  H20  single    0.970  0.020  1.090
 6ZD  N30  H21  single    0.860  0.020  1.020
 6ZD  C32  H22  single    0.970  0.020  1.090
 6ZD  C32  H23  single    0.970  0.020  1.090
 6ZD  C32  CL1  single    1.775  0.020  1.775

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
 6ZD  H1   C10  C12  109.98  3.000
 6ZD  H1   C10  O11  111.00  3.000
 6ZD  C12  C10  O11  110.00  3.000
 6ZD  H1   C10  C08  108.94  3.000
 6ZD  C12  C10  C08  101.56  3.000
 6ZD  O11  C10  C08  114.94  3.000
 6ZD  C18  C17  C16  118.83  3.000
 6ZD  C16  C17  N15  109.44  3.000
 6ZD  C18  C17  N15  131.70  3.000
 6ZD  N22  C20  N21  116.38  3.000
 6ZD  N21  C20  N19  119.75  3.000
 6ZD  N22  C20  N19  123.85  3.000
 6ZD  H3   C28  H2   107.91  3.000
 6ZD  H3   C28  C29  109.32  3.000
 6ZD  H2   C28  C29  107.99  3.000
 6ZD  H3   C28  N27  108.88  3.000
 6ZD  H2   C28  N27  112.33  3.000
 6ZD  C29  C28  N27  110.35  3.000
 6ZD  O35  S02  N27  106.16  3.000
 6ZD  O35  S02  C03  109.26  3.000
 6ZD  N27  S02  C03  105.98  3.000
 6ZD  O35  S02  O01  119.27  3.000
 6ZD  N27  S02  O01  106.77  3.000
 6ZD  C03  S02  O01  108.59  3.000
 6ZD  H5   C03  H4   108.59  3.000
 6ZD  H5   C03  P04  111.06  3.000
 6ZD  H4   C03  P04  109.71  3.000
 6ZD  H5   C03  S02  107.15  3.000
 6ZD  H4   C03  S02  106.54  3.000
 6ZD  P04  C03  S02  113.58  3.000
 6ZD  O26  P04  O25  122.73  3.000
 6ZD  O26  P04  O05  106.15  3.000
 6ZD  O25  P04  O05  109.61  3.000
 6ZD  O05  P04  C03   98.05  3.000
 6ZD  O26  P04  C03  108.33  3.000
 6ZD  O25  P04  C03  109.14  3.000
 6ZD  H7   C06  H6   106.84  3.000
 6ZD  H7   C06  C07  108.10  3.000
 6ZD  H6   C06  C07  110.65  3.000
 6ZD  H7   C06  O05  111.29  3.000
 6ZD  H6   C06  O05  111.51  3.000
 6ZD  C07  C06  O05  108.41  3.000
 6ZD  H8   C07  O24  107.29  3.000
 6ZD  H8   C07  C08  111.18  3.000
 6ZD  O24  C07  C08  104.39  3.000
 6ZD  H8   C07  C06  108.86  3.000
 6ZD  O24  C07  C06  112.04  3.000
 6ZD  C08  C07  C06  112.91  3.000
 6ZD  H9   C08  O09  112.13  3.000
 6ZD  H9   C08  C07  112.35  3.000
 6ZD  O09  C08  C07  108.21  3.000
 6ZD  H9   C08  C10  111.50  3.000
 6ZD  O09  C08  C10  111.39  3.000
 6ZD  C07  C08  C10  100.69  3.000
 6ZD  H10  O09  C08  108.64  3.000
 6ZD  H11  O11  C10  108.85  3.000
 6ZD  H12  C12  O24  110.53  3.000
 6ZD  H12  C12  N13  107.71  3.000
 6ZD  O24  C12  N13  108.58  3.000
 6ZD  H12  C12  C10  110.89  3.000
 6ZD  O24  C12  C10  106.94  3.000
 6ZD  N13  C12  C10  112.19  3.000
 6ZD  C16  N13  C14  105.35  3.000
 6ZD  C16  N13  C12  127.43  3.000
 6ZD  C14  N13  C12  127.18  3.000
 6ZD  H13  C14  N15  126.00  3.000
 6ZD  H13  C14  N13  121.36  3.000
 6ZD  N15  C14  N13  112.64  3.000
 6ZD  C14  N15  C17  105.35  3.000
 6ZD  N22  C16  N13  129.84  3.000
 6ZD  N22  C16  C17  122.94  3.000
 6ZD  N13  C16  C17  107.22  3.000
 6ZD  O23  C18  N19  120.45  3.000
 6ZD  N19  C18  C17  115.53  3.000
 6ZD  O23  C18  C17  124.02  3.000
 6ZD  C18  N19  C20  122.66  3.000
 6ZD  H16  N22  C16  121.26  3.000
 6ZD  H16  N22  C20  122.50  3.000
 6ZD  C16  N22  C20  116.09  3.000
 6ZD  C12  O24  C07  110.89  3.000
 6ZD  H18  N27  S02  110.17  3.000
 6ZD  H18  N27  C28  112.43  3.000
 6ZD  S02  N27  C28  116.71  3.000
 6ZD  H20  C29  H19  107.38  3.000
 6ZD  H20  C29  N30  107.42  3.000
 6ZD  H19  C29  N30  110.59  3.000
 6ZD  H20  C29  C28  110.11  3.000
 6ZD  H19  C29  C28  110.86  3.000
 6ZD  N30  C29  C28  110.38  3.000
 6ZD  H21  N30  C31  117.99  3.000
 6ZD  H21  N30  C29  117.21  3.000
 6ZD  C31  N30  C29  122.43  3.000
 6ZD  O34  C31  C32  122.94  3.000
 6ZD  C32  C31  N30  112.21  3.000
 6ZD  O34  C31  N30  124.83  3.000
 6ZD  CL1  C32  H23  108.30  3.000
 6ZD  CL1  C32  H22  108.47  3.000
 6ZD  H23  C32  H22  108.00  3.000
 6ZD  CL1  C32  C31  111.55  3.000
 6ZD  H23  C32  C31  108.91  3.000
 6ZD  H22  C32  C31  111.49  3.000
 6ZD  C06  O05  P04  119.73  3.000
 6ZD  H15  N21  H14  116.64  3.000
 6ZD  H15  N21  C20  121.48  3.000
 6ZD  H14  N21  C20  117.53  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
 6ZD  CONST_01  N13  C14  N15  C17     0.00   0.0  0
 6ZD  CONST_02  C14  N13  C16  C17     0.00   0.0  0
 6ZD  CONST_03  N15  C17  C16  N13     0.00   0.0  0
 6ZD  CONST_04  C16  C17  N15  C14     0.00   0.0  0
 6ZD  CONST_05  C16  N13  C14  N15     0.00   0.0  0
 6ZD  CONST_06  C12  N13  C16  C17   180.00   0.0  0
 6ZD  CONST_07  N15  C14  N13  C12   180.00   0.0  0
 6ZD  CONST_08  N22  C16  N13  C12     0.00   0.0  0
 6ZD  CONST_09  N19  C20  N22  C16     0.00   0.0  0
 6ZD  CONST_10  N22  C20  N19  C18     0.00   0.0  0
 6ZD  CONST_11  N21  C20  N22  C16   180.00   0.0  0
 6ZD  CONST_12  N21  C20  N19  C18   180.00   0.0  0
 6ZD  CONST_13  H13  C14  N15  C17   180.00   0.0  0
 6ZD  CONST_14  H16  N22  C20  N19   180.00   0.0  0
 6ZD  CONST_15  H14  N21  C20  N19     0.00   0.0  0
 6ZD  CONST_17  O34  C31  N30  C29     0.00   0.0  0
 6ZD  CONST_18  C32  C31  N30  C29   180.00   0.0  0
 6ZD  CONST_19  H21  N30  C31  C32     0.00   0.0  0
 6ZD  Var_01    C07  C06  O05  P04  -177.18  30.0  3
 6ZD  Var_02    C31  N30  C29  C28    76.00  30.0  3
 6ZD  Var_03    O01  S02  N27  C28   -60.69  30.0  1
 6ZD  Var_04    P04  C03  S02  O01   -75.59  30.0  3
 6ZD  Var_05    O25  P04  C03  S02   -78.12  30.0  3
 6ZD  Var_06    C29  C28  N27  S02   175.71  30.0  1
 6ZD  Var_07    N30  C29  C28  N27   169.22  30.0  3
 6ZD  Var_08    CL1  C32  C31  N30  -167.45  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
 6ZD  chir_01  C10  O11  C08  C12  positiv
 6ZD  chir_03  C07  C06  C08  O24  positiv
 6ZD  chir_04  C08  O09  C07  C10  positiv
 6ZD  chir_05  C12  O24  N13  C10  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
 6ZD  plan-1  C17  0.020
 6ZD  plan-1  C20  0.020
 6ZD  plan-1  C12  0.020
 6ZD  plan-1  N13  0.020
 6ZD  plan-1  C14  0.020
 6ZD  plan-1  N15  0.020
 6ZD  plan-1  C16  0.020
 6ZD  plan-1  C18  0.020
 6ZD  plan-1  N19  0.020
 6ZD  plan-1  N22  0.020
 6ZD  plan-1  O23  0.020
 6ZD  plan-1  H13  0.020
 6ZD  plan-1  H14  0.020
 6ZD  plan-1  H15  0.020
 6ZD  plan-1  H16  0.020
 6ZD  plan-1  N21  0.020
 6ZD  plan-2  C29  0.020
 6ZD  plan-2  N30  0.020
 6ZD  plan-2  C31  0.020
 6ZD  plan-2  C32  0.020
 6ZD  plan-2  O34  0.020
 6ZD  plan-2  H21  0.020

