# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 01:25:37 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3cc(CO)cc(N)c23
#
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
 RRW  RRW  '[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate'  ligand  62  33  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RRW
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
 RRW  N    N  NH2   0  -0.800    0.1085  -0.8545  -28.7763
 RRW  CA   C  CH1   0  -0.202   -1.2428  -0.4047  -28.5829
 RRW  C    C  C     0   0.573   -2.2477  -1.4137  -28.0248
 RRW  O    O  O     0  -0.425   -3.3330  -1.0945  -27.5988
 RRW  CB   C  CH2   0  -0.428   -1.8222   0.1514  -29.8900
 RRW  CG   C  CH1   0  -0.223   -1.0133   1.2950  -30.5050
 RRW  CD1  C  CH3   0  -0.667   -0.8811   2.4786  -29.5530
 RRW  CD2  C  CH3   0  -0.653   -1.6589   1.7264  -31.8184
 RRW  C1   C  CR16  0  -0.386  -11.1567  -3.8542  -26.5314
 RRW  C1'  C  CH1   0   0.212   -7.3251  -3.7889  -29.0922
 RRW  C2   C  CR6   0   0.064  -11.0298  -4.6981  -25.4139
 RRW  C2'  C  CH1   0  -0.035   -6.6327  -2.4347  -28.8967
 RRW  C2M  C  CH2   0  -0.220  -12.1885  -4.8327  -24.4655
 RRW  C3   C  CR16  0  -0.411   -9.8435  -5.3571  -25.1682
 RRW  C3'  C  CH1   0  -0.031   -5.7307  -2.3723  -30.1320
 RRW  C4   C  CR56  0   0.127   -8.7914  -5.1606  -26.0672
 RRW  C4'  C  CH1   0  -0.023   -5.3423  -3.8380  -30.3197
 RRW  C5   C  CR56  0   0.299   -8.9378  -4.3395  -27.1934
 RRW  C5'  C  CH2   0  -0.218   -4.0120  -4.2404  -29.7286
 RRW  C6   C  CR6   0   0.265  -10.1331  -3.6408  -27.4457
 RRW  C8   C  CR15  0   0.107   -6.9426  -5.2532  -27.1079
 RRW  N3S  N  NC1   0  -0.831   -1.8419  -2.7301  -28.0722
 RRW  N6   N  NH2   0  -0.878  -10.3086  -2.8324  -28.5602
 RRW  N7   N  NR5   0  -0.550   -7.7241  -4.4294  -27.8552
 RRW  N9   N  N     0  -0.473   -7.5347  -5.7131  -26.0455
 RRW  O1S  O  OS    0  -0.606   -3.1568  -3.7086  -26.1177
 RRW  O2'  O  OH1   0  -0.658   -7.5840  -1.4069  -28.8466
 RRW  O2M  O  OH1   0  -0.669  -13.3502  -5.1810  -25.1880
 RRW  O2S  O  OS    0  -0.628   -1.9634  -5.1763  -27.7633
 RRW  O3'  O  OH1   0  -0.666   -6.4650  -1.9807  -31.2624
 RRW  O4'  O  O2    0  -0.495   -6.3945  -4.6069  -29.7392
 RRW  O5'  O  OC2   0  -0.577   -4.0523  -3.9459  -28.3197
 RRW  S    S  S     0   1.640   -2.7254  -3.9931  -27.4563
 RRW  H1   H  HNH2  0   0.368    0.5364  -1.2397  -27.9466
 RRW  H2   H  HNH2  0   0.360    0.2228  -1.4925  -29.5522
 RRW  H4   H  HCH1  0   0.283   -1.2337   0.3959  -27.8367
 RRW  H5   H  HCH2  0   0.241   -2.8431   0.4965  -29.7041
 RRW  H6   H  HCH2  0   0.236   -1.8971  -0.6641  -30.6196
 RRW  H7   H  HCH1  0   0.224   -0.0092   0.9226  -30.7272
 RRW  H8   H  HCH3  0   0.230   -0.3255   2.2182  -28.6515
 RRW  H9   H  HCH3  0   0.231   -0.3505   3.3036  -30.0306
 RRW  H10  H  HCH3  0   0.215   -1.8626   2.8482  -29.2455
 RRW  H11  H  HCH3  0   0.227   -1.0793   2.5170  -32.2974
 RRW  H12  H  HCH3  0   0.225   -1.7289   0.8947  -32.5219
 RRW  H13  H  HCH3  0   0.214   -2.6696   2.1088  -31.6555
 RRW  H15  H  HCH1  0   0.265   -8.2268  -3.6734  -29.7022
 RRW  H16  H  HCH1  0   0.271   -6.0238  -2.4602  -27.9888
 RRW  H17  H  HCH2  0   0.210  -11.9455  -5.5831  -23.7025
 RRW  H18  H  HCH2  0   0.212  -12.3292  -3.8817  -23.9357
 RRW  H19  H  HCR6  0   0.244   -9.7223  -6.0108  -24.3135
 RRW  H20  H  HCH1  0   0.246   -4.8583  -1.7254  -29.9753
 RRW  H21  H  HCH1  0   0.288   -5.2763  -4.0673  -31.3880
 RRW  H22  H  HCH2  0   0.292   -3.8319  -5.3060  -29.8748
 RRW  H23  H  HCH2  0   0.267   -3.2147  -3.6763  -30.2199
 RRW  H24  H  HCR5  0   0.284   -5.9358  -5.5026  -27.3995
 RRW  H25  H  HNC1  0   0.441   -0.9175  -2.9615  -28.4172
 RRW  H26  H  HNH2  0   0.378  -11.1802  -2.3235  -28.5387
 RRW  H27  H  HNH2  0   0.382   -9.5462  -2.1895  -28.7339
 RRW  H28  H  HOH1  0   0.478   -7.2934  -0.7253  -28.2331
 RRW  H29  H  HOH1  0   0.456  -14.1060  -5.0668  -24.6045
 RRW  H30  H  HOH1  0   0.453   -6.9614  -1.1861  -31.0337
 RRW  H14  H  HCR6  0   0.248  -12.0930  -3.3297  -26.6872

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
 RRW  CD2  CG   single    1.526  0.020  1.526
 RRW  O3'  C3'  single    1.404  0.020  1.404
 RRW  CG   CB   single    1.530  0.020  1.530
 RRW  CG   CD1  single    1.525  0.020  1.525
 RRW  C4'  C3'  single    1.528  0.020  1.528
 RRW  C4'  O4'  single    1.427  0.020  1.427
 RRW  C4'  C5'  single    1.510  0.020  1.510
 RRW  C3'  C2'  single    1.531  0.020  1.531
 RRW  CB   CA   single    1.534  0.020  1.534
 RRW  O4'  C1'  single    1.398  0.020  1.398
 RRW  C5'  O5'  single    1.440  0.020  1.440
 RRW  C1'  C2'  single    1.534  0.020  1.534
 RRW  C1'  N7   single    1.449  0.020  1.449
 RRW  O2'  C2'  single    1.401  0.020  1.401
 RRW  N    CA   single    1.437  0.020  1.437
 RRW  CA   C    single    1.529  0.020  1.529
 RRW  N6   C6   single    1.388  0.020  1.388
 RRW  O5'  S    single    1.584  0.020  1.584
 RRW  N7   C8   aromatic  1.359  0.020  1.359
 RRW  N7   C5   aromatic  1.385  0.020  1.385
 RRW  C    N3S  single    1.378  0.020  1.378
 RRW  C    O    double    1.209  0.020  1.209
 RRW  N3S  S    single    1.660  0.020  1.660
 RRW  C6   C5   aromatic  1.407  0.020  1.407
 RRW  C6   C1   aromatic  1.389  0.020  1.389
 RRW  C8   N9   aromatic  1.300  0.020  1.300
 RRW  C5   C4   aromatic  1.401  0.020  1.401
 RRW  S    O2S  double    1.440  0.020  1.440
 RRW  S    O1S  double    1.435  0.020  1.435
 RRW  C1   C2   aromatic  1.406  0.020  1.406
 RRW  N9   C4   aromatic  1.373  0.020  1.373
 RRW  C4   C3   aromatic  1.398  0.020  1.398
 RRW  C2   C3   aromatic  1.379  0.020  1.379
 RRW  C2   C2M  single    1.503  0.020  1.503
 RRW  O2M  C2M  single    1.412  0.020  1.412
 RRW  N    H1   single    0.890  0.020  1.040
 RRW  N    H2   single    0.890  0.020  1.040
 RRW  CA   H4   single    0.970  0.020  1.090
 RRW  CB   H5   single    0.970  0.020  1.090
 RRW  CB   H6   single    0.970  0.020  1.090
 RRW  CG   H7   single    0.970  0.020  1.090
 RRW  CD1  H8   single    0.970  0.020  1.090
 RRW  CD1  H9   single    0.970  0.020  1.090
 RRW  CD1  H10  single    0.970  0.020  1.090
 RRW  CD2  H11  single    0.970  0.020  1.090
 RRW  CD2  H12  single    0.970  0.020  1.090
 RRW  CD2  H13  single    0.970  0.020  1.090
 RRW  C1   H14  single    0.930  0.020  1.080
 RRW  C1'  H15  single    0.970  0.020  1.090
 RRW  C2'  H16  single    0.970  0.020  1.090
 RRW  C2M  H17  single    0.970  0.020  1.090
 RRW  C2M  H18  single    0.970  0.020  1.090
 RRW  C3   H19  single    0.930  0.020  1.080
 RRW  C3'  H20  single    0.970  0.020  1.090
 RRW  C4'  H21  single    0.970  0.020  1.090
 RRW  C5'  H22  single    0.970  0.020  1.090
 RRW  C5'  H23  single    0.970  0.020  1.090
 RRW  C8   H24  single    0.930  0.020  1.080
 RRW  N3S  H25  single    0.860  0.020  1.020
 RRW  N6   H26  single    0.890  0.020  1.040
 RRW  N6   H27  single    0.890  0.020  1.040
 RRW  O2'  H28  single    0.850  0.020  0.980
 RRW  O2M  H29  single    0.850  0.020  0.980
 RRW  O3'  H30  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
 RRW  H2   N    H1   109.99  3.000
 RRW  H2   N    CA   114.02  3.000
 RRW  H1   N    CA   114.03  3.000
 RRW  H4   CA   CB   108.60  3.000
 RRW  H4   CA   C    103.84  3.000
 RRW  CB   CA   C    107.57  3.000
 RRW  H4   CA   N    108.23  3.000
 RRW  C    CA   N    117.41  3.000
 RRW  CB   CA   N    110.72  3.000
 RRW  N3S  C    O    121.92  3.000
 RRW  O    C    CA   122.97  3.000
 RRW  N3S  C    CA   115.09  3.000
 RRW  H6   CB   H5   106.49  3.000
 RRW  H6   CB   CG   108.94  3.000
 RRW  H5   CB   CG   109.03  3.000
 RRW  H6   CB   CA   108.85  3.000
 RRW  H5   CB   CA   108.79  3.000
 RRW  CG   CB   CA   114.45  3.000
 RRW  H7   CG   CD2  108.05  3.000
 RRW  H7   CG   CD1  108.15  3.000
 RRW  CD2  CG   CD1  110.78  3.000
 RRW  H7   CG   CB   108.21  3.000
 RRW  CD1  CG   CB   112.03  3.000
 RRW  CD2  CG   CB   109.49  3.000
 RRW  H10  CD1  H9   107.70  3.000
 RRW  H10  CD1  H8   107.80  3.000
 RRW  H9   CD1  H8   107.14  3.000
 RRW  H10  CD1  CG   111.12  3.000
 RRW  H9   CD1  CG   110.85  3.000
 RRW  H8   CD1  CG   112.03  3.000
 RRW  H13  CD2  H12  107.67  3.000
 RRW  H13  CD2  H11  107.65  3.000
 RRW  H12  CD2  H11  107.65  3.000
 RRW  H13  CD2  CG   111.22  3.000
 RRW  H12  CD2  CG   111.50  3.000
 RRW  H11  CD2  CG   110.97  3.000
 RRW  H14  C1   C6   117.86  3.000
 RRW  H14  C1   C2   118.84  3.000
 RRW  C6   C1   C2   123.29  3.000
 RRW  H15  C1'  O4'  110.62  3.000
 RRW  H15  C1'  N7   107.19  3.000
 RRW  O4'  C1'  N7   108.65  3.000
 RRW  H15  C1'  C2'  110.47  3.000
 RRW  N7   C1'  C2'  113.94  3.000
 RRW  O4'  C1'  C2'  105.97  3.000
 RRW  C3   C2   C2M  120.52  3.000
 RRW  C2M  C2   C1   119.05  3.000
 RRW  C3   C2   C1   120.39  3.000
 RRW  H16  C2'  O2'  111.44  3.000
 RRW  H16  C2'  C3'  110.05  3.000
 RRW  O2'  C2'  C3'  113.51  3.000
 RRW  H16  C2'  C1'  109.67  3.000
 RRW  O2'  C2'  C1'  110.22  3.000
 RRW  C3'  C2'  C1'  101.49  3.000
 RRW  H18  C2M  H17  106.57  3.000
 RRW  H18  C2M  O2M  110.81  3.000
 RRW  H17  C2M  O2M  111.68  3.000
 RRW  H18  C2M  C2   109.01  3.000
 RRW  H17  C2M  C2   109.23  3.000
 RRW  O2M  C2M  C2   109.48  3.000
 RRW  H19  C3   C4   120.55  3.000
 RRW  H19  C3   C2   121.69  3.000
 RRW  C4   C3   C2   117.76  3.000
 RRW  H20  C3'  O3'  111.50  3.000
 RRW  H20  C3'  C4'  112.39  3.000
 RRW  O3'  C3'  C4'  107.56  3.000
 RRW  H20  C3'  C2'  112.16  3.000
 RRW  C4'  C3'  C2'  102.11  3.000
 RRW  O3'  C3'  C2'  110.67  3.000
 RRW  N9   C4   C5   110.12  3.000
 RRW  N9   C4   C3   128.49  3.000
 RRW  C5   C4   C3   121.37  3.000
 RRW  H21  C4'  O4'  109.19  3.000
 RRW  H21  C4'  C5'  105.85  3.000
 RRW  O4'  C4'  C5'  110.29  3.000
 RRW  H21  C4'  C3'  109.65  3.000
 RRW  C5'  C4'  C3'  115.56  3.000
 RRW  O4'  C4'  C3'  106.24  3.000
 RRW  N7   C5   C6   133.68  3.000
 RRW  C6   C5   C4   121.58  3.000
 RRW  N7   C5   C4   104.74  3.000
 RRW  H23  C5'  H22  108.87  3.000
 RRW  H23  C5'  O5'  110.77  3.000
 RRW  H22  C5'  O5'  109.61  3.000
 RRW  H23  C5'  C4'  109.21  3.000
 RRW  H22  C5'  C4'  110.69  3.000
 RRW  O5'  C5'  C4'  107.68  3.000
 RRW  N6   C6   C5   122.72  3.000
 RRW  C5   C6   C1   115.57  3.000
 RRW  N6   C6   C1   121.66  3.000
 RRW  H24  C8   N9   124.39  3.000
 RRW  H24  C8   N7   121.92  3.000
 RRW  N9   C8   N7   113.68  3.000
 RRW  H25  N3S  S    115.98  3.000
 RRW  H25  N3S  C    119.89  3.000
 RRW  S    N3S  C    123.86  3.000
 RRW  H27  N6   H26  109.50  3.000
 RRW  H27  N6   C6   114.36  3.000
 RRW  H26  N6   C6   112.68  3.000
 RRW  C8   N7   C5   106.28  3.000
 RRW  C5   N7   C1'  128.35  3.000
 RRW  C8   N7   C1'  125.37  3.000
 RRW  C8   N9   C4   105.17  3.000
 RRW  H28  O2'  C2'  109.72  3.000
 RRW  H29  O2M  C2M  107.87  3.000
 RRW  H30  O3'  C3'  107.94  3.000
 RRW  C4'  O4'  C1'  111.34  3.000
 RRW  S    O5'  C5'  120.25  3.000
 RRW  O5'  S    O2S  110.58  3.000
 RRW  O2S  S    O1S  121.38  3.000
 RRW  O5'  S    O1S  104.52  3.000
 RRW  O1S  S    N3S  110.82  3.000
 RRW  O2S  S    N3S  105.33  3.000
 RRW  O5'  S    N3S  102.77  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
 RRW  CONST_01  N7   C5   C6   C1    180.00   0.0  0
 RRW  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 RRW  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 RRW  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 RRW  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 RRW  CONST_06  N9   C4   C3   C2    180.00   0.0  0
 RRW  CONST_07  N7   C5   C4   C3    180.00   0.0  0
 RRW  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 RRW  CONST_09  C8   N9   C4   C3    180.00   0.0  0
 RRW  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 RRW  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 RRW  CONST_12  N7   C8   N9   C4      0.00   0.0  0
 RRW  CONST_13  N9   C8   N7   C5      0.00   0.0  0
 RRW  CONST_14  C8   N9   C4   C5      0.00   0.0  0
 RRW  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 RRW  CONST_16  N9   C4   C5   C6    180.00   0.0  0
 RRW  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 RRW  CONST_18  N9   C8   N7   C1'   180.00   0.0  0
 RRW  CONST_19  C6   C5   N7   C1'     0.00   0.0  0
 RRW  CONST_20  C4   C5   N7   C1'   180.00   0.0  0
 RRW  CONST_21  N6   C6   C1   C2    180.00   0.0  0
 RRW  CONST_22  C6   C1   C2   C2M   180.00   0.0  0
 RRW  CONST_23  C4   C3   C2   C2M   180.00   0.0  0
 RRW  CONST_24  N6   C6   C5   C4    180.00   0.0  0
 RRW  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 RRW  CONST_26  H19  C3   C2   C1    180.00   0.0  0
 RRW  CONST_27  H24  C8   N7   C1'     0.00   0.0  0
 RRW  CONST_28  H14  C1   C2   C3    180.00   0.0  0
 RRW  CONST_29  H26  N6   C6   C1      0.00   0.0  0
 RRW  CONST_31  S    N3S  C    CA    180.00   0.0  0
 RRW  CONST_32  S    N3S  C    O       0.00   0.0  0
 RRW  CONST_33  H25  N3S  C    CA      0.00   0.0  0
 RRW  Var_01    O2M  C2M  C2   C1     53.10  30.0  2
 RRW  Var_02    CD2  CG   CB   CA    178.01  30.0  2
 RRW  Var_03    O5'  S    N3S  C      62.05  30.0  3
 RRW  Var_04    N3S  S    O5'  C5'    66.66  30.0  3
 RRW  Var_05    H11  CD2  CG   CB   -177.86  30.0  3
 RRW  Var_06    H8   CD1  CG   CB     63.59  30.0  3
 RRW  Var_07    H22  C5'  O5'  S      71.11  30.0  2

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
 RRW  chir_01  CA   CB   N    C    positiv
 RRW  chir_02  C1'  O4'  C2'  N7   positiv
 RRW  chir_03  C2'  O2'  C1'  C3'  negativ
 RRW  chir_04  C3'  O3'  C4'  C2'  positiv
 RRW  chir_05  C4'  O4'  C3'  C5'  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
 RRW  plan-1  C1   0.020
 RRW  plan-1  C1'  0.020
 RRW  plan-1  C2   0.020
 RRW  plan-1  C2M  0.020
 RRW  plan-1  C3   0.020
 RRW  plan-1  C4   0.020
 RRW  plan-1  C5   0.020
 RRW  plan-1  C6   0.020
 RRW  plan-1  C8   0.020
 RRW  plan-1  N6   0.020
 RRW  plan-1  N7   0.020
 RRW  plan-1  N9   0.020
 RRW  plan-1  H19  0.020
 RRW  plan-1  H24  0.020
 RRW  plan-1  H14  0.020
 RRW  plan-2  C6   0.020
 RRW  plan-2  N6   0.020
 RRW  plan-2  H26  0.020
 RRW  plan-2  H27  0.020
 RRW  plan-3  CA   0.020
 RRW  plan-3  C    0.020
 RRW  plan-3  O    0.020
 RRW  plan-3  N3S  0.020
 RRW  plan-3  S    0.020
 RRW  plan-3  H25  0.020

