# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 22:11:48 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2R,3R,4S,5R,8R,10R,13R,14S,15R,16R)-24-amino-18-bromo-3,4,8,10,14,15-hexahydroxy-7,9,11,25,26-pentaoxa-17,19,22-triaza-1-azonia-8,10-diphosphapentacyclo[18.3.1.1~2,5~.1~13,16~.0~17,21~]hexacosa-1(24),18,20,22-tetraene 8,10-dioxide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1c2nc(Br)n3[C@@H]4O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]5O[C@H]([C@H](O)[C@@H]5O)[n+]1cnc23)[C@@H](O)[C@H]4O
#
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
 CV1  CV1  '(2R,3R,4S,5R,8R,10R,13R,14S,15R,16R)-24-amino-18-bromo-3,4,8,10,14,15-hexahydroxy-7,9,11,25,26-pentaoxa-17,19,22-triaza-1-azonia-8,10-diphosphapentacyclo[18.3.1.1~2,5~.1~13,16~.0~17,21~]hexacosa-1(24),18,20,22-tetraene 8,10-dioxide (non-preferred name)'  ligand  55  36  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CV1
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
 CV1  N1    N   NR6    1  -0.554  -1.5903   2.3986  -0.0993
 CV1  BR1   BR  BR     0   0.079   4.5123   2.4726   0.8964
 CV1  C2    C   CR16   0   0.193  -1.2537   1.2820  -0.8314
 CV1  N3    N   N      0  -0.400  -0.0631   0.8403  -1.0133
 CV1  C4    C   CR56   0   0.540   0.8734   1.5555  -0.3811
 CV1  C5    C   CR56   0   0.043   0.6840   2.7454   0.2743
 CV1  C6    C   CR6    0   0.670  -0.6324   3.2221   0.4197
 CV1  N6    N   NH2    0  -0.804  -0.9051   4.3446   1.0417
 CV1  N7    N   N      0  -0.412   1.8621   3.2085   0.7794
 CV1  C8    C   CR5    0   0.300   2.7259   2.2936   0.4672
 CV1  N9    N   NR5    0  -0.574   2.1925   1.2475  -0.2500
 CV1  PA    P   P      0   1.366  -0.5556  -3.6423   1.0474
 CV1  PB    P   P      0   1.371  -2.4903  -2.3174  -0.6837
 CV1  C1'   C   CH1    0   0.225   2.6139  -0.1005  -0.6196
 CV1  O1A   O   O      0  -0.805  -0.0426  -4.6471   0.0647
 CV1  O1B   O   OP    -1  -0.786  -2.1855  -1.6010  -1.9650
 CV1  C1D   C   CH1    0   0.167  -3.0034   2.4822   0.3296
 CV1  C2'   C   CH1    0  -0.022   3.9995  -0.6079  -0.2481
 CV1  O2'   O   OH1    0  -0.654   4.9828  -0.1180  -1.1048
 CV1  O2A   O   OP    -1  -0.792  -1.4935  -4.0180   2.1484
 CV1  O2B   O   O      0  -0.793  -3.1135  -3.6773  -0.7056
 CV1  C2D   C   CH1    0  -0.047  -4.0190   2.6263  -0.8040
 CV1  O2D   O   OH1    0  -0.651  -4.2145   3.9790  -1.0774
 CV1  C3'   C   CH1    0  -0.056   3.7549  -2.1314  -0.3803
 CV1  O3'   O   OH1    0  -0.662   3.9351  -2.5666  -1.7009
 CV1  O3A   O   O2     0  -0.725  -1.1531  -2.3282   0.2498
 CV1  C3D   C   CH1    0  -0.028  -5.2305   1.9009  -0.1913
 CV1  O3D   O   OH1    0  -0.663  -5.8853   2.7211   0.7372
 CV1  C4'   C   CH1    0   0.004   2.2696  -2.2715  -0.0101
 CV1  O4'   O   O2     0  -0.474   1.7668  -0.9457   0.0915
 CV1  C4D   C   CH1    0  -0.047  -4.5503   0.7630   0.5579
 CV1  O4D   O   O2     0  -0.464  -3.2969   1.3033   0.9964
 CV1  C5'   C   CH2    0  -0.167   2.0366  -2.9834   1.3071
 CV1  O5'   O   O2     0  -0.615   0.7121  -2.8873   1.7781
 CV1  C5D   C   CH2    0  -0.167  -4.3426  -0.4572  -0.3293
 CV1  O5D   O   O2     0  -0.620  -3.4039  -1.3169   0.2664
 CV1  H2    H   HCR6   0   0.304  -2.0662   0.7329  -1.2835
 CV1  HN6   H   HNH2   0   0.449  -1.8220   4.7532   1.1126
 CV1  HN6A  H   HNH2   0   0.450  -0.1446   4.8864   1.4239
 CV1  H1'   H   HCH1   0   0.259   2.4700  -0.1786  -1.7054
 CV1  H1D   H   HCH1   0   0.271  -3.0936   3.3359   1.0035
 CV1  H2'   H   HCH1   0   0.256   4.1993  -0.3879   0.8056
 CV1  HO2'  H   HOH1   0   0.470   5.8299  -0.1230  -0.6489
 CV1  H2D   H   HCH1   0   0.267  -3.6907   2.0834  -1.6973
 CV1  HO2D  H   HOH1   0   0.474  -4.5526   4.0732  -1.9734
 CV1  H3'   H   HCH1   0   0.248   4.4048  -2.6821   0.3130
 CV1  HO3'  H   HOH1   0   0.450   4.8016  -2.2658  -1.9979
 CV1  H3D   H   HCH1   0   0.261  -5.9113   1.5307  -0.9689
 CV1  HO3D  H   HOH1   0   0.453  -6.0720   3.5674   0.3145
 CV1  H4'   H   HCH1   0   0.249   1.7452  -2.8006  -0.8125
 CV1  H4D   H   HCH1   0   0.273  -5.1128   0.4808   1.4512
 CV1  H5'   H   HCH2   0   0.218   2.3532  -4.0246   1.1877
 CV1  H5'A  H   HCH2   0   0.224   2.6691  -2.5381   2.0806
 CV1  H5D   H   HCH2   0   0.238  -5.3160  -0.9471  -0.4533
 CV1  H5DA  H   HCH2   0   0.210  -4.0215  -0.1509  -1.3307

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
 CV1  N1   C2    aromatic  1.377  0.020  1.377
 CV1  N1   C6    aromatic  1.366  0.020  1.366
 CV1  N1   C1D   single    1.479  0.020  1.479
 CV1  BR1  C8    single    1.846  0.020  1.846
 CV1  C2   N3    aromatic  1.283  0.020  1.283
 CV1  N3   C4    aromatic  1.337  0.020  1.337
 CV1  C4   C5    aromatic  1.372  0.020  1.372
 CV1  C4   N9    aromatic  1.361  0.020  1.361
 CV1  C5   C6    aromatic  1.408  0.020  1.408
 CV1  C5   N7    aromatic  1.363  0.020  1.363
 CV1  C6   N6    single    1.312  0.020  1.312
 CV1  N7   C8    aromatic  1.296  0.020  1.296
 CV1  C8   N9    aromatic  1.376  0.020  1.376
 CV1  N9   C1'   single    1.460  0.020  1.460
 CV1  PA   O1A   deloc     1.496  0.020  1.496
 CV1  PA   O2A   deloc     1.494  0.020  1.494
 CV1  PA   O3A   single    1.649  0.020  1.649
 CV1  PA   O5'   single    1.647  0.020  1.647
 CV1  PB   O1B   deloc     1.499  0.020  1.499
 CV1  PB   O2B   deloc     1.496  0.020  1.496
 CV1  PB   O3A   single    1.631  0.020  1.631
 CV1  PB   O5D   single    1.655  0.020  1.655
 CV1  C1'  C2'   single    1.522  0.020  1.522
 CV1  C1'  O4'   single    1.392  0.020  1.392
 CV1  C1D  C2D   single    1.529  0.020  1.529
 CV1  C1D  O4D   single    1.386  0.020  1.386
 CV1  C2'  O2'   single    1.393  0.020  1.393
 CV1  C2'  C3'   single    1.549  0.020  1.549
 CV1  C2D  O2D   single    1.394  0.020  1.394
 CV1  C2D  C3D   single    1.539  0.020  1.539
 CV1  C3'  O3'   single    1.402  0.020  1.402
 CV1  C3'  C4'   single    1.537  0.020  1.537
 CV1  C3D  O3D   single    1.401  0.020  1.401
 CV1  C3D  C4D   single    1.523  0.020  1.523
 CV1  C4'  O4'   single    1.422  0.020  1.422
 CV1  C4'  C5'   single    1.515  0.020  1.515
 CV1  C4D  O4D   single    1.434  0.020  1.434
 CV1  C4D  C5D   single    1.523  0.020  1.523
 CV1  C5'  O5'   single    1.409  0.020  1.409
 CV1  C5D  O5D   single    1.405  0.020  1.405
 CV1  C2   H2    single    0.930  0.020  1.080
 CV1  N6   HN6   single    0.860  0.020  1.020
 CV1  N6   HN6A  single    0.860  0.020  1.020
 CV1  C1'  H1'   single    0.970  0.020  1.090
 CV1  C1D  H1D   single    0.970  0.020  1.090
 CV1  C2'  H2'   single    0.970  0.020  1.090
 CV1  O2'  HO2'  single    0.850  0.020  0.980
 CV1  C2D  H2D   single    0.970  0.020  1.090
 CV1  O2D  HO2D  single    0.850  0.020  0.980
 CV1  C3'  H3'   single    0.970  0.020  1.090
 CV1  O3'  HO3'  single    0.850  0.020  0.980
 CV1  C3D  H3D   single    0.970  0.020  1.090
 CV1  O3D  HO3D  single    0.850  0.020  0.980
 CV1  C4'  H4'   single    0.970  0.020  1.090
 CV1  C4D  H4D   single    0.970  0.020  1.090
 CV1  C5'  H5'   single    0.970  0.020  1.090
 CV1  C5'  H5'A  single    0.970  0.020  1.090
 CV1  C5D  H5D   single    0.970  0.020  1.090
 CV1  C5D  H5DA  single    0.970  0.020  1.090

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
 CV1  C1D   N1   C6   121.72  3.000
 CV1  C1D   N1   C2   115.70  3.000
 CV1  C6    N1   C2   121.30  3.000
 CV1  H2    C2   N3   117.64  3.000
 CV1  H2    C2   N1   116.80  3.000
 CV1  N3    C2   N1   125.56  3.000
 CV1  C4    N3   C2   113.50  3.000
 CV1  N9    C4   C5   106.51  3.000
 CV1  N9    C4   N3   127.10  3.000
 CV1  C5    C4   N3   126.38  3.000
 CV1  N7    C5   C6   130.92  3.000
 CV1  N7    C5   C4   110.64  3.000
 CV1  C6    C5   C4   118.19  3.000
 CV1  N6    C6   C5   122.21  3.000
 CV1  N6    C6   N1   123.39  3.000
 CV1  C5    C6   N1   114.36  3.000
 CV1  HN6A  N6   HN6  116.24  3.000
 CV1  HN6A  N6   C6   118.84  3.000
 CV1  HN6   N6   C6   124.76  3.000
 CV1  C8    N7   C5   104.30  3.000
 CV1  N9    C8   N7   113.81  3.000
 CV1  N9    C8   BR1  124.75  3.000
 CV1  N7    C8   BR1  121.36  3.000
 CV1  C1'   N9   C8   136.23  3.000
 CV1  C1'   N9   C4   117.67  3.000
 CV1  C8    N9   C4   104.71  3.000
 CV1  O5'   PA   O3A   97.37  3.000
 CV1  O5'   PA   O2A  105.76  3.000
 CV1  O3A   PA   O2A  109.22  3.000
 CV1  O5'   PA   O1A  109.60  3.000
 CV1  O3A   PA   O1A  109.98  3.000
 CV1  O2A   PA   O1A  122.03  3.000
 CV1  O5D   PB   O3A   97.36  3.000
 CV1  O5D   PB   O2B  109.15  3.000
 CV1  O3A   PB   O2B  110.11  3.000
 CV1  O5D   PB   O1B  108.30  3.000
 CV1  O3A   PB   O1B  109.01  3.000
 CV1  O2B   PB   O1B  120.43  3.000
 CV1  H1'   C1'  O4'  112.47  3.000
 CV1  H1'   C1'  C2'  109.70  3.000
 CV1  O4'   C1'  C2'  103.12  3.000
 CV1  H1'   C1'  N9   106.15  3.000
 CV1  O4'   C1'  N9   104.81  3.000
 CV1  C2'   C1'  N9   120.59  3.000
 CV1  H1D   C1D  O4D  110.54  3.000
 CV1  H1D   C1D  C2D  109.22  3.000
 CV1  O4D   C1D  C2D  107.23  3.000
 CV1  H1D   C1D  N1   107.59  3.000
 CV1  O4D   C1D  N1   107.08  3.000
 CV1  C2D   C1D  N1   115.15  3.000
 CV1  H2'   C2'  C3'  107.97  3.000
 CV1  H2'   C2'  O2'  113.11  3.000
 CV1  C3'   C2'  O2'  113.89  3.000
 CV1  H2'   C2'  C1'  109.52  3.000
 CV1  C3'   C2'  C1'   99.40  3.000
 CV1  O2'   C2'  C1'  112.04  3.000
 CV1  HO2'  O2'  C2'  109.16  3.000
 CV1  H2D   C2D  C3D  109.07  3.000
 CV1  H2D   C2D  O2D  111.28  3.000
 CV1  C3D   C2D  O2D  115.15  3.000
 CV1  H2D   C2D  C1D  111.03  3.000
 CV1  C3D   C2D  C1D  100.56  3.000
 CV1  O2D   C2D  C1D  109.28  3.000
 CV1  HO2D  O2D  C2D  109.08  3.000
 CV1  H3'   C3'  C4'  111.96  3.000
 CV1  H3'   C3'  O3'  111.28  3.000
 CV1  C4'   C3'  O3'  108.83  3.000
 CV1  H3'   C3'  C2'  110.24  3.000
 CV1  C4'   C3'  C2'  102.81  3.000
 CV1  O3'   C3'  C2'  111.43  3.000
 CV1  HO3'  O3'  C3'  107.99  3.000
 CV1  PB    O3A  PA   125.39  3.000
 CV1  H3D   C3D  C4D  111.93  3.000
 CV1  H3D   C3D  O3D  112.14  3.000
 CV1  C4D   C3D  O3D  108.67  3.000
 CV1  H3D   C3D  C2D  111.41  3.000
 CV1  C4D   C3D  C2D  101.33  3.000
 CV1  O3D   C3D  C2D  110.84  3.000
 CV1  HO3D  O3D  C3D  108.29  3.000
 CV1  H4'   C4'  C5'  109.66  3.000
 CV1  H4'   C4'  O4'  109.49  3.000
 CV1  C5'   C4'  O4'  108.76  3.000
 CV1  H4'   C4'  C3'  109.29  3.000
 CV1  C5'   C4'  C3'  113.63  3.000
 CV1  O4'   C4'  C3'  105.90  3.000
 CV1  C4'   O4'  C1'  108.33  3.000
 CV1  H4D   C4D  C5D  109.85  3.000
 CV1  H4D   C4D  O4D  107.30  3.000
 CV1  C5D   C4D  O4D  111.16  3.000
 CV1  H4D   C4D  C3D  111.42  3.000
 CV1  C5D   C4D  C3D  111.90  3.000
 CV1  O4D   C4D  C3D  105.04  3.000
 CV1  C4D   O4D  C1D  111.01  3.000
 CV1  H5'A  C5'  H5'  107.28  3.000
 CV1  H5'A  C5'  O5'  106.22  3.000
 CV1  H5'   C5'  O5'  111.91  3.000
 CV1  H5'A  C5'  C4'  109.54  3.000
 CV1  H5'   C5'  C4'  107.91  3.000
 CV1  O5'   C5'  C4'  113.77  3.000
 CV1  C5'   O5'  PA   122.96  3.000
 CV1  H5DA  C5D  H5D  106.37  3.000
 CV1  H5DA  C5D  O5D  111.27  3.000
 CV1  H5D   C5D  O5D  111.56  3.000
 CV1  H5DA  C5D  C4D  110.40  3.000
 CV1  H5D   C5D  C4D  107.63  3.000
 CV1  O5D   C5D  C4D  109.53  3.000
 CV1  C5D   O5D  PB   119.69  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
 CV1  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CV1  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 CV1  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 CV1  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 CV1  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 CV1  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 CV1  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 CV1  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 CV1  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 CV1  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 CV1  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 CV1  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 CV1  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 CV1  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 CV1  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 CV1  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 CV1  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 CV1  CONST_18  C5    N7   C8   BR1   180.00   0.0  0
 CV1  CONST_19  C4    N9   C8   BR1   180.00   0.0  0
 CV1  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 CV1  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 CV1  CONST_24  N7    C5   C6   N6      0.00   0.0  0
 CV1  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 CV1  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 CV1  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 CV1  Var_01    O5D   PB   O3A  PA    114.09  30.0  1
 CV1  Var_02    C4'   C5'  O5'  PA     69.31  30.0  1
 CV1  Var_03    O5'   PA   O3A  PB   -178.09  30.0  1
 CV1  Var_04    C4D   C5D  O5D  PB   -152.86  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
 CV1  chir_03  C1'  N9   C2'  O4'  negativ
 CV1  chir_04  C1D  N1   C2D  O4D  negativ
 CV1  chir_05  C2'  C1'  O2'  C3'  positiv
 CV1  chir_06  C2D  C1D  O2D  C3D  positiv
 CV1  chir_07  C3'  C2'  O3'  C4'  positiv
 CV1  chir_08  C3D  C2D  O3D  C4D  positiv
 CV1  chir_09  C4'  O4'  C3'  C5'  negativ
 CV1  chir_10  C4D  O4D  C3D  C5D  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
 CV1  plan-1  N1    0.020
 CV1  plan-1  BR1   0.020
 CV1  plan-1  C2    0.020
 CV1  plan-1  N3    0.020
 CV1  plan-1  C4    0.020
 CV1  plan-1  C5    0.020
 CV1  plan-1  C6    0.020
 CV1  plan-1  N6    0.020
 CV1  plan-1  N7    0.020
 CV1  plan-1  C8    0.020
 CV1  plan-1  N9    0.020
 CV1  plan-1  C1'   0.020
 CV1  plan-1  C1D   0.020
 CV1  plan-1  H2    0.020
 CV1  plan-2  C6    0.020
 CV1  plan-2  N6    0.020
 CV1  plan-2  HN6   0.020
 CV1  plan-2  HN6A  0.020

