# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:25:03 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 6-[5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1~{H}-1,2,4-triazol-3-yl]naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2[nH]nc(n2)c3ccc4cc(ccc4c3)C(O)=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
 CJW  CJW  '6-[5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1~{H}-1,2,4-triazol-3-yl]naphthalene-2-carboxylic acid'  ligand  47  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CJW
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
 CJW  O5'  O  O2     0  -0.492  -3.8070  -0.9083   0.3593
 CJW  C5'  C  CH1    0  -0.017  -5.1907  -1.0974   0.1284
 CJW  C4'  C  CH1    0   0.036  -5.6276  -0.2875  -1.0941
 CJW  C3'  C  CH1    0  -0.017  -5.2624   1.1799  -0.8951
 CJW  C2'  C  CH1    0   0.011  -3.7808   1.3161  -0.5629
 CJW  C1'  C  CH1    0  -0.070  -3.4685   0.4257   0.6394
 CJW  C1   C  C      0   0.502  -2.0157   0.4718   0.9648
 CJW  O2'  O  OH1    0  -0.671  -3.4349   2.6353  -0.2197
 CJW  O3'  O  OH1    0  -0.674  -5.6024   1.8689  -2.0769
 CJW  O4'  O  OH1    0  -0.672  -7.0140  -0.4536  -1.2557
 CJW  C6'  C  CH2    0  -0.158  -5.4245  -2.5802  -0.0637
 CJW  O6'  O  OH1    0  -0.670  -5.0981  -3.2497   1.1302
 CJW  N5   N  N      0  -0.475  -1.0257   0.1195   0.1769
 CJW  C4   C  C      0   0.311   0.0765   0.3684   0.9206
 CJW  N3   N  N      0  -0.267  -0.1910   0.8532   2.1167
 CJW  N2   N  NC1    0  -0.467  -1.5190   0.9067   2.1231
 CJW  C6   C  CR6    0   0.007   1.4385   0.1325   0.4412
 CJW  C11  C  CR16   0  -0.302   1.6395  -0.4212  -0.8468
 CJW  C10  C  CR16   0  -0.300   2.9022  -0.6436  -1.3179
 CJW  C9   C  CR6    0   0.135   4.0384  -0.3249  -0.5368
 CJW  C8   C  CR6    0   0.141   3.8403   0.2289   0.7540
 CJW  C7   C  CR16   0  -0.369   2.5270   0.4463   1.2193
 CJW  C15  C  C1     0  -0.363   5.3550  -0.5368  -1.0018
 CJW  C14  C  C      0  -0.101   6.4464  -0.2173  -0.2341
 CJW  C13  C  C1     0  -0.291   6.2371   0.3333   1.0533
 CJW  C12  C  C1     0  -0.306   4.9766   0.5504   1.5346
 CJW  C16  C  C      0   0.403   7.8614  -0.4457  -0.7536
 CJW  O18  O  OC    -1  -0.591   8.7901  -0.1202   0.0104
 CJW  O17  O  O      0  -0.590   7.9670  -0.9356  -1.8937
 CJW  H1   H  HCH1   0   0.226  -5.7656  -0.7507   1.0029
 CJW  H2   H  HCH1   0   0.214  -5.0785  -0.6664  -1.9716
 CJW  H3   H  HCH1   0   0.220  -5.8433   1.5616  -0.0409
 CJW  H4   H  HCH1   0   0.234  -3.1878   0.9572  -1.4148
 CJW  H5   H  HCH1   0   0.253  -4.0343   0.7971   1.5093
 CJW  H6   H  HOH1   0   0.464  -3.1672   3.1032  -1.0153
 CJW  H7   H  HOH1   0   0.459  -5.7303   2.7988  -1.8683
 CJW  H8   H  HOH1   0   0.454  -7.2932   0.0886  -2.0012
 CJW  H9   H  HCH2   0   0.214  -6.4732  -2.7296  -0.3402
 CJW  H10  H  HCH2   0   0.199  -4.8155  -2.9286  -0.9095
 CJW  H11  H  HOH1   0   0.457  -5.2814  -4.1850   1.0057
 CJW  H13  H  HCR6   0   0.252   0.7807  -0.6665  -1.4573
 CJW  H14  H  HCR6   0   0.254   3.0450  -1.0688  -2.3041
 CJW  H15  H  HCR6   0   0.249   2.3869   0.8717   2.2060
 CJW  H16  H  H      0   0.242   5.5002  -0.9583  -1.9891
 CJW  H17  H  H      0   0.246   7.0970   0.5842   1.6598
 CJW  H18  H  H      0   0.248   4.8324   0.9741   2.5218
 CJW  H12  H  HNC1   0   0.434  -2.0158   1.2473   2.9332

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
 CJW  O3'  C3'  single    1.410  0.020  1.410
 CJW  O4'  C4'  single    1.406  0.020  1.406
 CJW  C3'  C4'  single    1.525  0.020  1.525
 CJW  C3'  C2'  single    1.524  0.020  1.524
 CJW  C4'  C5'  single    1.530  0.020  1.530
 CJW  O2'  C2'  single    1.406  0.020  1.406
 CJW  C2'  C1'  single    1.528  0.020  1.528
 CJW  O6'  C6'  single    1.407  0.020  1.407
 CJW  C5'  C6'  single    1.513  0.020  1.513
 CJW  C5'  O5'  single    1.415  0.020  1.415
 CJW  C1'  O5'  single    1.404  0.020  1.404
 CJW  C1'  C1   single    1.490  0.020  1.490
 CJW  N2   C1   aromatic  1.333  0.020  1.333
 CJW  N2   N3   aromatic  1.329  0.020  1.329
 CJW  C1   N5   aromatic  1.313  0.020  1.313
 CJW  N3   C4   aromatic  1.318  0.020  1.318
 CJW  N5   C4   aromatic  1.353  0.020  1.353
 CJW  C4   C6   single    1.463  0.020  1.463
 CJW  C6   C7   aromatic  1.374  0.020  1.374
 CJW  C6   C11  aromatic  1.416  0.020  1.416
 CJW  C7   C8   aromatic  1.410  0.020  1.410
 CJW  C11  C10  aromatic  1.366  0.020  1.366
 CJW  C8   C12  aromatic  1.416  0.020  1.416
 CJW  C8   C9   aromatic  1.418  0.020  1.418
 CJW  C12  C13  aromatic  1.367  0.020  1.367
 CJW  C10  C9   aromatic  1.415  0.020  1.415
 CJW  C9   C15  aromatic  1.412  0.020  1.412
 CJW  C13  C14  aromatic  1.416  0.020  1.416
 CJW  C15  C14  aromatic  1.372  0.020  1.372
 CJW  C14  C16  single    1.525  0.020  1.525
 CJW  C16  O17  deloc     1.245  0.020  1.245
 CJW  C16  O18  deloc     1.246  0.020  1.246
 CJW  C5'  H1   single    0.970  0.020  1.090
 CJW  C4'  H2   single    0.970  0.020  1.090
 CJW  C3'  H3   single    0.970  0.020  1.090
 CJW  C2'  H4   single    0.970  0.020  1.090
 CJW  C1'  H5   single    0.970  0.020  1.090
 CJW  O2'  H6   single    0.850  0.020  0.980
 CJW  O3'  H7   single    0.850  0.020  0.980
 CJW  O4'  H8   single    0.850  0.020  0.980
 CJW  C6'  H9   single    0.970  0.020  1.090
 CJW  C6'  H10  single    0.970  0.020  1.090
 CJW  O6'  H11  single    0.850  0.020  0.980
 CJW  C11  H13  single    0.930  0.020  1.080
 CJW  C10  H14  single    0.930  0.020  1.080
 CJW  C7   H15  single    0.930  0.020  1.080
 CJW  C15  H16  single    0.930  0.020  1.080
 CJW  C13  H17  single    0.930  0.020  1.080
 CJW  C12  H18  single    0.930  0.020  1.080
 CJW  N2   H12  single    0.860  0.020  1.020

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
 CJW  C1'  O5'  C5'  113.27  3.000
 CJW  H1   C5'  C6'  109.16  3.000
 CJW  H1   C5'  C4'  108.57  3.000
 CJW  C6'  C5'  C4'  111.90  3.000
 CJW  H1   C5'  O5'  109.78  3.000
 CJW  C6'  C5'  O5'  107.62  3.000
 CJW  C4'  C5'  O5'  109.80  3.000
 CJW  H2   C4'  O4'  111.05  3.000
 CJW  H2   C4'  C3'  108.38  3.000
 CJW  O4'  C4'  C3'  111.40  3.000
 CJW  H2   C4'  C5'  108.17  3.000
 CJW  C3'  C4'  C5'  109.67  3.000
 CJW  O4'  C4'  C5'  108.11  3.000
 CJW  H3   C3'  O3'  110.71  3.000
 CJW  H3   C3'  C2'  108.22  3.000
 CJW  O3'  C3'  C2'  111.92  3.000
 CJW  H3   C3'  C4'  107.97  3.000
 CJW  C2'  C3'  C4'  110.31  3.000
 CJW  O3'  C3'  C4'  107.65  3.000
 CJW  H4   C2'  O2'  111.29  3.000
 CJW  H4   C2'  C1'  108.03  3.000
 CJW  O2'  C2'  C1'  107.71  3.000
 CJW  H4   C2'  C3'  109.06  3.000
 CJW  C1'  C2'  C3'  108.54  3.000
 CJW  O2'  C2'  C3'  112.09  3.000
 CJW  H5   C1'  C1   108.53  3.000
 CJW  H5   C1'  C2'  108.64  3.000
 CJW  C1   C1'  C2'  110.68  3.000
 CJW  H5   C1'  O5'  110.72  3.000
 CJW  C1   C1'  O5'  107.94  3.000
 CJW  C2'  C1'  O5'  110.31  3.000
 CJW  N2   C1   N5   109.14  3.000
 CJW  N5   C1   C1'  126.57  3.000
 CJW  N2   C1   C1'  124.28  3.000
 CJW  H6   O2'  C2'  108.85  3.000
 CJW  H7   O3'  C3'  108.84  3.000
 CJW  H8   O4'  C4'  107.96  3.000
 CJW  H10  C6'  H9   107.05  3.000
 CJW  H10  C6'  O6'  111.94  3.000
 CJW  H9   C6'  O6'  111.81  3.000
 CJW  H10  C6'  C5'  108.83  3.000
 CJW  H9   C6'  C5'  108.29  3.000
 CJW  O6'  C6'  C5'  108.82  3.000
 CJW  H11  O6'  C6'  107.99  3.000
 CJW  C4   N5   C1   103.59  3.000
 CJW  C6   C4   N3   123.07  3.000
 CJW  C6   C4   N5   123.28  3.000
 CJW  N3   C4   N5   113.65  3.000
 CJW  N2   N3   C4   102.82  3.000
 CJW  H12  N2   N3   120.61  3.000
 CJW  H12  N2   C1   128.60  3.000
 CJW  N3   N2   C1   110.79  3.000
 CJW  C7   C6   C11  119.45  3.000
 CJW  C11  C6   C4   119.55  3.000
 CJW  C7   C6   C4   121.00  3.000
 CJW  H13  C11  C10  120.15  3.000
 CJW  H13  C11  C6   119.28  3.000
 CJW  C10  C11  C6   120.57  3.000
 CJW  H14  C10  C9   119.01  3.000
 CJW  H14  C10  C11  119.98  3.000
 CJW  C9   C10  C11  121.01  3.000
 CJW  C15  C9   C8   119.24  3.000
 CJW  C15  C9   C10  122.21  3.000
 CJW  C8   C9   C10  118.55  3.000
 CJW  C12  C8   C7   122.05  3.000
 CJW  C12  C8   C9   118.58  3.000
 CJW  C7   C8   C9   119.38  3.000
 CJW  H15  C7   C8   118.78  3.000
 CJW  H15  C7   C6   120.18  3.000
 CJW  C8   C7   C6   121.04  3.000
 CJW  H16  C15  C14  119.60  3.000
 CJW  H16  C15  C9   118.91  3.000
 CJW  C14  C15  C9   121.49  3.000
 CJW  C16  C14  C13  120.35  3.000
 CJW  C16  C14  C15  120.84  3.000
 CJW  C13  C14  C15  118.80  3.000
 CJW  H17  C13  C12  119.93  3.000
 CJW  H17  C13  C14  118.85  3.000
 CJW  C12  C13  C14  121.23  3.000
 CJW  H18  C12  C13  120.37  3.000
 CJW  H18  C12  C8   118.96  3.000
 CJW  C13  C12  C8   120.67  3.000
 CJW  O17  C16  O18  126.93  3.000
 CJW  O18  C16  C14  116.35  3.000
 CJW  O17  C16  C14  116.72  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
 CJW  CONST_01  C4   N3   N2   C1     0.00   0.0  0
 CJW  CONST_02  N3   C4   N5   C1     0.00   0.0  0
 CJW  CONST_03  C6   C4   N5   C1   180.00   0.0  0
 CJW  CONST_04  N3   N2   C1   N5     0.00   0.0  0
 CJW  CONST_05  N2   N3   C4   N5     0.00   0.0  0
 CJW  CONST_06  C7   C6   C4   N5   180.00   0.0  0
 CJW  CONST_07  C11  C6   C4   N5     0.00   0.0  0
 CJW  CONST_08  N2   C1   N5   C4     0.00   0.0  0
 CJW  CONST_09  C8   C7   C6   C4   180.00   0.0  0
 CJW  CONST_10  C10  C11  C6   C4   180.00   0.0  0
 CJW  CONST_11  C7   C6   C4   N3     0.00   0.0  0
 CJW  CONST_12  C11  C6   C4   N3   180.00   0.0  0
 CJW  CONST_13  C6   C4   N3   N2   180.00   0.0  0
 CJW  CONST_14  C12  C8   C7   C6   180.00   0.0  0
 CJW  CONST_15  C9   C8   C7   C6     0.00   0.0  0
 CJW  CONST_16  C9   C10  C11  C6     0.00   0.0  0
 CJW  CONST_17  C8   C7   C6   C11    0.00   0.0  0
 CJW  CONST_18  C8   C9   C10  C11    0.00   0.0  0
 CJW  CONST_19  C15  C9   C10  C11  180.00   0.0  0
 CJW  CONST_20  C7   C6   C11  C10    0.00   0.0  0
 CJW  CONST_21  C7   C8   C9   C10    0.00   0.0  0
 CJW  CONST_22  C12  C8   C9   C10  180.00   0.0  0
 CJW  CONST_23  C14  C15  C9   C10  180.00   0.0  0
 CJW  CONST_24  C13  C12  C8   C9     0.00   0.0  0
 CJW  CONST_25  C13  C14  C15  C9     0.00   0.0  0
 CJW  CONST_26  C14  C13  C12  C8     0.00   0.0  0
 CJW  CONST_27  C14  C15  C9   C8     0.00   0.0  0
 CJW  CONST_28  C13  C12  C8   C7   180.00   0.0  0
 CJW  CONST_29  C15  C9   C8   C7   180.00   0.0  0
 CJW  CONST_30  C12  C8   C9   C15    0.00   0.0  0
 CJW  CONST_31  C12  C13  C14  C15    0.00   0.0  0
 CJW  CONST_32  N3   N2   C1   C1'  180.00   0.0  0
 CJW  CONST_33  C4   N5   C1   C1'  180.00   0.0  0
 CJW  CONST_34  C16  C14  C15  C9   180.00   0.0  0
 CJW  CONST_35  C16  C14  C13  C12  180.00   0.0  0
 CJW  CONST_36  H12  N2   C1   C1'    0.00   0.0  0
 CJW  CONST_37  H15  C7   C6   C4     0.00   0.0  0
 CJW  CONST_38  H13  C11  C6   C4     0.00   0.0  0
 CJW  CONST_39  H14  C10  C11  C6   180.00   0.0  0
 CJW  CONST_40  H16  C15  C9   C10    0.00   0.0  0
 CJW  CONST_41  H18  C12  C8   C9   180.00   0.0  0
 CJW  CONST_42  H17  C13  C12  C8   180.00   0.0  0
 CJW  Var_01    O17  C16  C14  C15   -0.26  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
 CJW  chir_01  C5'  C4'  C6'  O5'  negativ
 CJW  chir_02  C4'  O4'  C5'  C3'  positiv
 CJW  chir_03  C3'  O3'  C4'  C2'  negativ
 CJW  chir_04  C2'  O2'  C3'  C1'  positiv
 CJW  chir_05  C1'  O5'  C2'  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
 CJW  plan-1  C1'  0.020
 CJW  plan-1  C1   0.020
 CJW  plan-1  N5   0.020
 CJW  plan-1  C4   0.020
 CJW  plan-1  N3   0.020
 CJW  plan-1  N2   0.020
 CJW  plan-1  C6   0.020
 CJW  plan-1  H12  0.020
 CJW  plan-2  C4   0.020
 CJW  plan-2  C6   0.020
 CJW  plan-2  C11  0.020
 CJW  plan-2  C10  0.020
 CJW  plan-2  C9   0.020
 CJW  plan-2  C8   0.020
 CJW  plan-2  C7   0.020
 CJW  plan-2  C15  0.020
 CJW  plan-2  C14  0.020
 CJW  plan-2  C13  0.020
 CJW  plan-2  C12  0.020
 CJW  plan-2  C16  0.020
 CJW  plan-2  H13  0.020
 CJW  plan-2  H14  0.020
 CJW  plan-2  H15  0.020
 CJW  plan-2  H16  0.020
 CJW  plan-2  H17  0.020
 CJW  plan-2  H18  0.020
 CJW  plan-3  C14  0.020
 CJW  plan-3  C16  0.020
 CJW  plan-3  O18  0.020
 CJW  plan-3  O17  0.020

