# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 11 15:21:10 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-[[1-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-10~{H}-acridin-9-one
#   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)N2C=CC(=NC2=O)Nc3ccc4Nc5ccccc5C(=O)c4c3
#
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
 7LS  7LS  2-[[1-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-10~{H}-acridin-9-one  ligand  56  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7LS
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
 7LS  C1   C  CR66  0   0.356  -4.9884   1.0567  -0.1257
 7LS  C2   C  CR66  0   0.367  -6.5735  -0.7292  -0.2745
 7LS  C3   C  CR66  0  -0.106  -5.5455  -1.6858  -0.2863
 7LS  C4   C  CR6   0   0.620   1.5451   0.2210   0.0783
 7LS  O1   O  O     0  -0.494   1.7111  -0.9860   0.0525
 7LS  C5   C  CR16  0  -0.376  -2.5935   0.6543  -0.0625
 7LS  C6   C  CR66  0  -0.074  -3.9078   0.1677  -0.1320
 7LS  C7   C  CR6   0   0.410  -4.1431  -1.2764  -0.2129
 7LS  O2   O  O     0  -0.442  -3.2242  -2.0887  -0.2193
 7LS  C8   C  CR16  0  -0.293  -5.8870  -3.0446  -0.3695
 7LS  C9   C  CR16  0  -0.262  -7.2002  -3.4434  -0.4387
 7LS  C10  C  CR16  0  -0.249  -8.2160  -2.4770  -0.4258
 7LS  C11  C  CR16  0  -0.328  -7.9148  -1.1388  -0.3449
 7LS  N1   N  NR16  0  -0.795  -6.2680   0.5946  -0.1950
 7LS  C12  C  CR16  0  -0.315  -4.7375   2.4352  -0.0477
 7LS  C13  C  CR16  0  -0.347  -3.4502   2.8941   0.0178
 7LS  C14  C  CR6   0   0.374  -2.3499   2.0116   0.0101
 7LS  N2   N  NH1   0  -0.769  -1.0912   2.6135   0.0737
 7LS  C15  C  CR6   0   0.579   0.1462   2.0779   0.0882
 7LS  C16  C  CR16  0  -0.502   1.2492   2.9834   0.1364
 7LS  C17  C  CR16  0   0.101   2.4753   2.4281   0.1554
 7LS  N3   N  N     0  -0.553   0.3109   0.7789   0.0580
 7LS  N4   N  NR6   0  -0.573   2.6547   1.0836   0.1303
 7LS  C18  C  CH1   0   0.216   4.0060   0.5609   0.1981
 7LS  O3   O  O2    0  -0.479   4.2642  -0.1668  -0.9614
 7LS  C19  C  CH1   0  -0.022   5.6138  -0.5781  -1.0842
 7LS  C20  C  CH2   0  -0.156   5.7484  -1.3010  -2.4065
 7LS  O4   O  OH1   0  -0.670   5.4583  -0.4003  -3.4483
 7LS  C21  C  CH1   0   0.026   5.9938  -1.4660   0.1028
 7LS  O5   O  OH1   0  -0.672   7.3517  -1.8094  -0.0263
 7LS  C22  C  CH1   0  -0.027   5.7309  -0.7072   1.4033
 7LS  O6   O  OH1   0  -0.675   5.9848  -1.5145   2.5324
 7LS  C23  C  CH1   0  -0.001   4.2758  -0.2616   1.4568
 7LS  O7   O  OH1   0  -0.668   4.0082   0.5702   2.5543
 7LS  H1   H  HCR6  0   0.297  -1.7782  -0.0500  -0.0679
 7LS  H2   H  HCR6  0   0.262  -5.0935  -3.7797  -0.3781
 7LS  H3   H  HCR6  0   0.260  -7.4503  -4.4935  -0.5027
 7LS  H4   H  HCR6  0   0.269  -9.2524  -2.7836  -0.4809
 7LS  H5   H  HCR6  0   0.277  -8.7025  -0.3959  -0.3355
 7LS  H6   H  HNR6  0   0.420  -7.0219   1.2649  -0.1896
 7LS  H7   H  HCR6  0   0.283  -5.5620   3.1364  -0.0411
 7LS  H8   H  HCR6  0   0.285  -3.2802   3.9629   0.0750
 7LS  H9   H  HNH1  0   0.425  -1.1156   3.6215   0.1036
 7LS  H10  H  HCR6  0   0.295   1.1244   4.0554   0.1559
 7LS  H11  H  HCR6  0   0.324   3.3686   3.0357   0.1879
 7LS  H12  H  HCH1  0   0.247   4.6626   1.4430   0.2427
 7LS  H13  H  HCH1  0   0.226   6.2738   0.3056  -1.0846
 7LS  H14  H  HCH2  0   0.214   6.7668  -1.6947  -2.4811
 7LS  H15  H  HCH2  0   0.199   5.0664  -2.1624  -2.4093
 7LS  H16  H  HOH1  0   0.457   5.5801  -0.8635  -4.2818
 7LS  H17  H  HCH1  0   0.219   5.3538  -2.3617   0.0847
 7LS  H18  H  HOH1  0   0.456   7.5496  -2.5058   0.6073
 7LS  H19  H  HCH1  0   0.225   6.3707   0.1875   1.4142
 7LS  H20  H  HOH1  0   0.463   6.8702  -1.3305   2.8570
 7LS  H21  H  HCH1  0   0.242   3.6380  -1.1525   1.4600
 7LS  H22  H  HOH1  0   0.456   4.2247   0.0815   3.3554

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
 7LS  O6   C22  single    1.411  0.020  1.411
 7LS  O5   C21  single    1.407  0.020  1.407
 7LS  C22  C21  single    1.528  0.020  1.528
 7LS  C22  C23  single    1.523  0.020  1.523
 7LS  C21  C19  single    1.530  0.020  1.530
 7LS  O7   C23  single    1.403  0.020  1.403
 7LS  C23  C18  single    1.528  0.020  1.528
 7LS  O4   C20  single    1.407  0.020  1.407
 7LS  C19  C20  single    1.513  0.020  1.513
 7LS  C19  O3   single    1.416  0.020  1.416
 7LS  C18  O3   single    1.393  0.020  1.393
 7LS  C18  N4   single    1.450  0.020  1.450
 7LS  C17  N4   single    1.357  0.020  1.357
 7LS  C17  C16  double    1.346  0.020  1.346
 7LS  N4   C4   single    1.406  0.020  1.406
 7LS  C16  C15  single    1.428  0.020  1.428
 7LS  C4   O1   double    1.219  0.020  1.219
 7LS  C4   N3   single    1.355  0.020  1.355
 7LS  C15  N3   double    1.310  0.020  1.310
 7LS  C15  N2   single    1.348  0.020  1.348
 7LS  N2   C14  single    1.397  0.020  1.397
 7LS  C14  C5   aromatic  1.381  0.020  1.381
 7LS  C14  C13  aromatic  1.411  0.020  1.411
 7LS  C5   C6   aromatic  1.403  0.020  1.403
 7LS  C13  C12  aromatic  1.368  0.020  1.368
 7LS  C6   C7   single    1.465  0.020  1.465
 7LS  C6   C1   aromatic  1.399  0.020  1.399
 7LS  O2   C7   double    1.227  0.020  1.227
 7LS  C12  C1   aromatic  1.403  0.020  1.403
 7LS  C7   C3   single    1.463  0.020  1.463
 7LS  C1   N1   single    1.362  0.020  1.362
 7LS  C3   C2   aromatic  1.404  0.020  1.404
 7LS  C3   C8   aromatic  1.404  0.020  1.404
 7LS  N1   C2   single    1.361  0.020  1.361
 7LS  C2   C11  aromatic  1.404  0.020  1.404
 7LS  C8   C9   aromatic  1.374  0.020  1.374
 7LS  C11  C10  aromatic  1.374  0.020  1.374
 7LS  C9   C10  aromatic  1.402  0.020  1.402
 7LS  C5   H1   single    0.930  0.020  1.080
 7LS  C8   H2   single    0.930  0.020  1.080
 7LS  C9   H3   single    0.930  0.020  1.080
 7LS  C10  H4   single    0.930  0.020  1.080
 7LS  C11  H5   single    0.930  0.020  1.080
 7LS  N1   H6   single    0.860  0.020  1.020
 7LS  C12  H7   single    0.930  0.020  1.080
 7LS  C13  H8   single    0.930  0.020  1.080
 7LS  N2   H9   single    0.860  0.020  1.020
 7LS  C16  H10  single    0.930  0.020  1.080
 7LS  C17  H11  single    0.930  0.020  1.080
 7LS  C18  H12  single    0.970  0.020  1.090
 7LS  C19  H13  single    0.970  0.020  1.090
 7LS  C20  H14  single    0.970  0.020  1.090
 7LS  C20  H15  single    0.970  0.020  1.090
 7LS  O4   H16  single    0.850  0.020  0.980
 7LS  C21  H17  single    0.970  0.020  1.090
 7LS  O5   H18  single    0.850  0.020  0.980
 7LS  C22  H19  single    0.970  0.020  1.090
 7LS  O6   H20  single    0.850  0.020  0.980
 7LS  C23  H21  single    0.970  0.020  1.090
 7LS  O7   H22  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
 7LS  C12  C1   N1   120.26  3.000
 7LS  N1   C1   C6   120.64  3.000
 7LS  C12  C1   C6   119.10  3.000
 7LS  N1   C2   C11  120.07  3.000
 7LS  C11  C2   C3   120.01  3.000
 7LS  N1   C2   C3   119.92  3.000
 7LS  C8   C3   C7   120.48  3.000
 7LS  C8   C3   C2   118.81  3.000
 7LS  C7   C3   C2   120.72  3.000
 7LS  N4   C4   N3   117.82  3.000
 7LS  N3   C4   O1   122.12  3.000
 7LS  N4   C4   O1   120.06  3.000
 7LS  H1   C5   C14  120.62  3.000
 7LS  H1   C5   C6   118.80  3.000
 7LS  C14  C5   C6   120.58  3.000
 7LS  C7   C6   C5   119.67  3.000
 7LS  C7   C6   C1   120.15  3.000
 7LS  C5   C6   C1   120.18  3.000
 7LS  O2   C7   C6   122.19  3.000
 7LS  O2   C7   C3   122.18  3.000
 7LS  C6   C7   C3   115.63  3.000
 7LS  H2   C8   C9   120.22  3.000
 7LS  H2   C8   C3   118.68  3.000
 7LS  C9   C8   C3   121.10  3.000
 7LS  H3   C9   C10  120.15  3.000
 7LS  H3   C9   C8   120.39  3.000
 7LS  C10  C9   C8   119.46  3.000
 7LS  H4   C10  C11  119.27  3.000
 7LS  H4   C10  C9   119.87  3.000
 7LS  C11  C10  C9   120.86  3.000
 7LS  H5   C11  C10  120.61  3.000
 7LS  H5   C11  C2   119.63  3.000
 7LS  C10  C11  C2   119.76  3.000
 7LS  H6   N1   C2   118.62  3.000
 7LS  H6   N1   C1   118.45  3.000
 7LS  C2   N1   C1   122.93  3.000
 7LS  H7   C12  C13  119.94  3.000
 7LS  H7   C12  C1   120.04  3.000
 7LS  C13  C12  C1   120.02  3.000
 7LS  H8   C13  C14  119.67  3.000
 7LS  H8   C13  C12  118.74  3.000
 7LS  C14  C13  C12  121.59  3.000
 7LS  N2   C14  C13  115.66  3.000
 7LS  C13  C14  C5   118.53  3.000
 7LS  N2   C14  C5   125.80  3.000
 7LS  H9   N2   C15  114.76  3.000
 7LS  H9   N2   C14  114.22  3.000
 7LS  C15  N2   C14  131.02  3.000
 7LS  N3   C15  C16  122.18  3.000
 7LS  N3   C15  N2   120.60  3.000
 7LS  C16  C15  N2   117.22  3.000
 7LS  H10  C16  C17  120.98  3.000
 7LS  H10  C16  C15  122.76  3.000
 7LS  C17  C16  C15  116.26  3.000
 7LS  H11  C17  N4   116.64  3.000
 7LS  H11  C17  C16  121.42  3.000
 7LS  N4   C17  C16  121.94  3.000
 7LS  C15  N3   C4   121.52  3.000
 7LS  C18  N4   C17  118.65  3.000
 7LS  C17  N4   C4   120.28  3.000
 7LS  C18  N4   C4   121.05  3.000
 7LS  H12  C18  C23  107.02  3.000
 7LS  H12  C18  O3   109.99  3.000
 7LS  C23  C18  O3   111.83  3.000
 7LS  H12  C18  N4   105.60  3.000
 7LS  O3   C18  N4   108.78  3.000
 7LS  C23  C18  N4   113.40  3.000
 7LS  C19  O3   C18  113.61  3.000
 7LS  H13  C19  C21  108.45  3.000
 7LS  H13  C19  C20  109.23  3.000
 7LS  C21  C19  C20  112.25  3.000
 7LS  H13  C19  O3   109.73  3.000
 7LS  C20  C19  O3   107.42  3.000
 7LS  C21  C19  O3   109.75  3.000
 7LS  H15  C20  H14  107.18  3.000
 7LS  H15  C20  O4   111.83  3.000
 7LS  H14  C20  O4   111.81  3.000
 7LS  H15  C20  C19  108.76  3.000
 7LS  H14  C20  C19  108.32  3.000
 7LS  O4   C20  C19  108.84  3.000
 7LS  H16  O4   C20  107.90  3.000
 7LS  H17  C21  C22  108.53  3.000
 7LS  H17  C21  O5   111.16  3.000
 7LS  C22  C21  O5   111.43  3.000
 7LS  H17  C21  C19  108.35  3.000
 7LS  C22  C21  C19  109.23  3.000
 7LS  O5   C21  C19  108.07  3.000
 7LS  H18  O5   C21  108.35  3.000
 7LS  H19  C22  C23  108.50  3.000
 7LS  H19  C22  O6   110.66  3.000
 7LS  C23  C22  O6   108.13  3.000
 7LS  H19  C22  C21  108.19  3.000
 7LS  C23  C22  C21  109.85  3.000
 7LS  O6   C22  C21  111.47  3.000
 7LS  H20  O6   C22  109.06  3.000
 7LS  H21  C23  O7   111.64  3.000
 7LS  H21  C23  C22  108.56  3.000
 7LS  O7   C23  C22  112.54  3.000
 7LS  H21  C23  C18  109.72  3.000
 7LS  O7   C23  C18  106.96  3.000
 7LS  C22  C23  C18  107.30  3.000
 7LS  H22  O7   C23  107.88  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
 7LS  CONST_01  C14  C5   C6   C1     0.00  0.0  0
 7LS  CONST_02  C14  C13  C12  C1     0.00  0.0  0
 7LS  CONST_03  C9   C8   C3   C2     0.00  0.0  0
 7LS  CONST_04  C9   C10  C11  C2     0.00  0.0  0
 7LS  CONST_05  C10  C11  C2   C3     0.00  0.0  0
 7LS  CONST_06  C10  C9   C8   C3     0.00  0.0  0
 7LS  CONST_07  C12  C13  C14  C5     0.00  0.0  0
 7LS  CONST_08  C12  C1   C6   C5     0.00  0.0  0
 7LS  CONST_09  C13  C14  C5   C6     0.00  0.0  0
 7LS  CONST_10  C13  C12  C1   C6     0.00  0.0  0
 7LS  CONST_11  C11  C2   C3   C8     0.00  0.0  0
 7LS  CONST_12  C11  C10  C9   C8     0.00  0.0  0
 7LS  CONST_13  C16  C15  N3   C4     0.00  0.0  0
 7LS  CONST_14  N4   C4   N3   C15    0.00  0.0  0
 7LS  CONST_15  N3   C4   N4   C17    0.00  0.0  0
 7LS  CONST_16  C18  N4   C4   N3   180.00  0.0  0
 7LS  CONST_17  N2   C14  C5   C6   180.00  0.0  0
 7LS  CONST_18  N2   C14  C13  C12  180.00  0.0  0
 7LS  CONST_19  C15  N2   C14  C5     0.00  0.0  0
 7LS  CONST_20  C15  N2   C14  C13  180.00  0.0  0
 7LS  CONST_21  C16  C15  N2   C14  180.00  0.0  0
 7LS  CONST_22  N3   C15  N2   C14    0.00  0.0  0
 7LS  CONST_23  N2   C15  N3   C4   180.00  0.0  0
 7LS  CONST_24  C18  N4   C4   O1     0.00  0.0  0
 7LS  CONST_25  C17  N4   C4   O1   180.00  0.0  0
 7LS  CONST_26  C15  N3   C4   O1   180.00  0.0  0
 7LS  CONST_27  H1   C5   C6   C1   180.00  0.0  0
 7LS  CONST_28  H8   C13  C12  C1   180.00  0.0  0
 7LS  CONST_29  H2   C8   C3   C2   180.00  0.0  0
 7LS  CONST_30  H4   C10  C11  C2   180.00  0.0  0
 7LS  CONST_31  H5   C11  C2   C3   180.00  0.0  0
 7LS  CONST_32  H3   C9   C8   C3   180.00  0.0  0
 7LS  CONST_33  H7   C12  C1   C6   180.00  0.0  0
 7LS  CONST_34  H9   N2   C14  C5   180.00  0.0  0

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
 7LS  chir_01  C18  C23  O3   N4   negativ
 7LS  chir_02  C19  O3   C20  C21  positiv
 7LS  chir_03  C21  O5   C19  C22  positiv
 7LS  chir_04  C22  O6   C21  C23  negativ
 7LS  chir_05  C23  O7   C22  C18  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
 7LS  plan-1  C1   0.020
 7LS  plan-1  C2   0.020
 7LS  plan-1  C3   0.020
 7LS  plan-1  C5   0.020
 7LS  plan-1  C6   0.020
 7LS  plan-1  C7   0.020
 7LS  plan-1  O2   0.020
 7LS  plan-1  C8   0.020
 7LS  plan-1  C9   0.020
 7LS  plan-1  C10  0.020
 7LS  plan-1  C11  0.020
 7LS  plan-1  N1   0.020
 7LS  plan-1  C12  0.020
 7LS  plan-1  C13  0.020
 7LS  plan-1  C14  0.020
 7LS  plan-1  N2   0.020
 7LS  plan-1  H1   0.020
 7LS  plan-1  H2   0.020
 7LS  plan-1  H3   0.020
 7LS  plan-1  H4   0.020
 7LS  plan-1  H5   0.020
 7LS  plan-1  H6   0.020
 7LS  plan-1  H7   0.020
 7LS  plan-1  H8   0.020
 7LS  plan-2  C4   0.020
 7LS  plan-2  O1   0.020
 7LS  plan-2  C14  0.020
 7LS  plan-2  N2   0.020
 7LS  plan-2  C15  0.020
 7LS  plan-2  C16  0.020
 7LS  plan-2  C17  0.020
 7LS  plan-2  N3   0.020
 7LS  plan-2  N4   0.020
 7LS  plan-2  C18  0.020
 7LS  plan-2  H9   0.020
 7LS  plan-2  H10  0.020
 7LS  plan-2  H11  0.020

