# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 04:09:26 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5,6-tetrakis(oxidanyl)hexanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@@H](O)C=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
 LBL  LBL  "(2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5,6-tetrakis(oxidanyl)hexanal"
  ligand  45  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LBL
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
 LBL  C1   C  C1    0   0.133  -18.0419  6.7128  13.5654
 LBL  C10  C  CH1   0  -0.021  -11.8549  4.5279  14.0574
 LBL  C11  C  CH1   0   0.019  -15.5232  5.4052  15.6847
 LBL  C12  C  CH2   0  -0.189  -15.5108  4.0586  16.4063
 LBL  C2   C  CH1   0  -0.105  -17.9370  5.2047  13.6906
 LBL  C3   C  CH1   0   0.005  -16.5162  4.6707  13.3971
 LBL  C4   C  CH1   0  -0.026  -15.3590  5.3430  14.1633
 LBL  C5   C  CH1   0   0.288  -13.0455  5.3042  13.4905
 LBL  C6   C  CH1   0  -0.014  -11.8193  6.0177  11.6162
 LBL  C7   C  CH2   0  -0.156  -11.9310  6.1588  10.1128
 LBL  C8   C  CH1   0   0.001  -10.5550  5.2801  12.0444
 LBL  C9   C  CH1   0   0.006  -10.5576  5.1561  13.5655
 LBL  O1   O  O     0  -0.368  -17.5384  7.3470  12.6714
 LBL  O10  O  OH1   0  -0.661  -14.5155  6.2679  16.1602
 LBL  O2   O  OH1   0  -0.659  -18.3838  4.7668  14.9448
 LBL  O3   O  OH1   0  -0.652  -16.2759  4.7172  12.0152
 LBL  O4   O  O2    0  -0.500  -14.1945  4.6173  13.8266
 LBL  O5   O  O2    0  -0.489  -12.9753  5.3595  12.0889
 LBL  O6   O  OH1   0  -0.666  -13.0023  7.0261   9.8237
 LBL  O7   O  OH1   0  -0.669  -10.5166  4.0243  11.4131
 LBL  O8   O  OH1   0  -0.672   -9.4268  4.4051  13.9383
 LBL  O9   O  OH1   0  -0.703  -11.8309  4.5537  15.4584
 LBL  H1   H  H     0   0.218  -18.6358  7.2068  14.3573
 LBL  H16  H  HCH1  0   0.201  -11.9190  3.4980  13.6718
 LBL  H18  H  HCH1  0   0.224  -16.5119  5.8320  15.8939
 LBL  H20  H  HCH2  0   0.227  -15.8212  4.2424  17.4421
 LBL  H21  H  HCH2  0   0.210  -16.2722  3.4058  15.9675
 LBL  H2   H  HCH1  0   0.291  -18.5651  4.7916  12.8868
 LBL  H4   H  HCH1  0   0.257  -16.5352  3.6087  13.6615
 LBL  H6   H  HCH1  0   0.241  -15.2681  6.3812  13.8125
 LBL  H7   H  HCH1  0   0.188  -13.0482  6.3272  13.9042
 LBL  H8   H  HCH1  0   0.223  -11.7547  7.0302  12.0484
 LBL  H10  H  HCH2  0   0.205  -12.0751  5.1722   9.6579
 LBL  H9   H  HCH2  0   0.200  -10.9767  6.5525   9.7390
 LBL  H12  H  HCH1  0   0.227   -9.6932  5.8987  11.7499
 LBL  H14  H  HCH1  0   0.206  -10.4993  6.1771  13.9765
 LBL  H19  H  HOH1  0   0.452  -14.6088  6.3547  17.1145
 LBL  H22  H  HOH1  0   0.466  -14.1640  2.8638  17.1442
 LBL  H3   H  HOH1  0   0.468  -19.3460  4.7439  14.9492
 LBL  H5   H  HOH1  0   0.442  -16.2400  5.6394  11.7353
 LBL  H11  H  HOH1  0   0.453  -13.1048  7.0664   8.8688
 LBL  H13  H  HOH1  0   0.449   -9.7772  3.5297  11.7827
 LBL  H15  H  HOH1  0   0.452   -9.4927  4.2014  14.8774
 LBL  H17  H  HOH1  0   0.461  -12.6744  4.2017  15.7980
 LBL  O11  O  OH1   0  -0.662  -14.2363  3.4436  16.3807

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
 LBL  C7   O6   single  1.408  0.020  1.408
 LBL  C7   C6   single  1.514  0.020  1.514
 LBL  O7   C8   single  1.406  0.020  1.406
 LBL  C6   C8   single  1.525  0.020  1.525
 LBL  C6   O5   single  1.412  0.020  1.412
 LBL  C8   C9   single  1.526  0.020  1.526
 LBL  O3   C3   single  1.403  0.020  1.403
 LBL  O5   C5   single  1.405  0.020  1.405
 LBL  O1   C1   double  1.206  0.020  1.206
 LBL  C9   O8   single  1.408  0.020  1.408
 LBL  C9   C10  single  1.523  0.020  1.523
 LBL  C3   C2   single  1.546  0.020  1.546
 LBL  C3   C4   single  1.542  0.020  1.542
 LBL  C2   C1   single  1.517  0.020  1.517
 LBL  C2   O2   single  1.402  0.020  1.402
 LBL  C5   C10  single  1.530  0.020  1.530
 LBL  C5   O4   single  1.380  0.020  1.380
 LBL  C10  O9   single  1.401  0.020  1.401
 LBL  C4   O4   single  1.413  0.020  1.413
 LBL  C4   C11  single  1.531  0.020  1.531
 LBL  C11  O10  single  1.409  0.020  1.409
 LBL  C11  C12  single  1.528  0.020  1.528
 LBL  C12  O11  single  1.415  0.020  1.415
 LBL  C1   H1   single  0.930  0.020  1.080
 LBL  C10  H16  single  0.970  0.020  1.090
 LBL  C11  H18  single  0.970  0.020  1.090
 LBL  C12  H20  single  0.970  0.020  1.090
 LBL  C12  H21  single  0.970  0.020  1.090
 LBL  C2   H2   single  0.970  0.020  1.090
 LBL  C3   H4   single  0.970  0.020  1.090
 LBL  C4   H6   single  0.970  0.020  1.090
 LBL  C5   H7   single  0.970  0.020  1.090
 LBL  C6   H8   single  0.970  0.020  1.090
 LBL  C7   H10  single  0.970  0.020  1.090
 LBL  C7   H9   single  0.970  0.020  1.090
 LBL  C8   H12  single  0.970  0.020  1.090
 LBL  C9   H14  single  0.970  0.020  1.090
 LBL  O10  H19  single  0.850  0.020  0.980
 LBL  O11  H22  single  0.850  0.020  0.980
 LBL  O2   H3   single  0.850  0.020  0.980
 LBL  O3   H5   single  0.850  0.020  0.980
 LBL  O6   H11  single  0.850  0.020  0.980
 LBL  O7   H13  single  0.850  0.020  0.980
 LBL  O8   H15  single  0.850  0.020  0.980
 LBL  O9   H17  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
 LBL  H1   C1   O1   121.32  3.000
 LBL  H1   C1   C2   114.96  3.000
 LBL  O1   C1   C2   123.72  3.000
 LBL  H16  C10  O9   111.60  3.000
 LBL  H16  C10  C9   108.79  3.000
 LBL  O9   C10  C9   107.50  3.000
 LBL  H16  C10  C5   107.42  3.000
 LBL  O9   C10  C5   111.98  3.000
 LBL  C9   C10  C5   109.50  3.000
 LBL  H18  C11  O10  109.99  3.000
 LBL  H18  C11  C4   107.57  3.000
 LBL  O10  C11  C4   106.46  3.000
 LBL  H18  C11  C12  105.08  3.000
 LBL  O10  C11  C12  111.99  3.000
 LBL  C4   C11  C12  115.63  3.000
 LBL  H21  C12  H20  106.36  3.000
 LBL  H21  C12  O11  111.10  3.000
 LBL  H20  C12  O11  110.17  3.000
 LBL  H21  C12  C11  109.30  3.000
 LBL  H20  C12  C11  107.22  3.000
 LBL  O11  C12  C11  112.44  3.000
 LBL  H2   C2   O2   110.76  3.000
 LBL  H2   C2   C3   104.84  3.000
 LBL  O2   C2   C3   110.79  3.000
 LBL  H2   C2   C1   105.87  3.000
 LBL  O2   C2   C1   111.25  3.000
 LBL  C3   C2   C1   113.03  3.000
 LBL  H4   C3   O3   105.84  3.000
 LBL  H4   C3   C4   108.42  3.000
 LBL  O3   C3   C4   110.26  3.000
 LBL  H4   C3   C2   105.86  3.000
 LBL  C4   C3   C2   116.41  3.000
 LBL  O3   C3   C2   109.44  3.000
 LBL  H6   C4   O4   109.93  3.000
 LBL  H6   C4   C3   108.37  3.000
 LBL  O4   C4   C3   106.03  3.000
 LBL  H6   C4   C11  106.70  3.000
 LBL  O4   C4   C11  110.24  3.000
 LBL  C3   C4   C11  115.52  3.000
 LBL  H7   C5   O5   109.74  3.000
 LBL  H7   C5   O4   111.60  3.000
 LBL  O5   C5   O4   107.71  3.000
 LBL  H7   C5   C10  109.47  3.000
 LBL  O4   C5   C10  107.76  3.000
 LBL  O5   C5   C10  110.54  3.000
 LBL  H8   C6   O5   110.17  3.000
 LBL  H8   C6   C8   106.59  3.000
 LBL  O5   C6   C8   111.06  3.000
 LBL  H8   C6   C7   107.93  3.000
 LBL  O5   C6   C7   108.39  3.000
 LBL  C8   C6   C7   112.64  3.000
 LBL  H9   C7   H10  107.20  3.000
 LBL  H9   C7   O6   111.74  3.000
 LBL  H10  C7   O6   111.66  3.000
 LBL  H9   C7   C6   107.90  3.000
 LBL  H10  C7   C6   109.75  3.000
 LBL  O6   C7   C6   108.50  3.000
 LBL  H12  C8   O7   111.12  3.000
 LBL  H12  C8   C9   108.27  3.000
 LBL  O7   C8   C9   112.02  3.000
 LBL  H12  C8   C6   107.58  3.000
 LBL  C9   C8   C6   108.53  3.000
 LBL  O7   C8   C6   109.18  3.000
 LBL  H14  C9   O8   110.67  3.000
 LBL  H14  C9   C8   107.23  3.000
 LBL  O8   C9   C8   107.82  3.000
 LBL  H14  C9   C10  107.86  3.000
 LBL  O8   C9   C10  112.25  3.000
 LBL  C8   C9   C10  110.91  3.000
 LBL  H19  O10  C11  108.69  3.000
 LBL  H3   O2   C2   109.28  3.000
 LBL  H5   O3   C3   108.89  3.000
 LBL  C5   O4   C4   119.25  3.000
 LBL  C6   O5   C5   113.16  3.000
 LBL  H11  O6   C7   108.11  3.000
 LBL  H13  O7   C8   107.90  3.000
 LBL  H15  O8   C9   108.43  3.000
 LBL  H17  O9   C10  109.07  3.000
 LBL  H22  O11  C12  108.38  3.000

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
 LBL  chir_01  C10  C9   C5   O9   positiv
 LBL  chir_02  C11  O10  C4   C12  negativ
 LBL  chir_03  C2   O2   C3   C1   positiv
 LBL  chir_04  C3   O3   C2   C4   positiv
 LBL  chir_05  C4   O4   C11  C3   positiv
 LBL  chir_06  C5   O4   O5   C10  positiv
 LBL  chir_07  C6   O5   C7   C8   positiv
 LBL  chir_08  C8   O7   C6   C9   negativ
 LBL  chir_09  C9   O8   C8   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
 LBL  plan-1  C1  0.020
 LBL  plan-1  C2  0.020
 LBL  plan-1  O1  0.020
 LBL  plan-1  H1  0.020

