# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:36:14 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2~{R},3~{R},4~{S})-4-[4-(methoxymethyl)-1,2,3-triazol-1-yl]-3-(2-methylpropanoylamino)-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1cn(nn1)[C@H]2C=C(O[C@@H]([C@H](O)[C@H](O)CO)[C@@H]2NC(=O)C(C)C)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
 6Y6  6Y6  '(2~{R},3~{R},4~{S})-4-[4-(methoxymethyl)-1,2,3-triazol-1-yl]-3-(2-methylpropanoylamino)-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid'  D-saccharide  54  29  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6Y6
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
 6Y6  O1A  O  OC    -1  -0.587  -2.6924  -3.9404  -0.0025
 6Y6  O1B  O  O      0  -0.585  -0.9536  -4.5636  -1.2596
 6Y6  C01  C  C      0   0.380  -1.6616  -3.7353  -0.6605
 6Y6  C02  C  C      0   0.179  -1.1993  -2.2809  -0.7428
 6Y6  C03  C  C1     0  -0.367  -0.0826  -1.9045  -1.3680
 6Y6  C04  C  CH1    0  -0.078   0.3821  -0.4848  -1.3852
 6Y6  N04  N  NR5    0  -0.261   1.8139  -0.3961  -1.1578
 6Y6  C05  C  CH1    0  -0.111  -0.3642   0.3316  -0.3219
 6Y6  N05  N  NH1    0  -0.652  -0.1515   1.7409  -0.4986
 6Y6  C06  C  CH1    0   0.024  -1.8470  -0.0328  -0.4000
 6Y6  O06  O  O2     0  -0.478  -2.0246  -1.4125  -0.1220
 6Y6  C07  C  CH1    0  -0.032  -2.6998   0.7323   0.6083
 6Y6  O07  O  OH1    0  -0.658  -2.2037   0.5874   1.9168
 6Y6  C08  C  CH1    0  -0.017  -4.1884   0.3475   0.5175
 6Y6  O08  O  OH1    0  -0.661  -4.6547   0.4238  -0.8103
 6Y6  C09  C  CH2    0  -0.160  -5.0229   1.2030   1.4579
 6Y6  O09  O  OH1    0  -0.671  -6.3578   0.7561   1.4091
 6Y6  C41  C  CR15   0  -0.084   2.5431  -1.0035  -0.2035
 6Y6  N41  N  N      0  -0.090   2.5517   0.4450  -1.8556
 6Y6  C42  C  CR5    0   0.112   3.7972  -0.4784  -0.3662
 6Y6  N42  N  N      0  -0.327   3.7523   0.4013  -1.3883
 6Y6  C43  C  CH2    0  -0.174   5.0483  -0.7694   0.3862
 6Y6  O44  O  O2     0  -0.485   4.7241  -1.5831   1.4782
 6Y6  C45  C  CH3    0  -0.397   5.8504  -1.9364   2.2415
 6Y6  C51  C  C      0   0.585   0.7477   2.4545   0.2173
 6Y6  O52  O  O      0  -0.483   1.3769   1.9823   1.1492
 6Y6  C52  C  CH1    0  -0.388   0.9343   3.8870  -0.2515
 6Y6  C53  C  CH3    0  -0.649   1.2015   4.8188   0.9226
 6Y6  C54  C  CH3    0  -0.643   2.0758   3.9280  -1.2715
 6Y6  H2   H  H      0   0.266   0.5058  -2.6508  -1.8820
 6Y6  H3   H  HCH1   0   0.292   0.2213  -0.0336  -2.3690
 6Y6  H4   H  HCH1   0   0.281   0.0150   0.0618   0.6655
 6Y6  H5   H  HNH1   0   0.400  -0.5791   2.1841  -1.2977
 6Y6  H6   H  HCH1   0   0.248  -2.2110   0.1789  -1.4145
 6Y6  H7   H  HCH1   0   0.247  -2.6076   1.7975   0.3689
 6Y6  H8   H  HOH1   0   0.446  -2.2463  -0.3442   2.1615
 6Y6  H9   H  HCH1   0   0.237  -4.3018  -0.7021   0.8102
 6Y6  H10  H  HOH1   0   0.445  -4.6685   1.3485  -1.0819
 6Y6  H11  H  HCH2   0   0.209  -4.6117   1.1321   2.4699
 6Y6  H12  H  HCH2   0   0.189  -4.9373   2.2577   1.1520
 6Y6  H13  H  HOH1   0   0.455  -6.8571   1.2409   2.0717
 6Y6  H14  H  HCR5   0   0.307   2.1271  -1.7229   0.4804
 6Y6  H15  H  HCH2   0   0.224   5.7773  -1.2640  -0.2727
 6Y6  H16  H  HCH2   0   0.224   5.5146   0.1724   0.7098
 6Y6  H17  H  HCH3   0   0.208   6.5901  -2.4876   1.6492
 6Y6  H18  H  HCH3   0   0.208   6.3478  -1.0585   2.6701
 6Y6  H19  H  HCH3   0   0.238   5.5146  -2.5752   3.0571
 6Y6  H20  H  HCH1   0   0.250   0.0182   4.2136  -0.7535
 6Y6  H21  H  HCH3   0   0.225   2.1248   4.5528   1.4366
 6Y6  H22  H  HCH3   0   0.232   1.3011   5.8447   0.5671
 6Y6  H23  H  HCH3   0   0.233   0.3894   4.7967   1.6498
 6Y6  H24  H  HCH3   0   0.235   2.2131   4.9452  -1.6391
 6Y6  H25  H  HCH3   0   0.227   3.0136   3.5997  -0.8213
 6Y6  H26  H  HCH3   0   0.235   1.8747   3.2825  -2.1261

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
 6Y6  O09  C09  single    1.409  0.020  1.409
 6Y6  C54  C52  single    1.531  0.020  1.531
 6Y6  C09  C08  single    1.521  0.020  1.521
 6Y6  C52  C53  single    1.523  0.020  1.523
 6Y6  C52  C51  single    1.519  0.020  1.519
 6Y6  O07  C07  single    1.407  0.020  1.407
 6Y6  C08  C07  single    1.540  0.020  1.540
 6Y6  C08  O08  single    1.409  0.020  1.409
 6Y6  C07  C06  single    1.526  0.020  1.526
 6Y6  O52  C51  double    1.220  0.020  1.220
 6Y6  C51  N05  single    1.353  0.020  1.353
 6Y6  N05  C05  single    1.436  0.020  1.436
 6Y6  C06  C05  single    1.529  0.020  1.529
 6Y6  C06  O06  single    1.419  0.020  1.419
 6Y6  C05  C04  single    1.534  0.020  1.534
 6Y6  O06  C02  single    1.349  0.020  1.349
 6Y6  C04  N04  single    1.452  0.020  1.452
 6Y6  C04  C03  single    1.494  0.020  1.494
 6Y6  N04  C41  aromatic  1.346  0.020  1.346
 6Y6  N04  N41  aromatic  1.319  0.020  1.319
 6Y6  C41  C42  aromatic  1.369  0.020  1.369
 6Y6  N41  N42  aromatic  1.289  0.020  1.289
 6Y6  C42  N42  aromatic  1.349  0.020  1.349
 6Y6  C42  C43  single    1.489  0.020  1.489
 6Y6  C02  C03  double    1.334  0.020  1.334
 6Y6  C02  C01  single    1.528  0.020  1.528
 6Y6  C43  O44  single    1.400  0.020  1.400
 6Y6  O1B  C01  deloc     1.243  0.020  1.243
 6Y6  O44  C45  single    1.406  0.020  1.406
 6Y6  C01  O1A  deloc     1.240  0.020  1.240
 6Y6  C03  H2   single    0.930  0.020  1.080
 6Y6  C04  H3   single    0.970  0.020  1.090
 6Y6  C05  H4   single    0.970  0.020  1.090
 6Y6  N05  H5   single    0.860  0.020  1.020
 6Y6  C06  H6   single    0.970  0.020  1.090
 6Y6  C07  H7   single    0.970  0.020  1.090
 6Y6  O07  H8   single    0.850  0.020  0.980
 6Y6  C08  H9   single    0.970  0.020  1.090
 6Y6  O08  H10  single    0.850  0.020  0.980
 6Y6  C09  H11  single    0.970  0.020  1.090
 6Y6  C09  H12  single    0.970  0.020  1.090
 6Y6  O09  H13  single    0.850  0.020  0.980
 6Y6  C41  H14  single    0.930  0.020  1.080
 6Y6  C43  H15  single    0.970  0.020  1.090
 6Y6  C43  H16  single    0.970  0.020  1.090
 6Y6  C45  H17  single    0.970  0.020  1.090
 6Y6  C45  H18  single    0.970  0.020  1.090
 6Y6  C45  H19  single    0.970  0.020  1.090
 6Y6  C52  H20  single    0.970  0.020  1.090
 6Y6  C53  H21  single    0.970  0.020  1.090
 6Y6  C53  H22  single    0.970  0.020  1.090
 6Y6  C53  H23  single    0.970  0.020  1.090
 6Y6  C54  H24  single    0.970  0.020  1.090
 6Y6  C54  H25  single    0.970  0.020  1.090
 6Y6  C54  H26  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
 6Y6  C02  C01  O1B  115.83  3.000
 6Y6  O1B  C01  O1A  128.22  3.000
 6Y6  C02  C01  O1A  115.94  3.000
 6Y6  O06  C02  C03  123.10  3.000
 6Y6  C03  C02  C01  123.16  3.000
 6Y6  O06  C02  C01  113.74  3.000
 6Y6  H2   C03  C04  118.79  3.000
 6Y6  H2   C03  C02  118.94  3.000
 6Y6  C04  C03  C02  122.27  3.000
 6Y6  H3   C04  C05  109.40  3.000
 6Y6  H3   C04  N04  105.10  3.000
 6Y6  C05  C04  N04  109.79  3.000
 6Y6  H3   C04  C03  110.88  3.000
 6Y6  N04  C04  C03  111.28  3.000
 6Y6  C05  C04  C03  110.27  3.000
 6Y6  N41  N04  C41  111.10  3.000
 6Y6  N41  N04  C04  120.51  3.000
 6Y6  C41  N04  C04  128.14  3.000
 6Y6  H4   C05  C06  108.92  3.000
 6Y6  H4   C05  N05  107.60  3.000
 6Y6  C06  C05  N05  111.79  3.000
 6Y6  H4   C05  C04  109.04  3.000
 6Y6  C06  C05  C04  108.03  3.000
 6Y6  N05  C05  C04  111.40  3.000
 6Y6  H5   N05  C51  117.97  3.000
 6Y6  H5   N05  C05  117.76  3.000
 6Y6  C51  N05  C05  123.43  3.000
 6Y6  H6   C06  C07  109.17  3.000
 6Y6  H6   C06  O06  109.08  3.000
 6Y6  C07  C06  O06  106.75  3.000
 6Y6  H6   C06  C05  108.83  3.000
 6Y6  O06  C06  C05  110.07  3.000
 6Y6  C07  C06  C05  112.87  3.000
 6Y6  C06  O06  C02  117.33  3.000
 6Y6  H7   C07  C08  108.14  3.000
 6Y6  H7   C07  O07  105.88  3.000
 6Y6  C08  C07  O07  111.70  3.000
 6Y6  H7   C07  C06  107.22  3.000
 6Y6  C08  C07  C06  112.08  3.000
 6Y6  O07  C07  C06  111.46  3.000
 6Y6  H8   O07  C07  108.66  3.000
 6Y6  H9   C08  C09  108.48  3.000
 6Y6  H9   C08  O08  105.62  3.000
 6Y6  C09  C08  O08  111.76  3.000
 6Y6  H9   C08  C07  108.88  3.000
 6Y6  O08  C08  C07  111.20  3.000
 6Y6  C09  C08  C07  110.69  3.000
 6Y6  H10  O08  C08  108.79  3.000
 6Y6  H12  C09  H11  106.83  3.000
 6Y6  H12  C09  O09  111.58  3.000
 6Y6  H11  C09  O09  111.56  3.000
 6Y6  H12  C09  C08  108.93  3.000
 6Y6  H11  C09  C08  109.22  3.000
 6Y6  O09  C09  C08  108.67  3.000
 6Y6  H13  O09  C09  107.97  3.000
 6Y6  H14  C41  C42  133.30  3.000
 6Y6  H14  C41  N04  122.88  3.000
 6Y6  C42  C41  N04  103.82  3.000
 6Y6  N42  N41  N04  107.91  3.000
 6Y6  C43  C42  N42  122.57  3.000
 6Y6  C43  C42  C41  129.40  3.000
 6Y6  N42  C42  C41  108.03  3.000
 6Y6  C42  N42  N41  109.13  3.000
 6Y6  H16  C43  H15  106.28  3.000
 6Y6  H16  C43  O44  111.50  3.000
 6Y6  H15  C43  O44  111.06  3.000
 6Y6  H16  C43  C42  109.74  3.000
 6Y6  H15  C43  C42  110.00  3.000
 6Y6  O44  C43  C42  108.25  3.000
 6Y6  C45  O44  C43  112.58  3.000
 6Y6  H19  C45  H18  108.47  3.000
 6Y6  H19  C45  H17  108.53  3.000
 6Y6  H18  C45  H17  107.93  3.000
 6Y6  H19  C45  O44  107.87  3.000
 6Y6  H18  C45  O44  112.00  3.000
 6Y6  H17  C45  O44  111.94  3.000
 6Y6  C52  C51  O52  122.53  3.000
 6Y6  O52  C51  N05  122.89  3.000
 6Y6  C52  C51  N05  114.57  3.000
 6Y6  H20  C52  C54  108.09  3.000
 6Y6  H20  C52  C53  108.54  3.000
 6Y6  C54  C52  C53  111.49  3.000
 6Y6  H20  C52  C51  108.68  3.000
 6Y6  C53  C52  C51  111.15  3.000
 6Y6  C54  C52  C51  108.81  3.000
 6Y6  H23  C53  H22  107.73  3.000
 6Y6  H23  C53  H21  108.16  3.000
 6Y6  H22  C53  H21  107.83  3.000
 6Y6  H23  C53  C52  111.79  3.000
 6Y6  H22  C53  C52  109.90  3.000
 6Y6  H21  C53  C52  111.29  3.000
 6Y6  H26  C54  H25  107.71  3.000
 6Y6  H26  C54  H24  108.15  3.000
 6Y6  H25  C54  H24  108.16  3.000
 6Y6  H26  C54  C52  111.65  3.000
 6Y6  H25  C54  C52  110.97  3.000
 6Y6  H24  C54  C52  110.08  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
 6Y6  CONST_01  N42  C42  C41  N04    0.00   0.0  0
 6Y6  CONST_02  C42  N42  N41  N04    0.00   0.0  0
 6Y6  CONST_03  N42  N41  N04  C41    0.00   0.0  0
 6Y6  CONST_04  N41  N42  C42  C41    0.00   0.0  0
 6Y6  CONST_05  C42  C41  N04  N41    0.00   0.0  0
 6Y6  CONST_06  C42  C41  N04  C04  180.00   0.0  0
 6Y6  CONST_07  N42  N41  N04  C04  180.00   0.0  0
 6Y6  CONST_08  C43  C42  C41  N04  180.00   0.0  0
 6Y6  CONST_09  C43  C42  N42  N41  180.00   0.0  0
 6Y6  CONST_10  H14  C41  N04  C04    0.00   0.0  0
 6Y6  CONST_11  C52  C51  N05  C05  180.00   0.0  0
 6Y6  CONST_12  O52  C51  N05  C05    0.00   0.0  0
 6Y6  CONST_13  H5   N05  C51  O52  180.00   0.0  0
 6Y6  Var_01    O06  C02  C03  C04    2.63  30.0  1
 6Y6  Var_02    O44  C43  C42  C41   -8.10  30.0  2
 6Y6  Var_03    C54  C52  C51  N05  -91.54  30.0  1
 6Y6  Var_04    H17  C45  O44  C43  -59.94  30.0  3
 6Y6  Var_05    H24  C54  C52  C51  178.74  30.0  3
 6Y6  Var_06    H21  C53  C52  C51   62.39  30.0  3

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
 6Y6  chir_01  C04  C05  N04  C03  negativ
 6Y6  chir_02  C05  N05  C06  C04  negativ
 6Y6  chir_03  C06  O06  C05  C07  positiv
 6Y6  chir_04  C07  O07  C06  C08  negativ
 6Y6  chir_05  C08  O08  C07  C09  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
 6Y6  plan-1  C04  0.020
 6Y6  plan-1  N04  0.020
 6Y6  plan-1  C41  0.020
 6Y6  plan-1  N41  0.020
 6Y6  plan-1  C42  0.020
 6Y6  plan-1  N42  0.020
 6Y6  plan-1  C43  0.020
 6Y6  plan-1  H14  0.020
 6Y6  plan-2  C05  0.020
 6Y6  plan-2  N05  0.020
 6Y6  plan-2  C51  0.020
 6Y6  plan-2  O52  0.020
 6Y6  plan-2  C52  0.020
 6Y6  plan-2  H5   0.020
 6Y6  plan-3  O1A  0.020
 6Y6  plan-3  O1B  0.020
 6Y6  plan-3  C01  0.020
 6Y6  plan-3  C02  0.020

