# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:33:11 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (2R,3R,4S,5R,6E)-N-(2,3-dihydro-1H-inden-2-yl)-3,4,5-trihydroxy-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]([C@H](O)[C@@H](O)[C@H](O)/C=C/C(C)(C)C)C(=O)NC1Cc2ccccc2C1
#
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
 Y10  Y10  '(2R,3R,4S,5R,6E)-N-(2,3-dihydro-1H-inden-2-yl)-3,4,5-trihydroxy-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)'  ligand  58  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y10
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
 Y10  N     N  NH1   0  -0.645  -2.2601  -0.9994  -0.6121
 Y10  O1    O  OH1   0  -0.661   2.7387   2.1764   0.1562
 Y10  O2    O  OH1   0  -0.656   0.1230   0.8096   0.3710
 Y10  O3    O  OH1   0  -0.663   2.3688   0.0088  -1.5779
 Y10  O4    O  O     0  -0.492  -1.5178  -2.0726   1.2323
 Y10  O5    O  O2    0  -0.484   0.7911  -2.6762  -0.2427
 Y10  C01   C  CT    0  -0.136   6.9947   1.2180   0.0795
 Y10  C04   C  CH1   0  -0.018   3.0918   0.8829   0.5824
 Y10  C05   C  CH1   0  -0.011   2.3096  -0.2059  -0.1874
 Y10  C06   C  CH1   0  -0.025   0.8798  -0.3769   0.3376
 Y10  C07   C  CH1   0  -0.070   0.1134  -1.4700  -0.4238
 Y10  C08   C  CH3   0  -0.659   7.3736  -0.2137   0.4477
 Y10  C09   C  CH3   0  -0.633   7.4320   1.5077  -1.3623
 Y10  C10   C  CH3   0  -0.635   7.7139   2.1907   1.0225
 Y10  C11   C  C     0   0.529  -1.3045  -1.5481   0.1503
 Y10  C12   C  CR15  0  -0.066  -3.6188  -0.8223  -0.1636
 Y10  C13   C  CH2   0  -0.513  -4.5904  -0.5751  -1.3273
 Y10  C14   C  CR56  0   0.089  -5.7050   0.1810  -0.6631
 Y10  C15   C  CR56  0   0.090  -5.2726   0.7215   0.5470
 Y10  C16   C  CH2   0  -0.488  -3.8339   0.3687   0.7920
 Y10  C17   C  CR16  0  -0.321  -7.0027   0.3859  -1.1035
 Y10  C18   C  CR16  0  -0.261  -7.8703   1.1402  -0.3192
 Y10  C19   C  CR16  0  -0.259  -7.4395   1.6805   0.8876
 Y10  C20   C  CR16  0  -0.327  -6.1360   1.4726   1.3286
 Y10  HN    H  HNH1  0   0.397  -1.9871  -0.5359  -1.4648
 Y10  HO1   H  HOH1  0   0.449   3.2581   2.4012  -0.6238
 Y10  HO2   H  HOH1  0   0.442   0.0279   1.1671  -0.5179
 Y10  HO3   H  HOH1  0   0.439   2.0455   0.8946  -1.7757
 Y10  H02   H  H     0   0.225   5.2366   2.5033  -0.0635
 Y10  H03   H  H     0   0.249   4.8371  -0.4110   0.7772
 Y10  H04   H  HCH1  0   0.249   2.7943   0.8128   1.6364
 Y10  H05   H  HCH1  0   0.252   2.8135  -1.1593  -0.0089
 Y10  H06   H  HCH1  0   0.252   0.9648  -0.7008   1.3802
 Y10  H07   H  HCH1  0   0.232   0.0675  -1.2049  -1.4920
 Y10  H08   H  HCH3  0   0.226   6.9083  -0.9426  -0.2186
 Y10  H08A  H  HCH3  0   0.232   8.4547  -0.3439   0.3748
 Y10  H08B  H  HCH3  0   0.227   7.0799  -0.4578   1.4701
 Y10  H09   H  HCH3  0   0.227   6.9394   0.8353  -2.0669
 Y10  H09A  H  HCH3  0   0.224   7.1899   2.5319  -1.6541
 Y10  H09B  H  HCH3  0   0.225   8.5111   1.3793  -1.4715
 Y10  H10   H  HCH3  0   0.226   8.7971   2.0816   0.9332
 Y10  H10A  H  HCH3  0   0.225   7.4643   3.2281   0.7900
 Y10  H10B  H  HCH3  0   0.227   7.4424   2.0070   2.0636
 Y10  H12   H  HCR5  0   0.268  -3.9284  -1.7344   0.3509
 Y10  H13   H  HCH2  0   0.254  -4.1213   0.0463  -2.0995
 Y10  H13A  H  HCH2  0   0.264  -4.9114  -1.4994  -1.8089
 Y10  H16   H  HCH2  0   0.257  -3.6128   0.1162   1.8296
 Y10  H16A  H  HCH2  0   0.251  -3.1765   1.1991   0.5135
 Y10  H17   H  HCR6  0   0.248  -7.3425  -0.0385  -2.0404
 Y10  H18   H  HCR6  0   0.252  -8.8892   1.3025  -0.6470
 Y10  H19   H  HCR6  0   0.252  -8.1249   2.2628   1.4901
 Y10  H20   H  HCR6  0   0.247  -5.8068   1.8894   2.2729
 Y10  H21   H  HCH3  0   0.212   0.4452  -3.4362  -2.1485
 Y10  H21A  H  HCH3  0   0.241   0.9826  -4.5783  -0.9036
 Y10  H21B  H  HCH3  0   0.212  -0.6875  -3.9972  -0.9030
 Y10  C21   C  CH3   0  -0.408   0.3526  -3.7104  -1.0919
 Y10  C03   C  C1    0  -0.277   4.5680   0.6064   0.5112
 Y10  C02   C  C1    0  -0.182   5.5128   1.4772   0.1753

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
 Y10  C12  N     single    1.442  0.020  1.442
 Y10  N    C11   single    1.340  0.020  1.340
 Y10  N    HN    single    0.860  0.020  1.020
 Y10  C04  O1    single    1.407  0.020  1.407
 Y10  O1   HO1   single    0.850  0.020  0.980
 Y10  C06  O2    single    1.408  0.020  1.408
 Y10  O2   HO2   single    0.850  0.020  0.980
 Y10  C05  O3    single    1.408  0.020  1.408
 Y10  O3   HO3   single    0.850  0.020  0.980
 Y10  O4   C11   double    1.221  0.020  1.221
 Y10  C07  O5    single    1.395  0.020  1.395
 Y10  O5   C21   single    1.408  0.020  1.408
 Y10  C09  C01   single    1.534  0.020  1.534
 Y10  C10  C01   single    1.534  0.020  1.534
 Y10  C01  C08   single    1.526  0.020  1.526
 Y10  C01  C02   single    1.508  0.020  1.508
 Y10  C02  C03   double    1.328  0.020  1.328
 Y10  C02  H02   single    0.930  0.020  1.080
 Y10  C03  C04   single    1.504  0.020  1.504
 Y10  C03  H03   single    0.930  0.020  1.080
 Y10  C04  C05   single    1.546  0.020  1.546
 Y10  C04  H04   single    0.970  0.020  1.090
 Y10  C06  C05   single    1.533  0.020  1.533
 Y10  C05  H05   single    0.970  0.020  1.090
 Y10  C07  C06   single    1.537  0.020  1.537
 Y10  C06  H06   single    0.970  0.020  1.090
 Y10  C11  C07   single    1.532  0.020  1.532
 Y10  C07  H07   single    0.970  0.020  1.090
 Y10  C08  H08   single    0.970  0.020  1.090
 Y10  C08  H08A  single    0.970  0.020  1.090
 Y10  C08  H08B  single    0.970  0.020  1.090
 Y10  C09  H09   single    0.970  0.020  1.090
 Y10  C09  H09A  single    0.970  0.020  1.090
 Y10  C09  H09B  single    0.970  0.020  1.090
 Y10  C10  H10   single    0.970  0.020  1.090
 Y10  C10  H10A  single    0.970  0.020  1.090
 Y10  C10  H10B  single    0.970  0.020  1.090
 Y10  C16  C12   single    1.542  0.020  1.542
 Y10  C12  C13   single    1.536  0.020  1.536
 Y10  C12  H12   single    0.970  0.020  1.090
 Y10  C14  C13   single    1.502  0.020  1.502
 Y10  C13  H13   single    0.970  0.020  1.090
 Y10  C13  H13A  single    0.970  0.020  1.090
 Y10  C15  C14   aromatic  1.394  0.020  1.394
 Y10  C17  C14   aromatic  1.386  0.020  1.386
 Y10  C20  C15   aromatic  1.386  0.020  1.386
 Y10  C15  C16   single    1.502  0.020  1.502
 Y10  C16  H16   single    0.970  0.020  1.090
 Y10  C16  H16A  single    0.970  0.020  1.090
 Y10  C18  C17   aromatic  1.392  0.020  1.392
 Y10  C17  H17   single    0.930  0.020  1.080
 Y10  C19  C18   aromatic  1.391  0.020  1.391
 Y10  C18  H18   single    0.930  0.020  1.080
 Y10  C19  C20   aromatic  1.392  0.020  1.392
 Y10  C19  H19   single    0.930  0.020  1.080
 Y10  C20  H20   single    0.930  0.020  1.080
 Y10  C21  H21   single    0.970  0.020  1.090
 Y10  C21  H21A  single    0.970  0.020  1.090
 Y10  C21  H21B  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
 Y10  HN    N    C12   117.50  3.000
 Y10  HN    N    C11   118.45  3.000
 Y10  C12   N    C11   123.05  3.000
 Y10  HO1   O1   C04   108.93  3.000
 Y10  HO2   O2   C06   110.13  3.000
 Y10  HO3   O3   C05   109.20  3.000
 Y10  C21   O5   C07   113.91  3.000
 Y10  C10   C01  C09   108.93  3.000
 Y10  C10   C01  C08   109.29  3.000
 Y10  C09   C01  C08   109.46  3.000
 Y10  C08   C01  C02   112.96  3.000
 Y10  C10   C01  C02   108.23  3.000
 Y10  C09   C01  C02   107.90  3.000
 Y10  H04   C04  C05   107.23  3.000
 Y10  H04   C04  C03   107.45  3.000
 Y10  C05   C04  C03   110.10  3.000
 Y10  H04   C04  O1    106.36  3.000
 Y10  C05   C04  O1    111.70  3.000
 Y10  C03   C04  O1    113.65  3.000
 Y10  H05   C05  C06   106.07  3.000
 Y10  H05   C05  C04   107.44  3.000
 Y10  C06   C05  C04   112.33  3.000
 Y10  H05   C05  O3    105.95  3.000
 Y10  C06   C05  O3    113.23  3.000
 Y10  C04   C05  O3    111.28  3.000
 Y10  H06   C06  C07   107.46  3.000
 Y10  H06   C06  C05   106.66  3.000
 Y10  C07   C06  C05   112.01  3.000
 Y10  H06   C06  O2    105.57  3.000
 Y10  C07   C06  O2    110.07  3.000
 Y10  C05   C06  O2    114.56  3.000
 Y10  H07   C07  C11   109.70  3.000
 Y10  H07   C07  C06   109.27  3.000
 Y10  C11   C07  C06   108.19  3.000
 Y10  H07   C07  O5    110.74  3.000
 Y10  C11   C07  O5    110.91  3.000
 Y10  C06   C07  O5    107.96  3.000
 Y10  H08B  C08  H08A  107.60  3.000
 Y10  H08B  C08  H08   107.93  3.000
 Y10  H08A  C08  H08   107.57  3.000
 Y10  H08B  C08  C01   111.65  3.000
 Y10  H08A  C08  C01   109.98  3.000
 Y10  H08   C08  C01   111.92  3.000
 Y10  H09B  C09  H09A  107.61  3.000
 Y10  H09B  C09  H09   108.00  3.000
 Y10  H09A  C09  H09   107.77  3.000
 Y10  H09B  C09  C01   110.69  3.000
 Y10  H09A  C09  C01   111.40  3.000
 Y10  H09   C09  C01   111.20  3.000
 Y10  H10B  C10  H10A  107.82  3.000
 Y10  H10B  C10  H10   107.92  3.000
 Y10  H10A  C10  H10   107.71  3.000
 Y10  H10B  C10  C01   111.29  3.000
 Y10  H10A  C10  C01   111.38  3.000
 Y10  H10   C10  C01   110.57  3.000
 Y10  C07   C11  O4    121.05  3.000
 Y10  C07   C11  N     115.22  3.000
 Y10  O4    C11  N     123.74  3.000
 Y10  H12   C12  C16   108.28  3.000
 Y10  H12   C12  C13   108.19  3.000
 Y10  C16   C12  C13   104.89  3.000
 Y10  H12   C12  N     108.13  3.000
 Y10  C13   C12  N     112.35  3.000
 Y10  C16   C12  N     114.78  3.000
 Y10  H13A  C13  H13   107.17  3.000
 Y10  H13A  C13  C14   113.80  3.000
 Y10  H13   C13  C14   110.10  3.000
 Y10  H13A  C13  C12   112.60  3.000
 Y10  H13   C13  C12   110.74  3.000
 Y10  C14   C13  C12   102.44  3.000
 Y10  C17   C14  C15   120.60  3.000
 Y10  C17   C14  C13   128.98  3.000
 Y10  C15   C14  C13   110.42  3.000
 Y10  C20   C15  C16   129.22  3.000
 Y10  C16   C15  C14   110.35  3.000
 Y10  C20   C15  C14   120.43  3.000
 Y10  H16A  C16  H16   107.21  3.000
 Y10  H16A  C16  C15   110.83  3.000
 Y10  H16   C16  C15   113.82  3.000
 Y10  H16A  C16  C12   110.14  3.000
 Y10  H16   C16  C12   112.49  3.000
 Y10  C15   C16  C12   102.36  3.000
 Y10  H17   C17  C18   120.27  3.000
 Y10  H17   C17  C14   120.71  3.000
 Y10  C18   C17  C14   119.01  3.000
 Y10  H18   C18  C19   119.74  3.000
 Y10  H18   C18  C17   119.83  3.000
 Y10  C19   C18  C17   120.43  3.000
 Y10  H19   C19  C20   119.80  3.000
 Y10  H19   C19  C18   119.73  3.000
 Y10  C20   C19  C18   120.47  3.000
 Y10  H20   C20  C19   120.22  3.000
 Y10  H20   C20  C15   120.72  3.000
 Y10  C19   C20  C15   119.07  3.000
 Y10  H21B  C21  H21A  108.11  3.000
 Y10  H21B  C21  H21   108.18  3.000
 Y10  H21A  C21  H21   108.50  3.000
 Y10  H21B  C21  O5    112.58  3.000
 Y10  H21A  C21  O5    107.52  3.000
 Y10  H21   C21  O5    111.81  3.000
 Y10  H03   C03  C04   113.84  3.000
 Y10  H03   C03  C02   120.01  3.000
 Y10  C04   C03  C02   126.15  3.000
 Y10  H02   C02  C03   119.53  3.000
 Y10  H02   C02  C01   113.41  3.000
 Y10  C03   C02  C01   127.06  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
 Y10  CONST_01  C19  C20  C15  C14     0.00   0.0  0
 Y10  CONST_02  C19  C18  C17  C14     0.00   0.0  0
 Y10  CONST_03  C18  C17  C14  C15     0.00   0.0  0
 Y10  CONST_04  C18  C19  C20  C15     0.00   0.0  0
 Y10  CONST_05  C20  C15  C14  C17     0.00   0.0  0
 Y10  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 Y10  CONST_07  H17  C17  C14  C13     0.00   0.0  0
 Y10  CONST_08  H20  C20  C15  C14   180.00   0.0  0
 Y10  CONST_09  H18  C18  C17  C14   180.00   0.0  0
 Y10  CONST_10  H19  C19  C20  C15   180.00   0.0  0
 Y10  CONST_11  C12  N    C11  O4      0.00   0.0  0
 Y10  CONST_12  C12  N    C11  C07   180.00   0.0  0
 Y10  CONST_13  HN   N    C11  O4    180.00   0.0  0
 Y10  Var_01    C14  C15  C16  C12   -18.50  30.0  1
 Y10  Var_02    C15  C14  C13  C12    18.75  30.0  1
 Y10  Var_03    C04  C03  C02  C01  -179.12   0.0  2
 Y10  Var_04    C09  C01  C02  C03   119.94  30.0  3
 Y10  Var_05    H09  C09  C01  C02   -62.63  30.0  3
 Y10  Var_06    H10  C10  C01  C02  -176.19  30.0  3
 Y10  Var_07    H08  C08  C01  C02    61.24  30.0  3
 Y10  Var_08    H21  C21  O5   C07    57.89  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
 Y10  chir_01  C04  O1  C03  C05  positiv
 Y10  chir_02  C05  O3  C04  C06  negativ
 Y10  chir_03  C06  O2  C07  C05  negativ
 Y10  chir_04  C07  O5  C06  C11  positiv
 Y10  chir_05  C12  N   C16  C13  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
 Y10  plan-1  N    0.020
 Y10  plan-1  O4   0.020
 Y10  plan-1  C07  0.020
 Y10  plan-1  C11  0.020
 Y10  plan-1  C12  0.020
 Y10  plan-1  HN   0.020
 Y10  plan-2  C13  0.020
 Y10  plan-2  C14  0.020
 Y10  plan-2  C15  0.020
 Y10  plan-2  C16  0.020
 Y10  plan-2  C17  0.020
 Y10  plan-2  C18  0.020
 Y10  plan-2  C19  0.020
 Y10  plan-2  C20  0.020
 Y10  plan-2  H17  0.020
 Y10  plan-2  H18  0.020
 Y10  plan-2  H19  0.020
 Y10  plan-2  H20  0.020
 Y10  plan-3  C01  0.020
 Y10  plan-3  C04  0.020
 Y10  plan-3  H02  0.020
 Y10  plan-3  H03  0.020
 Y10  plan-3  C03  0.020
 Y10  plan-3  C02  0.020

