# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:06:00 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2R,3R,4S,5R,6E)-N-(2-amino-2-oxoethyl)-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)NCC(N)=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
 Y16  Y16  '(2R,3R,4S,5R,6E)-N-(2-amino-2-oxoethyl)-3,4,5-trihydroxy-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)'  ligand  48  22  .  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_Y16
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
 Y16  N1    N  NH1   0  -0.639  -3.6483   0.2206   0.1368
 Y16  O1    O  OH1   0  -0.660   1.9005  -2.0227  -0.6836
 Y16  N2    N  NH2   0  -0.797  -7.0078  -1.1087   0.3674
 Y16  O2    O  OH1   0  -0.658  -0.9174  -1.1441  -0.8395
 Y16  O3    O  OH1   0  -0.663   0.9974  -0.2323   1.3258
 Y16  O4    O  O     0  -0.494  -2.9695   1.3708  -1.6791
 Y16  O5    O  O     0  -0.484  -5.2404  -1.1533   1.7716
 Y16  O6    O  O2    0  -0.484  -0.9117   2.3506   0.0150
 Y16  C01   C  CT    0  -0.134   5.8820  -0.4380   0.1499
 Y16  C04   C  CH1   0  -0.020   2.0617  -0.6331  -0.8351
 Y16  C05   C  CH1   0  -0.013   1.0165   0.1640  -0.0257
 Y16  C06   C  CH1   0  -0.017  -0.3734   0.1425  -0.6714
 Y16  C07   C  CH1   0  -0.067  -1.3690   1.0331   0.0860
 Y16  C08   C  CH3   0  -0.631   6.1924  -0.8570   1.5926
 Y16  C09   C  CH3   0  -0.636   6.8563  -1.1526  -0.7949
 Y16  C10   C  CH3   0  -0.662   6.0523   1.0718   0.0095
 Y16  C11   C  C     0   0.530  -2.7423   0.8954  -0.5768
 Y16  C12   C  CH2   0  -0.374  -4.9672  -0.0657  -0.3506
 Y16  C13   C  C     0   0.493  -5.7471  -0.8298   0.7076
 Y16  HN1   H  HNH1  0   0.401  -3.4138  -0.1393   1.0501
 Y16  HO1   H  HOH1  0   0.449   2.3441  -2.3052   0.1236
 Y16  HN2   H  HNH2  0   0.414  -7.3974  -0.8276  -0.5163
 Y16  HN2A  H  HNH2  0   0.408  -7.6061  -1.6181   0.9972
 Y16  HO2   H  HOH1  0   0.441  -0.9974  -1.5811   0.0146
 Y16  HO3   H  HOH1  0   0.439   0.8588  -1.1843   1.3779
 Y16  H02   H  H     0   0.224   4.3733  -1.9871  -0.1368
 Y16  H03   H  H     0   0.247   3.5627   0.9294  -0.5775
 Y16  H04   H  HCH1  0   0.248   1.8786  -0.4158  -1.8950
 Y16  H05   H  HCH1  0   0.252   1.3348   1.2099  -0.0283
 Y16  H06   H  HCH1  0   0.250  -0.2648   0.5538  -1.6806
 Y16  H07   H  HCH1  0   0.232  -1.4314   0.7002   1.1346
 Y16  H08   H  HCH3  0   0.227   5.5261  -0.3608   2.3002
 Y16  H08A  H  HCH3  0   0.224   6.0781  -1.9349   1.7245
 Y16  H08B  H  HCH3  0   0.225   7.2199  -0.5980   1.8574
 Y16  H09   H  HCH3  0   0.226   7.8891  -0.8874  -0.5592
 Y16  H09A  H  HCH3  0   0.224   6.7644  -2.2377  -0.7096
 Y16  H09B  H  HCH3  0   0.228   6.6690  -0.8824  -1.8356
 Y16  H10   H  HCH3  0   0.232   7.0755   1.3599   0.2573
 Y16  H10A  H  HCH3  0   0.226   5.8552   1.4078  -1.0106
 Y16  H10B  H  HCH3  0   0.227   5.3855   1.6204   0.6774
 Y16  H12   H  HCH2  0   0.281  -5.5034   0.8540  -0.6011
 Y16  H12A  H  HCH2  0   0.282  -4.9308  -0.6649  -1.2660
 Y16  H14   H  HCH3  0   0.212  -1.5749   2.9262   1.9018
 Y16  H14A  H  HCH3  0   0.242  -1.1241   4.2152   0.7720
 Y16  H14B  H  HCH3  0   0.213  -2.6574   3.3598   0.5636
 Y16  C14   C  CH3   0  -0.408  -1.6076   3.2429   0.8537
 Y16  C03   C  C1    0  -0.273   3.4474  -0.1481  -0.5116
 Y16  C02   C  C1    0  -0.181   4.4870  -0.9050  -0.1811

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
 Y16  N1   C12   single  1.435  0.020  1.435
 Y16  N1   C11   single  1.336  0.020  1.336
 Y16  N1   HN1   single  0.860  0.020  1.020
 Y16  O1   C04   single  1.407  0.020  1.407
 Y16  O1   HO1   single  0.850  0.020  0.980
 Y16  C13  N2    single  1.335  0.020  1.335
 Y16  N2   HN2   single  0.860  0.020  1.020
 Y16  N2   HN2A  single  0.860  0.020  1.020
 Y16  O2   C06   single  1.407  0.020  1.407
 Y16  O2   HO2   single  0.850  0.020  0.980
 Y16  O3   C05   single  1.408  0.020  1.408
 Y16  O3   HO3   single  0.850  0.020  0.980
 Y16  C11  O4    double  1.222  0.020  1.222
 Y16  C13  O5    double  1.222  0.020  1.222
 Y16  C07  O6    single  1.396  0.020  1.396
 Y16  C14  O6    single  1.408  0.020  1.408
 Y16  C02  C01   single  1.508  0.020  1.508
 Y16  C01  C10   single  1.526  0.020  1.526
 Y16  C01  C08   single  1.534  0.020  1.534
 Y16  C01  C09   single  1.534  0.020  1.534
 Y16  C03  C02   double  1.328  0.020  1.328
 Y16  C02  H02   single  0.930  0.020  1.080
 Y16  C04  C03   single  1.503  0.020  1.503
 Y16  C03  H03   single  0.930  0.020  1.080
 Y16  C05  C04   single  1.544  0.020  1.544
 Y16  C04  H04   single  0.970  0.020  1.090
 Y16  C05  C06   single  1.533  0.020  1.533
 Y16  C05  H05   single  0.970  0.020  1.090
 Y16  C06  C07   single  1.536  0.020  1.536
 Y16  C06  H06   single  0.970  0.020  1.090
 Y16  C07  C11   single  1.531  0.020  1.531
 Y16  C07  H07   single  0.970  0.020  1.090
 Y16  C08  H08   single  0.970  0.020  1.090
 Y16  C08  H08A  single  0.970  0.020  1.090
 Y16  C08  H08B  single  0.970  0.020  1.090
 Y16  C09  H09   single  0.970  0.020  1.090
 Y16  C09  H09A  single  0.970  0.020  1.090
 Y16  C09  H09B  single  0.970  0.020  1.090
 Y16  C10  H10   single  0.970  0.020  1.090
 Y16  C10  H10A  single  0.970  0.020  1.090
 Y16  C10  H10B  single  0.970  0.020  1.090
 Y16  C12  C13   single  1.520  0.020  1.520
 Y16  C12  H12   single  0.970  0.020  1.090
 Y16  C12  H12A  single  0.970  0.020  1.090
 Y16  C14  H14   single  0.970  0.020  1.090
 Y16  C14  H14A  single  0.970  0.020  1.090
 Y16  C14  H14B  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
 Y16  HN1   N1   C12   116.73  3.000
 Y16  HN1   N1   C11   120.39  3.000
 Y16  C12   N1   C11   122.86  3.000
 Y16  HO1   O1   C04   109.09  3.000
 Y16  HN2A  N2   HN2   117.43  3.000
 Y16  HN2A  N2   C13   120.48  3.000
 Y16  HN2   N2   C13   122.09  3.000
 Y16  HO2   O2   C06   109.95  3.000
 Y16  HO3   O3   C05   109.38  3.000
 Y16  C14   O6   C07   113.93  3.000
 Y16  C10   C01  C09   109.48  3.000
 Y16  C09   C01  C08   108.87  3.000
 Y16  C10   C01  C08   109.53  3.000
 Y16  C09   C01  C02   107.95  3.000
 Y16  C08   C01  C02   108.00  3.000
 Y16  C10   C01  C02   112.93  3.000
 Y16  H04   C04  C05   106.93  3.000
 Y16  H04   C04  C03   107.32  3.000
 Y16  C05   C04  C03   110.16  3.000
 Y16  H04   C04  O1    106.29  3.000
 Y16  C05   C04  O1    112.08  3.000
 Y16  C03   C04  O1    113.64  3.000
 Y16  H05   C05  C06   106.05  3.000
 Y16  H05   C05  C04   107.20  3.000
 Y16  C06   C05  C04   112.69  3.000
 Y16  H05   C05  O3    105.99  3.000
 Y16  C06   C05  O3    112.83  3.000
 Y16  C04   C05  O3    111.53  3.000
 Y16  H06   C06  C07   107.52  3.000
 Y16  H06   C06  C05   107.04  3.000
 Y16  C07   C06  C05   111.84  3.000
 Y16  H06   C06  O2    105.77  3.000
 Y16  C07   C06  O2    109.79  3.000
 Y16  C05   C06  O2    114.44  3.000
 Y16  H07   C07  C11   109.51  3.000
 Y16  H07   C07  C06   109.32  3.000
 Y16  C11   C07  C06   108.41  3.000
 Y16  H07   C07  O6    110.61  3.000
 Y16  C11   C07  O6    110.89  3.000
 Y16  C06   C07  O6    108.05  3.000
 Y16  H08B  C08  H08A  107.66  3.000
 Y16  H08B  C08  H08   108.02  3.000
 Y16  H08A  C08  H08   107.85  3.000
 Y16  H08B  C08  C01   110.71  3.000
 Y16  H08A  C08  C01   111.23  3.000
 Y16  H08   C08  C01   111.22  3.000
 Y16  H09B  C09  H09A  107.81  3.000
 Y16  H09B  C09  H09   107.94  3.000
 Y16  H09A  C09  H09   107.70  3.000
 Y16  H09B  C09  C01   111.29  3.000
 Y16  H09A  C09  C01   111.18  3.000
 Y16  H09   C09  C01   110.77  3.000
 Y16  H10B  C10  H10A  107.86  3.000
 Y16  H10B  C10  H10   107.52  3.000
 Y16  H10A  C10  H10   107.47  3.000
 Y16  H10B  C10  C01   111.89  3.000
 Y16  H10A  C10  C01   111.73  3.000
 Y16  H10   C10  C01   110.18  3.000
 Y16  C07   C11  O4    121.49  3.000
 Y16  C07   C11  N1    114.98  3.000
 Y16  O4    C11  N1    123.53  3.000
 Y16  H12A  C12  H12   106.56  3.000
 Y16  H12A  C12  C13   108.90  3.000
 Y16  H12   C12  C13   109.30  3.000
 Y16  H12A  C12  N1    111.27  3.000
 Y16  H12   C12  N1    111.14  3.000
 Y16  C13   C12  N1    109.59  3.000
 Y16  C12   C13  O5    121.76  3.000
 Y16  C12   C13  N2    114.32  3.000
 Y16  O5    C13  N2    123.92  3.000
 Y16  H14B  C14  H14A  108.08  3.000
 Y16  H14B  C14  H14   108.23  3.000
 Y16  H14A  C14  H14   108.47  3.000
 Y16  H14B  C14  O6    112.54  3.000
 Y16  H14A  C14  O6    107.56  3.000
 Y16  H14   C14  O6    111.83  3.000
 Y16  H03   C03  C04   113.89  3.000
 Y16  H03   C03  C02   119.86  3.000
 Y16  C04   C03  C02   126.25  3.000
 Y16  H02   C02  C03   119.66  3.000
 Y16  H02   C02  C01   113.30  3.000
 Y16  C03   C02  C01   127.04  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
 Y16  CONST_01  C12   N1   C11  O4      0.00   0.0  0
 Y16  CONST_02  C12   N1   C11  C07   180.00   0.0  0
 Y16  CONST_03  HN1   N1   C11  O4    180.00   0.0  0
 Y16  CONST_04  HN2   N2   C13  O5    180.00   0.0  0
 Y16  CONST_05  HN2A  N2   C13  O5      0.00   0.0  0
 Y16  Var_01    C04   C03  C02  C01  -179.83   0.0  2
 Y16  Var_02    N2    C13  C12  N1    177.95  30.0  3
 Y16  Var_03    C10   C01  C02  C03    -2.78  30.0  3
 Y16  Var_04    C13   C12  N1   C11  -179.34  30.0  3
 Y16  Var_05    H10   C10  C01  C02  -179.91  30.0  3
 Y16  Var_06    H08   C08  C01  C02   -63.64  30.0  3
 Y16  Var_07    H09   C09  C01  C02  -176.97  30.0  3
 Y16  Var_08    H14   C14  O6   C07    56.97  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
 Y16  chir_01  C04  O1  C03  C05  positiv
 Y16  chir_02  C05  O3  C04  C06  negativ
 Y16  chir_03  C06  O2  C07  C05  negativ
 Y16  chir_04  C07  O6  C06  C11  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
 Y16  plan-1  N1    0.020
 Y16  plan-1  O4    0.020
 Y16  plan-1  C07   0.020
 Y16  plan-1  C11   0.020
 Y16  plan-1  C12   0.020
 Y16  plan-1  HN1   0.020
 Y16  plan-2  N2    0.020
 Y16  plan-2  O5    0.020
 Y16  plan-2  C12   0.020
 Y16  plan-2  C13   0.020
 Y16  plan-2  HN2   0.020
 Y16  plan-2  HN2A  0.020
 Y16  plan-3  C01   0.020
 Y16  plan-3  C04   0.020
 Y16  plan-3  H02   0.020
 Y16  plan-3  H03   0.020
 Y16  plan-3  C03   0.020
 Y16  plan-3  C02   0.020

