# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:57:34 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: butyl (2S)-[(2S,3S,4S,5S)-1,3,4,5-tetrahydroxy-4-(hydroxymethyl)piperidin-2-yl](L-tyrosylamino)ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCOC(=O)[C@@H](NC(=O)[C@@H](N)Cc1ccc(O)cc1)[C@H]2[C@H](O)[C@](O)(CO)[C@@H](O)CN2O
#
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
 545  545  'butyl (2S)-[(2S,3S,4S,5S)-1,3,4,5-tetrahydroxy-4-(hydroxymethyl)piperidin-2-yl](L-tyrosylamino)ethanoate'  ligand  66  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_545
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
 545  C8    C  CR16  0  -0.303  -0.9332  -1.2331  -5.8593
 545  C7    C  CR16  0  -0.325  -0.9742  -0.7754  -7.1678
 545  C12   C  CR6   0   0.340  -1.1979   0.5741  -7.4247
 545  C11   C  CR16  0  -0.369  -1.3852   1.4490  -6.3568
 545  C10   C  CR16  0  -0.284  -1.3419   0.9726  -5.0559
 545  C9    C  CR6   0   0.103  -1.1164  -0.3736  -4.7787
 545  C14   C  CH2   0  -0.526  -1.0214  -0.8592  -3.3621
 545  C15   C  CH1   0  -0.222   0.3688  -0.5585  -2.7477
 545  C17   C  C     0   0.583   0.3437  -1.0266  -1.3040
 545  N19   N  NH1   0  -0.609  -0.1421  -0.1397  -0.4240
 545  C20   C  CH1   0  -0.262  -0.4501  -0.4636   0.9413
 545  C21   C  C     0   0.623  -1.8582   0.0147   1.2671
 545  O23   O  O2    0  -0.460  -2.1704  -0.2607   2.5198
 545  C24   C  CH2   0  -0.165  -3.4752   0.1024   2.9972
 545  C25   C  CH2   0  -0.458  -3.5396  -0.2494   4.4672
 545  C26   C  CH2   0  -0.433  -4.8969   0.1001   5.0667
 545  C27   C  CH3   0  -0.659  -4.9788  -0.2455   6.5469
 545  O18   O  O     0  -0.506   0.6924  -2.1622  -0.9932
 545  N16   N  NH2   0  -0.783   1.4905  -1.1642  -3.4275
 545  O22   O  O     0  -0.440  -2.6114   0.5040   0.4661
 545  C6    C  CH1   0  -0.124   0.6265   0.0081   1.9348
 545  N5    N  NT    0  -0.164   0.8182   1.4447   1.8354
 545  C4    C  CH2   0  -0.371   1.8053   1.9425   2.7753
 545  C3    C  CH1   0   0.025   3.1643   1.2928   2.5506
 545  C2    C  CT    0   0.167   3.0670  -0.2469   2.6035
 545  C1    C  CH1   0   0.048   1.9695  -0.6853   1.6249
 545  O28   O  OH1   0  -0.564  -0.3881   2.1195   2.0399
 545  O32   O  OH1   0  -0.664   3.7038   1.6394   1.2975
 545  O29   O  OH1   0  -0.678   4.2624  -0.8312   2.1504
 545  C30   C  CH2   0  -0.182   2.7893  -0.7299   4.0319
 545  O31   O  OH1   0  -0.675   3.9246  -0.4171   4.8132
 545  O64   O  OH1   0  -0.686   1.8329  -2.0793   1.6588
 545  O13   O  OH1   0  -0.634  -1.2271   0.9778  -8.7117
 545  H8    H  HCR6  0   0.251  -0.7641  -2.2888  -5.6823
 545  H7    H  HCR6  0   0.261  -0.8326  -1.4638  -7.9917
 545  H11   H  HCR6  0   0.270  -1.5662   2.5026  -6.5376
 545  H10   H  HCR6  0   0.251  -1.4913   1.6718  -4.2407
 545  H141  H  HCH2  0   0.258  -1.1973  -1.9377  -3.3200
 545  H142  H  HCH2  0   0.253  -1.7964  -0.3865  -2.7525
 545  H15   H  HCH1  0   0.268   0.5127   0.5267  -2.7641
 545  H19   H  HNH1  0   0.406  -0.3638   0.7889  -0.7484
 545  H20   H  HCH1  0   0.312  -0.5029  -1.5529   1.0291
 545  H241  H  HCH2  0   0.237  -4.2367  -0.4394   2.4310
 545  H242  H  HCH2  0   0.234  -3.6379   1.1721   2.8448
 545  H251  H  HCH2  0   0.230  -2.7523   0.2868   5.0054
 545  H252  H  HCH2  0   0.231  -3.3457  -1.3182   4.5978
 545  H261  H  HCH2  0   0.221  -5.6847  -0.4299   4.5237
 545  H262  H  HCH2  0   0.222  -5.0946   1.1671   4.9284
 545  H271  H  HCH3  0   0.230  -5.9574   0.0025   6.9587
 545  H272  H  HCH3  0   0.219  -4.8100  -1.3108   6.7127
 545  H273  H  HCH3  0   0.219  -4.2286   0.3005   7.1215
 545  H161  H  HNH2  0   0.345   1.4004  -2.1730  -3.4117
 545  H162  H  HNH2  0   0.357   1.4774  -0.8926  -4.4029
 545  H6    H  HCH1  0   0.242   0.2911  -0.2950   2.9401
 545  H41   H  HCH2  0   0.223   1.4885   1.7866   3.8198
 545  H42   H  HCH2  0   0.270   1.8956   3.0234   2.6386
 545  H3    H  HCH1  0   0.233   3.8193   1.6398   3.3615
 545  H1    H  HCH1  0   0.242   2.2918  -0.3481   0.6319
 545  H28   H  HOH1  0   0.446  -0.6331   2.0241   2.9765
 545  H32   H  HOH1  0   0.451   3.6761   2.5976   1.2139
 545  H29   H  HOH1  0   0.442   4.9118  -0.7494   2.8592
 545  H301  H  HCH2  0   0.204   1.8908  -0.2618   4.4463
 545  H302  H  HCH2  0   0.234   2.6091  -1.8089   4.0109
 545  H31   H  HOH1  0   0.465   3.9313  -0.9878   5.5863
 545  H64   H  HOH1  0   0.457   1.5043  -2.3565   0.7897
 545  H13   H  HOH1  0   0.473  -1.3623   1.9307  -8.7626

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
 545  C8   C7    aromatic  1.387  0.020  1.387
 545  C8   C9    aromatic  1.393  0.020  1.393
 545  C8   H8    single    0.930  0.020  1.080
 545  C7   C12   aromatic  1.392  0.020  1.392
 545  C7   H7    single    0.930  0.020  1.080
 545  C12  C11   aromatic  1.393  0.020  1.393
 545  C12  O13   single    1.349  0.020  1.349
 545  C11  C10   aromatic  1.386  0.020  1.386
 545  C11  H11   single    0.930  0.020  1.080
 545  C10  C9    aromatic  1.393  0.020  1.393
 545  C10  H10   single    0.930  0.020  1.080
 545  C9   C14   single    1.501  0.020  1.501
 545  C14  C15   single    1.549  0.020  1.549
 545  C14  H141  single    0.970  0.020  1.090
 545  C14  H142  single    0.970  0.020  1.090
 545  C15  C17   single    1.518  0.020  1.518
 545  C15  N16   single    1.445  0.020  1.445
 545  C15  H15   single    0.970  0.020  1.090
 545  C17  N19   single    1.341  0.020  1.341
 545  C17  O18   double    1.228  0.020  1.228
 545  N19  C20   single    1.437  0.020  1.437
 545  N19  H19   single    0.860  0.020  1.020
 545  C20  C21   single    1.522  0.020  1.522
 545  C20  C6    single    1.539  0.020  1.539
 545  C20  H20   single    0.970  0.020  1.090
 545  C21  O23   single    1.320  0.020  1.320
 545  C21  O22   double    1.203  0.020  1.203
 545  O23  C24   single    1.436  0.020  1.436
 545  C24  C25   single    1.513  0.020  1.513
 545  C24  H241  single    0.970  0.020  1.090
 545  C24  H242  single    0.970  0.020  1.090
 545  C25  C26   single    1.524  0.020  1.524
 545  C25  H251  single    0.970  0.020  1.090
 545  C25  H252  single    0.970  0.020  1.090
 545  C26  C27   single    1.522  0.020  1.522
 545  C26  H261  single    0.970  0.020  1.090
 545  C26  H262  single    0.970  0.020  1.090
 545  C27  H271  single    0.970  0.020  1.090
 545  C27  H272  single    0.970  0.020  1.090
 545  C27  H273  single    0.970  0.020  1.090
 545  N16  H161  single    0.890  0.020  1.040
 545  N16  H162  single    0.890  0.020  1.040
 545  C6   N5    single    1.453  0.020  1.453
 545  C6   C1    single    1.543  0.020  1.543
 545  C6   H6    single    0.970  0.020  1.090
 545  N5   C4    single    1.451  0.020  1.451
 545  N5   O28   single    1.397  0.020  1.397
 545  C4   C3    single    1.523  0.020  1.523
 545  C4   H41   single    0.970  0.020  1.090
 545  C4   H42   single    0.970  0.020  1.090
 545  C3   C2    single    1.544  0.020  1.544
 545  C3   O32   single    1.408  0.020  1.408
 545  C3   H3    single    0.970  0.020  1.090
 545  C2   C1    single    1.534  0.020  1.534
 545  C2   O29   single    1.405  0.020  1.405
 545  C2   C30   single    1.533  0.020  1.533
 545  C1   O64   single    1.401  0.020  1.401
 545  C1   H1    single    0.970  0.020  1.090
 545  O28  H28   single    0.850  0.020  0.980
 545  O32  H32   single    0.850  0.020  0.980
 545  O29  H29   single    0.850  0.020  0.980
 545  C30  O31   single    1.413  0.020  1.413
 545  C30  H301  single    0.970  0.020  1.090
 545  C30  H302  single    0.970  0.020  1.090
 545  O31  H31   single    0.850  0.020  0.980
 545  O64  H64   single    0.850  0.020  0.980
 545  O13  H13   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
 545  H8    C8   C9    119.67  3.000
 545  H8    C8   C7    118.70  3.000
 545  C9    C8   C7    121.63  3.000
 545  H7    C7   C12   119.80  3.000
 545  H7    C7   C8    120.27  3.000
 545  C12   C7   C8    119.93  3.000
 545  O13   C12  C11   122.71  3.000
 545  O13   C12  C7    118.02  3.000
 545  C11   C12  C7    119.27  3.000
 545  H11   C11  C10   119.71  3.000
 545  H11   C11  C12   120.32  3.000
 545  C10   C11  C12   119.96  3.000
 545  H10   C10  C9    119.73  3.000
 545  H10   C10  C11   118.66  3.000
 545  C9    C10  C11   121.60  3.000
 545  C14   C9   C10   120.73  3.000
 545  C14   C9   C8    121.63  3.000
 545  C10   C9   C8    117.60  3.000
 545  H142  C14  H141  106.91  3.000
 545  H142  C14  C15   109.33  3.000
 545  H141  C14  C15   108.70  3.000
 545  H142  C14  C9    109.97  3.000
 545  H141  C14  C9    110.20  3.000
 545  C15   C14  C9    111.61  3.000
 545  H15   C15  N16   107.84  3.000
 545  H15   C15  C17   108.79  3.000
 545  N16   C15  C17   109.33  3.000
 545  H15   C15  C14   107.72  3.000
 545  N16   C15  C14   115.38  3.000
 545  C17   C15  C14   107.61  3.000
 545  O18   C17  N19   123.28  3.000
 545  O18   C17  C15   121.42  3.000
 545  N19   C17  C15   115.23  3.000
 545  H19   N19  C20   117.79  3.000
 545  H19   N19  C17   118.54  3.000
 545  C20   N19  C17   123.53  3.000
 545  H20   C20  C6    106.68  3.000
 545  H20   C20  C21   104.54  3.000
 545  C6    C20  C21   114.37  3.000
 545  H20   C20  N19   108.12  3.000
 545  C6    C20  N19   113.23  3.000
 545  C21   C20  N19   109.32  3.000
 545  O22   C21  O23   124.64  3.000
 545  O22   C21  C20   124.35  3.000
 545  O23   C21  C20   110.87  3.000
 545  C24   O23  C21   118.53  3.000
 545  H242  C24  H241  108.02  3.000
 545  H242  C24  C25   110.90  3.000
 545  H241  C24  C25   111.01  3.000
 545  H242  C24  O23   109.66  3.000
 545  H241  C24  O23   109.61  3.000
 545  C25   C24  O23   107.63  3.000
 545  H252  C25  H251  107.01  3.000
 545  H252  C25  C26   109.56  3.000
 545  H251  C25  C26   109.56  3.000
 545  H252  C25  C24   109.61  3.000
 545  H251  C25  C24   109.48  3.000
 545  C26   C25  C24   111.51  3.000
 545  H262  C26  H261  106.24  3.000
 545  H262  C26  C27   109.55  3.000
 545  H261  C26  C27   109.51  3.000
 545  H262  C26  C25   109.56  3.000
 545  H261  C26  C25   109.57  3.000
 545  C27   C26  C25   112.23  3.000
 545  H273  C27  H272  107.58  3.000
 545  H273  C27  H271  107.72  3.000
 545  H272  C27  H271  107.67  3.000
 545  H273  C27  C26   111.18  3.000
 545  H272  C27  C26   111.16  3.000
 545  H271  C27  C26   111.35  3.000
 545  H162  N16  H161  106.32  3.000
 545  H162  N16  C15   109.31  3.000
 545  H161  N16  C15   109.94  3.000
 545  H6    C6   C1    108.93  3.000
 545  H6    C6   N5    111.99  3.000
 545  C1    C6   N5    108.41  3.000
 545  H6    C6   C20   106.96  3.000
 545  C1    C6   C20   109.97  3.000
 545  N5    C6   C20   110.56  3.000
 545  O28   N5   C4    109.08  3.000
 545  O28   N5   C6    110.71  3.000
 545  C4    N5   C6    112.62  3.000
 545  H42   C4   H41   106.38  3.000
 545  H42   C4   C3    109.25  3.000
 545  H41   C4   C3    109.63  3.000
 545  H42   C4   N5    108.32  3.000
 545  H41   C4   N5    111.69  3.000
 545  C3    C4   N5    111.42  3.000
 545  H3    C3   O32   110.53  3.000
 545  H3    C3   C2    109.11  3.000
 545  O32   C3   C2    107.47  3.000
 545  H3    C3   C4    106.76  3.000
 545  O32   C3   C4    111.61  3.000
 545  C2    C3   C4    111.36  3.000
 545  C30   C2   O29   108.87  3.000
 545  C30   C2   C1    112.00  3.000
 545  O29   C2   C1    106.50  3.000
 545  C30   C2   C3    110.94  3.000
 545  O29   C2   C3    110.49  3.000
 545  C1    C2   C3    107.95  3.000
 545  H1    C1   O64   110.88  3.000
 545  H1    C1   C2    106.22  3.000
 545  O64   C1   C2    109.79  3.000
 545  H1    C1   C6    107.42  3.000
 545  O64   C1   C6    110.94  3.000
 545  C2    C1   C6    111.47  3.000
 545  H28   O28  N5    108.12  3.000
 545  H32   O32  C3    108.15  3.000
 545  H29   O29  C2    107.49  3.000
 545  H302  C30  H301  107.09  3.000
 545  H302  C30  O31   111.17  3.000
 545  H301  C30  O31   110.83  3.000
 545  H302  C30  C2    108.82  3.000
 545  H301  C30  C2    111.51  3.000
 545  O31   C30  C2    107.44  3.000
 545  H31   O31  C30   108.59  3.000
 545  H64   O64  C1    107.21  3.000
 545  H13   O13  C12   110.44  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
 545  CONST_01  C11   C12  C7   C8      0.00   0.0  0
 545  CONST_02  C11   C10  C9   C8      0.00   0.0  0
 545  CONST_03  C10   C9   C8   C7      0.00   0.0  0
 545  CONST_04  C10   C11  C12  C7      0.00   0.0  0
 545  CONST_05  C9    C8   C7   C12     0.00   0.0  0
 545  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 545  CONST_07  O13   C12  C7   C8    180.00   0.0  0
 545  CONST_08  C14   C9   C8   C7    180.00   0.0  0
 545  CONST_09  C14   C9   C10  C11   180.00   0.0  0
 545  CONST_10  O13   C12  C11  C10   180.00   0.0  0
 545  CONST_11  H10   C10  C9   C8    180.00   0.0  0
 545  CONST_12  H11   C11  C12  C7    180.00   0.0  0
 545  CONST_13  H8    C8   C7   C12   180.00   0.0  0
 545  CONST_14  H7    C7   C12  C11   180.00   0.0  0
 545  CONST_15  C20   N19  C17  C15   180.00   0.0  0
 545  CONST_16  O18   C17  N19  C20     0.00   0.0  0
 545  CONST_17  H19   N19  C17  C15     0.00   0.0  0
 545  Var_01    C3    C4   N5   C6     59.63  30.0  1
 545  Var_02    C15   C14  C9   C8     98.45  30.0  2
 545  Var_03    C25   C24  O23  C21  -176.78  30.0  3
 545  Var_04    C26   C25  C24  O23  -179.93  30.0  3
 545  Var_05    O22   C21  O23  C24    -3.25  30.0  1
 545  Var_06    C27   C26  C25  C24  -179.91  30.0  3
 545  Var_07    H271  C27  C26  C25  -179.53  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
 545  chir_01  C15  C14  C17  N16  negativ
 545  chir_02  C20  N19  C21  C6   positiv
 545  chir_03  C6   N5   C1   C20  positiv
 545  chir_04  C3   O32  C2   C4   positiv
 545  chir_05  C2   C30  C1   C3   negativ
 545  chir_06  C1   O64  C2   C6   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
 545  plan-1  C8   0.020
 545  plan-1  C7   0.020
 545  plan-1  C12  0.020
 545  plan-1  C11  0.020
 545  plan-1  C10  0.020
 545  plan-1  C9   0.020
 545  plan-1  C14  0.020
 545  plan-1  O13  0.020
 545  plan-1  H8   0.020
 545  plan-1  H7   0.020
 545  plan-1  H11  0.020
 545  plan-1  H10  0.020
 545  plan-2  C15  0.020
 545  plan-2  C17  0.020
 545  plan-2  N19  0.020
 545  plan-2  C20  0.020
 545  plan-2  O18  0.020
 545  plan-2  H19  0.020
 545  plan-3  C20  0.020
 545  plan-3  C21  0.020
 545  plan-3  O23  0.020
 545  plan-3  O22  0.020

