# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  2 16:40:30 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: methyl 6,8-dideoxy-6-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}-1-thio-D-glycero-alpha-D-galacto-octopyranosid-7-ulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H]1C[C@H](N(C)C1)C(=O)N[C@@H]([C@H]2O[C@H](SC)[C@H](O)[C@@H](O)[C@H]2O)C(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
 LN0  LN0  'methyl 6,8-dideoxy-6-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}-1-thio-D-glycero-alpha-D-galacto-octopyranosid-7-ulose'  ligand  59  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LN0
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
 LN0  C4   C  CH1   0   0.004   1.9819  -0.1391   0.0764
 LN0  C14  C  CH2   0  -0.242  -5.0835  -1.0940   0.2057
 LN0  C5   C  CH1   0  -0.146   4.2434   0.5898   0.0286
 LN0  C6   C  CH3   0  -0.767   3.6697   3.0556  -1.0776
 LN0  C11  C  CH1   0  -0.195  -2.7475  -0.9820  -0.0680
 LN0  C7   C  CH1   0  -0.170   0.7213   0.1237   0.9026
 LN0  C8   C  C     0   0.413   0.4892   1.6400   0.9943
 LN0  C9   C  CH3   0  -0.774   0.8500   2.2975   2.2875
 LN0  C12  C  CH2   0  -0.468  -3.4026   0.1567  -0.8812
 LN0  C13  C  CH1   0  -0.243  -4.7903   0.3260  -0.2586
 LN0  N1   N  NH1   0  -0.659  -0.3984  -0.5215   0.2704
 LN0  N2   N  NT    0  -0.417  -3.8127  -1.5380   0.7365
 LN0  C3   C  CH1   0   0.008   2.3653  -1.6121   0.0059
 LN0  C18  C  CH3   0  -0.662  -8.1869   1.7391  -1.5614
 LN0  C16  C  CH2   0  -0.412  -5.8176   0.9111  -1.2147
 LN0  C15  C  CH3   0  -0.523  -3.7026  -2.9477   1.0044
 LN0  O8   O  O     0  -0.400   0.0221   2.2335   0.0510
 LN0  O5   O  O2    0  -0.474   3.0049   0.6243   0.6773
 LN0  O7   O  OH1   0  -0.668   2.4719  -2.1124   1.3125
 LN0  C2   C  CH1   0   0.006   3.6780  -1.7312  -0.7638
 LN0  O6   O  OH1   0  -0.672   4.0474  -3.0877  -0.7594
 LN0  C1   C  CH1   0   0.010   4.7468  -0.8527  -0.1255
 LN0  O4   O  OH1   0  -0.658   5.8939  -0.9306  -0.9290
 LN0  S1   S  S2    0  -0.043   4.2308   1.4186  -1.6001
 LN0  H1   H  HCH1  0   0.255   1.8048   0.2121  -0.9513
 LN0  H2   H  HCH2  0   0.232  -5.8576  -1.1510   0.9749
 LN0  H3   H  HCH2  0   0.184  -5.4273  -1.7028  -0.6502
 LN0  H4   H  HCH1  0   0.292   4.9211   1.1534   0.6750
 LN0  H5   H  HCH3  0   0.276   3.7797   3.7201  -1.9323
 LN0  H6   H  HCH3  0   0.265   2.6259   3.0506  -0.7736
 LN0  H7   H  HCH3  0   0.263   4.2848   3.4353  -0.2627
 LN0  H8   H  HCH1  0   0.244  -2.3192  -1.7254  -0.7573
 LN0  H9   H  HCH1  0   0.283   0.8615  -0.2778   1.9096
 LN0  H10  H  HCH3  0   0.264   1.8470   2.0024   2.6134
 LN0  H11  H  HCH3  0   0.260   0.7902   3.3815   2.2187
 LN0  H12  H  HCH3  0   0.270   0.1526   1.9500   3.0533
 LN0  H13  H  HCH2  0   0.254  -2.8170   1.0776  -0.8841
 LN0  H14  H  HCH2  0   0.243  -3.5030  -0.1602  -1.9216
 LN0  H15  H  HCH1  0   0.231  -4.7149   0.9706   0.6240
 LN0  H16  H  HNH1  0   0.405  -0.3024  -0.8691  -0.6713
 LN0  H18  H  HCH1  0   0.243   1.5930  -2.1477  -0.5653
 LN0  H19  H  HCH3  0   0.227  -9.1688   1.8647  -1.1040
 LN0  H20  H  HCH3  0   0.217  -7.8395   2.7251  -1.8762
 LN0  H21  H  HCH3  0   0.216  -8.3163   1.1346  -2.4609
 LN0  H22  H  HCH2  0   0.213  -7.1162   1.7041   0.3044
 LN0  H23  H  HCH2  0   0.219  -7.5923   0.1235  -0.2745
 LN0  H24  H  HCH2  0   0.221  -5.4581   1.8811  -1.5751
 LN0  H25  H  HCH2  0   0.209  -5.8917   0.2674  -2.0988
 LN0  H26  H  HCH3  0   0.233  -2.7478  -3.1706   1.4839
 LN0  H27  H  HCH3  0   0.234  -4.4907  -3.2616   1.6902
 LN0  H28  H  HCH3  0   0.196  -3.7753  -3.5707   0.0995
 LN0  H29  H  HOH1  0   0.457   2.8086  -3.0135   1.2629
 LN0  H30  H  HCH1  0   0.223   3.4949  -1.3785  -1.7903
 LN0  H31  H  HOH1  0   0.457   4.9092  -3.1730  -1.1808
 LN0  H32  H  HCH1  0   0.249   4.9449  -1.2296   0.8869
 LN0  H33  H  HOH1  0   0.462   6.6427  -0.5687  -0.4447
 LN0  C10  C  C     0   0.564  -1.6317  -0.4302   0.8046
 LN0  C17  C  CH2   0  -0.426  -7.2003   1.0919  -0.5990
 LN0  O9   O  O     0  -0.480  -1.8254   0.1048   1.8837

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
 LN0  C6   S1   single  1.808  0.020  1.808
 LN0  S1   C5   single  1.827  0.020  1.827
 LN0  O8   C8   double  1.208  0.020  1.208
 LN0  O4   C1   single  1.403  0.020  1.403
 LN0  C5   C1   single  1.536  0.020  1.536
 LN0  C5   O5   single  1.399  0.020  1.399
 LN0  C8   C9   single  1.495  0.020  1.495
 LN0  C8   C7   single  1.537  0.020  1.537
 LN0  C1   C2   single  1.524  0.020  1.524
 LN0  O5   C4   single  1.411  0.020  1.411
 LN0  C4   C7   single  1.530  0.020  1.530
 LN0  C4   C3   single  1.524  0.020  1.524
 LN0  C2   C3   single  1.526  0.020  1.526
 LN0  C2   O6   single  1.406  0.020  1.406
 LN0  C7   N1   single  1.439  0.020  1.439
 LN0  C3   O7   single  1.403  0.020  1.403
 LN0  N1   C10  single  1.347  0.020  1.347
 LN0  C10  C11  single  1.520  0.020  1.520
 LN0  C10  O9   double  1.220  0.020  1.220
 LN0  C11  C12  single  1.545  0.020  1.545
 LN0  C11  N2   single  1.446  0.020  1.446
 LN0  C15  N2   single  1.439  0.020  1.439
 LN0  C12  C13  single  1.530  0.020  1.530
 LN0  C18  C17  single  1.523  0.020  1.523
 LN0  N2   C14  single  1.447  0.020  1.447
 LN0  C16  C13  single  1.520  0.020  1.520
 LN0  C16  C17  single  1.524  0.020  1.524
 LN0  C14  C13  single  1.522  0.020  1.522
 LN0  C4   H1   single  0.970  0.020  1.090
 LN0  C14  H2   single  0.970  0.020  1.090
 LN0  C14  H3   single  0.970  0.020  1.090
 LN0  C5   H4   single  0.970  0.020  1.090
 LN0  C6   H5   single  0.970  0.020  1.090
 LN0  C6   H6   single  0.970  0.020  1.090
 LN0  C6   H7   single  0.970  0.020  1.090
 LN0  C11  H8   single  0.970  0.020  1.090
 LN0  C7   H9   single  0.970  0.020  1.090
 LN0  C9   H10  single  0.970  0.020  1.090
 LN0  C9   H11  single  0.970  0.020  1.090
 LN0  C9   H12  single  0.970  0.020  1.090
 LN0  C12  H13  single  0.970  0.020  1.090
 LN0  C12  H14  single  0.970  0.020  1.090
 LN0  C13  H15  single  0.970  0.020  1.090
 LN0  N1   H16  single  0.860  0.020  1.020
 LN0  C3   H18  single  0.970  0.020  1.090
 LN0  C18  H19  single  0.970  0.020  1.090
 LN0  C18  H20  single  0.970  0.020  1.090
 LN0  C18  H21  single  0.970  0.020  1.090
 LN0  C17  H22  single  0.970  0.020  1.090
 LN0  C17  H23  single  0.970  0.020  1.090
 LN0  C16  H24  single  0.970  0.020  1.090
 LN0  C16  H25  single  0.970  0.020  1.090
 LN0  C15  H26  single  0.970  0.020  1.090
 LN0  C15  H27  single  0.970  0.020  1.090
 LN0  C15  H28  single  0.970  0.020  1.090
 LN0  O7   H29  single  0.850  0.020  0.980
 LN0  C2   H30  single  0.970  0.020  1.090
 LN0  O6   H31  single  0.850  0.020  0.980
 LN0  C1   H32  single  0.970  0.020  1.090
 LN0  O4   H33  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
 LN0  H1   C4   O5   109.99  3.000
 LN0  H1   C4   C3   107.81  3.000
 LN0  O5   C4   C3   111.12  3.000
 LN0  H1   C4   C7   108.48  3.000
 LN0  C3   C4   C7   113.47  3.000
 LN0  O5   C4   C7   105.93  3.000
 LN0  H3   C14  H2   107.21  3.000
 LN0  H3   C14  N2   112.85  3.000
 LN0  H2   C14  N2   110.36  3.000
 LN0  H3   C14  C13  109.73  3.000
 LN0  H2   C14  C13  113.56  3.000
 LN0  N2   C14  C13  103.24  3.000
 LN0  H4   C5   S1   107.30  3.000
 LN0  H4   C5   C1   109.91  3.000
 LN0  S1   C5   C1   109.81  3.000
 LN0  H4   C5   O5   105.19  3.000
 LN0  C1   C5   O5   111.10  3.000
 LN0  S1   C5   O5   113.33  3.000
 LN0  H7   C6   H6   109.54  3.000
 LN0  H7   C6   H5   108.52  3.000
 LN0  H6   C6   H5   108.63  3.000
 LN0  H7   C6   S1   110.89  3.000
 LN0  H6   C6   S1   112.01  3.000
 LN0  H5   C6   S1   107.14  3.000
 LN0  H8   C11  N2   112.05  3.000
 LN0  H8   C11  C12  109.47  3.000
 LN0  N2   C11  C12  105.30  3.000
 LN0  H8   C11  C10  108.60  3.000
 LN0  N2   C11  C10  111.15  3.000
 LN0  C12  C11  C10  110.23  3.000
 LN0  H9   C7   N1   109.87  3.000
 LN0  H9   C7   C8   109.08  3.000
 LN0  N1   C7   C8   110.56  3.000
 LN0  H9   C7   C4   109.19  3.000
 LN0  N1   C7   C4   109.08  3.000
 LN0  C8   C7   C4   109.04  3.000
 LN0  O8   C8   C9   123.54  3.000
 LN0  C9   C8   C7   116.69  3.000
 LN0  O8   C8   C7   119.77  3.000
 LN0  H12  C9   H11  109.04  3.000
 LN0  H12  C9   H10  106.75  3.000
 LN0  H11  C9   H10  109.83  3.000
 LN0  H12  C9   C8   108.20  3.000
 LN0  H11  C9   C8   111.73  3.000
 LN0  H10  C9   C8   111.13  3.000
 LN0  H14  C12  H13  106.96  3.000
 LN0  H14  C12  C13  109.65  3.000
 LN0  H13  C12  C13  113.22  3.000
 LN0  H14  C12  C11  109.06  3.000
 LN0  H13  C12  C11  113.31  3.000
 LN0  C13  C12  C11  104.59  3.000
 LN0  H15  C13  C16  109.06  3.000
 LN0  H15  C13  C12  109.30  3.000
 LN0  C16  C13  C12  113.54  3.000
 LN0  H15  C13  C14  108.44  3.000
 LN0  C16  C13  C14  114.87  3.000
 LN0  C12  C13  C14  101.28  3.000
 LN0  H16  N1   C10  118.74  3.000
 LN0  H16  N1   C7   119.40  3.000
 LN0  C10  N1   C7   120.52  3.000
 LN0  C15  N2   C11  115.08  3.000
 LN0  C15  N2   C14  115.85  3.000
 LN0  C11  N2   C14  108.95  3.000
 LN0  H18  C3   C2   107.70  3.000
 LN0  H18  C3   O7   111.30  3.000
 LN0  C2   C3   O7   112.11  3.000
 LN0  H18  C3   C4   108.55  3.000
 LN0  O7   C3   C4   108.71  3.000
 LN0  C2   C3   C4   108.37  3.000
 LN0  H21  C18  H20  107.47  3.000
 LN0  H21  C18  H19  107.62  3.000
 LN0  H20  C18  H19  107.66  3.000
 LN0  H21  C18  C17  111.24  3.000
 LN0  H20  C18  C17  111.10  3.000
 LN0  H19  C18  C17  111.55  3.000
 LN0  H25  C16  H24  106.07  3.000
 LN0  H25  C16  C17  109.51  3.000
 LN0  H24  C16  C17  109.00  3.000
 LN0  H25  C16  C13  109.08  3.000
 LN0  H24  C16  C13  109.02  3.000
 LN0  C17  C16  C13  113.86  3.000
 LN0  H28  C15  H27  107.83  3.000
 LN0  H28  C15  H26  107.66  3.000
 LN0  H27  C15  H26  107.28  3.000
 LN0  H28  C15  N2   113.34  3.000
 LN0  H27  C15  N2   110.09  3.000
 LN0  H26  C15  N2   110.41  3.000
 LN0  C5   O5   C4   115.54  3.000
 LN0  H29  O7   C3   108.20  3.000
 LN0  H30  C2   C1   108.82  3.000
 LN0  H30  C2   O6   110.84  3.000
 LN0  C1   C2   O6   111.76  3.000
 LN0  H30  C2   C3   107.59  3.000
 LN0  O6   C2   C3   107.44  3.000
 LN0  C1   C2   C3   110.31  3.000
 LN0  H31  O6   C2   108.62  3.000
 LN0  H32  C1   O4   111.19  3.000
 LN0  H32  C1   C2   108.35  3.000
 LN0  O4   C1   C2   107.56  3.000
 LN0  H32  C1   C5   106.80  3.000
 LN0  C2   C1   C5   110.71  3.000
 LN0  O4   C1   C5   112.19  3.000
 LN0  H33  O4   C1   109.10  3.000
 LN0  C6   S1   C5    98.93  3.000
 LN0  O9   C10  N1   121.73  3.000
 LN0  O9   C10  C11  123.39  3.000
 LN0  N1   C10  C11  114.82  3.000
 LN0  H23  C17  H22  106.12  3.000
 LN0  H23  C17  C16  109.87  3.000
 LN0  H22  C17  C16  109.27  3.000
 LN0  H23  C17  C18  109.36  3.000
 LN0  H22  C17  C18  109.50  3.000
 LN0  C16  C17  C18  112.51  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
 LN0  CONST_01  C7   N1   C10  C11   180.00   0.0  0
 LN0  CONST_02  H16  N1   C10  C11     0.00   0.0  0
 LN0  CONST_03  O9   C10  N1   C7      0.00   0.0  0
 LN0  Var_01    C13  C14  N2   C11   -36.03  30.0  1
 LN0  Var_02    H26  C15  N2   C14  -174.86  30.0  3
 LN0  Var_03    C18  C17  C16  C13   177.33  30.0  3
 LN0  Var_04    H5   C6   S1   C5    170.28  30.0  3
 LN0  Var_05    H10  C9   C8   C7     48.75  30.0  3
 LN0  Var_06    H19  C18  C17  C16  -179.76  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
 LN0  chir_01  C4   O5   C7   C3   positiv
 LN0  chir_02  C5   S1   O5   C1   negativ
 LN0  chir_03  C11  N2   C10  C12  positiv
 LN0  chir_04  C7   N1   C8   C4   positiv
 LN0  chir_05  C13  C14  C16  C12  positiv
 LN0  chir_06  C3   C4   C2   O7   negativ
 LN0  chir_07  C2   O6   C3   C1   negativ
 LN0  chir_08  C1   O4   C2   C5   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
 LN0  plan-1  C11  0.020
 LN0  plan-1  C7   0.020
 LN0  plan-1  N1   0.020
 LN0  plan-1  H16  0.020
 LN0  plan-1  C10  0.020
 LN0  plan-1  O9   0.020
 LN0  plan-2  C7   0.020
 LN0  plan-2  C8   0.020
 LN0  plan-2  C9   0.020
 LN0  plan-2  O8   0.020

