# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 08:27:54 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: methyl 7-chloro-6,7,8-trideoxy-6-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}-1-thio-L-threo-alpha-D-galacto-octopyranoside
#   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](C)Cl)[C@H]2O[C@H](SC)[C@H](O)[C@@H](O)[C@H]2O
#
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
 CLY  CLY  'methyl 7-chloro-6,7,8-trideoxy-6-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}-1-thio-L-threo-alpha-D-galacto-octopyranoside'  ligand  60  27  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CLY
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
 CLY  O4    O   OH1   0  -0.668   2.3209  -0.5059  -4.6497
 CLY  C1    C   CH1   0  -0.015   1.8022   0.4838  -3.7949
 CLY  C2    C   CH1   0  -0.034   2.2939   0.1823  -2.3703
 CLY  C3    C   CH1   0   0.057   1.6051  -1.0750  -1.8510
 CLY  C4    C   CH1   0  -0.001   0.0711  -0.9990  -1.9491
 CLY  O5    O   O2    0  -0.476  -0.2668  -0.6980  -3.2930
 CLY  C5    C   CH1   0  -0.124   0.2754   0.5012  -3.7997
 CLY  O6    O   OH1   0  -0.647   2.0231   1.2502  -1.5024
 CLY  O7    O   OH1   0  -0.654   1.9954  -1.4189  -0.5490
 CLY  S1    S   S2    0  -0.012  -0.3135   0.7074  -5.4913
 CLY  C6    C   CH3   0  -0.772  -2.0481   1.1075  -5.1815
 CLY  C7    C   CH1   0  -0.118  -0.6885  -0.0779  -0.9699
 CLY  C8    C   CH1   0  -0.255  -2.1870  -0.0150  -1.2758
 CLY  C9    C   CH3   0  -0.637  -2.9409   0.9294  -0.3680
 CLY  CL1   CL  CL    0  -0.178  -2.9209  -1.6727  -1.1237
 CLY  N1    N   NH1   0  -0.626  -0.4506  -0.4819   0.3891
 CLY  C10   C   C     0   0.560  -0.0001   0.3466   1.3497
 CLY  O8    O   O     0  -0.484   0.0919   1.5541   1.2150
 CLY  C11   C   CR15  0  -0.172   0.3178  -0.3422   2.6693
 CLY  C12   C   CH2   0  -0.468  -0.8194  -0.1542   3.7009
 CLY  C13   C   CR15  0  -0.235  -0.1451   0.4736   4.9316
 CLY  C14   C   CH2   0  -0.252   1.3182   0.1091   4.7178
 CLY  N2    N   NR5   0  -0.420   1.4830   0.2492   3.2885
 CLY  C15   C   CH3   0  -0.529   2.7385  -0.2291   2.7677
 CLY  C16   C   CH2   0  -0.418  -0.7262   0.0027   6.2550
 CLY  C17   C   CH2   0  -0.428  -0.0868   0.6609   7.4720
 CLY  C18   C   CH3   0  -0.661  -0.6893   0.1800   8.7845
 CLY  HO4   H   HOH1  0   0.461   2.3827  -0.1562  -5.5432
 CLY  H1    H   HCH1  0   0.249   2.1571   1.4825  -4.0827
 CLY  H2    H   HCH1  0   0.237   3.3755  -0.0138  -2.4290
 CLY  H3    H   HCH1  0   0.234   1.8810  -1.8769  -2.5499
 CLY  H4    H   HCH1  0   0.256  -0.3004  -2.0168  -1.7917
 CLY  H5    H   HCH1  0   0.256  -0.0654   1.3725  -3.2263
 CLY  HO6   H   HOH1  0   0.454   2.5390   2.0121  -1.7854
 CLY  HO7   H   HOH1  0   0.454   2.9229  -1.6747  -0.5740
 CLY  H61   H   HCH3  0   0.286  -2.4882   1.3992  -6.1329
 CLY  H62   H   HCH3  0   0.268  -2.5910   0.2468  -4.7971
 CLY  H63   H   HCH3  0   0.265  -2.1378   1.9424  -4.4880
 CLY  H7    H   HCH1  0   0.287  -0.3321   0.9486  -1.0645
 CLY  H8    H   HCH1  0   0.294  -2.3444   0.2654  -2.3154
 CLY  H91   H   HCH3  0   0.252  -3.9950   0.9636  -0.6380
 CLY  H92   H   HCH3  0   0.239  -2.8603   0.6329   0.6767
 CLY  H93   H   HCH3  0   0.242  -2.5347   1.9366  -0.4722
 CLY  HN1   H   HNH1  0   0.388  -0.4266  -1.4708   0.5791
 CLY  H11   H   HCR5  0   0.226   0.4662  -1.4213   2.4922
 CLY  H121  H   HCH2  0   0.240  -1.2513  -1.1246   3.9527
 CLY  H122  H   HCH2  0   0.250  -1.6339   0.4684   3.3271
 CLY  H13   H   HCR5  0   0.230  -0.2374   1.5632   4.8690
 CLY  H141  H   HCH2  0   0.234   2.0144   0.7613   5.2502
 CLY  H142  H   HCH2  0   0.182   1.5031  -0.9240   5.0680
 CLY  H151  H   HCH3  0   0.230   3.5651   0.2951   3.2491
 CLY  H152  H   HCH3  0   0.190   2.8854  -1.3092   2.9260
 CLY  H153  H   HCH3  0   0.242   2.8023  -0.0403   1.6955
 CLY  H161  H   HCH2  0   0.208  -0.6159  -1.0859   6.3265
 CLY  H162  H   HCH2  0   0.222  -1.8039   0.1981   6.2680
 CLY  H171  H   HCH2  0   0.213  -0.1960   1.7470   7.3921
 CLY  H172  H   HCH2  0   0.220   0.9899   0.4659   7.4745
 CLY  H181  H   HCH3  0   0.227  -0.2237   0.6674   9.6418
 CLY  H182  H   HCH3  0   0.216  -1.7603   0.3872   8.8273
 CLY  H183  H   HCH3  0   0.216  -0.5597  -0.8971   8.9055

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
 CLY  O4   C1    single  1.407  0.020  1.407
 CLY  O4   HO4   single  0.850  0.020  0.980
 CLY  C1   C2    single  1.537  0.020  1.537
 CLY  C1   C5    single  1.527  0.020  1.527
 CLY  C1   H1    single  0.970  0.020  1.090
 CLY  C2   C3    single  1.525  0.020  1.525
 CLY  C2   O6    single  1.402  0.020  1.402
 CLY  C2   H2    single  0.970  0.020  1.090
 CLY  C3   C4    single  1.539  0.020  1.539
 CLY  C3   O7    single  1.402  0.020  1.402
 CLY  C3   H3    single  0.970  0.020  1.090
 CLY  C4   O5    single  1.418  0.020  1.418
 CLY  C4   C7    single  1.544  0.020  1.544
 CLY  C4   H4    single  0.970  0.020  1.090
 CLY  O5   C5    single  1.410  0.020  1.410
 CLY  C5   S1    single  1.803  0.020  1.803
 CLY  C5   H5    single  0.970  0.020  1.090
 CLY  O6   HO6   single  0.850  0.020  0.980
 CLY  O7   HO7   single  0.850  0.020  0.980
 CLY  S1   C6    single  1.807  0.020  1.807
 CLY  C6   H61   single  0.970  0.020  1.090
 CLY  C6   H62   single  0.970  0.020  1.090
 CLY  C6   H63   single  0.970  0.020  1.090
 CLY  C7   C8    single  1.531  0.020  1.531
 CLY  C7   N1    single  1.438  0.020  1.438
 CLY  C7   H7    single  0.970  0.020  1.090
 CLY  C8   C9    single  1.511  0.020  1.511
 CLY  C8   CL1   single  1.819  0.020  1.819
 CLY  C8   H8    single  0.970  0.020  1.090
 CLY  C9   H91   single  0.970  0.020  1.090
 CLY  C9   H92   single  0.970  0.020  1.090
 CLY  C9   H93   single  0.970  0.020  1.090
 CLY  N1   C10   single  1.346  0.020  1.346
 CLY  N1   HN1   single  0.860  0.020  1.020
 CLY  C10  O8    double  1.218  0.020  1.218
 CLY  C10  C11   single  1.522  0.020  1.522
 CLY  C11  C12   single  1.547  0.020  1.547
 CLY  C11  N2    single  1.446  0.020  1.446
 CLY  C11  H11   single  0.970  0.020  1.090
 CLY  C12  C13   single  1.537  0.020  1.537
 CLY  C12  H121  single  0.970  0.020  1.090
 CLY  C12  H122  single  0.970  0.020  1.090
 CLY  C13  C14   single  1.523  0.020  1.523
 CLY  C13  C16   single  1.520  0.020  1.520
 CLY  C13  H13   single  0.970  0.020  1.090
 CLY  C14  N2    single  1.446  0.020  1.446
 CLY  C14  H141  single  0.970  0.020  1.090
 CLY  C14  H142  single  0.970  0.020  1.090
 CLY  N2   C15   single  1.441  0.020  1.441
 CLY  C15  H151  single  0.970  0.020  1.090
 CLY  C15  H152  single  0.970  0.020  1.090
 CLY  C15  H153  single  0.970  0.020  1.090
 CLY  C16  C17   single  1.524  0.020  1.524
 CLY  C16  H161  single  0.970  0.020  1.090
 CLY  C16  H162  single  0.970  0.020  1.090
 CLY  C17  C18   single  1.522  0.020  1.522
 CLY  C17  H171  single  0.970  0.020  1.090
 CLY  C17  H172  single  0.970  0.020  1.090
 CLY  C18  H181  single  0.970  0.020  1.090
 CLY  C18  H182  single  0.970  0.020  1.090
 CLY  C18  H183  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
 CLY  HO4   O4   C1    109.42  3.000
 CLY  H1    C1   C5    108.17  3.000
 CLY  H1    C1   C2    108.53  3.000
 CLY  C5    C1   C2    108.97  3.000
 CLY  H1    C1   O4    111.19  3.000
 CLY  C5    C1   O4    112.01  3.000
 CLY  C2    C1   O4    107.89  3.000
 CLY  H2    C2   O6    111.00  3.000
 CLY  H2    C2   C3    108.37  3.000
 CLY  O6    C2   C3    109.26  3.000
 CLY  H2    C2   C1    107.45  3.000
 CLY  O6    C2   C1    111.25  3.000
 CLY  C3    C2   C1    109.45  3.000
 CLY  H3    C3   O7    109.98  3.000
 CLY  H3    C3   C4    104.22  3.000
 CLY  O7    C3   C4    110.41  3.000
 CLY  H3    C3   C2    105.77  3.000
 CLY  O7    C3   C2    113.13  3.000
 CLY  C4    C3   C2    112.82  3.000
 CLY  H4    C4   C7    107.25  3.000
 CLY  H4    C4   O5    104.64  3.000
 CLY  C7    C4   O5    110.93  3.000
 CLY  H4    C4   C3    106.45  3.000
 CLY  C7    C4   C3    118.64  3.000
 CLY  O5    C4   C3    107.96  3.000
 CLY  C5    O5   C4    115.43  3.000
 CLY  H5    C5   S1    107.34  3.000
 CLY  H5    C5   O5    111.60  3.000
 CLY  S1    C5   O5    107.98  3.000
 CLY  H5    C5   C1    108.54  3.000
 CLY  S1    C5   C1    109.32  3.000
 CLY  O5    C5   C1    111.94  3.000
 CLY  HO6   O6   C2    108.50  3.000
 CLY  HO7   O7   C3    108.02  3.000
 CLY  C6    S1   C5    100.25  3.000
 CLY  H63   C6   H62   109.90  3.000
 CLY  H63   C6   H61   108.54  3.000
 CLY  H62   C6   H61   108.62  3.000
 CLY  H63   C6   S1    110.98  3.000
 CLY  H62   C6   S1    111.38  3.000
 CLY  H61   C6   S1    107.32  3.000
 CLY  H7    C7   N1    107.00  3.000
 CLY  H7    C7   C8    105.30  3.000
 CLY  N1    C7   C8    111.25  3.000
 CLY  H7    C7   C4    110.22  3.000
 CLY  N1    C7   C4    110.51  3.000
 CLY  C8    C7   C4    112.29  3.000
 CLY  H8    C8   CL1   104.85  3.000
 CLY  H8    C8   C9    109.92  3.000
 CLY  CL1   C8   C9    108.54  3.000
 CLY  H8    C8   C7    110.07  3.000
 CLY  CL1   C8   C7    109.93  3.000
 CLY  C9    C8   C7    113.20  3.000
 CLY  H93   C9   H92   108.39  3.000
 CLY  H93   C9   H91   107.93  3.000
 CLY  H92   C9   H91   108.55  3.000
 CLY  H93   C9   C8    109.50  3.000
 CLY  H92   C9   C8    111.66  3.000
 CLY  H91   C9   C8    110.70  3.000
 CLY  HN1   N1   C10   117.49  3.000
 CLY  HN1   N1   C7    117.27  3.000
 CLY  C10   N1   C7    123.85  3.000
 CLY  C11   C10  O8    121.90  3.000
 CLY  C11   C10  N1    114.21  3.000
 CLY  O8    C10  N1    123.80  3.000
 CLY  H11   C11  N2    111.11  3.000
 CLY  H11   C11  C12   108.95  3.000
 CLY  N2    C11  C12   104.90  3.000
 CLY  H11   C11  C10   109.36  3.000
 CLY  N2    C11  C10   110.76  3.000
 CLY  C12   C11  C10   111.69  3.000
 CLY  H122  C12  H121  106.91  3.000
 CLY  H122  C12  C13   111.63  3.000
 CLY  H121  C12  C13   110.60  3.000
 CLY  H122  C12  C11   112.93  3.000
 CLY  H121  C12  C11   109.68  3.000
 CLY  C13   C12  C11   105.13  3.000
 CLY  H13   C13  C16   109.01  3.000
 CLY  H13   C13  C14   108.12  3.000
 CLY  C16   C13  C14   114.54  3.000
 CLY  H13   C13  C12   108.88  3.000
 CLY  C16   C13  C12   113.75  3.000
 CLY  C14   C13  C12   102.20  3.000
 CLY  H142  C14  H141  107.26  3.000
 CLY  H142  C14  N2    112.61  3.000
 CLY  H141  C14  N2    110.56  3.000
 CLY  H142  C14  C13   109.86  3.000
 CLY  H141  C14  C13   113.64  3.000
 CLY  N2    C14  C13   103.01  3.000
 CLY  C15   N2   C14   115.12  3.000
 CLY  C15   N2   C11   114.31  3.000
 CLY  C14   N2   C11   106.97  3.000
 CLY  H153  C15  H152  107.65  3.000
 CLY  H153  C15  H151  107.84  3.000
 CLY  H152  C15  H151  107.86  3.000
 CLY  H153  C15  N2    110.42  3.000
 CLY  H152  C15  N2    112.94  3.000
 CLY  H151  C15  N2    109.96  3.000
 CLY  H162  C16  H161  105.99  3.000
 CLY  H162  C16  C17   109.04  3.000
 CLY  H161  C16  C17   109.54  3.000
 CLY  H162  C16  C13   109.34  3.000
 CLY  H161  C16  C13   109.01  3.000
 CLY  C17   C16  C13   113.64  3.000
 CLY  H172  C17  H171  105.98  3.000
 CLY  H172  C17  C18   109.35  3.000
 CLY  H171  C17  C18   109.69  3.000
 CLY  H172  C17  C16   109.73  3.000
 CLY  H171  C17  C16   109.17  3.000
 CLY  C18   C17  C16   112.70  3.000
 CLY  H183  C18  H182  107.42  3.000
 CLY  H183  C18  H181  107.64  3.000
 CLY  H182  C18  H181  107.65  3.000
 CLY  H183  C18  C17   111.12  3.000
 CLY  H182  C18  C17   111.24  3.000
 CLY  H181  C18  C17   111.57  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
 CLY  CONST_01  C11   C10  N1   C7    180.00   0.0  0
 CLY  CONST_02  HN1   N1   C10  C11     0.00   0.0  0
 CLY  CONST_03  O8    C10  N1   C7      0.00   0.0  0
 CLY  Var_01    C13   C14  N2   C11   -42.97  30.0  1
 CLY  Var_02    H151  C15  N2   C11   177.35  30.0  3
 CLY  Var_03    C18   C17  C16  C13   179.68  30.0  3
 CLY  Var_04    H61   C6   S1   C5    171.93  30.0  3
 CLY  Var_05    H181  C18  C17  C16  -179.60  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
 CLY  chir_01  C1   O4   C2   C5   positiv
 CLY  chir_02  C2   O6   C1   C3   positiv
 CLY  chir_03  C3   O7   C2   C4   positiv
 CLY  chir_04  C4   O5   C7   C3   positiv
 CLY  chir_05  C5   S1   O5   C1   negativ
 CLY  chir_06  C7   N1   C8   C4   positiv
 CLY  chir_07  C8   CL1  C7   C9   positiv
 CLY  chir_08  C11  N2   C10  C12  positiv
 CLY  chir_09  C13  C16  C14  C12  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
 CLY  plan-1  C7   0.020
 CLY  plan-1  N1   0.020
 CLY  plan-1  C10  0.020
 CLY  plan-1  O8   0.020
 CLY  plan-1  C11  0.020
 CLY  plan-1  HN1  0.020

