# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:42:33 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)N[C@H]1CNC[C@H](O)[C@@H](O)[C@@H]1O
#
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
 8MP  8MP  N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide  ligand  36  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8MP
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
 8MP  C9   C  CH2   0  -0.580   3.6571   0.4030   0.2617
 8MP  N1   N  NH1   0  -0.598  -1.3992  -2.2769   0.2906
 8MP  C10  C  CH2   0  -0.418   4.9164  -0.1839  -0.3548
 8MP  C2   C  CH2   0  -0.332  -0.4308  -1.3297   0.7971
 8MP  N2   N  NH1   0  -0.643   1.2504   0.3599   0.2290
 8MP  C11  C  CH3   0  -0.666   6.1725   0.4478   0.2293
 8MP  C3   C  CH1   0  -0.089  -0.0832  -0.1128  -0.0856
 8MP  C4   C  CH1   0   0.028  -1.0565   1.0392   0.1556
 8MP  O4   O  OH1   0  -0.671  -0.5702   2.1700  -0.5308
 8MP  C5   C  CH1   0   0.021  -2.4985   0.7735  -0.2753
 8MP  O5   O  OH1   0  -0.683  -3.2054   1.9206   0.1446
 8MP  C6   C  CH1   0   0.003  -3.1574  -0.4975   0.2678
 8MP  O6   O  OH1   0  -0.682  -4.5208  -0.3637  -0.0925
 8MP  C7   C  CH2   0  -0.319  -2.5840  -1.7608  -0.3716
 8MP  C8   C  C     0   0.560   2.3690  -0.2008  -0.2629
 8MP  O8   O  O     0  -0.505   2.3447  -1.1226  -1.0678
 8MP  H16  H  HCH2  0   0.262   3.6787   0.2708   1.3490
 8MP  H13  H  HCH2  0   0.260   3.6300   1.4857   0.1016
 8MP  H17  H  HCH2  0   0.223   4.9407  -1.2632  -0.1908
 8MP  H01  H  HCH2  0   0.223   4.9027  -0.0381  -1.4370
 8MP  H03  H  HCH2  0   0.222  -0.7477  -0.9599   1.7793
 8MP  H14  H  HCH2  0   0.260   0.4850  -1.8919   0.9788
 8MP  H04  H  HNH1  0   0.398   1.3464   1.0982   0.9084
 8MP  H19  H  HCH3  0   0.219   6.1948   1.5251   0.0546
 8MP  H18  H  HCH3  0   0.219   6.2311   0.2904   1.3080
 8MP  H20  H  HCH3  0   0.231   7.0720   0.0222  -0.2158
 8MP  H05  H  HCH1  0   0.251  -0.1004  -0.4066  -1.1401
 8MP  H06  H  HCH1  0   0.211  -1.0704   1.2259   1.2432
 8MP  H07  H  HOH1  0   0.450  -1.1879   2.8938  -0.3799
 8MP  H08  H  HCH1  0   0.206  -2.5093   0.6938  -1.3757
 8MP  H09  H  HOH1  0   0.453  -4.1332   1.7958  -0.0822
 8MP  H10  H  HCH1  0   0.224  -3.0514  -0.5441   1.3612
 8MP  H11  H  HOH1  0   0.460  -5.0316  -1.0310   0.3758
 8MP  H12  H  HCH2  0   0.206  -2.4245  -1.5558  -1.4412
 8MP  H15  H  HCH2  0   0.238  -3.3537  -2.5374  -0.3286
 8MP  H1   H  HNH1  0   0.356  -0.9377  -2.9234  -0.3329

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
 8MP  C11  C10  single  1.522  0.020  1.522
 8MP  C10  C9   single  1.520  0.020  1.520
 8MP  C2   N1   single  1.446  0.020  1.446
 8MP  C2   C3   single  1.543  0.020  1.543
 8MP  N1   C7   single  1.452  0.020  1.452
 8MP  C9   C8   single  1.516  0.020  1.516
 8MP  O8   C8   double  1.224  0.020  1.224
 8MP  C8   N2   single  1.344  0.020  1.344
 8MP  N2   C3   single  1.449  0.020  1.449
 8MP  O6   C6   single  1.417  0.020  1.417
 8MP  C3   C4   single  1.527  0.020  1.527
 8MP  C7   C6   single  1.528  0.020  1.528
 8MP  C6   C5   single  1.531  0.020  1.531
 8MP  C4   C5   single  1.528  0.020  1.528
 8MP  C4   O4   single  1.409  0.020  1.409
 8MP  C5   O5   single  1.411  0.020  1.411
 8MP  C9   H16  single  0.970  0.020  1.090
 8MP  C9   H13  single  0.970  0.020  1.090
 8MP  N1   H1   single  0.890  0.020  1.040
 8MP  C10  H17  single  0.970  0.020  1.090
 8MP  C10  H01  single  0.970  0.020  1.090
 8MP  C2   H03  single  0.970  0.020  1.090
 8MP  C2   H14  single  0.970  0.020  1.090
 8MP  N2   H04  single  0.860  0.020  1.020
 8MP  C11  H19  single  0.970  0.020  1.090
 8MP  C11  H18  single  0.970  0.020  1.090
 8MP  C11  H20  single  0.970  0.020  1.090
 8MP  C3   H05  single  0.970  0.020  1.090
 8MP  C4   H06  single  0.970  0.020  1.090
 8MP  O4   H07  single  0.850  0.020  0.980
 8MP  C5   H08  single  0.970  0.020  1.090
 8MP  O5   H09  single  0.850  0.020  0.980
 8MP  C6   H10  single  0.970  0.020  1.090
 8MP  O6   H11  single  0.850  0.020  0.980
 8MP  C7   H12  single  0.970  0.020  1.090
 8MP  C7   H15  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
 8MP  H13  C9   H16  105.36  3.000
 8MP  H13  C9   C8   108.79  3.000
 8MP  H16  C9   C8   108.19  3.000
 8MP  H13  C9   C10  110.06  3.000
 8MP  H16  C9   C10  109.85  3.000
 8MP  C8   C9   C10  114.19  3.000
 8MP  H1   N1   C7   108.59  3.000
 8MP  H1   N1   C2   109.24  3.000
 8MP  C7   N1   C2   118.25  3.000
 8MP  H01  C10  H17  106.32  3.000
 8MP  H01  C10  C11  109.58  3.000
 8MP  H17  C10  C11  109.52  3.000
 8MP  H01  C10  C9   109.87  3.000
 8MP  H17  C10  C9   109.83  3.000
 8MP  C11  C10  C9   111.57  3.000
 8MP  H14  C2   H03  105.52  3.000
 8MP  H14  C2   C3   108.23  3.000
 8MP  H03  C2   C3   108.16  3.000
 8MP  H14  C2   N1   106.45  3.000
 8MP  H03  C2   N1   109.94  3.000
 8MP  C3   C2   N1   117.84  3.000
 8MP  H04  N2   C8   118.22  3.000
 8MP  H04  N2   C3   118.21  3.000
 8MP  C8   N2   C3   123.37  3.000
 8MP  H20  C11  H18  107.63  3.000
 8MP  H20  C11  H19  107.64  3.000
 8MP  H18  C11  H19  107.41  3.000
 8MP  H20  C11  C10  111.23  3.000
 8MP  H18  C11  C10  111.32  3.000
 8MP  H19  C11  C10  111.41  3.000
 8MP  H05  C3   C4   110.15  3.000
 8MP  H05  C3   N2   108.12  3.000
 8MP  C4   C3   N2   107.82  3.000
 8MP  H05  C3   C2   109.62  3.000
 8MP  C4   C3   C2   111.16  3.000
 8MP  N2   C3   C2   109.90  3.000
 8MP  H06  C4   C5   107.18  3.000
 8MP  H06  C4   O4   110.40  3.000
 8MP  C5   C4   O4   109.13  3.000
 8MP  H06  C4   C3   106.93  3.000
 8MP  O4   C4   C3   107.96  3.000
 8MP  C5   C4   C3   115.19  3.000
 8MP  H07  O4   C4   107.77  3.000
 8MP  H08  C5   C6   106.83  3.000
 8MP  H08  C5   O5   110.52  3.000
 8MP  C6   C5   O5   110.71  3.000
 8MP  H08  C5   C4   107.64  3.000
 8MP  O5   C5   C4   104.32  3.000
 8MP  C6   C5   C4   116.76  3.000
 8MP  H09  O5   C5   107.88  3.000
 8MP  H10  C6   C7   110.18  3.000
 8MP  H10  C6   O6   110.47  3.000
 8MP  C7   C6   O6   109.45  3.000
 8MP  H10  C6   C5   110.28  3.000
 8MP  C7   C6   C5   112.12  3.000
 8MP  O6   C6   C5   104.21  3.000
 8MP  H11  O6   C6   108.77  3.000
 8MP  H15  C7   H12  105.80  3.000
 8MP  H15  C7   C6   107.85  3.000
 8MP  H12  C7   C6   107.89  3.000
 8MP  H15  C7   N1   107.69  3.000
 8MP  H12  C7   N1   113.02  3.000
 8MP  C6   C7   N1   114.16  3.000
 8MP  O8   C8   N2   122.56  3.000
 8MP  N2   C8   C9   114.47  3.000
 8MP  O8   C8   C9   122.98  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
 8MP  CONST_01  C3   N2   C8   C9    180.00   0.0  0
 8MP  CONST_02  O8   C8   N2   C3      0.00   0.0  0
 8MP  CONST_03  H04  N2   C8   C9      0.00   0.0  0
 8MP  Var_01    O8   C8   C9   C10     3.16  30.0  3
 8MP  Var_02    C8   C9   C10  C11  -179.09  30.0  3
 8MP  Var_03    H19  C11  C10  C9    -59.96  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
 8MP  chir_01  C3  C2  N2  C4  positiv
 8MP  chir_02  C4  O4  C3  C5  positiv
 8MP  chir_03  C5  O5  C4  C6  negativ
 8MP  chir_04  C6  O6  C5  C7  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
 8MP  plan-1  C9   0.020
 8MP  plan-1  N2   0.020
 8MP  plan-1  C3   0.020
 8MP  plan-1  C8   0.020
 8MP  plan-1  O8   0.020
 8MP  plan-1  H04  0.020

