# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:26:29 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-D-mannose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](C=O)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 MN9  MN9  2-(acetylamino)-2-deoxy-D-mannose  ligand  30  15  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MN9
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
 MN9  O1    O  O     0  -0.365  -3.1733   1.8246  -0.7148
 MN9  C2    C  CH1   0  -0.240  -1.3248   0.6557   0.2741
 MN9  N2    N  NH1   0  -0.626  -1.7481  -0.4914  -0.4732
 MN9  C7    C  C     0   0.530  -2.6934  -1.3472  -0.0286
 MN9  C     C  C1    0   0.197  -2.2343   1.8455   0.0369
 MN9  O7    O  O     0  -0.495  -3.1742  -1.2721   1.0916
 MN9  C8    C  CH3   0  -0.782  -3.1131  -2.4052  -1.0153
 MN9  C3    C  CH1   0   0.016   0.1428   1.0051  -0.0595
 MN9  O3    O  OH1   0  -0.658   0.5162   2.2254   0.5293
 MN9  C4    C  CH1   0  -0.018   1.0880  -0.1356   0.3424
 MN9  O4    O  OH1   0  -0.661   1.0541  -0.3377   1.7390
 MN9  C5    C  CH1   0  -0.034   2.5221   0.0976  -0.1634
 MN9  C6    C  CH2   0  -0.159   3.4159  -1.0875   0.1714
 MN9  O6    O  OH1   0  -0.668   4.7299  -0.7861  -0.2311
 MN9  O5    O  OH1   0  -0.656   2.5351   0.3884  -1.5403
 MN9  H81C  H  HCH3  0   0.272  -4.1058  -2.1634  -1.3977
 MN9  H82C  H  HCH3  0   0.251  -2.4366  -2.4978  -1.8625
 MN9  H83C  H  HCH3  0   0.266  -3.1821  -3.3686  -0.5132
 MN9  H2    H  HNH1  0   0.403  -1.4921  -0.5341  -1.4476
 MN9  HA    H  HCH1  0   0.291  -1.3901   0.4282   1.3448
 MN9  H3    H  HCH1  0   0.261   0.2190   1.1588  -1.1393
 MN9  HB    H  HOH1  0   0.444   0.4208   2.1583   1.4860
 MN9  H4    H  HCH1  0   0.239   0.7126  -1.0620  -0.1076
 MN9  HC    H  HOH1  0   0.448   1.6724   0.2632   2.1693
 MN9  H5    H  HCH1  0   0.234   2.9247   0.9896   0.3317
 MN9  HD    H  HOH1  0   0.446   2.3058  -0.4096  -2.0295
 MN9  H61C  H  HCH2  0   0.208   3.3597  -1.2944   1.2454
 MN9  H62C  H  HCH2  0   0.192   3.0278  -1.9817  -0.3414
 MN9  H6    H  HOH1  0   0.456   5.2986  -1.5086   0.0485
 MN9  H     H  H     0   0.207  -1.9910   2.7451   0.6233

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
 MN9  C8  C7    single  1.506  0.020  1.506
 MN9  C7  O7    double  1.221  0.020  1.221
 MN9  C7  N2    single  1.350  0.020  1.350
 MN9  N2  C2    single  1.433  0.020  1.433
 MN9  C2  C     single  1.516  0.020  1.516
 MN9  C2  C3    single  1.545  0.020  1.545
 MN9  C   O1    double  1.203  0.020  1.203
 MN9  C3  O3    single  1.405  0.020  1.405
 MN9  C3  C4    single  1.535  0.020  1.535
 MN9  C4  O4    single  1.412  0.020  1.412
 MN9  C4  C5    single  1.539  0.020  1.539
 MN9  C5  O5    single  1.407  0.020  1.407
 MN9  C5  C6    single  1.522  0.020  1.522
 MN9  C6  O6    single  1.407  0.020  1.407
 MN9  C   H     single  0.930  0.020  1.080
 MN9  C8  H81C  single  0.970  0.020  1.090
 MN9  C8  H82C  single  0.970  0.020  1.090
 MN9  C8  H83C  single  0.970  0.020  1.090
 MN9  N2  H2    single  0.860  0.020  1.020
 MN9  C2  HA    single  0.970  0.020  1.090
 MN9  C3  H3    single  0.970  0.020  1.090
 MN9  O3  HB    single  0.850  0.020  0.980
 MN9  C4  H4    single  0.970  0.020  1.090
 MN9  O4  HC    single  0.850  0.020  0.980
 MN9  C5  H5    single  0.970  0.020  1.090
 MN9  O5  HD    single  0.850  0.020  0.980
 MN9  C6  H61C  single  0.970  0.020  1.090
 MN9  C6  H62C  single  0.970  0.020  1.090
 MN9  O6  H6    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
 MN9  HA    C2  C3    108.32  3.000
 MN9  HA    C2  C     106.25  3.000
 MN9  C3    C2  C     111.01  3.000
 MN9  HA    C2  N2    109.00  3.000
 MN9  C3    C2  N2    110.43  3.000
 MN9  C     C2  N2    111.68  3.000
 MN9  H2    N2  C7    117.97  3.000
 MN9  H2    N2  C2    117.57  3.000
 MN9  C7    N2  C2    122.84  3.000
 MN9  C8    C7  O7    122.30  3.000
 MN9  O7    C7  N2    122.59  3.000
 MN9  C8    C7  N2    115.12  3.000
 MN9  H     C   C2    115.17  3.000
 MN9  H     C   O1    121.30  3.000
 MN9  C2    C   O1    123.53  3.000
 MN9  H83C  C8  H82C  108.86  3.000
 MN9  H83C  C8  H81C  107.47  3.000
 MN9  H82C  C8  H81C  108.16  3.000
 MN9  H83C  C8  C7    109.70  3.000
 MN9  H82C  C8  C7    113.36  3.000
 MN9  H81C  C8  C7    109.12  3.000
 MN9  H3    C3  C4    108.67  3.000
 MN9  H3    C3  O3    105.86  3.000
 MN9  C4    C3  O3    111.84  3.000
 MN9  H3    C3  C2    108.13  3.000
 MN9  C4    C3  C2    111.12  3.000
 MN9  O3    C3  C2    110.99  3.000
 MN9  HB    O3  C3    109.21  3.000
 MN9  H4    C4  C5    108.20  3.000
 MN9  H4    C4  O4    106.08  3.000
 MN9  C5    C4  O4    111.67  3.000
 MN9  H4    C4  C3    108.04  3.000
 MN9  C5    C4  C3    112.04  3.000
 MN9  O4    C4  C3    110.53  3.000
 MN9  HC    O4  C4    109.70  3.000
 MN9  H5    C5  O5    105.67  3.000
 MN9  H5    C5  C6    108.57  3.000
 MN9  O5    C5  C6    111.76  3.000
 MN9  H5    C5  C4    108.49  3.000
 MN9  C6    C5  C4    110.93  3.000
 MN9  O5    C5  C4    111.20  3.000
 MN9  H62C  C6  H61C  106.57  3.000
 MN9  H62C  C6  O6    111.71  3.000
 MN9  H61C  C6  O6    111.65  3.000
 MN9  H62C  C6  C5    108.84  3.000
 MN9  H61C  C6  C5    109.44  3.000
 MN9  O6    C6  C5    108.59  3.000
 MN9  H6    O6  C6    107.96  3.000
 MN9  HD    O5  C5    108.86  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
 MN9  CONST_01  C8    C7  N2  C2   180.00   0.0  0
 MN9  CONST_02  O7    C7  N2  C2     0.00   0.0  0
 MN9  CONST_03  H2    N2  C7  O7   180.00   0.0  0
 MN9  Var_01    H81C  C8  C7  N2  -106.44  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
 MN9  chir_01  C2  N2  C   C3  positiv
 MN9  chir_02  C3  O3  C2  C4  positiv
 MN9  chir_03  C4  O4  C3  C5  negativ
 MN9  chir_04  C5  O5  C4  C6  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
 MN9  plan-1  C2  0.020
 MN9  plan-1  N2  0.020
 MN9  plan-1  C7  0.020
 MN9  plan-1  O7  0.020
 MN9  plan-1  C8  0.020
 MN9  plan-1  H2  0.020
 MN9  plan-2  O1  0.020
 MN9  plan-2  C2  0.020
 MN9  plan-2  C   0.020
 MN9  plan-2  H   0.020

