# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:11:18 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-(acetylamino)-3,5-dideoxy-D-erythro-L-manno-nononic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]([C@@H](O)C[C@@H](O)C(O)=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
 HMN  HMN  '5-(acetylamino)-3,5-dideoxy-D-erythro-L-manno-nononic acid'  ligand  41  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HMN
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
 HMN  C1    C  C      0   0.404   0.2584  -0.4509   4.9178
 HMN  O1A   O  O      0  -0.607   0.3538   0.5202   5.7038
 HMN  O1B   O  OC    -1  -0.590  -0.4033  -1.4873   5.0684
 HMN  C2    C  CH1    0  -0.087   1.0612  -0.2932   3.6087
 HMN  O2    O  OH1    0  -0.705   1.8187   0.9008   3.6852
 HMN  C3    C  CH2    0  -0.486   0.1285  -0.2878   2.3970
 HMN  C4    C  CH1    0   0.082   0.8718  -0.0458   1.0860
 HMN  O4    O  OH1    0  -0.706   1.4167   1.2564   1.0248
 HMN  C5    C  CH1    0  -0.164  -0.0415  -0.2230  -0.1306
 HMN  N2    N  NH1    0  -0.627  -1.1268   0.7290  -0.0778
 HMN  C10   C  C      0   0.521  -2.4319   0.4077  -0.0103
 HMN  O10   O  O      0  -0.500  -2.8473  -0.7426  -0.0303
 HMN  C11   C  CH3    0  -0.778  -3.3729   1.5843   0.0806
 HMN  C6    C  CH1    0   0.056   0.7230  -0.0739  -1.4612
 HMN  O6    O  OH1    0  -0.669   1.8633  -0.9064  -1.4924
 HMN  C7    C  CH1    0  -0.024  -0.1747  -0.3351  -2.6769
 HMN  O7    O  OH1    0  -0.664  -0.6723  -1.6573  -2.6727
 HMN  C8    C  CH1    0  -0.026   0.5372  -0.0139  -4.0040
 HMN  O8    O  OH1    0  -0.660   1.0794   1.2871  -3.9939
 HMN  C9    C  CH2    0  -0.158  -0.3993  -0.2171  -5.1854
 HMN  O9    O  OH1    0  -0.671   0.3180   0.0066  -6.3770
 HMN  HC2   H  HCH1   0   0.215   1.7492  -1.1441   3.5114
 HMN  HO2   H  HOH1   0   0.438   1.4825   1.3013   4.5137
 HMN  HC31  H  HCH2   0   0.226  -0.6472   0.4736   2.5299
 HMN  HC32  H  HCH2   0   0.234  -0.3761  -1.2553   2.3518
 HMN  HC4   H  HCH1   0   0.196   1.6677  -0.8029   1.0169
 HMN  HO4   H  HOH1   0   0.450   1.6941   1.4806   1.9275
 HMN  HC5   H  HCH1   0   0.262  -0.4792  -1.2228  -0.0842
 HMN  HN2   H  HNH1   0   0.392  -0.8697   1.7000   0.0069
 HMN  H111  H  HCH3   0   0.264  -3.9916   1.4869   0.9723
 HMN  H112  H  HCH3   0   0.247  -2.8676   2.5478   0.1144
 HMN  H113  H  HCH3   0   0.265  -4.0414   1.5764  -0.7803
 HMN  HC6   H  HCH1   0   0.236   1.0957   0.9504  -1.5289
 HMN  HO6   H  HOH1   0   0.442   1.6059  -1.8005  -1.2431
 HMN  HC7   H  HCH1   0   0.233  -1.0518   0.3180  -2.6060
 HMN  HO7   H  HOH1   0   0.442   0.0253  -2.2573  -2.9589
 HMN  HC8   H  HCH1   0   0.228   1.3933  -0.6898  -4.1136
 HMN  HO8   H  HOH1   0   0.444   0.3549   1.9223  -3.9702
 HMN  HC91  H  HCH2   0   0.204  -0.8158  -1.2292  -5.1510
 HMN  HC92  H  HCH2   0   0.189  -1.2481   0.4781  -5.0877
 HMN  HO9   H  HOH1   0   0.455  -0.2763  -0.1577  -7.1142

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
 HMN  C1   O1A   deloc   1.253  0.020  1.253
 HMN  C1   O1B   deloc   1.239  0.020  1.239
 HMN  C1   C2    single  1.544  0.020  1.544
 HMN  C2   O2    single  1.416  0.020  1.416
 HMN  C2   C3    single  1.529  0.020  1.529
 HMN  C2   HC2   single  0.970  0.020  1.090
 HMN  O2   HO2   single  0.850  0.020  0.980
 HMN  C3   C4    single  1.526  0.020  1.526
 HMN  C3   HC31  single  0.970  0.020  1.090
 HMN  C3   HC32  single  0.970  0.020  1.090
 HMN  C4   O4    single  1.413  0.020  1.413
 HMN  C4   C5    single  1.532  0.020  1.532
 HMN  C4   HC4   single  0.970  0.020  1.090
 HMN  O4   HO4   single  0.850  0.020  0.980
 HMN  C5   N2    single  1.445  0.020  1.445
 HMN  C5   C6    single  1.542  0.020  1.542
 HMN  C5   HC5   single  0.970  0.020  1.090
 HMN  N2   C10   single  1.346  0.020  1.346
 HMN  N2   HN2   single  0.860  0.020  1.020
 HMN  C10  O10   double  1.223  0.020  1.223
 HMN  C10  C11   single  1.509  0.020  1.509
 HMN  C11  H111  single  0.970  0.020  1.090
 HMN  C11  H112  single  0.970  0.020  1.090
 HMN  C11  H113  single  0.970  0.020  1.090
 HMN  C6   O6    single  1.412  0.020  1.412
 HMN  C6   C7    single  1.534  0.020  1.534
 HMN  C6   HC6   single  0.970  0.020  1.090
 HMN  O6   HO6   single  0.850  0.020  0.980
 HMN  C7   O7    single  1.413  0.020  1.413
 HMN  C7   C8    single  1.540  0.020  1.540
 HMN  C7   HC7   single  0.970  0.020  1.090
 HMN  O7   HO7   single  0.850  0.020  0.980
 HMN  C8   O8    single  1.409  0.020  1.409
 HMN  C8   C9    single  1.521  0.020  1.521
 HMN  C8   HC8   single  0.970  0.020  1.090
 HMN  O8   HO8   single  0.850  0.020  0.980
 HMN  C9   O9    single  1.409  0.020  1.409
 HMN  C9   HC91  single  0.970  0.020  1.090
 HMN  C9   HC92  single  0.970  0.020  1.090
 HMN  O9   HO9   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
 HMN  C2    C1   O1B   117.80  3.000
 HMN  C2    C1   O1A   114.41  3.000
 HMN  O1B   C1   O1A   127.79  3.000
 HMN  HC2   C2   C3    108.33  3.000
 HMN  HC2   C2   O2    108.83  3.000
 HMN  C3    C2   O2    111.48  3.000
 HMN  HC2   C2   C1    108.76  3.000
 HMN  C3    C2   C1    110.81  3.000
 HMN  O2    C2   C1    108.57  3.000
 HMN  HO2   O2   C2    101.94  3.000
 HMN  HC32  C3   HC31  107.08  3.000
 HMN  HC32  C3   C4    109.27  3.000
 HMN  HC31  C3   C4    109.81  3.000
 HMN  HC32  C3   C2    108.15  3.000
 HMN  HC31  C3   C2    109.77  3.000
 HMN  C4    C3   C2    112.59  3.000
 HMN  HC4   C4   C5    107.56  3.000
 HMN  HC4   C4   O4    110.63  3.000
 HMN  C5    C4   O4    107.59  3.000
 HMN  HC4   C4   C3    107.28  3.000
 HMN  C5    C4   C3    111.93  3.000
 HMN  O4    C4   C3    111.79  3.000
 HMN  HO4   O4   C4    106.43  3.000
 HMN  HC5   C5   C6    108.90  3.000
 HMN  HC5   C5   N2    107.50  3.000
 HMN  C6    C5   N2    109.90  3.000
 HMN  HC5   C5   C4    108.12  3.000
 HMN  C6    C5   C4    112.25  3.000
 HMN  N2    C5   C4    110.04  3.000
 HMN  HN2   N2   C10   118.23  3.000
 HMN  HN2   N2   C5    116.51  3.000
 HMN  C10   N2   C5    124.96  3.000
 HMN  C11   C10  O10   121.49  3.000
 HMN  C11   C10  N2    114.93  3.000
 HMN  O10   C10  N2    123.57  3.000
 HMN  H113  C11  H112  108.40  3.000
 HMN  H113  C11  H111  107.30  3.000
 HMN  H112  C11  H111  108.49  3.000
 HMN  H113  C11  C10   109.22  3.000
 HMN  H112  C11  C10   113.73  3.000
 HMN  H111  C11  C10   109.49  3.000
 HMN  HC6   C6   C7    108.08  3.000
 HMN  HC6   C6   O6    106.02  3.000
 HMN  C7    C6   O6    110.78  3.000
 HMN  HC6   C6   C5    108.26  3.000
 HMN  C7    C6   C5    112.17  3.000
 HMN  O6    C6   C5    111.25  3.000
 HMN  HO6   O6   C6    109.01  3.000
 HMN  HC7   C7   C8    107.54  3.000
 HMN  HC7   C7   O7    106.00  3.000
 HMN  C8    C7   O7    111.14  3.000
 HMN  HC7   C7   C6    108.40  3.000
 HMN  C8    C7   C6    112.15  3.000
 HMN  O7    C7   C6    111.30  3.000
 HMN  HO7   O7   C7    109.08  3.000
 HMN  HC8   C8   C9    108.71  3.000
 HMN  HC8   C8   O8    105.63  3.000
 HMN  C9    C8   O8    111.45  3.000
 HMN  HC8   C8   C7    108.58  3.000
 HMN  C9    C8   C7    110.91  3.000
 HMN  O8    C8   C7    111.36  3.000
 HMN  HO8   O8   C8    108.62  3.000
 HMN  HC92  C9   HC91  106.71  3.000
 HMN  HC92  C9   O9    111.54  3.000
 HMN  HC91  C9   O9    111.53  3.000
 HMN  HC92  C9   C8    108.74  3.000
 HMN  HC91  C9   C8    109.47  3.000
 HMN  O9    C9   C8    108.80  3.000
 HMN  HO9   O9   C9    107.86  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
 HMN  CONST_01  O10   C10  N2   C5      0.00   0.0  0
 HMN  CONST_02  C11   C10  N2   C5    180.00   0.0  0
 HMN  CONST_03  HN2   N2   C10  O10   180.00   0.0  0
 HMN  Var_01    H111  C11  C10  N2   -123.54  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
 HMN  chir_01  C2  C1  O2  C3  positiv
 HMN  chir_02  C4  O4  C5  C3  positiv
 HMN  chir_03  C5  N2  C6  C4  negativ
 HMN  chir_04  C6  O6  C5  C7  positiv
 HMN  chir_05  C7  O7  C6  C8  negativ
 HMN  chir_06  C8  O8  C7  C9  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
 HMN  plan-1  C5   0.020
 HMN  plan-1  N2   0.020
 HMN  plan-1  C10  0.020
 HMN  plan-1  O10  0.020
 HMN  plan-1  C11  0.020
 HMN  plan-1  HN2  0.020
 HMN  plan-2  C1   0.020
 HMN  plan-2  O1A  0.020
 HMN  plan-2  O1B  0.020
 HMN  plan-2  C2   0.020

