# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:52:50 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: N-[(3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxopiperidin-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)NC1=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
 LTM  LTM  N-[(3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxopiperidin-3-yl]acetamide  saccharide  29  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LTM
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
 LTM  O7    O  O     0  -0.495   3.2487   0.1713   1.4445
 LTM  C7    C  C     0   0.527   3.2278   0.0277   0.2318
 LTM  C8    C  CH3   0  -0.782   4.4876   0.0434  -0.5944
 LTM  N2    N  NH1   0  -0.630   2.0886  -0.1629  -0.4673
 LTM  C2    C  CH1   0  -0.245   0.7801  -0.0903   0.1160
 LTM  C3    C  CH1   0   0.030  -0.0839  -1.2703  -0.3177
 LTM  O3    O  OH1   0  -0.666   0.4369  -2.4830   0.1595
 LTM  C4    C  CH1   0   0.025  -1.4766  -1.1020   0.2710
 LTM  O4    O  OH1   0  -0.666  -2.3173  -2.1762  -0.0541
 LTM  C5    C  CH1   0  -0.102  -2.1211   0.1555  -0.2965
 LTM  C6    C  CH2   0  -0.142  -3.3992   0.5094   0.4476
 LTM  O6    O  OH1   0  -0.672  -3.9614   1.6442  -0.1720
 LTM  N5    N  NH1   0  -0.645  -1.2065   1.2820  -0.2334
 LTM  C1    C  C     0   0.543   0.1337   1.2634  -0.1711
 LTM  O1    O  O     0  -0.479   0.8147   2.2694  -0.2835
 LTM  H81C  H  HCH3  0   0.267   5.2274  -0.6189  -0.1471
 LTM  H82C  H  HCH3  0   0.250   4.3336  -0.2530  -1.6300
 LTM  H83C  H  HCH3  0   0.271   4.9054   1.0509  -0.5872
 LTM  H2    H  HNH1  0   0.404   2.1457  -0.1794  -1.4740
 LTM  HA    H  HCH1  0   0.301   0.9027  -0.1440   1.2027
 LTM  H3    H  HCH1  0   0.229  -0.1661  -1.2803  -1.4161
 LTM  HB    H  HOH1  0   0.459   1.2387  -2.6912  -0.3306
 LTM  H4    H  HCH1  0   0.222  -1.3761  -0.9913   1.3629
 LTM  HC    H  HOH1  0   0.457  -1.9340  -2.9798   0.3127
 LTM  H5    H  HCH1  0   0.257  -2.3724  -0.0446  -1.3466
 LTM  H61C  H  HCH2  0   0.217  -4.0797  -0.3471   0.4140
 LTM  H62C  H  HCH2  0   0.207  -3.1543   0.7008   1.4999
 LTM  HD    H  HNH1  0   0.396  -1.6224   2.1857  -0.4143
 LTM  H6    H  HOH1  0   0.463  -4.6555   1.9894   0.3964

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
 LTM  O7  C7    double  1.221  0.020  1.221
 LTM  C7  C8    single  1.507  0.020  1.507
 LTM  C7  N2    single  1.350  0.020  1.350
 LTM  N2  C2    single  1.435  0.020  1.435
 LTM  C2  C3    single  1.525  0.020  1.525
 LTM  C2  C1    single  1.527  0.020  1.527
 LTM  C3  O3    single  1.403  0.020  1.403
 LTM  C3  C4    single  1.521  0.020  1.521
 LTM  C4  O4    single  1.402  0.020  1.402
 LTM  C4  C5    single  1.523  0.020  1.523
 LTM  C5  C6    single  1.521  0.020  1.521
 LTM  C5  N5    single  1.452  0.020  1.452
 LTM  C6  O6    single  1.410  0.020  1.410
 LTM  N5  C1    single  1.342  0.020  1.342
 LTM  C1  O1    double  1.220  0.020  1.220
 LTM  C8  H81C  single  0.970  0.020  1.090
 LTM  C8  H82C  single  0.970  0.020  1.090
 LTM  C8  H83C  single  0.970  0.020  1.090
 LTM  N2  H2    single  0.860  0.020  1.020
 LTM  C2  HA    single  0.970  0.020  1.090
 LTM  C3  H3    single  0.970  0.020  1.090
 LTM  O3  HB    single  0.850  0.020  0.980
 LTM  C4  H4    single  0.970  0.020  1.090
 LTM  O4  HC    single  0.850  0.020  0.980
 LTM  C5  H5    single  0.970  0.020  1.090
 LTM  C6  H61C  single  0.970  0.020  1.090
 LTM  C6  H62C  single  0.970  0.020  1.090
 LTM  N5  HD    single  0.860  0.020  1.020
 LTM  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
 LTM  N2    C7  C8    115.03  3.000
 LTM  N2    C7  O7    123.04  3.000
 LTM  C8    C7  O7    121.94  3.000
 LTM  H83C  C8  H82C  108.19  3.000
 LTM  H83C  C8  H81C  107.38  3.000
 LTM  H82C  C8  H81C  108.75  3.000
 LTM  H83C  C8  C7    109.04  3.000
 LTM  H82C  C8  C7    113.62  3.000
 LTM  H81C  C8  C7    109.66  3.000
 LTM  H2    N2  C2    117.28  3.000
 LTM  H2    N2  C7    118.13  3.000
 LTM  C2    N2  C7    123.50  3.000
 LTM  HA    C2  C1    106.11  3.000
 LTM  HA    C2  C3    107.92  3.000
 LTM  C1    C2  C3    113.11  3.000
 LTM  HA    C2  N2    107.39  3.000
 LTM  C1    C2  N2    110.76  3.000
 LTM  C3    C2  N2    111.21  3.000
 LTM  H3    C3  C4    108.57  3.000
 LTM  H3    C3  O3    111.04  3.000
 LTM  C4    C3  O3    107.68  3.000
 LTM  H3    C3  C2    109.44  3.000
 LTM  C4    C3  C2    108.84  3.000
 LTM  O3    C3  C2    111.20  3.000
 LTM  HB    O3  C3    108.84  3.000
 LTM  H4    C4  C5    108.95  3.000
 LTM  H4    C4  O4    111.18  3.000
 LTM  C5    C4  O4    107.00  3.000
 LTM  H4    C4  C3    108.12  3.000
 LTM  C5    C4  C3    109.55  3.000
 LTM  O4    C4  C3    111.99  3.000
 LTM  HC    O4  C4    108.20  3.000
 LTM  H5    C5  N5    109.08  3.000
 LTM  H5    C5  C6    108.54  3.000
 LTM  N5    C5  C6    109.12  3.000
 LTM  H5    C5  C4    107.62  3.000
 LTM  N5    C5  C4    110.96  3.000
 LTM  C6    C5  C4    111.44  3.000
 LTM  H62C  C6  H61C  107.74  3.000
 LTM  H62C  C6  O6    111.72  3.000
 LTM  H61C  C6  O6    111.62  3.000
 LTM  H62C  C6  C5    108.80  3.000
 LTM  H61C  C6  C5    108.99  3.000
 LTM  O6    C6  C5    107.90  3.000
 LTM  H6    O6  C6    108.49  3.000
 LTM  HD    N5  C1    115.57  3.000
 LTM  HD    N5  C5    115.24  3.000
 LTM  C1    N5  C5    128.33  3.000
 LTM  O1    C1  N5    122.80  3.000
 LTM  O1    C1  C2    120.79  3.000
 LTM  N5    C1  C2    116.34  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
 LTM  CONST_01  C5    N5  C1  C2    0.00   0.0  0
 LTM  CONST_02  O1    C1  N5  C5  180.00   0.0  0
 LTM  CONST_03  HD    N5  C1  C2  180.00   0.0  0
 LTM  CONST_04  C2    N2  C7  O7    0.00   0.0  0
 LTM  CONST_05  C2    N2  C7  C8  180.00   0.0  0
 LTM  CONST_06  H2    N2  C7  O7  180.00   0.0  0
 LTM  Var_01    H81C  C8  C7  O7   48.85  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
 LTM  chir_01  C2  N2  C3  C1  positiv
 LTM  chir_02  C3  O3  C2  C4  positiv
 LTM  chir_03  C4  O4  C3  C5  negativ
 LTM  chir_04  C5  N5  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
 LTM  plan-1  O7  0.020
 LTM  plan-1  C7  0.020
 LTM  plan-1  C8  0.020
 LTM  plan-1  N2  0.020
 LTM  plan-1  C2  0.020
 LTM  plan-1  H2  0.020
 LTM  plan-2  C2  0.020
 LTM  plan-2  C5  0.020
 LTM  plan-2  N5  0.020
 LTM  plan-2  C1  0.020
 LTM  plan-2  O1  0.020
 LTM  plan-2  HD  0.020

