# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 12:14:49 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: methyl 5-(acetylamino)-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CNC(=O)C(N)=O)C(O)=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
 NXD  NXD  'methyl 5-(acetylamino)-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  49  27  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NXD
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
 NXD  C11   C  CH3    0  -0.782  -3.0751   4.1466   1.4967
 NXD  C10   C  C      0   0.522  -2.9498   3.1647   0.3575
 NXD  O10   O  O      0  -0.503  -3.1105   3.5084  -0.8050
 NXD  N5    N  NH1    0  -0.632  -2.6194   1.9126   0.7240
 NXD  C5    C  CH1    0  -0.122  -2.4616   0.8001  -0.1799
 NXD  C4    C  CH1    0   0.069  -3.5923  -0.2088  -0.0121
 NXD  O4    O  OH1    0  -0.666  -4.7957   0.4342  -0.3599
 NXD  C3    C  CH2    0  -0.527  -3.3202  -1.4303  -0.8763
 NXD  C2    C  CT     0   0.435  -1.9701  -2.0443  -0.5302
 NXD  C1    C  C      0   0.345  -1.9622  -2.6964   0.8946
 NXD  O1A   O  OC    -1  -0.574  -0.9803  -2.4823   1.6219
 NXD  O1B   O  O      0  -0.595  -2.9541  -3.4062   1.1449
 NXD  O2    O  O2     0  -0.508  -1.7068  -3.0064  -1.5026
 NXD  CB    C  CH3    0  -0.420  -0.5505  -3.7986  -1.3202
 NXD  O6    O  O2     0  -0.521  -0.9692  -1.0593  -0.6729
 NXD  C6    C  CH1    0   0.029  -1.1068   0.1220   0.0776
 NXD  C7    C  CH1    0  -0.005   0.0665   1.0065  -0.3489
 NXD  O7    O  OH1    0  -0.667   0.1258   1.1266  -1.7491
 NXD  C8    C  CH1    0  -0.019   1.3904   0.4925   0.2406
 NXD  O8    O  OH1    0  -0.659   1.3841   0.6000   1.6482
 NXD  C9    C  CH2    0  -0.281   2.5871   1.2269  -0.3577
 NXD  NAB   N  NH1    0  -0.620   3.8072   0.7880   0.2775
 NXD  CAC   C  C      0   0.442   4.9512   0.5733  -0.3613
 NXD  OAD   O  O      0  -0.481   5.1434   0.7057  -1.5610
 NXD  CAF   C  C      0   0.423   6.0817   0.1177   0.5804
 NXD  OAG   O  O      0  -0.470   5.8939  -0.0035   1.7808
 NXD  NAK   N  NH2    0  -0.783   7.2265  -0.1109  -0.0526
 NXD  H111  H  HCH3   0   0.247  -3.0610   3.6802   2.4802
 NXD  H112  H  HCH3   0   0.267  -2.2513   4.8594   1.4459
 NXD  H113  H  HCH3   0   0.263  -4.0008   4.7109   1.3935
 NXD  HN5   H  HNH1   0   0.396  -2.5387   1.7158   1.7096
 NXD  H5    H  HCH1   0   0.257  -2.4871   1.1889  -1.2003
 NXD  H4    H  HCH1   0   0.200  -3.6200  -0.5197   1.0443
 NXD  HO4   H  HOH1   0   0.451  -5.5214  -0.1721  -0.1799
 NXD  H31   H  HCH2   0   0.233  -3.3160  -1.1300  -1.9294
 NXD  H32   H  HCH2   0   0.248  -4.1094  -2.1711  -0.7420
 NXD  HB1   H  HCH3   0   0.217   0.3569  -3.2015  -1.2092
 NXD  HB2   H  HCH3   0   0.209  -0.6321  -4.4697  -0.4602
 NXD  HB3   H  HCH3   0   0.232  -0.4507  -4.4112  -2.2152
 NXD  H6    H  HCH1   0   0.234  -1.0192  -0.0855   1.1509
 NXD  H7    H  HCH1   0   0.239  -0.0975   2.0188   0.0390
 NXD  HO7   H  HOH1   0   0.444   0.0517   0.2376  -2.1166
 NXD  H8    H  HCH1   0   0.250   1.4964  -0.5756   0.0279
 NXD  HO8   H  HOH1   0   0.446   1.2697   1.5272   1.8884
 NXD  H91   H  HCH2   0   0.261   2.6578   1.0334  -1.4254
 NXD  H92   H  HCH2   0   0.243   2.4675   2.3097  -0.2305
 NXD  HAB   H  HNH1   0   0.403   3.8015   0.6632   1.2799
 NXD  HAK1  H  HNH2   0   0.415   7.3007   0.0152  -1.0483
 NXD  HAK2  H  HNH2   0   0.413   8.0436  -0.4102   0.4541

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
 NXD  C11  C10   single  1.509  0.020  1.509
 NXD  C11  H111  single  0.970  0.020  1.090
 NXD  C11  H112  single  0.970  0.020  1.090
 NXD  C11  H113  single  0.970  0.020  1.090
 NXD  C10  O10   double  1.223  0.020  1.223
 NXD  C10  N5    single  1.346  0.020  1.346
 NXD  N5   C5    single  1.442  0.020  1.442
 NXD  N5   HN5   single  0.860  0.020  1.020
 NXD  C5   C4    single  1.525  0.020  1.525
 NXD  C5   C6    single  1.537  0.020  1.537
 NXD  C5   H5    single  0.970  0.020  1.090
 NXD  C4   O4    single  1.408  0.020  1.408
 NXD  C4   C3    single  1.521  0.020  1.521
 NXD  C4   H4    single  0.970  0.020  1.090
 NXD  O4   HO4   single  0.850  0.020  0.980
 NXD  C3   C2    single  1.523  0.020  1.523
 NXD  C3   H31   single  0.970  0.020  1.090
 NXD  C3   H32   single  0.970  0.020  1.090
 NXD  C2   C1    single  1.567  0.020  1.567
 NXD  C2   O2    single  1.393  0.020  1.393
 NXD  C2   O6    single  1.412  0.020  1.412
 NXD  C1   O1A   deloc   1.241  0.020  1.241
 NXD  C1   O1B   deloc   1.245  0.020  1.245
 NXD  O2   CB    single  1.413  0.020  1.413
 NXD  CB   HB1   single  0.970  0.020  1.090
 NXD  CB   HB2   single  0.970  0.020  1.090
 NXD  CB   HB3   single  0.970  0.020  1.090
 NXD  O6   C6    single  1.406  0.020  1.406
 NXD  C6   C7    single  1.530  0.020  1.530
 NXD  C6   H6    single  0.970  0.020  1.090
 NXD  C7   O7    single  1.407  0.020  1.407
 NXD  C7   C8    single  1.538  0.020  1.538
 NXD  C7   H7    single  0.970  0.020  1.090
 NXD  O7   HO7   single  0.850  0.020  0.980
 NXD  C8   O8    single  1.412  0.020  1.412
 NXD  C8   C9    single  1.526  0.020  1.526
 NXD  C8   H8    single  0.970  0.020  1.090
 NXD  O8   HO8   single  0.850  0.020  0.980
 NXD  C9   NAB   single  1.444  0.020  1.444
 NXD  C9   H91   single  0.970  0.020  1.090
 NXD  C9   H92   single  0.970  0.020  1.090
 NXD  NAB  CAC   single  1.328  0.020  1.328
 NXD  NAB  HAB   single  0.860  0.020  1.020
 NXD  CAC  OAD   double  1.222  0.020  1.222
 NXD  CAC  CAF   single  1.540  0.020  1.540
 NXD  CAF  OAG   double  1.221  0.020  1.221
 NXD  CAF  NAK   single  1.328  0.020  1.328
 NXD  NAK  HAK1  single  0.860  0.020  1.020
 NXD  NAK  HAK2  single  0.860  0.020  1.020

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
 NXD  H113  C11  H112  107.40  3.000
 NXD  H113  C11  H111  108.58  3.000
 NXD  H112  C11  H111  108.20  3.000
 NXD  H113  C11  C10   109.64  3.000
 NXD  H112  C11  C10   109.11  3.000
 NXD  H111  C11  C10   113.71  3.000
 NXD  N5    C10  O10   123.55  3.000
 NXD  N5    C10  C11   114.85  3.000
 NXD  O10   C10  C11   121.58  3.000
 NXD  HN5   N5   C5    116.96  3.000
 NXD  HN5   N5   C10   117.87  3.000
 NXD  C5    N5   C10   125.02  3.000
 NXD  H5    C5   C6    109.53  3.000
 NXD  H5    C5   C4    108.73  3.000
 NXD  C6    C5   C4    110.08  3.000
 NXD  H5    C5   N5    107.96  3.000
 NXD  C6    C5   N5    109.38  3.000
 NXD  C4    C5   N5    111.12  3.000
 NXD  H4    C4   C3    108.83  3.000
 NXD  H4    C4   O4    110.13  3.000
 NXD  C3    C4   O4    112.29  3.000
 NXD  H4    C4   C5    108.12  3.000
 NXD  C3    C4   C5    109.65  3.000
 NXD  O4    C4   C5    107.73  3.000
 NXD  HO4   O4   C4    108.09  3.000
 NXD  H32   C3   H31   107.90  3.000
 NXD  H32   C3   C2    109.86  3.000
 NXD  H31   C3   C2    109.01  3.000
 NXD  H32   C3   C4    110.25  3.000
 NXD  H31   C3   C4    109.08  3.000
 NXD  C2    C3   C4    110.69  3.000
 NXD  O6    C2   O2    106.10  3.000
 NXD  O6    C2   C1    112.25  3.000
 NXD  O2    C2   C1    110.26  3.000
 NXD  O6    C2   C3    108.93  3.000
 NXD  O2    C2   C3    106.71  3.000
 NXD  C1    C2   C3    112.26  3.000
 NXD  O1B   C1   O1A   127.66  3.000
 NXD  O1B   C1   C2    114.58  3.000
 NXD  O1A   C1   C2    117.73  3.000
 NXD  CB    O2   C2    116.85  3.000
 NXD  HB3   CB   HB2   107.92  3.000
 NXD  HB3   CB   HB1   108.36  3.000
 NXD  HB2   CB   HB1   108.52  3.000
 NXD  HB3   CB   O2    106.51  3.000
 NXD  HB2   CB   O2    112.60  3.000
 NXD  HB1   CB   O2    112.74  3.000
 NXD  C6    O6   C2    117.57  3.000
 NXD  H6    C6   C7    108.72  3.000
 NXD  H6    C6   O6    110.83  3.000
 NXD  C7    C6   O6    105.18  3.000
 NXD  H6    C6   C5    108.54  3.000
 NXD  C7    C6   C5    111.97  3.000
 NXD  O6    C6   C5    111.56  3.000
 NXD  H7    C7   C8    107.57  3.000
 NXD  H7    C7   O7    106.24  3.000
 NXD  C8    C7   O7    111.95  3.000
 NXD  H7    C7   C6    108.69  3.000
 NXD  C8    C7   C6    111.10  3.000
 NXD  O7    C7   C6    111.05  3.000
 NXD  HO7   O7   C7    107.29  3.000
 NXD  H8    C8   C9    108.51  3.000
 NXD  H8    C8   O8    105.59  3.000
 NXD  C9    C8   O8    110.96  3.000
 NXD  H8    C8   C7    109.58  3.000
 NXD  C9    C8   C7    111.34  3.000
 NXD  O8    C8   C7    110.67  3.000
 NXD  HO8   O8   C8    108.79  3.000
 NXD  H92   C9   H91   107.26  3.000
 NXD  H92   C9   NAB   109.95  3.000
 NXD  H91   C9   NAB   108.85  3.000
 NXD  H92   C9   C8    110.12  3.000
 NXD  H91   C9   C8    110.51  3.000
 NXD  NAB   C9   C8    110.11  3.000
 NXD  HAB   NAB  CAC   117.54  3.000
 NXD  HAB   NAB  C9    117.99  3.000
 NXD  CAC   NAB  C9    124.43  3.000
 NXD  CAF   CAC  OAD   121.11  3.000
 NXD  CAF   CAC  NAB   112.70  3.000
 NXD  OAD   CAC  NAB   126.18  3.000
 NXD  NAK   CAF  OAG   125.74  3.000
 NXD  NAK   CAF  CAC   113.09  3.000
 NXD  OAG   CAF  CAC   121.17  3.000
 NXD  HAK2  NAK  HAK1  118.38  3.000
 NXD  HAK2  NAK  CAF   120.72  3.000
 NXD  HAK1  NAK  CAF   120.90  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
 NXD  CONST_01  C5    N5   C10  C11  180.00   0.0  0
 NXD  CONST_02  C5    N5   C10  O10    0.00   0.0  0
 NXD  CONST_03  OAD   CAC  NAB  C9     0.00   0.0  0
 NXD  CONST_04  CAF   CAC  NAB  C9   180.00   0.0  0
 NXD  CONST_05  NAK   CAF  CAC  NAB  180.00   0.0  0
 NXD  CONST_06  NAK   CAF  CAC  OAD    0.00   0.0  0
 NXD  CONST_07  HN5   N5   C10  C11    0.00   0.0  0
 NXD  CONST_08  HAK1  NAK  CAF  CAC    0.00   0.0  0
 NXD  CONST_09  HAK2  NAK  CAF  CAC  180.00   0.0  0
 NXD  CONST_10  HAB   NAB  CAC  OAD  180.00   0.0  0
 NXD  Var_01    HB1   CB   O2   C2   -55.50  30.0  3
 NXD  Var_02    CAC   NAB  C9   C8   139.85  30.0  3
 NXD  Var_03    H111  C11  C10  O10  171.02  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
 NXD  chir_01  C5  N5  C4  C6  positiv
 NXD  chir_02  C4  O4  C5  C3  positiv
 NXD  chir_03  C2  O6  C1  C3  negativ
 NXD  chir_04  C6  O6  C5  C7  positiv
 NXD  chir_05  C7  O7  C6  C8  negativ
 NXD  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
 NXD  plan-1  C11   0.020
 NXD  plan-1  C10   0.020
 NXD  plan-1  O10   0.020
 NXD  plan-1  N5    0.020
 NXD  plan-1  C5    0.020
 NXD  plan-1  HN5   0.020
 NXD  plan-2  C9    0.020
 NXD  plan-2  NAB   0.020
 NXD  plan-2  CAC   0.020
 NXD  plan-2  OAD   0.020
 NXD  plan-2  CAF   0.020
 NXD  plan-2  OAG   0.020
 NXD  plan-2  NAK   0.020
 NXD  plan-2  HAB   0.020
 NXD  plan-2  HAK1  0.020
 NXD  plan-2  HAK2  0.020
 NXD  plan-3  C2    0.020
 NXD  plan-3  C1    0.020
 NXD  plan-3  O1A   0.020
 NXD  plan-3  O1B   0.020

