# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 21:23:48 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,5-dideoxy-2-prop-2-en-1-yl-D-erythro-L-manno-nononic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@@](CC=C)(O[C@H]1[C@H](O)[C@H](O)CO)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
 CNP  CNP  '5-(acetylamino)-2,6-anhydro-3,5-dideoxy-2-prop-2-en-1-yl-D-erythro-L-manno-nononic acid'  D-saccharide  45  23  .  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_CNP
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
 CNP  C1    C  C      0   0.410  -1.9585  -1.1859  -1.5524
 CNP  O1A   O  O      0  -0.608  -3.1604  -1.5207  -1.5634
 CNP  O1B   O  OC    -1  -0.578  -0.9855  -1.8745  -1.8972
 CNP  C2    C  CT     0   0.109  -1.6885   0.2787  -1.1023
 CNP  C12   C  CH2    0  -0.500  -2.0771   1.2060  -2.2612
 CNP  C13   C  C1     0  -0.142  -1.3609   0.9087  -3.5399
 CNP  C14   C  C2     0  -0.544  -1.9622   0.6989  -4.7053
 CNP  C3    C  CH2    0  -0.472  -2.4809   0.6519   0.1487
 CNP  C4    C  CH1    0   0.070  -1.9543  -0.0815   1.3727
 CNP  O4    O  OH1    0  -0.669  -2.6001   0.3196   2.5596
 CNP  C5    C  CH1    0  -0.117  -0.4659   0.2003   1.5379
 CNP  N5    N  NH1    0  -0.630   0.0919  -0.5753   2.6198
 CNP  C10   C  C      0   0.519   0.5875  -0.0615   3.7599
 CNP  O10   O  O      0  -0.504   0.6522   1.1387   3.9884
 CNP  C11   C  CH3    0  -0.781   1.1014  -1.0809   4.7470
 CNP  C6    C  CH1    0   0.035   0.2783  -0.1182   0.2321
 CNP  O6    O  O2     0  -0.518  -0.3152   0.5318  -0.8642
 CNP  C7    C  CH1    0  -0.005   1.7248   0.3780   0.2553
 CNP  O7    O  OH1    0  -0.671   1.7638   1.7861   0.2433
 CNP  C8    C  CH1    0  -0.029   2.5400  -0.2495  -0.8912
 CNP  O8    O  OH1    0  -0.661   2.6717  -1.6390  -0.6811
 CNP  C9    C  CH2    0  -0.158   3.8919   0.4254  -1.0549
 CNP  O9    O  OH1    0  -0.672   4.5814  -0.2024  -2.1129
 CNP  H121  H  HCH2   0   0.239  -3.1563   1.1472  -2.4143
 CNP  H122  H  HCH2   0   0.238  -1.8527   2.2347  -1.9544
 CNP  H13   H  H      0   0.240  -0.2768   0.8881  -3.4936
 CNP  H141  H  H      0   0.229  -1.3980   0.5093  -5.6097
 CNP  H142  H  H      0   0.226  -3.0424   0.7095  -4.7993
 CNP  H31   H  HCH2   0   0.240  -3.5373   0.4222   0.0012
 CNP  H32   H  HCH2   0   0.223  -2.4007   1.7316   0.3197
 CNP  H4    H  HCH1   0   0.196  -2.0852  -1.1643   1.2153
 CNP  HO4   H  HOH1   0   0.450  -3.5347   0.1052   2.4777
 CNP  H5    H  HCH1   0   0.252  -0.3354   1.2567   1.7843
 CNP  HN5   H  HNH1   0   0.394   0.0481  -1.5789   2.5353
 CNP  H111  H  HCH3   0   0.262   0.7119  -0.8570   5.7391
 CNP  H112  H  HCH3   0   0.247   0.8402  -2.1067   4.4938
 CNP  H113  H  HCH3   0   0.267   2.1885  -1.0100   4.8011
 CNP  H6    H  HCH1   0   0.226   0.2767  -1.2048   0.0868
 CNP  H7    H  HCH1   0   0.231   2.1911   0.0652   1.1974
 CNP  HO7   H  HOH1   0   0.441   1.1578   2.0809  -0.4475
 CNP  H8    H  HCH1   0   0.236   1.9802  -0.1472  -1.8266
 CNP  HO8   H  HOH1   0   0.440   3.2120  -1.7767   0.1048
 CNP  H91   H  HCH2   0   0.205   3.7409   1.4910  -1.2526
 CNP  H92   H  HCH2   0   0.184   4.4538   0.3534  -0.1096
 CNP  HO9   H  HOH1   0   0.453   5.4092   0.2678  -2.2433

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
 CNP  C1   O1A   deloc   1.248  0.020  1.248
 CNP  C1   O1B   deloc   1.241  0.020  1.241
 CNP  C1   C2    single  1.556  0.020  1.556
 CNP  C2   C12   single  1.534  0.020  1.534
 CNP  C2   C3    single  1.527  0.020  1.527
 CNP  C2   O6    single  1.417  0.020  1.417
 CNP  C12  C13   single  1.495  0.020  1.495
 CNP  C12  H121  single  0.970  0.020  1.090
 CNP  C12  H122  single  0.970  0.020  1.090
 CNP  C13  C14   double  1.328  0.020  1.328
 CNP  C13  H13   single  0.930  0.020  1.080
 CNP  C14  H141  single  0.930  0.020  1.080
 CNP  C14  H142  single  0.930  0.020  1.080
 CNP  C3   C4    single  1.521  0.020  1.521
 CNP  C3   H31   single  0.970  0.020  1.090
 CNP  C3   H32   single  0.970  0.020  1.090
 CNP  C4   O4    single  1.409  0.020  1.409
 CNP  C4   C5    single  1.524  0.020  1.524
 CNP  C4   H4    single  0.970  0.020  1.090
 CNP  O4   HO4   single  0.850  0.020  0.980
 CNP  C5   N5    single  1.443  0.020  1.443
 CNP  C5   C6    single  1.536  0.020  1.536
 CNP  C5   H5    single  0.970  0.020  1.090
 CNP  N5   C10   single  1.345  0.020  1.345
 CNP  N5   HN5   single  0.860  0.020  1.020
 CNP  C10  O10   double  1.224  0.020  1.224
 CNP  C10  C11   single  1.509  0.020  1.509
 CNP  C11  H111  single  0.970  0.020  1.090
 CNP  C11  H112  single  0.970  0.020  1.090
 CNP  C11  H113  single  0.970  0.020  1.090
 CNP  C6   O6    single  1.406  0.020  1.406
 CNP  C6   C7    single  1.529  0.020  1.529
 CNP  C6   H6    single  0.970  0.020  1.090
 CNP  C7   O7    single  1.409  0.020  1.409
 CNP  C7   C8    single  1.540  0.020  1.540
 CNP  C7   H7    single  0.970  0.020  1.090
 CNP  O7   HO7   single  0.850  0.020  0.980
 CNP  C8   O8    single  1.411  0.020  1.411
 CNP  C8   C9    single  1.520  0.020  1.520
 CNP  C8   H8    single  0.970  0.020  1.090
 CNP  O8   HO8   single  0.850  0.020  0.980
 CNP  C9   O9    single  1.410  0.020  1.410
 CNP  C9   H91   single  0.970  0.020  1.090
 CNP  C9   H92   single  0.970  0.020  1.090
 CNP  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
 CNP  C2    C1   O1B   117.82  3.000
 CNP  C2    C1   O1A   114.98  3.000
 CNP  O1B   C1   O1A   127.15  3.000
 CNP  O6    C2   C3    108.77  3.000
 CNP  O6    C2   C12   105.33  3.000
 CNP  C3    C2   C12   109.86  3.000
 CNP  O6    C2   C1    112.65  3.000
 CNP  C3    C2   C1    112.15  3.000
 CNP  C12   C2   C1    107.85  3.000
 CNP  H122  C12  H121  106.98  3.000
 CNP  H122  C12  C13   109.13  3.000
 CNP  H121  C12  C13   110.05  3.000
 CNP  H122  C12  C2    107.68  3.000
 CNP  H121  C12  C2    108.89  3.000
 CNP  C13   C12  C2    113.86  3.000
 CNP  H13   C13  C14   119.12  3.000
 CNP  H13   C13  C12   116.47  3.000
 CNP  C14   C13  C12   124.40  3.000
 CNP  H142  C14  H141  116.64  3.000
 CNP  H142  C14  C13   121.71  3.000
 CNP  H141  C14  C13   121.65  3.000
 CNP  H32   C3   H31   107.42  3.000
 CNP  H32   C3   C4    108.91  3.000
 CNP  H31   C3   C4    110.03  3.000
 CNP  H32   C3   C2    109.30  3.000
 CNP  H31   C3   C2    109.89  3.000
 CNP  C4    C3   C2    111.20  3.000
 CNP  H4    C4   C5    108.26  3.000
 CNP  H4    C4   O4    110.21  3.000
 CNP  C5    C4   O4    107.68  3.000
 CNP  H4    C4   C3    108.52  3.000
 CNP  C5    C4   C3    109.65  3.000
 CNP  O4    C4   C3    112.44  3.000
 CNP  HO4   O4   C4    108.06  3.000
 CNP  H5    C5   C6    109.53  3.000
 CNP  H5    C5   N5    107.72  3.000
 CNP  C6    C5   N5    109.78  3.000
 CNP  H5    C5   C4    108.66  3.000
 CNP  C6    C5   C4    110.03  3.000
 CNP  N5    C5   C4    111.06  3.000
 CNP  HN5   N5   C10   117.86  3.000
 CNP  HN5   N5   C5    117.09  3.000
 CNP  C10   N5   C5    124.92  3.000
 CNP  C11   C10  O10   121.50  3.000
 CNP  C11   C10  N5    114.95  3.000
 CNP  O10   C10  N5    123.54  3.000
 CNP  H113  C11  H112  108.18  3.000
 CNP  H113  C11  H111  107.33  3.000
 CNP  H112  C11  H111  108.65  3.000
 CNP  H113  C11  C10   109.14  3.000
 CNP  H112  C11  C10   113.75  3.000
 CNP  H111  C11  C10   109.58  3.000
 CNP  H6    C6   C7    108.96  3.000
 CNP  H6    C6   O6    110.75  3.000
 CNP  C7    C6   O6    105.13  3.000
 CNP  H6    C6   C5    108.51  3.000
 CNP  C7    C6   C5    112.21  3.000
 CNP  O6    C6   C5    111.25  3.000
 CNP  C6    O6   C2    117.23  3.000
 CNP  H7    C7   C8    107.35  3.000
 CNP  H7    C7   O7    106.30  3.000
 CNP  C8    C7   O7    112.72  3.000
 CNP  H7    C7   C6    108.82  3.000
 CNP  C8    C7   C6    110.92  3.000
 CNP  O7    C7   C6    110.51  3.000
 CNP  HO7   O7   C7    107.10  3.000
 CNP  H8    C8   C9    108.74  3.000
 CNP  H8    C8   O8    105.48  3.000
 CNP  C9    C8   O8    111.72  3.000
 CNP  H8    C8   C7    109.10  3.000
 CNP  C9    C8   C7    111.72  3.000
 CNP  O8    C8   C7    109.86  3.000
 CNP  HO8   O8   C8    108.33  3.000
 CNP  H92   C9   H91   106.80  3.000
 CNP  H92   C9   O9    111.42  3.000
 CNP  H91   C9   O9    111.43  3.000
 CNP  H92   C9   C8    109.40  3.000
 CNP  H91   C9   C8    109.22  3.000
 CNP  O9    C9   C8    108.54  3.000
 CNP  HO9   O9   C9    107.77  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
 CNP  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 CNP  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 CNP  CONST_03  HN5   N5   C10  O10   180.00   0.0  0
 CNP  Var_01    C14   C13  C12  C2    126.94  30.0  3
 CNP  Var_02    H141  C14  C13  C12   178.57   0.0  2
 CNP  Var_03    H111  C11  C10  N5   -132.53  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
 CNP  chir_01  C2  C12  C3  O6  positiv
 CNP  chir_02  C4  O4   C5  C3  positiv
 CNP  chir_03  C5  N5   C6  C4  negativ
 CNP  chir_04  C6  O6   C5  C7  positiv
 CNP  chir_05  C7  O7   C6  C8  negativ
 CNP  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
 CNP  plan-1  C5    0.020
 CNP  plan-1  N5    0.020
 CNP  plan-1  C10   0.020
 CNP  plan-1  O10   0.020
 CNP  plan-1  C11   0.020
 CNP  plan-1  HN5   0.020
 CNP  plan-2  C1    0.020
 CNP  plan-2  O1A   0.020
 CNP  plan-2  O1B   0.020
 CNP  plan-2  C2    0.020
 CNP  plan-3  C12   0.020
 CNP  plan-3  C13   0.020
 CNP  plan-3  C14   0.020
 CNP  plan-3  H13   0.020
 CNP  plan-3  H141  0.020
 CNP  plan-3  H142  0.020

