# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:06:47 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R)-2-[(1R,2S)-2-hydroxycyclopentyl]pent-4-enal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCC[C@@H]1[C@@H](CC=C)C=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
 1NB  1NB  (2R)-2-[(1R,2S)-2-hydroxycyclopentyl]pent-4-enal  ligand  28  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1NB
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
 1NB  C7    C  CH1   0  -0.355  -0.1172   0.0901  -0.6922
 1NB  C8    C  CH1   0  -0.259   0.3258  -0.2902   0.7208
 1NB  C9    C  CH2   0  -0.450   1.7798   0.0581   1.0501
 1NB  O4    O  OH1   0  -0.665  -1.7786  -0.0082   1.8552
 1NB  C26   C  CH2   0  -0.446   1.8371   0.1727   2.5915
 1NB  C29   C  CH1   0   0.082  -0.4433   0.4352   1.8186
 1NB  C27   C  CH2   0  -0.508   0.7152  -0.6624  -1.7531
 1NB  C28   C  CH2   0  -0.477   0.3760   0.1435   3.0736
 1NB  C19   C  C2    0  -0.533   1.1439   0.3591  -3.9942
 1NB  C30   C  C1    0   0.212  -1.5647  -0.2609  -0.9017
 1NB  H7    H  HCH1  0   0.249   0.0089   1.1682  -0.8381
 1NB  H8    H  HCH1  0   0.236   0.1759  -1.3701   0.8612
 1NB  H91   H  HCH2  0   0.229   2.0390   1.0149   0.5884
 1NB  H92   H  HCH2  0   0.244   2.4821  -0.6787   0.6614
 1NB  H17   H  H     0   0.246  -0.6214  -0.6324  -3.5165
 1NB  HO4   H  HOH1  0   0.455  -2.2989   0.6180   2.3669
 1NB  H261  H  HCH2  0   0.232   2.3349   1.0961   2.8883
 1NB  H262  H  HCH2  0   0.235   2.4091  -0.6439   3.0319
 1NB  H29   H  HCH1  0   0.198  -0.3995   1.5147   1.6061
 1NB  H271  H  HCH2  0   0.268   1.7701  -0.4414  -1.5818
 1NB  H272  H  HCH2  0   0.245   0.5911  -1.7401  -1.5977
 1NB  H281  H  HCH2  0   0.236   0.1793   0.8499   3.8818
 1NB  H282  H  HCH2  0   0.225   0.1113  -0.8523   3.4394
 1NB  H191  H  H     0   0.238   0.8373   0.5902  -5.0059
 1NB  H192  H  H     0   0.234   2.1282   0.7007  -3.6947
 1NB  H30   H  H     0   0.175  -1.8062  -1.3166  -0.6744
 1NB  C17   C  C1    0  -0.154   0.3540  -0.3100  -3.1628
 1NB  O5    O  O     0  -0.391  -2.4052   0.4828  -1.3455

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
 1NB  C7   C8    single  1.529  0.020  1.529
 1NB  C7   C27   single  1.544  0.020  1.544
 1NB  C7   C30   single  1.504  0.020  1.504
 1NB  C7   H7    single  0.970  0.020  1.090
 1NB  C8   C9    single  1.531  0.020  1.531
 1NB  C8   C29   single  1.524  0.020  1.524
 1NB  C8   H8    single  0.970  0.020  1.090
 1NB  C9   C26   single  1.547  0.020  1.547
 1NB  C9   H91   single  0.970  0.020  1.090
 1NB  C9   H92   single  0.970  0.020  1.090
 1NB  C17  C27   single  1.497  0.020  1.497
 1NB  C17  C19   double  1.328  0.020  1.328
 1NB  C17  H17   single  0.930  0.020  1.080
 1NB  O5   C30   double  1.207  0.020  1.207
 1NB  O4   C29   single  1.407  0.020  1.407
 1NB  O4   HO4   single  0.850  0.020  0.980
 1NB  C26  C28   single  1.539  0.020  1.539
 1NB  C26  H261  single  0.970  0.020  1.090
 1NB  C26  H262  single  0.970  0.020  1.090
 1NB  C29  C28   single  1.527  0.020  1.527
 1NB  C29  H29   single  0.970  0.020  1.090
 1NB  C27  H271  single  0.970  0.020  1.090
 1NB  C27  H272  single  0.970  0.020  1.090
 1NB  C28  H281  single  0.970  0.020  1.090
 1NB  C28  H282  single  0.970  0.020  1.090
 1NB  C19  H191  single  0.930  0.020  1.080
 1NB  C19  H192  single  0.930  0.020  1.080
 1NB  C30  H30   single  0.930  0.020  1.080

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
 1NB  H7    C7   C30   108.78  3.000
 1NB  H7    C7   C27   109.04  3.000
 1NB  C30   C7   C27   108.02  3.000
 1NB  H7    C7   C8    109.55  3.000
 1NB  C30   C7   C8    110.45  3.000
 1NB  C27   C7   C8    110.95  3.000
 1NB  H8    C8   C29   107.87  3.000
 1NB  H8    C8   C9    108.99  3.000
 1NB  C29   C8   C9    102.47  3.000
 1NB  H8    C8   C7    108.84  3.000
 1NB  C29   C8   C7    113.65  3.000
 1NB  C9    C8   C7    114.67  3.000
 1NB  H92   C9   H91   106.76  3.000
 1NB  H92   C9   C26   112.44  3.000
 1NB  H91   C9   C26   110.31  3.000
 1NB  H92   C9   C8    112.43  3.000
 1NB  H91   C9   C8    109.47  3.000
 1NB  C26   C9   C8    105.45  3.000
 1NB  HO4   O4   C29   108.79  3.000
 1NB  H262  C26  H261  106.56  3.000
 1NB  H262  C26  C28   110.94  3.000
 1NB  H261  C26  C28   111.37  3.000
 1NB  H262  C26  C9    111.50  3.000
 1NB  H261  C26  C9    110.55  3.000
 1NB  C28   C26  C9    106.00  3.000
 1NB  H29   C29  C28   108.95  3.000
 1NB  H29   C29  O4    110.58  3.000
 1NB  C28   C29  O4    115.31  3.000
 1NB  H29   C29  C8    107.91  3.000
 1NB  C28   C29  C8    103.32  3.000
 1NB  O4    C29  C8    110.33  3.000
 1NB  H272  C27  H271  106.64  3.000
 1NB  H272  C27  C17   109.73  3.000
 1NB  H271  C27  C17   109.47  3.000
 1NB  H272  C27  C7    108.71  3.000
 1NB  H271  C27  C7    108.34  3.000
 1NB  C17   C27  C7    113.71  3.000
 1NB  H282  C28  H281  107.35  3.000
 1NB  H282  C28  C29   108.61  3.000
 1NB  H281  C28  C29   112.85  3.000
 1NB  H282  C28  C26   110.61  3.000
 1NB  H281  C28  C26   113.01  3.000
 1NB  C29   C28  C26   104.38  3.000
 1NB  H192  C19  H191  116.64  3.000
 1NB  H192  C19  C17   121.73  3.000
 1NB  H191  C19  C17   121.63  3.000
 1NB  H30   C30  O5    120.76  3.000
 1NB  H30   C30  C7    113.83  3.000
 1NB  O5    C30  C7    125.28  3.000
 1NB  H17   C17  C19   118.67  3.000
 1NB  H17   C17  C27   116.95  3.000
 1NB  C19   C17  C27   124.37  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
 1NB  Var_01  C28   C26  C9   C8    -10.12  30.0  1
 1NB  Var_02  C29   C28  C26  C9    -16.40  30.0  1
 1NB  Var_03  C19   C17  C27  C7    111.61  30.0  1
 1NB  Var_04  H191  C19  C17  C27  -180.00   0.0  2

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
 1NB  chir_01  C7   C8   C27  C30  negativ
 1NB  chir_02  C8   C29  C9   C7   positiv
 1NB  chir_03  C29  O4   C8   C28  positiv

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
 1NB  plan-1  C27   0.020
 1NB  plan-1  C19   0.020
 1NB  plan-1  H17   0.020
 1NB  plan-1  H191  0.020
 1NB  plan-1  H192  0.020
 1NB  plan-1  C17   0.020
 1NB  plan-2  C7    0.020
 1NB  plan-2  C30   0.020
 1NB  plan-2  H30   0.020
 1NB  plan-2  O5    0.020

