# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:43:55 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: (1~{S},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-5-(octylamino)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCN[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@H]1CO
#
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
 N0T  N0T  (1~{S},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-5-(octylamino)cyclopentane-1,2,3-triol  ligand  48  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N0T
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
 N0T  C4   C  CR15  0  -0.061  63.5748  28.2250  33.5329
 N0T  C5   C  CR15  0  -0.326  63.1717  29.0828  34.7634
 N0T  C6   C  CR15  0   0.011  61.6404  28.8449  34.9655
 N0T  C7   C  CH3   0  -0.660  72.4803  32.5177  33.5063
 N0T  C8   C  CH2   0  -0.157  63.9786  28.7462  36.0063
 N0T  C2   C  CR15  0   0.027  61.2252  28.1033  33.6906
 N0T  C3   C  CR15  0   0.013  62.4338  27.2299  33.3954
 N0T  N7   N  NH1   0  -0.620  64.8678  27.5852  33.6505
 N0T  O9   O  OH1   0  -0.682  63.4488  29.5031  37.0866
 N0T  O10  O  OH1   0  -0.677  61.3289  28.0233  36.0652
 N0T  O11  O  OH1   0  -0.670  60.0592  27.3335  33.7812
 N0T  O12  O  OH1   0  -0.673  62.4471  26.6427  32.1190
 N0T  C16  C  CH2   0  -0.434  67.3094  27.8602  33.7049
 N0T  C17  C  CH2   0  -0.424  68.4969  28.7001  33.2518
 N0T  C18  C  CH2   0  -0.421  69.8283  28.1686  33.7705
 N0T  C19  C  CH2   0  -0.420  71.0532  28.8967  33.2244
 N0T  C20  C  CH2   0  -0.412  71.1270  30.3722  33.6016
 N0T  C1   C  CH2   0  -0.418  72.4158  31.0414  33.1396
 N0T  H1   H  HCR5  0   0.217  63.5315  28.8733  32.6408
 N0T  H2   H  HCR5  0   0.247  63.3327  30.1404  34.5390
 N0T  H3   H  HCR5  0   0.212  61.1170  29.8058  35.0505
 N0T  H4   H  HCH3  0   0.225  73.4093  32.9767  33.1654
 N0T  H5   H  HCH3  0   0.215  71.6536  33.0721  33.0577
 N0T  H6   H  HCH3  0   0.215  72.4206  32.6581  34.5873
 N0T  H7   H  HCH2  0   0.203  63.9376  27.6725  36.2152
 N0T  H8   H  HCH2  0   0.225  65.0323  28.9939  35.8466
 N0T  H9   H  HCH2  0   0.220  65.8427  29.4155  33.7824
 N0T  H10  H  HCH2  0   0.201  65.9869  28.6731  32.2033
 N0T  H11  H  HCR5  0   0.207  61.1458  28.8474  32.8825
 N0T  H12  H  HCR5  0   0.209  62.5253  26.4654  34.1826
 N0T  H13  H  HNH1  0   0.344  64.8869  26.7693  33.0494
 N0T  H15  H  HOH1  0   0.460  63.9287  29.2618  37.8845
 N0T  H16  H  HOH1  0   0.448  61.7142  28.4502  36.8416
 N0T  H17  H  HOH1  0   0.452  59.3034  27.9235  33.8565
 N0T  H18  H  HOH1  0   0.453  61.7916  25.9391  32.0989
 N0T  H19  H  HCH2  0   0.211  67.4099  26.8461  33.3016
 N0T  H20  H  HCH2  0   0.214  67.3179  27.7586  34.7948
 N0T  H21  H  HCH2  0   0.208  68.5216  28.7312  32.1567
 N0T  H22  H  HCH2  0   0.214  68.3533  29.7344  33.5802
 N0T  H23  H  HCH2  0   0.207  69.8360  28.2192  34.8649
 N0T  H24  H  HCH2  0   0.216  69.9076  27.1061  33.5185
 N0T  H25  H  HCH2  0   0.206  71.0759  28.7993  32.1331
 N0T  H26  H  HCH2  0   0.215  71.9541  28.3933  33.5904
 N0T  H27  H  HCH2  0   0.212  70.2746  30.9111  33.1761
 N0T  H28  H  HCH2  0   0.204  71.0366  30.4736  34.6895
 N0T  H29  H  HCH2  0   0.210  72.5137  30.9280  32.0553
 N0T  H30  H  HCH2  0   0.209  73.2718  30.5176  33.5766
 N0T  C15  C  CH2   0  -0.275  65.9751  28.4512  33.2822

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
 N0T  O12  C3   single  1.405  0.020  1.405
 N0T  C3   C4   single  1.520  0.020  1.520
 N0T  C3   C2   single  1.520  0.020  1.520
 N0T  C17  C16  single  1.523  0.020  1.523
 N0T  C17  C18  single  1.524  0.020  1.524
 N0T  C7   C1   single  1.523  0.020  1.523
 N0T  C15  C16  single  1.519  0.020  1.519
 N0T  C15  N7   single  1.453  0.020  1.453
 N0T  C20  C19  single  1.525  0.020  1.525
 N0T  C20  C1   single  1.524  0.020  1.524
 N0T  C4   N7   single  1.447  0.020  1.447
 N0T  C4   C5   single  1.553  0.020  1.553
 N0T  C19  C18  single  1.526  0.020  1.526
 N0T  C2   O11  single  1.400  0.020  1.400
 N0T  C2   C6   single  1.532  0.020  1.532
 N0T  C5   C6   single  1.563  0.020  1.563
 N0T  C5   C8   single  1.520  0.020  1.520
 N0T  C6   O10  single  1.408  0.020  1.408
 N0T  C8   O9   single  1.421  0.020  1.421
 N0T  C4   H1   single  0.970  0.020  1.090
 N0T  C5   H2   single  0.970  0.020  1.090
 N0T  C6   H3   single  0.970  0.020  1.090
 N0T  C7   H4   single  0.970  0.020  1.090
 N0T  C7   H5   single  0.970  0.020  1.090
 N0T  C7   H6   single  0.970  0.020  1.090
 N0T  C8   H7   single  0.970  0.020  1.090
 N0T  C8   H8   single  0.970  0.020  1.090
 N0T  C15  H9   single  0.970  0.020  1.090
 N0T  C15  H10  single  0.970  0.020  1.090
 N0T  C2   H11  single  0.970  0.020  1.090
 N0T  C3   H12  single  0.970  0.020  1.090
 N0T  N7   H13  single  0.890  0.020  1.040
 N0T  O9   H15  single  0.850  0.020  0.980
 N0T  O10  H16  single  0.850  0.020  0.980
 N0T  O11  H17  single  0.850  0.020  0.980
 N0T  O12  H18  single  0.850  0.020  0.980
 N0T  C16  H19  single  0.970  0.020  1.090
 N0T  C16  H20  single  0.970  0.020  1.090
 N0T  C17  H21  single  0.970  0.020  1.090
 N0T  C17  H22  single  0.970  0.020  1.090
 N0T  C18  H23  single  0.970  0.020  1.090
 N0T  C18  H24  single  0.970  0.020  1.090
 N0T  C19  H25  single  0.970  0.020  1.090
 N0T  C19  H26  single  0.970  0.020  1.090
 N0T  C20  H27  single  0.970  0.020  1.090
 N0T  C20  H28  single  0.970  0.020  1.090
 N0T  C1   H29  single  0.970  0.020  1.090
 N0T  C1   H30  single  0.970  0.020  1.090

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
 N0T  H1   C4   N7   111.13  3.000
 N0T  H1   C4   C3   106.38  3.000
 N0T  N7   C4   C3   112.86  3.000
 N0T  H1   C4   C5   107.80  3.000
 N0T  N7   C4   C5   114.31  3.000
 N0T  C3   C4   C5   103.79  3.000
 N0T  H2   C5   C8   107.70  3.000
 N0T  H2   C5   C6   108.55  3.000
 N0T  C8   C5   C6   112.38  3.000
 N0T  H2   C5   C4   109.48  3.000
 N0T  C8   C5   C4   112.82  3.000
 N0T  C6   C5   C4   105.83  3.000
 N0T  H3   C6   O10  110.19  3.000
 N0T  H3   C6   C2   111.04  3.000
 N0T  O10  C6   C2   107.91  3.000
 N0T  H3   C6   C5   110.12  3.000
 N0T  O10  C6   C5   114.00  3.000
 N0T  C2   C6   C5   103.39  3.000
 N0T  H6   C7   H5   107.47  3.000
 N0T  H6   C7   H4   107.57  3.000
 N0T  H5   C7   H4   107.63  3.000
 N0T  H6   C7   C1   111.15  3.000
 N0T  H5   C7   C1   111.18  3.000
 N0T  H4   C7   C1   111.64  3.000
 N0T  H8   C8   H7   106.62  3.000
 N0T  H8   C8   O9   110.45  3.000
 N0T  H7   C8   O9   111.31  3.000
 N0T  H8   C8   C5   109.99  3.000
 N0T  H7   C8   C5   110.70  3.000
 N0T  O9   C8   C5   107.80  3.000
 N0T  H11  C2   O11  111.04  3.000
 N0T  H11  C2   C3   107.64  3.000
 N0T  O11  C2   C3   111.03  3.000
 N0T  H11  C2   C6   107.64  3.000
 N0T  O11  C2   C6   115.97  3.000
 N0T  C3   C2   C6   102.96  3.000
 N0T  H12  C3   O12  111.01  3.000
 N0T  H12  C3   C2   109.03  3.000
 N0T  O12  C3   C2   115.09  3.000
 N0T  H12  C3   C4   109.12  3.000
 N0T  C2   C3   C4   101.72  3.000
 N0T  O12  C3   C4   110.40  3.000
 N0T  H13  N7   C15  108.37  3.000
 N0T  H13  N7   C4   108.93  3.000
 N0T  C15  N7   C4   113.37  3.000
 N0T  H15  O9   C8   108.11  3.000
 N0T  H16  O10  C6   106.36  3.000
 N0T  H17  O11  C2   108.79  3.000
 N0T  H18  O12  C3   108.56  3.000
 N0T  H20  C16  H19  106.26  3.000
 N0T  H20  C16  C17  109.95  3.000
 N0T  H19  C16  C17  109.22  3.000
 N0T  H20  C16  C15  108.66  3.000
 N0T  H19  C16  C15  109.76  3.000
 N0T  C17  C16  C15  112.79  3.000
 N0T  H22  C17  H21  106.02  3.000
 N0T  H22  C17  C18  109.99  3.000
 N0T  H21  C17  C18  109.29  3.000
 N0T  H22  C17  C16  109.23  3.000
 N0T  H21  C17  C16  109.29  3.000
 N0T  C18  C17  C16  112.79  3.000
 N0T  H24  C18  H23  105.92  3.000
 N0T  H24  C18  C19  108.82  3.000
 N0T  H23  C18  C19  109.26  3.000
 N0T  H24  C18  C17  108.86  3.000
 N0T  H23  C18  C17  109.27  3.000
 N0T  C19  C18  C17  114.38  3.000
 N0T  H26  C19  H25  105.96  3.000
 N0T  H26  C19  C20  108.81  3.000
 N0T  H25  C19  C20  109.36  3.000
 N0T  H26  C19  C18  108.74  3.000
 N0T  H25  C19  C18  109.30  3.000
 N0T  C20  C19  C18  114.33  3.000
 N0T  H28  C20  H27  106.02  3.000
 N0T  H28  C20  C1   109.26  3.000
 N0T  H27  C20  C1   108.94  3.000
 N0T  H28  C20  C19  109.33  3.000
 N0T  H27  C20  C19  110.04  3.000
 N0T  C1   C20  C19  113.01  3.000
 N0T  H30  C1   H29  106.02  3.000
 N0T  H30  C1   C20  109.28  3.000
 N0T  H29  C1   C20  109.29  3.000
 N0T  H30  C1   C7   109.56  3.000
 N0T  H29  C1   C7   109.59  3.000
 N0T  C20  C1   C7   112.87  3.000
 N0T  H10  C15  H9   105.75  3.000
 N0T  H10  C15  C16  109.97  3.000
 N0T  H9   C15  C16  108.78  3.000
 N0T  H10  C15  N7   112.11  3.000
 N0T  H9   C15  N7   108.48  3.000
 N0T  C16  C15  N7   111.52  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
 N0T  Var_01  C16  C15  N7   C4    167.45  30.0  1
 N0T  Var_02  C19  C20  C1   C7    179.45  30.0  1
 N0T  Var_03  C18  C17  C16  C15   175.39  30.0  2
 N0T  Var_04  C17  C16  C15  N7    176.21  30.0  3
 N0T  Var_05  C19  C18  C17  C16   174.09  30.0  3
 N0T  Var_06  C20  C19  C18  C17    62.67  30.0  2
 N0T  Var_07  C1   C20  C19  C18   175.25  30.0  1
 N0T  Var_08  H4   C7   C1   C20  -179.92  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
 N0T  chir_01  C4  C3   N7  C5  positiv
 N0T  chir_02  C5  C4   C6  C8  negativ
 N0T  chir_03  C6  O10  C5  C2  negativ
 N0T  chir_04  C2  O11  C6  C3  negativ
 N0T  chir_05  C3  O12  C2  C4  positiv

