# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:28:49 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S)-2-amino-1-hydroxyoctadecan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)[C@@H](N)CO
#
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
 VSD  VSD  (2S)-2-amino-1-hydroxyoctadecan-3-one  ligand  58  21  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VSD
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
 VSD  C15  C  CH2   0  -0.576  202.4605  210.1645  214.0282
 VSD  C16  C  C     0   0.394  202.4650  209.1062  215.1056
 VSD  C10  C  CH2   0  -0.420  206.8587  208.0404  209.8621
 VSD  C11  C  CH2   0  -0.420  206.3632  208.5613  211.2078
 VSD  C12  C  CH2   0  -0.415  204.8745  208.8896  211.2440
 VSD  C13  C  CH2   0  -0.415  204.4055  209.3466  212.6185
 VSD  C14  C  CH2   0  -0.421  202.9178  209.6763  212.6612
 VSD  C01  C  CH3   0  -0.659  208.9307  211.0544  198.9896
 VSD  C02  C  CH2   0  -0.417  208.9166  210.0045  200.0917
 VSD  C03  C  CH2   0  -0.404  208.4004  210.5461  201.4186
 VSD  C04  C  CH2   0  -0.409  208.3918  209.5079  202.5330
 VSD  C05  C  CH2   0  -0.409  207.8728  210.0519  203.8576
 VSD  C06  C  CH2   0  -0.410  207.8744  209.0179  204.9761
 VSD  C07  C  CH2   0  -0.409  207.3450  209.5598  206.2974
 VSD  C08  C  CH2   0  -0.408  207.3623  208.5312  207.4207
 VSD  C09  C  CH2   0  -0.416  206.8152  209.0684  208.7372
 VSD  C18  C  CH1   0  -0.222  202.7743  209.5929  216.5122
 VSD  C19  C  CH2   0  -0.138  204.2911  209.7439  216.6286
 VSD  N21  N  NH2   0  -0.794  202.3009  208.6617  217.5105
 VSD  O17  O  O     0  -0.388  202.2131  207.9480  214.8693
 VSD  O20  O  OH1   0  -0.662  204.5730  210.3550  217.8659
 VSD  H1   H  HCH2  0   0.250  203.0463  211.0314  214.3448
 VSD  H2   H  HCH2  0   0.285  201.4251  210.5244  213.9776
 VSD  H3   H  HCH2  0   0.205  206.2721  207.1608  209.5742
 VSD  H4   H  HCH2  0   0.214  207.8896  207.6901  209.9754
 VSD  H5   H  HCH2  0   0.215  206.5752  207.8144  211.9796
 VSD  H6   H  HCH2  0   0.205  206.9374  209.4522  211.4858
 VSD  H7   H  HCH2  0   0.214  204.6415  209.6674  210.5102
 VSD  H8   H  HCH2  0   0.214  204.6357  208.5689  213.3545
 VSD  H9   H  HCH2  0   0.229  202.7002  210.4523  211.9229
 VSD  H10  H  HCH2  0   0.221  202.3335  208.8019  212.3643
 VSD  H11  H  HCH3  0   0.224  209.3075  210.6467  198.0507
 VSD  H12  H  HCH3  0   0.215  207.9282  211.4433  198.8017
 VSD  H13  H  HCH3  0   0.214  209.5651  211.9003  199.2607
 VSD  H14  H  HCH2  0   0.209  208.2995  209.1550  199.7826
 VSD  H15  H  HCH2  0   0.208  209.9274  209.6085  200.2313
 VSD  H16  H  HCH2  0   0.205  209.0141  211.4010  201.7243
 VSD  H17  H  HCH2  0   0.204  207.3864  210.9372  201.2797
 VSD  H18  H  HCH2  0   0.205  207.7802  208.6518  202.2272
 VSD  H19  H  HCH2  0   0.205  208.4795  210.9128  204.1597
 VSD  H20  H  HCH2  0   0.205  207.2742  208.1531  204.6720
 VSD  H21  H  HCH2  0   0.205  207.9371  210.4318  206.5964
 VSD  H22  H  HCH2  0   0.205  206.7810  207.6531  207.1181
 VSD  H23  H  HCH2  0   0.204  207.3895  209.9525  209.0366
 VSD  H24  H  HCH1  0   0.238  202.3424  210.6050  216.5982
 VSD  H25  H  HCH2  0   0.206  204.7425  208.7469  216.5544
 VSD  H26  H  HCH2  0   0.206  204.6752  210.3404  215.7918
 VSD  H27  H  HNH2  0   0.350  202.5663  208.9972  218.4273
 VSD  H28  H  HNH2  0   0.348  201.2894  208.6300  217.5059
 VSD  H30  H  HOH1  0   0.457  205.5183  210.2871  218.0290
 VSD  H29  H  HCH2  0   0.205  209.4067  209.1194  202.6727
 VSD  H31  H  HCH2  0   0.205  206.8552  210.4335  203.7191
 VSD  H32  H  HCH2  0   0.205  208.8937  208.6427  205.1196
 VSD  H33  H  HCH2  0   0.205  206.3214  209.9239  206.1555
 VSD  H34  H  HCH2  0   0.204  208.3884  208.1774  207.5707
 VSD  H35  H  HCH2  0   0.211  205.7885  209.4134  208.5803
 VSD  H36  H  HCH2  0   0.207  204.3037  208.0049  210.9405
 VSD  H37  H  HCH2  0   0.210  204.9771  210.2302  212.9231

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
 VSD  C01  C02  single  1.522  0.020  1.522
 VSD  C02  C03  single  1.523  0.020  1.523
 VSD  C03  C04  single  1.523  0.020  1.523
 VSD  C04  C05  single  1.523  0.020  1.523
 VSD  C05  C06  single  1.523  0.020  1.523
 VSD  C06  C07  single  1.523  0.020  1.523
 VSD  C07  C08  single  1.523  0.020  1.523
 VSD  C08  C09  single  1.523  0.020  1.523
 VSD  C09  C10  single  1.525  0.020  1.525
 VSD  C10  C11  single  1.526  0.020  1.526
 VSD  C11  C12  single  1.525  0.020  1.525
 VSD  C12  C13  single  1.523  0.020  1.523
 VSD  C13  C14  single  1.524  0.020  1.524
 VSD  C14  C15  single  1.522  0.020  1.522
 VSD  C15  C16  single  1.510  0.020  1.510
 VSD  O17  C16  double  1.209  0.020  1.209
 VSD  C16  C18  single  1.520  0.020  1.520
 VSD  C18  N21  single  1.445  0.020  1.445
 VSD  C18  C19  single  1.529  0.020  1.529
 VSD  C19  O20  single  1.408  0.020  1.408
 VSD  C15  H1   single  0.970  0.020  1.090
 VSD  C15  H2   single  0.970  0.020  1.090
 VSD  C10  H3   single  0.970  0.020  1.090
 VSD  C10  H4   single  0.970  0.020  1.090
 VSD  C11  H5   single  0.970  0.020  1.090
 VSD  C11  H6   single  0.970  0.020  1.090
 VSD  C12  H7   single  0.970  0.020  1.090
 VSD  C13  H8   single  0.970  0.020  1.090
 VSD  C14  H9   single  0.970  0.020  1.090
 VSD  C14  H10  single  0.970  0.020  1.090
 VSD  C01  H11  single  0.970  0.020  1.090
 VSD  C01  H12  single  0.970  0.020  1.090
 VSD  C01  H13  single  0.970  0.020  1.090
 VSD  C02  H14  single  0.970  0.020  1.090
 VSD  C02  H15  single  0.970  0.020  1.090
 VSD  C03  H16  single  0.970  0.020  1.090
 VSD  C03  H17  single  0.970  0.020  1.090
 VSD  C04  H18  single  0.970  0.020  1.090
 VSD  C05  H19  single  0.970  0.020  1.090
 VSD  C06  H20  single  0.970  0.020  1.090
 VSD  C07  H21  single  0.970  0.020  1.090
 VSD  C08  H22  single  0.970  0.020  1.090
 VSD  C09  H23  single  0.970  0.020  1.090
 VSD  C18  H24  single  0.970  0.020  1.090
 VSD  C19  H25  single  0.970  0.020  1.090
 VSD  C19  H26  single  0.970  0.020  1.090
 VSD  N21  H27  single  0.890  0.020  1.040
 VSD  N21  H28  single  0.890  0.020  1.040
 VSD  O20  H30  single  0.850  0.020  0.980
 VSD  C04  H29  single  0.970  0.020  1.090
 VSD  C05  H31  single  0.970  0.020  1.090
 VSD  C06  H32  single  0.970  0.020  1.090
 VSD  C07  H33  single  0.970  0.020  1.090
 VSD  C08  H34  single  0.970  0.020  1.090
 VSD  C09  H35  single  0.970  0.020  1.090
 VSD  C12  H36  single  0.970  0.020  1.090
 VSD  C13  H37  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
 VSD  H2   C15  H1   105.00  3.000
 VSD  H2   C15  C14  110.33  3.000
 VSD  H1   C15  C14  110.71  3.000
 VSD  H2   C15  C16  105.40  3.000
 VSD  H1   C15  C16  110.33  3.000
 VSD  C14  C15  C16  114.53  3.000
 VSD  O17  C16  C18  122.01  3.000
 VSD  C18  C16  C15  115.87  3.000
 VSD  O17  C16  C15  122.10  3.000
 VSD  H4   C10  H3   105.93  3.000
 VSD  H4   C10  C09  108.60  3.000
 VSD  H3   C10  C09  109.40  3.000
 VSD  H4   C10  C11  108.89  3.000
 VSD  H3   C10  C11  109.39  3.000
 VSD  C09  C10  C11  114.29  3.000
 VSD  H6   C11  H5   105.93  3.000
 VSD  H6   C11  C12  109.30  3.000
 VSD  H5   C11  C12  108.62  3.000
 VSD  H6   C11  C10  109.34  3.000
 VSD  H5   C11  C10  109.02  3.000
 VSD  C12  C11  C10  114.30  3.000
 VSD  H36  C12  H7   106.09  3.000
 VSD  H36  C12  C13  109.38  3.000
 VSD  H7   C12  C13  109.05  3.000
 VSD  H36  C12  C11  109.16  3.000
 VSD  H7   C12  C11  110.18  3.000
 VSD  C13  C12  C11  112.76  3.000
 VSD  H37  C13  H8   106.03  3.000
 VSD  H37  C13  C14  109.09  3.000
 VSD  H8   C13  C14  109.87  3.000
 VSD  H37  C13  C12  109.41  3.000
 VSD  H8   C13  C12  109.20  3.000
 VSD  C14  C13  C12  113.01  3.000
 VSD  H10  C14  H9   106.15  3.000
 VSD  H10  C14  C13  109.95  3.000
 VSD  H9   C14  C13  109.20  3.000
 VSD  H10  C14  C15  109.88  3.000
 VSD  H9   C14  C15  108.61  3.000
 VSD  C13  C14  C15  112.81  3.000
 VSD  H13  C01  H12  107.48  3.000
 VSD  H13  C01  H11  107.62  3.000
 VSD  H12  C01  H11  107.59  3.000
 VSD  H13  C01  C02  111.10  3.000
 VSD  H12  C01  C02  111.21  3.000
 VSD  H11  C01  C02  111.63  3.000
 VSD  H15  C02  H14  106.02  3.000
 VSD  H15  C02  C03  109.29  3.000
 VSD  H14  C02  C03  109.32  3.000
 VSD  H15  C02  C01  109.47  3.000
 VSD  H14  C02  C01  109.64  3.000
 VSD  C03  C02  C01  112.87  3.000
 VSD  H17  C03  H16  105.97  3.000
 VSD  H17  C03  C04  109.32  3.000
 VSD  H16  C03  C04  109.32  3.000
 VSD  H17  C03  C02  109.27  3.000
 VSD  H16  C03  C02  109.31  3.000
 VSD  C04  C03  C02  113.38  3.000
 VSD  H29  C04  H18  106.00  3.000
 VSD  H29  C04  C05  109.35  3.000
 VSD  H18  C04  C05  109.37  3.000
 VSD  H29  C04  C03  109.25  3.000
 VSD  H18  C04  C03  109.36  3.000
 VSD  C05  C04  C03  113.25  3.000
 VSD  H31  C05  H19  105.99  3.000
 VSD  H31  C05  C06  109.28  3.000
 VSD  H19  C05  C06  109.29  3.000
 VSD  H31  C05  C04  109.32  3.000
 VSD  H19  C05  C04  109.38  3.000
 VSD  C06  C05  C04  113.32  3.000
 VSD  H32  C06  H20  106.00  3.000
 VSD  H32  C06  C07  109.36  3.000
 VSD  H20  C06  C07  109.35  3.000
 VSD  H32  C06  C05  109.24  3.000
 VSD  H20  C06  C05  109.35  3.000
 VSD  C07  C06  C05  113.28  3.000
 VSD  H33  C07  H21  106.00  3.000
 VSD  H33  C07  C08  109.30  3.000
 VSD  H21  C07  C08  109.28  3.000
 VSD  H33  C07  C06  109.30  3.000
 VSD  H21  C07  C06  109.39  3.000
 VSD  C08  C07  C06  113.30  3.000
 VSD  H34  C08  H22  106.01  3.000
 VSD  H34  C08  C09  109.38  3.000
 VSD  H22  C08  C09  109.31  3.000
 VSD  H34  C08  C07  109.24  3.000
 VSD  H22  C08  C07  109.36  3.000
 VSD  C09  C08  C07  113.27  3.000
 VSD  H35  C09  H23  106.05  3.000
 VSD  H35  C09  C08  108.92  3.000
 VSD  H23  C09  C08  109.41  3.000
 VSD  H35  C09  C10  110.19  3.000
 VSD  H23  C09  C10  109.11  3.000
 VSD  C08  C09  C10  112.93  3.000
 VSD  H24  C18  N21  114.14  3.000
 VSD  H24  C18  C19  106.96  3.000
 VSD  N21  C18  C19  109.64  3.000
 VSD  H24  C18  C16  106.62  3.000
 VSD  C19  C18  C16  107.69  3.000
 VSD  N21  C18  C16  111.49  3.000
 VSD  H26  C19  H25  107.37  3.000
 VSD  H26  C19  O20  111.35  3.000
 VSD  H25  C19  O20  111.80  3.000
 VSD  H26  C19  C18  110.06  3.000
 VSD  H25  C19  C18  108.27  3.000
 VSD  O20  C19  C18  107.96  3.000
 VSD  H28  N21  H27  106.06  3.000
 VSD  H28  N21  C18  110.15  3.000
 VSD  H27  N21  C18  109.05  3.000
 VSD  H30  O20  C19  108.37  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
 VSD  Var_01  C12  C13  C14  C15  -178.62  30.0  1
 VSD  Var_02  C13  C14  C15  C16   -69.37  30.0  1
 VSD  Var_03  C07  C08  C09  C10  -178.99  30.0  1
 VSD  Var_04  C13  C12  C11  C10   177.43  30.0  3
 VSD  Var_05  C08  C09  C10  C11   177.96  30.0  1
 VSD  Var_06  C14  C13  C12  C11  -180.00  30.0  3
 VSD  Var_07  C09  C10  C11  C12    66.99  30.0  1
 VSD  Var_08  O17  C16  C15  C14   -33.72  30.0  3
 VSD  Var_09  C04  C03  C02  C01  -179.54  30.0  3
 VSD  Var_10  C05  C04  C03  C02  -179.89  30.0  3
 VSD  Var_11  C06  C05  C04  C03  -179.52  30.0  3
 VSD  Var_12  C07  C06  C05  C04  -179.55  30.0  3
 VSD  Var_13  C08  C07  C06  C05  -179.29  30.0  3
 VSD  Var_14  C09  C08  C07  C06  -179.22  30.0  3
 VSD  Var_15  H11  C01  C02  C03   179.75  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
 VSD  chir_01  C18  C16  N21  C19  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
 VSD  plan-1  C15  0.020
 VSD  plan-1  C16  0.020
 VSD  plan-1  C18  0.020
 VSD  plan-1  O17  0.020

