# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:38:56 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCCCC(=O)NO
#
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
 XS6  XS6  6-[(3-aminopropyl)amino]-N-hydroxyhexanamide  ligand  35  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XS6
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
 XS6  C2   C  CH2   0  -0.273   6.5946   0.3078   0.1276
 XS6  C3   C  CH2   0  -0.454   5.2740  -0.4470   0.1367
 XS6  C4   C  CH2   0  -0.252   4.0757   0.4812   0.0193
 XS6  C6   C  CH2   0  -0.248   1.6641   0.5938  -0.1200
 XS6  C7   C  CH2   0  -0.440   0.3725  -0.2064  -0.0613
 XS6  C8   C  CH2   0  -0.419  -0.8625   0.6626  -0.2582
 XS6  C9   C  CH2   0  -0.417  -2.1609  -0.1287  -0.1737
 XS6  C10  C  CH2   0  -0.583  -3.3838   0.7591  -0.3787
 XS6  C11  C  C     0   0.529  -4.6768  -0.0208  -0.3452
 XS6  N1   N  NH2   0  -0.800   7.7193  -0.6128   0.2220
 XS6  N5   N  NH1   0  -0.600   2.8267  -0.2557   0.0530
 XS6  N13  N  NH1   0  -0.377  -5.6132   0.5230   0.4555
 XS6  O12  O  O     0  -0.483  -4.8497  -1.0539  -0.9692
 XS6  O14  O  OH1   0  -0.545  -6.8878   0.0414   0.4417
 XS6  H1   H  HCH2  0   0.189   6.6315   0.9530  -0.7625
 XS6  H2   H  HCH2  0   0.213   6.6280   0.9782   0.9911
 XS6  H3   H  HCH2  0   0.214   5.2615  -1.1602  -0.6960
 XS6  H4   H  HCH2  0   0.219   5.1964  -1.0343   1.0559
 XS6  H5   H  HCH2  0   0.212   4.0799   1.1857   0.8581
 XS6  H6   H  HCH2  0   0.182   4.1768   1.0947  -0.8918
 XS6  H7   H  HCH2  0   0.183   1.6962   1.1658  -1.0628
 XS6  H8   H  HCH2  0   0.212   1.6619   1.3380   0.6835
 XS6  H9   H  HCH2  0   0.214   0.3922  -0.9876  -0.8296
 XS6  H10  H  HCH2  0   0.216   0.3149  -0.7215   0.9026
 XS6  H11  H  HCH2  0   0.215  -0.8716   1.4590   0.4938
 XS6  H12  H  HCH2  0   0.215  -0.8075   1.1639  -1.2307
 XS6  H13  H  HCH2  0   0.227  -2.1550  -0.9231  -0.9238
 XS6  H14  H  HCH2  0   0.227  -2.2246  -0.6211   0.8017
 XS6  H15  H  HCH2  0   0.250  -3.3890   1.5637   0.3614
 XS6  H16  H  HCH2  0   0.267  -3.3251   1.2446  -1.3583
 XS6  H17  H  HNH2  0   0.337   7.7642  -1.1657  -0.6256
 XS6  H18  H  HNH2  0   0.345   8.5833  -0.0865   0.2458
 XS6  H20  H  HNH1  0   0.333   2.8378  -0.9430  -0.6926
 XS6  H22  H  HNH1  0   0.414  -5.5142   1.4463   0.8524
 XS6  H23  H  HOH1  0   0.477  -6.9603  -0.5470   1.2040

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
 XS6  O14  N13  single  1.363  0.020  1.363
 XS6  O12  C11  double  1.219  0.020  1.219
 XS6  N13  C11  single  1.347  0.020  1.347
 XS6  N1   C2   single  1.456  0.020  1.456
 XS6  C11  C10  single  1.510  0.020  1.510
 XS6  C3   C2   single  1.521  0.020  1.521
 XS6  C3   C4   single  1.520  0.020  1.520
 XS6  C9   C10  single  1.525  0.020  1.525
 XS6  C9   C8   single  1.523  0.020  1.523
 XS6  C4   N5   single  1.451  0.020  1.451
 XS6  N5   C6   single  1.450  0.020  1.450
 XS6  C7   C8   single  1.523  0.020  1.523
 XS6  C7   C6   single  1.521  0.020  1.521
 XS6  C2   H1   single  0.970  0.020  1.090
 XS6  C2   H2   single  0.970  0.020  1.090
 XS6  C3   H3   single  0.970  0.020  1.090
 XS6  C3   H4   single  0.970  0.020  1.090
 XS6  C4   H5   single  0.970  0.020  1.090
 XS6  C4   H6   single  0.970  0.020  1.090
 XS6  C6   H7   single  0.970  0.020  1.090
 XS6  C6   H8   single  0.970  0.020  1.090
 XS6  C7   H9   single  0.970  0.020  1.090
 XS6  C7   H10  single  0.970  0.020  1.090
 XS6  C8   H11  single  0.970  0.020  1.090
 XS6  C8   H12  single  0.970  0.020  1.090
 XS6  C9   H13  single  0.970  0.020  1.090
 XS6  C9   H14  single  0.970  0.020  1.090
 XS6  C10  H15  single  0.970  0.020  1.090
 XS6  C10  H16  single  0.970  0.020  1.090
 XS6  N1   H17  single  0.890  0.020  1.040
 XS6  N1   H18  single  0.890  0.020  1.040
 XS6  N5   H20  single  0.890  0.020  1.040
 XS6  N13  H22  single  0.860  0.020  1.020
 XS6  O14  H23  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
 XS6  H2   C2   H1   106.17  3.000
 XS6  H2   C2   N1   108.22  3.000
 XS6  H1   C2   N1   113.40  3.000
 XS6  H2   C2   C3   109.03  3.000
 XS6  H1   C2   C3   108.96  3.000
 XS6  N1   C2   C3   110.88  3.000
 XS6  H4   C3   H3   106.75  3.000
 XS6  H4   C3   C4   109.68  3.000
 XS6  H3   C3   C4   109.24  3.000
 XS6  H4   C3   C2   109.46  3.000
 XS6  H3   C3   C2   109.16  3.000
 XS6  C4   C3   C2   112.39  3.000
 XS6  H6   C4   H5   105.93  3.000
 XS6  H6   C4   N5   112.37  3.000
 XS6  H5   C4   N5   108.19  3.000
 XS6  H6   C4   C3   109.34  3.000
 XS6  H5   C4   C3   109.30  3.000
 XS6  N5   C4   C3   111.52  3.000
 XS6  H8   C6   H7   105.94  3.000
 XS6  H8   C6   N5   108.19  3.000
 XS6  H7   C6   N5   112.48  3.000
 XS6  H8   C6   C7   109.12  3.000
 XS6  H7   C6   C7   109.30  3.000
 XS6  N5   C6   C7   111.60  3.000
 XS6  H10  C7   H9   106.43  3.000
 XS6  H10  C7   C8   109.87  3.000
 XS6  H9   C7   C8   109.31  3.000
 XS6  H10  C7   C6   109.05  3.000
 XS6  H9   C7   C6   109.44  3.000
 XS6  C8   C7   C6   112.56  3.000
 XS6  H12  C8   H11  106.09  3.000
 XS6  H12  C8   C9   109.26  3.000
 XS6  H11  C8   C9   109.43  3.000
 XS6  H12  C8   C7   109.59  3.000
 XS6  H11  C8   C7   109.44  3.000
 XS6  C9   C8   C7   112.81  3.000
 XS6  H14  C9   H13  106.56  3.000
 XS6  H14  C9   C10  109.57  3.000
 XS6  H13  C9   C10  109.59  3.000
 XS6  H14  C9   C8   109.44  3.000
 XS6  H13  C9   C8   109.58  3.000
 XS6  C10  C9   C8   111.95  3.000
 XS6  H16  C10  H15  106.23  3.000
 XS6  H16  C10  C11  107.14  3.000
 XS6  H15  C10  C11  111.16  3.000
 XS6  H16  C10  C9   109.60  3.000
 XS6  H15  C10  C9   109.96  3.000
 XS6  C11  C10  C9   112.51  3.000
 XS6  O12  C11  N13  123.21  3.000
 XS6  N13  C11  C10  113.57  3.000
 XS6  O12  C11  C10  123.20  3.000
 XS6  H18  N1   H17  105.41  3.000
 XS6  H18  N1   C2   109.39  3.000
 XS6  H17  N1   C2   108.97  3.000
 XS6  H20  N5   C6   108.54  3.000
 XS6  H20  N5   C4   108.53  3.000
 XS6  C6   N5   C4   112.95  3.000
 XS6  H22  N13  O14  114.76  3.000
 XS6  H22  N13  C11  122.32  3.000
 XS6  O14  N13  C11  120.11  3.000
 XS6  H23  O14  N13  106.11  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
 XS6  CONST_01  O14  N13  C11  C10   180.00   0.0  0
 XS6  CONST_02  O14  N13  C11  O12     0.00   0.0  0
 XS6  CONST_03  H22  N13  C11  C10     0.00   0.0  0
 XS6  Var_01    N5   C4   C3   C2   -179.01  30.0  3
 XS6  Var_02    C6   N5   C4   C3   -177.27  30.0  3
 XS6  Var_03    N1   C2   C3   C4   -179.17  30.0  3
 XS6  Var_04    C7   C6   N5   C4   -179.25  30.0  3
 XS6  Var_05    C9   C8   C7   C6   -178.89  30.0  3
 XS6  Var_06    C10  C9   C8   C7   -179.79  30.0  1
 XS6  Var_07    C11  C10  C9   C8    178.01  30.0  3
 XS6  Var_08    N5   C6   C7   C8   -179.28  30.0  3
 XS6  Var_09    O12  C11  C10  C9    -47.68  30.0  1
 XS6  Var_10    H17  N1   C2   C3     67.14  30.0  3

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
 XS6  plan-1  C10  0.020
 XS6  plan-1  C11  0.020
 XS6  plan-1  N13  0.020
 XS6  plan-1  O12  0.020
 XS6  plan-1  O14  0.020
 XS6  plan-1  H22  0.020

