# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:41:41 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: N~6~-(1,1-dihydroxyethyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(O)(O)NCCCC[C@H](N)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
 5OL  5OL  N~6~-(1,1-dihydroxyethyl)-L-lysine  L-peptide  31  14  .  2017-07-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_5OL
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
 5OL  CA   C  CH1    0  -0.189  6.1564  16.4556  -1.7932
 5OL  N    N  NH2    0  -0.794  6.9008  17.0505  -2.9024
 5OL  C    C  C      0   0.384  6.2541  17.2528  -0.4708
 5OL  O    O  O      0  -0.613  5.2057  17.4021   0.1898
 5OL  C03  C  CH2    0  -0.411  6.6588  15.0261  -1.5837
 5OL  C04  C  CH2    0  -0.423  5.8769  14.2174  -0.5564
 5OL  C05  C  CH2    0  -0.438  6.3128  12.7586  -0.5077
 5OL  C06  C  CH2    0  -0.252  5.5162  11.9483   0.5040
 5OL  N07  N  NH1    0  -0.637  5.9614  10.5623   0.5006
 5OL  C08  C  CT     0   0.581  5.3837   9.6755   1.4608
 5OL  O02  O  OH1    0  -0.662  5.7979  10.1439   2.7163
 5OL  O01  O  OH1    0  -0.671  3.9748   9.7181   1.3594
 5OL  C11  C  CH3    0  -0.710  5.8886   8.2556   1.2164
 5OL  OXT  O  OC    -1  -0.612  7.3938  17.6661  -0.1654
 5OL  H1   H  HCH1   0   0.191  5.1047  16.4007  -2.0946
 5OL  H2   H  HNH2   0   0.332  6.4943  17.9530  -3.1216
 5OL  H3   H  HNH2   0   0.320  7.8306  17.2670  -2.5586
 5OL  H5   H  HCH2   0   0.206  6.6220  14.5087  -2.5480
 5OL  H6   H  HCH2   0   0.200  7.7159  15.0597  -1.2951
 5OL  H7   H  HCH2   0   0.213  5.9888  14.6559   0.4389
 5OL  H8   H  HCH2   0   0.204  4.8083  14.2685  -0.7919
 5OL  H9   H  HCH2   0   0.209  6.1965  12.3145  -1.5029
 5OL  H10  H  HCH2   0   0.212  7.3778  12.6953  -0.2639
 5OL  H11  H  HCH2   0   0.218  5.6736  12.3692   1.4989
 5OL  H12  H  HCH2   0   0.193  4.4462  12.0592   0.2823
 5OL  H13  H  HNH1   0   0.348  5.8517  10.1718  -0.4270
 5OL  H15  H  HOH1   0   0.448  5.4920   9.5359   3.3980
 5OL  H16  H  HOH1   0   0.446  3.5898   9.0068   1.8842
 5OL  H17  H  HCH3   0   0.235  5.4733   7.5635   1.9529
 5OL  H18  H  HCH3   0   0.234  5.5982   7.8981   0.2277
 5OL  H19  H  HCH3   0   0.238  6.9743   8.2146   1.2905

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
 5OL  N    CA   single  1.458  0.019  1.458
 5OL  CA   C03  single  1.530  0.020  1.530
 5OL  CA   C    single  1.525  0.021  1.525
 5OL  C03  C04  single  1.523  0.020  1.523
 5OL  C05  C04  single  1.523  0.020  1.523
 5OL  C05  C06  single  1.521  0.020  1.521
 5OL  C    O    deloc   1.231  0.020  1.231
 5OL  N07  C06  single  1.456  0.020  1.456
 5OL  N07  C08  single  1.429  0.020  1.429
 5OL  O01  C08  single  1.413  0.020  1.413
 5OL  C08  C11  single  1.527  0.020  1.527
 5OL  C08  O02  single  1.403  0.020  1.403
 5OL  C    OXT  deloc   1.250  0.020  1.250
 5OL  CA   H1   single  0.970  0.020  1.090
 5OL  N    H2   single  0.890  0.020  1.040
 5OL  N    H3   single  0.890  0.020  1.040
 5OL  C03  H5   single  0.970  0.020  1.090
 5OL  C03  H6   single  0.970  0.020  1.090
 5OL  C04  H7   single  0.970  0.020  1.090
 5OL  C04  H8   single  0.970  0.020  1.090
 5OL  C05  H9   single  0.970  0.020  1.090
 5OL  C05  H10  single  0.970  0.020  1.090
 5OL  C06  H11  single  0.970  0.020  1.090
 5OL  C06  H12  single  0.970  0.020  1.090
 5OL  N07  H13  single  0.890  0.020  1.040
 5OL  O02  H15  single  0.850  0.020  0.980
 5OL  O01  H16  single  0.850  0.020  0.980
 5OL  C11  H17  single  0.970  0.020  1.090
 5OL  C11  H18  single  0.970  0.020  1.090
 5OL  C11  H19  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
 5OL  H1   CA   C03  107.84  3.000
 5OL  H1   CA   C    108.76  3.000
 5OL  C03  CA   C    110.10  3.000
 5OL  H1   CA   N    107.49  3.000
 5OL  C    CA   N    111.00  2.800
 5OL  C03  CA   N    108.48  3.000
 5OL  H3   N    H2   104.52  3.000
 5OL  H3   N    CA   107.24  3.000
 5OL  H2   N    CA   108.79  3.000
 5OL  OXT  C    O    126.65  3.000
 5OL  OXT  C    CA   120.80  1.700
 5OL  O    C    CA   120.80  1.700
 5OL  H6   C03  H5   106.19  3.000
 5OL  H6   C03  C04  109.49  3.000
 5OL  H5   C03  C04  109.01  3.000
 5OL  H6   C03  CA   108.92  3.000
 5OL  H5   C03  CA   108.05  3.000
 5OL  C04  C03  CA   114.83  3.000
 5OL  H8   C04  H7   106.07  3.000
 5OL  H8   C04  C05  109.31  3.000
 5OL  H7   C04  C05  109.00  3.000
 5OL  H8   C04  C03  109.33  3.000
 5OL  H7   C04  C03  110.39  3.000
 5OL  C05  C04  C03  112.53  3.000
 5OL  H10  C05  H9   106.38  3.000
 5OL  H10  C05  C06  109.31  3.000
 5OL  H9   C05  C06  109.42  3.000
 5OL  H10  C05  C04  109.94  3.000
 5OL  H9   C05  C04  109.19  3.000
 5OL  C06  C05  C04  112.43  3.000
 5OL  H12  C06  H11  106.59  3.000
 5OL  H12  C06  N07  113.18  3.000
 5OL  H11  C06  N07  108.97  3.000
 5OL  H12  C06  C05  108.79  3.000
 5OL  H11  C06  C05  108.98  3.000
 5OL  N07  C06  C05  110.21  3.000
 5OL  H13  N07  C08  109.42  3.000
 5OL  H13  N07  C06  109.64  3.000
 5OL  C08  N07  C06  117.75  3.000
 5OL  C11  C08  O01  110.25  3.000
 5OL  C11  C08  O02  110.87  3.000
 5OL  O01  C08  O02  110.40  3.000
 5OL  O02  C08  N07  105.95  3.000
 5OL  C11  C08  N07  109.63  3.000
 5OL  O01  C08  N07  109.64  3.000
 5OL  H15  O02  C08  109.20  3.000
 5OL  H16  O01  C08  109.68  3.000
 5OL  H19  C11  H18  108.35  3.000
 5OL  H19  C11  H17  108.01  3.000
 5OL  H18  C11  H17  107.59  3.000
 5OL  H19  C11  C08  110.72  3.000
 5OL  H18  C11  C08  111.22  3.000
 5OL  H17  C11  C08  110.82  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
 5OL  Var_01  C05  C04  C03  CA    173.21  30.0  3
 5OL  Var_02  C06  C05  C04  C03  -179.14  30.0  1
 5OL  Var_03  N07  C06  C05  C04   179.40  30.0  3
 5OL  Var_04  C08  N07  C06  C05   175.68  30.0  1
 5OL  Var_05  O01  C08  N07  C06    54.00  30.0  3
 5OL  Var_06  H17  C11  C08  N07   178.91  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
 5OL  chir_01  CA  N  C03  C  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
 5OL  plan-1  CA   0.020
 5OL  plan-1  C    0.020
 5OL  plan-1  O    0.020
 5OL  plan-1  OXT  0.020

