# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 04:26:17 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)(CO)NCC(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
 VLS  VLS  N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine  ligand  24  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VLS
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
 VLS  C10  C  C      0   0.388  -28.0275  -28.2588  -0.0985
 VLS  C02  C  CH2    0  -0.138  -25.4529  -25.9818   2.4167
 VLS  C03  C  CT     0  -0.009  -24.8438  -27.1756   1.6704
 VLS  C04  C  CH2    0  -0.131  -23.7943  -26.6804   0.6712
 VLS  C06  C  CH2    0  -0.148  -24.1167  -28.1196   2.6424
 VLS  C09  C  CH2    0  -0.396  -26.6997  -27.4758   0.0059
 VLS  N08  N  NH1    0  -0.621  -25.8302  -28.0287   1.0228
 VLS  O01  O  OH1    0  -0.672  -26.3290  -26.4658   3.4127
 VLS  O05  O  OH1    0  -0.667  -24.2926  -25.6361  -0.1354
 VLS  O07  O  OH1    0  -0.667  -23.2281  -27.4012   3.4661
 VLS  O11  O  OC    -1  -0.602  -28.3386  -28.9871   0.8662
 VLS  O12  O  O      0  -0.614  -28.6915  -28.0571  -1.1329
 VLS  H1   H  HCH2   0   0.190  -24.6516  -25.3673   2.8464
 VLS  H2   H  HCH2   0   0.205  -25.9876  -25.3412   1.7075
 VLS  H3   H  HCH2   0   0.195  -23.4831  -27.5422   0.0652
 VLS  H4   H  HCH2   0   0.201  -22.9141  -26.3429   1.2307
 VLS  H5   H  HCH2   0   0.202  -24.8623  -28.6588   3.2405
 VLS  H6   H  HCH2   0   0.203  -23.5900  -28.8751   2.0438
 VLS  H7   H  HCH2   0   0.203  -26.2127  -27.4813  -0.9727
 VLS  H8   H  HCH2   0   0.194  -26.9808  -26.4264   0.1864
 VLS  H9   H  HNH1   0   0.329  -26.4379  -28.4396   1.7220
 VLS  H11  H  HOH1   0   0.450  -26.7544  -25.7098   3.8260
 VLS  H12  H  HOH1   0   0.451  -23.5772  -25.3348  -0.7024
 VLS  H13  H  HOH1   0   0.453  -22.7206  -28.0335   3.9818

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
 VLS  O12  C10  deloc   1.246  0.020  1.246
 VLS  O11  C10  deloc   1.248  0.020  1.248
 VLS  O05  C04  single  1.411  0.020  1.411
 VLS  C10  C09  single  1.545  0.020  1.545
 VLS  C09  N08  single  1.448  0.020  1.448
 VLS  C04  C03  single  1.531  0.020  1.531
 VLS  N08  C03  single  1.456  0.020  1.456
 VLS  C03  C02  single  1.534  0.020  1.534
 VLS  C03  C06  single  1.538  0.020  1.538
 VLS  C02  O01  single  1.412  0.020  1.412
 VLS  C06  O07  single  1.409  0.020  1.409
 VLS  C02  H1   single  0.970  0.020  1.090
 VLS  C02  H2   single  0.970  0.020  1.090
 VLS  C04  H3   single  0.970  0.020  1.090
 VLS  C04  H4   single  0.970  0.020  1.090
 VLS  C06  H5   single  0.970  0.020  1.090
 VLS  C06  H6   single  0.970  0.020  1.090
 VLS  C09  H7   single  0.970  0.020  1.090
 VLS  C09  H8   single  0.970  0.020  1.090
 VLS  N08  H9   single  0.890  0.020  1.040
 VLS  O01  H11  single  0.850  0.020  0.980
 VLS  O05  H12  single  0.850  0.020  0.980
 VLS  O07  H13  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
 VLS  O12  C10  O11  127.12  3.000
 VLS  O11  C10  C09  117.24  3.000
 VLS  O12  C10  C09  115.61  3.000
 VLS  H2   C02  H1   106.41  3.000
 VLS  H2   C02  O01  110.75  3.000
 VLS  H1   C02  O01  111.64  3.000
 VLS  H2   C02  C03  109.51  3.000
 VLS  H1   C02  C03  109.66  3.000
 VLS  O01  C02  C03  108.83  3.000
 VLS  N08  C03  C06  103.99  3.000
 VLS  C06  C03  C04  106.67  3.000
 VLS  N08  C03  C04  111.32  3.000
 VLS  C06  C03  C02  110.98  3.000
 VLS  N08  C03  C02  113.79  3.000
 VLS  C04  C03  C02  109.75  3.000
 VLS  H4   C04  H3   107.19  3.000
 VLS  H4   C04  O05  110.34  3.000
 VLS  H3   C04  O05  111.43  3.000
 VLS  H4   C04  C03  108.47  3.000
 VLS  H3   C04  C03  107.49  3.000
 VLS  O05  C04  C03  111.74  3.000
 VLS  H6   C06  H5   106.55  3.000
 VLS  H6   C06  O07  111.53  3.000
 VLS  H5   C06  O07  111.13  3.000
 VLS  H6   C06  C03  107.73  3.000
 VLS  H5   C06  C03  108.95  3.000
 VLS  O07  C06  C03  110.78  3.000
 VLS  H8   C09  H7   105.38  3.000
 VLS  H8   C09  N08  113.71  3.000
 VLS  H7   C09  N08  111.06  3.000
 VLS  H8   C09  C10  105.93  3.000
 VLS  H7   C09  C10  108.65  3.000
 VLS  N08  C09  C10  111.72  3.000
 VLS  H9   N08  C09  106.22  3.000
 VLS  H9   N08  C03  109.69  3.000
 VLS  C09  N08  C03  119.70  3.000
 VLS  H11  O01  C02  107.96  3.000
 VLS  H12  O05  C04  107.85  3.000
 VLS  H13  O07  C06  108.15  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
 VLS  Var_01  C03  N08  C09  C10  -154.08  30.0  3
 VLS  Var_02  O05  C04  C03  C02   -49.87  30.0  2
 VLS  Var_03  C09  N08  C03  C02    60.29  30.0  2
 VLS  Var_04  O07  C06  C03  C02   -50.28  30.0  3
 VLS  Var_05  O01  C02  C03  C04  -174.87  30.0  3
 VLS  Var_06  O12  C10  C09  N08  -164.02  30.0  2

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
 VLS  plan-1  C10  0.020
 VLS  plan-1  C09  0.020
 VLS  plan-1  O11  0.020
 VLS  plan-1  O12  0.020

