# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:09:30 2021
#   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  25  12  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.527  -27.8126  -28.3157  -0.4307
 VLS  C02  C  CH2   0  -0.141  -25.3683  -25.9120   2.4684
 VLS  C03  C  CT    0  -0.014  -24.8897  -27.1714   1.7385
 VLS  C04  C  CH2   0  -0.139  -23.8921  -26.7994   0.6372
 VLS  C06  C  CH2   0  -0.148  -24.1570  -28.1268   2.6947
 VLS  C09  C  CH2   0  -0.404  -26.8941  -27.3522   0.2810
 VLS  N08  N  NH1   0  -0.611  -25.9869  -27.9828   1.2083
 VLS  O01  O  OH1   0  -0.675  -26.2140  -26.3047   3.5270
 VLS  O05  O  OH1   0  -0.669  -24.3511  -25.7165  -0.1451
 VLS  O07  O  OH1   0  -0.668  -23.1543  -27.4388   3.4012
 VLS  O11  O  OH1   0  -0.580  -27.5259  -29.5924  -0.2315
 VLS  O12  O  O     0  -0.463  -28.7246  -27.9430  -1.1298
 VLS  H1   H  HCH2  0   0.201  -24.5047  -25.3400   2.8297
 VLS  H2   H  HCH2  0   0.212  -25.8997  -25.2634   1.7637
 VLS  H3   H  HCH2  0   0.206  -23.7269  -27.6958   0.0245
 VLS  H4   H  HCH2  0   0.214  -22.9364  -26.5464   1.1095
 VLS  H5   H  HCH2  0   0.208  -24.8845  -28.5807   3.3798
 VLS  H6   H  HCH2  0   0.210  -23.7397  -28.9455   2.0937
 VLS  H7   H  HCH2  0   0.289  -26.3305  -26.8404  -0.5004
 VLS  H8   H  HCH2  0   0.247  -27.5432  -26.5843   0.7241
 VLS  H9   H  HNH1  0   0.347  -26.5210  -28.3395   1.9913
 VLS  H11  H  HOH1  0   0.455  -26.6027  -25.5132   3.9085
 VLS  H12  H  HOH1  0   0.458  -23.6626  -25.5016  -0.7811
 VLS  H13  H  HOH1  0   0.459  -22.6514  -28.0812   3.9091
 VLS  H14  H  HOH1  0   0.480  -28.1600  -30.1444  -0.7142

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  double  1.208  0.020  1.208
 VLS  O11  C10  single  1.324  0.020  1.324
 VLS  O05  C04  single  1.413  0.020  1.413
 VLS  C10  C09  single  1.509  0.020  1.509
 VLS  C09  N08  single  1.442  0.020  1.442
 VLS  C04  C03  single  1.532  0.020  1.532
 VLS  N08  C03  single  1.464  0.020  1.464
 VLS  C03  C02  single  1.532  0.020  1.532
 VLS  C03  C06  single  1.538  0.020  1.538
 VLS  C02  O01  single  1.411  0.020  1.411
 VLS  C06  O07  single  1.406  0.020  1.406
 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
 VLS  O11  H14  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  123.24  3.000
 VLS  O11  C10  C09  114.39  3.000
 VLS  O12  C10  C09  122.37  3.000
 VLS  H2   C02  H1   106.56  3.000
 VLS  H2   C02  O01  110.90  3.000
 VLS  H1   C02  O01  111.71  3.000
 VLS  H2   C02  C03  109.37  3.000
 VLS  H1   C02  C03  109.85  3.000
 VLS  O01  C02  C03  108.42  3.000
 VLS  N08  C03  C06  103.77  3.000
 VLS  C06  C03  C04  106.72  3.000
 VLS  N08  C03  C04  111.24  3.000
 VLS  C06  C03  C02  111.30  3.000
 VLS  N08  C03  C02  113.20  3.000
 VLS  C04  C03  C02  110.26  3.000
 VLS  H4   C04  H3   107.33  3.000
 VLS  H4   C04  O05  110.19  3.000
 VLS  H3   C04  O05  111.44  3.000
 VLS  H4   C04  C03  108.31  3.000
 VLS  H3   C04  C03  107.50  3.000
 VLS  O05  C04  C03  111.88  3.000
 VLS  H6   C06  H5   106.57  3.000
 VLS  H6   C06  O07  111.64  3.000
 VLS  H5   C06  O07  111.18  3.000
 VLS  H6   C06  C03  107.70  3.000
 VLS  H5   C06  C03  109.22  3.000
 VLS  O07  C06  C03  110.38  3.000
 VLS  H8   C09  H7   105.43  3.000
 VLS  H8   C09  N08  114.70  3.000
 VLS  H7   C09  N08  109.92  3.000
 VLS  H8   C09  C10  106.06  3.000
 VLS  H7   C09  C10  106.03  3.000
 VLS  N08  C09  C10  114.01  3.000
 VLS  H9   N08  C09  108.62  3.000
 VLS  H9   N08  C03  108.09  3.000
 VLS  C09  N08  C03  117.51  3.000
 VLS  H11  O01  C02  108.13  3.000
 VLS  H12  O05  C04  107.75  3.000
 VLS  H13  O07  C06  108.15  3.000
 VLS  H14  O11  C10  109.43  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  CONST_01  H14  O11  C10  C09   180.00   0.0  0
 VLS  Var_01    C03  N08  C09  C10   168.05  30.0  3
 VLS  Var_02    O05  C04  C03  C02   -46.72  30.0  2
 VLS  Var_03    C09  N08  C03  C02    58.05  30.0  3
 VLS  Var_04    O07  C06  C03  C02   -51.37  30.0  3
 VLS  Var_05    O01  C02  C03  C04  -176.21  30.0  3
 VLS  Var_06    O12  C10  C09  N08   171.93  30.0  1

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
 VLS  plan-1  H14  0.020

