# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:11:57 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: N-[(3-hydroxypyridin-2-yl)carbonyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1ncccc1O
#
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
 MD6  MD6  N-[(3-hydroxypyridin-2-yl)carbonyl]glycine  peptide  21  14  .  2016-04-26  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_MD6
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
 MD6  C    C  C      0   0.396  -4.2159  1.7810  -1.1810
 MD6  N    N  NH1    0  -0.627  -3.3554  2.2214   1.0806
 MD6  O    O  O      0  -0.600  -5.0013  1.1501  -1.9074
 MD6  CA   C  CH2    0  -0.412  -4.3356  1.4797   0.3295
 MD6  N2   N  N      0  -0.393  -1.5104  2.3675   4.0296
 MD6  OXT  O  OC    -1  -0.593  -3.3576  2.6171  -1.5239
 MD6  C3   C  C      0   0.516  -3.2433  2.1603   2.4070
 MD6  O3   O  O      0  -0.493  -3.9519  1.4518   3.1109
 MD6  C4   C  CR6    0   0.005  -2.1413  2.9799   3.0342
 MD6  C5   C  CR16   0  -0.104  -0.5361  2.9859   4.6734
 MD6  C6   C  CR16   0  -0.297  -0.1447  4.2811   4.3631
 MD6  C7   C  CR16   0  -0.275  -0.8006  4.9423   3.3439
 MD6  C8   C  CR6    0   0.323  -1.8190  4.2890   2.6545
 MD6  H2   H  HNH1   0   0.390  -2.7582  2.8096   0.5165
 MD6  HA2  H  HCH2   0   0.238  -5.3490  1.7270   0.6619
 MD6  HA3  H  HCH2   0   0.236  -4.2149  0.4037   0.4875
 MD6  HO4  H  HOH1   0   0.483  -2.1848  5.7708   1.5042
 MD6  H5   H  HCR6   0   0.261  -0.0478  2.4350   5.4688
 MD6  H6   H  HCR6   0   0.276   0.6525  4.7633   4.9119
 MD6  H7   H  HCR6   0   0.291  -0.5308  5.9592   3.0815
 MD6  O4   O  OH1    0  -0.621  -2.5061  4.8744   1.6612

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
 MD6  O    C    deloc     1.231  0.020  1.231
 MD6  OXT  C    deloc     1.246  0.020  1.246
 MD6  C    CA   single    1.516  0.018  1.516
 MD6  CA   N    single    1.451  0.016  1.451
 MD6  N    C3   single    1.333  0.020  1.333
 MD6  N    H2   single    0.860  0.020  1.020
 MD6  CA   HA2  single    0.970  0.020  1.090
 MD6  CA   HA3  single    0.970  0.020  1.090
 MD6  C4   N2   aromatic  1.328  0.020  1.328
 MD6  N2   C5   aromatic  1.321  0.020  1.321
 MD6  C3   O3   double    1.225  0.020  1.225
 MD6  C3   C4   single    1.510  0.020  1.510
 MD6  C8   C4   aromatic  1.401  0.020  1.401
 MD6  O4   C8   single    1.342  0.020  1.342
 MD6  O4   HO4  single    0.850  0.020  0.980
 MD6  C6   C5   aromatic  1.388  0.020  1.388
 MD6  C5   H5   single    0.930  0.020  1.080
 MD6  C7   C6   aromatic  1.381  0.020  1.381
 MD6  C6   H6   single    0.930  0.020  1.080
 MD6  C8   C7   aromatic  1.393  0.020  1.393
 MD6  C7   H7   single    0.930  0.020  1.080

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
 MD6  OXT  C   CA   116.95  3.000
 MD6  CA   C   O    120.80  2.100
 MD6  OXT  C   O    127.98  3.000
 MD6  H2   N   C3   122.19  3.000
 MD6  H2   N   CA   114.25  3.000
 MD6  C3   N   CA   123.56  3.000
 MD6  HA3  CA  HA2  106.28  3.000
 MD6  HA3  CA  N    110.85  3.000
 MD6  HA2  CA  N    110.81  3.000
 MD6  HA3  CA  C    108.93  3.000
 MD6  HA2  CA  C    108.94  3.000
 MD6  N    CA  C    113.30  2.900
 MD6  C5   N2  C4   119.98  3.000
 MD6  C4   C3  O3   119.85  3.000
 MD6  C4   C3  N    116.75  3.000
 MD6  O3   C3  N    123.36  3.000
 MD6  C8   C4  C3   124.24  3.000
 MD6  C8   C4  N2   121.66  3.000
 MD6  C3   C4  N2   114.07  3.000
 MD6  H5   C5  C6   120.75  3.000
 MD6  H5   C5  N2   116.87  3.000
 MD6  C6   C5  N2   122.38  3.000
 MD6  H6   C6  C7   120.75  3.000
 MD6  H6   C6  C5   120.70  3.000
 MD6  C7   C6  C5   118.55  3.000
 MD6  H7   C7  C8   120.14  3.000
 MD6  H7   C7  C6   120.64  3.000
 MD6  C8   C7  C6   119.22  3.000
 MD6  C7   C8  O4   122.42  3.000
 MD6  C7   C8  C4   118.20  3.000
 MD6  O4   C8  C4   119.37  3.000
 MD6  HO4  O4  C8   110.80  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
 MD6  CONST_01  C7  C8  C4  N2     0.00   0.0  0
 MD6  CONST_02  C7  C6  C5  N2     0.00   0.0  0
 MD6  CONST_03  C6  C5  N2  C4     0.00   0.0  0
 MD6  CONST_04  C6  C7  C8  C4     0.00   0.0  0
 MD6  CONST_05  C8  C4  N2  C5     0.00   0.0  0
 MD6  CONST_06  C8  C7  C6  C5     0.00   0.0  0
 MD6  CONST_07  O4  C8  C4  N2   180.00   0.0  0
 MD6  CONST_08  C5  N2  C4  C3   180.00   0.0  0
 MD6  CONST_09  C7  C8  C4  C3   180.00   0.0  0
 MD6  CONST_10  C6  C7  C8  O4   180.00   0.0  0
 MD6  CONST_11  H6  C6  C5  N2   180.00   0.0  0
 MD6  CONST_12  H5  C5  N2  C4   180.00   0.0  0
 MD6  CONST_13  H7  C7  C8  C4   180.00   0.0  0
 MD6  CONST_14  C4  C3  N   CA   180.00   0.0  0
 MD6  CONST_15  H2  N   C3  C4     0.00   0.0  0
 MD6  CONST_16  O3  C3  N   CA     0.00   0.0  0
 MD6  Var_01    N2  C4  C3  N   -139.89  30.0  2
 MD6  Var_02    C3  N   CA  C    179.33  30.0  3
 MD6  Var_03    O   C   CA  N    177.96  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
 MD6  plan-1  N2   0.020
 MD6  plan-1  C3   0.020
 MD6  plan-1  C4   0.020
 MD6  plan-1  C5   0.020
 MD6  plan-1  C6   0.020
 MD6  plan-1  C7   0.020
 MD6  plan-1  C8   0.020
 MD6  plan-1  H5   0.020
 MD6  plan-1  H6   0.020
 MD6  plan-1  H7   0.020
 MD6  plan-1  O4   0.020
 MD6  plan-2  N    0.020
 MD6  plan-2  CA   0.020
 MD6  plan-2  C3   0.020
 MD6  plan-2  O3   0.020
 MD6  plan-2  C4   0.020
 MD6  plan-2  H2   0.020
 MD6  plan-3  C    0.020
 MD6  plan-3  O    0.020
 MD6  plan-3  CA   0.020
 MD6  plan-3  OXT  0.020

