# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:11:54 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: N-benzylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNCc1ccccc1
#
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
 04Q  04Q  'N-benzylglycine          '  ligand  23  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_04Q
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
 04Q  N5    N  NH1   0  -0.595   0.9597   0.0838   0.1251
 04Q  C9    C  CH2   0  -0.304  -0.0765  -0.2682   1.0740
 04Q  C10   C  CH2   0  -0.380   2.2744   0.0318   0.7088
 04Q  C16   C  CR6   0   0.076  -1.4530  -0.1518   0.4728
 04Q  C17   C  C     0   0.518   3.3339   0.4483  -0.2790
 04Q  C21   C  CR16  0  -0.310  -2.4467  -1.0650   0.8137
 04Q  C22   C  CR16  0  -0.293  -1.7697   0.8834  -0.4050
 04Q  O23   O  OH1   0  -0.595   4.5379   0.4537   0.2818
 04Q  O24   O  O     0  -0.438   3.1347   0.7280  -1.4329
 04Q  C28   C  CR16  0  -0.241  -3.7320  -0.9448   0.3001
 04Q  C29   C  CR16  0  -0.239  -3.0516   1.0034  -0.9238
 04Q  C34   C  CR16  0  -0.270  -4.0385   0.0904  -0.5724
 04Q  H91C  H  HCH2  0   0.218   0.0478  -1.2766   1.4970
 04Q  H92C  H  HCH2  0   0.245  -0.0030   0.4220   1.9218
 04Q  H101  H  HCH2  0   0.276   2.3180   0.7152   1.5631
 04Q  H102  H  HCH2  0   0.249   2.5570  -0.9566   1.1047
 04Q  H21   H  HCR6  0   0.248  -2.2138  -1.8821   1.4872
 04Q  H22   H  HCR6  0   0.246  -1.0043   1.5952  -0.6864
 04Q  H23   H  HOH1  0   0.483   5.2073   0.7062  -0.3716
 04Q  H28   H  HCR6  0   0.253  -4.4915  -1.6646   0.5779
 04Q  H29   H  HCR6  0   0.252  -3.2808   1.8141  -1.6040
 04Q  H34   H  HCR6  0   0.253  -5.0376   0.1835  -0.9785
 04Q  H2    H  HNH1  0   0.350   0.9127  -0.5421  -0.6699

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
 04Q  N5   C9    single    1.448  0.020  1.448
 04Q  N5   C10   single    1.439  0.020  1.439
 04Q  C9   C16   single    1.507  0.020  1.507
 04Q  C10  C17   single    1.507  0.020  1.507
 04Q  C16  C21   aromatic  1.392  0.020  1.392
 04Q  C16  C22   aromatic  1.394  0.020  1.394
 04Q  C17  O23   single    1.328  0.020  1.328
 04Q  C17  O24   double    1.204  0.020  1.204
 04Q  C21  C28   aromatic  1.389  0.020  1.389
 04Q  C22  C29   aromatic  1.388  0.020  1.388
 04Q  C28  C34   aromatic  1.388  0.020  1.388
 04Q  C29  C34   aromatic  1.390  0.020  1.390
 04Q  C9   H91C  single    0.970  0.020  1.090
 04Q  C9   H92C  single    0.970  0.020  1.090
 04Q  C10  H101  single    0.970  0.020  1.090
 04Q  C10  H102  single    0.970  0.020  1.090
 04Q  C21  H21   single    0.930  0.020  1.080
 04Q  C22  H22   single    0.930  0.020  1.080
 04Q  O23  H23   single    0.850  0.020  0.980
 04Q  C28  H28   single    0.930  0.020  1.080
 04Q  C29  H29   single    0.930  0.020  1.080
 04Q  C34  H34   single    0.930  0.020  1.080
 04Q  N5   H2    single    0.890  0.020  1.040

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
 04Q  H2    N5   C10   109.78  3.000
 04Q  H2    N5   C9    109.32  3.000
 04Q  C10   N5   C9    112.27  3.000
 04Q  H92C  C9   H91C  105.79  3.000
 04Q  H92C  C9   C16   108.75  3.000
 04Q  H91C  C9   C16   109.11  3.000
 04Q  H92C  C9   N5    107.81  3.000
 04Q  H91C  C9   N5    113.18  3.000
 04Q  C16   C9   N5    111.93  3.000
 04Q  H102  C10  H101  105.63  3.000
 04Q  H102  C10  C17   107.64  3.000
 04Q  H101  C10  C17   108.11  3.000
 04Q  H102  C10  N5    114.36  3.000
 04Q  H101  C10  N5    109.29  3.000
 04Q  C17   C10  N5    111.49  3.000
 04Q  C22   C16  C21   118.64  3.000
 04Q  C22   C16  C9    121.08  3.000
 04Q  C21   C16  C9    120.26  3.000
 04Q  O24   C17  O23   123.63  3.000
 04Q  O24   C17  C10   125.17  3.000
 04Q  O23   C17  C10   111.20  3.000
 04Q  H21   C21  C28   119.58  3.000
 04Q  H21   C21  C16   119.55  3.000
 04Q  C28   C21  C16   120.87  3.000
 04Q  H22   C22  C29   119.93  3.000
 04Q  H22   C22  C16   119.44  3.000
 04Q  C29   C22  C16   120.63  3.000
 04Q  H23   O23  C17   110.03  3.000
 04Q  H28   C28  C34   120.14  3.000
 04Q  H28   C28  C21   119.78  3.000
 04Q  C34   C28  C21   120.08  3.000
 04Q  H29   C29  C34   120.02  3.000
 04Q  H29   C29  C22   119.67  3.000
 04Q  C34   C29  C22   120.30  3.000
 04Q  H34   C34  C29   120.27  3.000
 04Q  H34   C34  C28   120.25  3.000
 04Q  C29   C34  C28   119.48  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
 04Q  CONST_01  C34  C28  C21  C16     0.00   0.0  0
 04Q  CONST_02  C34  C29  C22  C16     0.00   0.0  0
 04Q  CONST_03  C29  C22  C16  C21     0.00   0.0  0
 04Q  CONST_04  C29  C34  C28  C21     0.00   0.0  0
 04Q  CONST_05  C28  C21  C16  C22     0.00   0.0  0
 04Q  CONST_06  C28  C34  C29  C22     0.00   0.0  0
 04Q  CONST_07  C28  C21  C16  C9    180.00   0.0  0
 04Q  CONST_08  C29  C22  C16  C9    180.00   0.0  0
 04Q  CONST_09  H28  C28  C21  C16   180.00   0.0  0
 04Q  CONST_10  H29  C29  C22  C16   180.00   0.0  0
 04Q  CONST_11  H22  C22  C16  C21   180.00   0.0  0
 04Q  CONST_12  H34  C34  C28  C21   180.00   0.0  0
 04Q  CONST_13  H21  C21  C16  C22   180.00   0.0  0
 04Q  CONST_14  H23  O23  C17  C10   180.00   0.0  0
 04Q  Var_01    C21  C16  C9   N5    143.29  30.0  2
 04Q  Var_02    C16  C9   N5   C10   177.45  30.0  3
 04Q  Var_03    O23  C17  C10  N5    177.31  30.0  3
 04Q  Var_04    C17  C10  N5   C9   -177.97  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
 04Q  plan-1  C9   0.020
 04Q  plan-1  C16  0.020
 04Q  plan-1  C21  0.020
 04Q  plan-1  C22  0.020
 04Q  plan-1  C28  0.020
 04Q  plan-1  C29  0.020
 04Q  plan-1  C34  0.020
 04Q  plan-1  H21  0.020
 04Q  plan-1  H22  0.020
 04Q  plan-1  H28  0.020
 04Q  plan-1  H29  0.020
 04Q  plan-1  H34  0.020
 04Q  plan-2  C10  0.020
 04Q  plan-2  C17  0.020
 04Q  plan-2  O23  0.020
 04Q  plan-2  O24  0.020
 04Q  plan-2  H23  0.020

