# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:19:47 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  22  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 OK
;

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  -0.592   0.9269   0.2676   0.1889
 04Q  C9    C  CH2    0  -0.308  -0.0965  -0.1624   1.1153
 04Q  C10   C  CH2    0  -0.402   2.2513   0.2651   0.7710
 04Q  C16   C  CR6    0   0.087  -1.4689  -0.1329   0.4953
 04Q  C17   C  C      0   0.390   3.3708   0.3176  -0.2844
 04Q  C21   C  CR16   0  -0.316  -2.3571  -1.1882   0.6813
 04Q  C22   C  CR16   0  -0.292  -1.8846   0.9624  -0.2612
 04Q  O23   O  OC    -1  -0.623   4.4952   0.6609   0.1297
 04Q  O24   O  O      0  -0.608   3.0736  -0.0246  -1.4457
 04Q  C28   C  CR16   0  -0.240  -3.6347  -1.1511   0.1349
 04Q  C29   C  CR16   0  -0.241  -3.1585   1.0027  -0.8095
 04Q  C34   C  CR16   0  -0.273  -4.0396  -0.0547  -0.6132
 04Q  H91C  H  HCH2   0   0.204   0.0928  -1.1663   1.5297
 04Q  H92C  H  HCH2   0   0.230  -0.0832   0.5181   1.9747
 04Q  H101  H  HCH2   0   0.215   2.3538   1.1142   1.4541
 04Q  H102  H  HCH2   0   0.193   2.4351  -0.6331   1.3894
 04Q  H21   H  HCR6   0   0.246  -2.0471  -2.0518   1.2589
 04Q  H22   H  HCR6   0   0.244  -1.2001   1.7856  -0.4222
 04Q  H28   H  HCR6   0   0.252  -4.3117  -1.9816   0.2907
 04Q  H29   H  HCR6   0   0.251  -3.4660   1.8619  -1.3924
 04Q  H34   H  HCR6   0   0.252  -5.0324  -0.0245  -1.0437
 04Q  H2    H  HNH1   0   0.331   0.9375  -0.3375  -0.6228

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    1.446  0.020  1.446
 04Q  N5   C10   single    1.447  0.020  1.447
 04Q  C9   C16   single    1.506  0.020  1.506
 04Q  C10  C17   single    1.539  0.020  1.539
 04Q  C16  C21   aromatic  1.392  0.020  1.392
 04Q  C16  C22   aromatic  1.395  0.020  1.395
 04Q  C17  O23   deloc     1.246  0.020  1.246
 04Q  C17  O24   deloc     1.247  0.020  1.247
 04Q  C21  C28   aromatic  1.390  0.020  1.390
 04Q  C22  C29   aromatic  1.387  0.020  1.387
 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  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   108.18  3.000
 04Q  H2    N5   C9    110.08  3.000
 04Q  C10   N5   C9    112.94  3.000
 04Q  H92C  C9   H91C  105.57  3.000
 04Q  H92C  C9   C16   108.76  3.000
 04Q  H91C  C9   C16   109.21  3.000
 04Q  H92C  C9   N5    108.00  3.000
 04Q  H91C  C9   N5    112.96  3.000
 04Q  C16   C9   N5    112.05  3.000
 04Q  H102  C10  H101  105.40  3.000
 04Q  H102  C10  C17   106.87  3.000
 04Q  H101  C10  C17   109.47  3.000
 04Q  H102  C10  N5    112.24  3.000
 04Q  H101  C10  N5    109.60  3.000
 04Q  C17   C10  N5    112.95  3.000
 04Q  C22   C16  C21   118.54  3.000
 04Q  C22   C16  C9    120.68  3.000
 04Q  C21   C16  C9    120.77  3.000
 04Q  O24   C17  O23   126.88  3.000
 04Q  O24   C17  C10   117.13  3.000
 04Q  O23   C17  C10   115.95  3.000
 04Q  H21   C21  C28   119.56  3.000
 04Q  H21   C21  C16   119.52  3.000
 04Q  C28   C21  C16   120.92  3.000
 04Q  H22   C22  C29   119.98  3.000
 04Q  H22   C22  C16   119.30  3.000
 04Q  C29   C22  C16   120.72  3.000
 04Q  H28   C28  C34   120.08  3.000
 04Q  H28   C28  C21   119.85  3.000
 04Q  C34   C28  C21   120.07  3.000
 04Q  H29   C29  C34   119.97  3.000
 04Q  H29   C29  C22   119.77  3.000
 04Q  C34   C29  C22   120.26  3.000
 04Q  H34   C34  C29   120.25  3.000
 04Q  H34   C34  C28   120.26  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  Var_01    C21  C16  C9   N5   135.78  30.0  2
 04Q  Var_02    C16  C9   N5   C10  179.16  30.0  3
 04Q  Var_03    O23  C17  C10  N5   162.21  30.0  3
 04Q  Var_04    C17  C10  N5   C9   163.28  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

