# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:19:27 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]-N-methyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N(C)C(=O)OCc1ccccc1)C(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
 RDY  RDY  N-[(benzyloxy)carbonyl]-N-methyl-L-alanine  ligand  31  17  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RDY
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
 RDY  O3   O  O2     0  -0.486  51.5529   9.7073  46.4130
 RDY  C4   C  C      0   0.765  51.4173   9.1691  45.1912
 RDY  C5   C  CH2    0  -0.215  50.9387   9.0137  47.4960
 RDY  C6   C  CR6    0   0.069  51.3145   9.7235  48.7636
 RDY  C7   C  CR16   0  -0.306  50.3329  10.1776  49.6369
 RDY  C8   C  CR16   0  -0.237  50.6784  10.8009  50.8304
 RDY  C9   C  CR16   0  -0.264  52.0140  10.9855  51.1551
 RDY  C10  C  CR16   0  -0.239  53.0022  10.5407  50.2836
 RDY  C11  C  CR16   0  -0.283  52.6550   9.9109  49.0986
 RDY  O2   O  O      0  -0.535  50.7549   8.1664  44.9871
 RDY  N    N  NT     0  -0.456  52.0889   9.8357  44.2393
 RDY  C3   C  CH3    0  -0.519  51.8825   9.3924  42.8749
 RDY  C1   C  CH1    0  -0.266  52.7811  11.1000  44.4505
 RDY  C2   C  C      0   0.419  51.9670  12.2977  43.8833
 RDY  O1   O  OC    -1  -0.598  52.6131  13.3431  43.6813
 RDY  O    O  O      0  -0.595  50.7457  12.1202  43.7279
 RDY  C    C  CH3    0  -0.646  54.2180  11.0349  43.9430
 RDY  H1   H  HCH2   0   0.243  49.8529   8.9943  47.3761
 RDY  H2   H  HCH2   0   0.241  51.2875   7.9779  47.5260
 RDY  H3   H  HCR6   0   0.254  49.2874  10.0439  49.3849
 RDY  H4   H  HCR6   0   0.255  49.9024  11.1463  51.5014
 RDY  H5   H  HCR6   0   0.255  52.2864  11.4729  52.0824
 RDY  H6   H  HCR6   0   0.255  54.0464  10.6803  50.5322
 RDY  H7   H  HCR6   0   0.250  53.4338   9.5601  48.4320
 RDY  H8   H  HCH3   0   0.233  50.8282   9.3975  42.5979
 RDY  H9   H  HCH3   0   0.241  52.4035  10.0627  42.1978
 RDY  H10  H  HCH3   0   0.232  52.2760   8.3884  42.7133
 RDY  H11  H  HCH1   0   0.265  52.8402  11.2644  45.5269
 RDY  H13  H  HCH3   0   0.218  54.7443  10.1884  44.3860
 RDY  H14  H  HCH3   0   0.217  54.2799  10.9399  42.8580
 RDY  H15  H  HCH3   0   0.230  54.7512  11.9412  44.2197

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
 RDY  C3   N    single    1.449  0.020  1.449
 RDY  O    C2   deloc     1.244  0.020  1.244
 RDY  O1   C2   deloc     1.246  0.020  1.246
 RDY  C2   C1   single    1.555  0.020  1.555
 RDY  C    C1   single    1.525  0.020  1.525
 RDY  N    C1   single    1.457  0.020  1.457
 RDY  N    C4   single    1.342  0.020  1.342
 RDY  O2   C4   double    1.219  0.020  1.219
 RDY  C4   O3   single    1.342  0.020  1.342
 RDY  O3   C5   single    1.425  0.020  1.425
 RDY  C5   C6   single    1.501  0.020  1.501
 RDY  C6   C7   aromatic  1.390  0.020  1.390
 RDY  C6   C11  aromatic  1.394  0.020  1.394
 RDY  C7   C8   aromatic  1.390  0.020  1.390
 RDY  C11  C10  aromatic  1.386  0.020  1.386
 RDY  C8   C9   aromatic  1.387  0.020  1.387
 RDY  C10  C9   aromatic  1.391  0.020  1.391
 RDY  C5   H1   single    0.970  0.020  1.090
 RDY  C5   H2   single    0.970  0.020  1.090
 RDY  C7   H3   single    0.930  0.020  1.080
 RDY  C8   H4   single    0.930  0.020  1.080
 RDY  C9   H5   single    0.930  0.020  1.080
 RDY  C10  H6   single    0.930  0.020  1.080
 RDY  C11  H7   single    0.930  0.020  1.080
 RDY  C3   H8   single    0.970  0.020  1.090
 RDY  C3   H9   single    0.970  0.020  1.090
 RDY  C3   H10  single    0.970  0.020  1.090
 RDY  C1   H11  single    0.970  0.020  1.090
 RDY  C    H13  single    0.970  0.020  1.090
 RDY  C    H14  single    0.970  0.020  1.090
 RDY  C    H15  single    0.970  0.020  1.090

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
 RDY  C5   O3   C4   116.94  3.000
 RDY  N    C4   O2   124.17  3.000
 RDY  O2   C4   O3   122.50  3.000
 RDY  N    C4   O3   113.32  3.000
 RDY  H2   C5   H1   107.65  3.000
 RDY  H2   C5   C6   110.18  3.000
 RDY  H1   C5   C6   110.49  3.000
 RDY  H2   C5   O3   110.15  3.000
 RDY  H1   C5   O3   110.70  3.000
 RDY  C6   C5   O3   107.68  3.000
 RDY  C11  C6   C7   118.95  3.000
 RDY  C11  C6   C5   120.48  3.000
 RDY  C7   C6   C5   120.55  3.000
 RDY  H3   C7   C8   119.65  3.000
 RDY  H3   C7   C6   119.67  3.000
 RDY  C8   C7   C6   120.68  3.000
 RDY  H4   C8   C9   120.19  3.000
 RDY  H4   C8   C7   119.81  3.000
 RDY  C9   C8   C7   120.00  3.000
 RDY  H5   C9   C10  120.14  3.000
 RDY  H5   C9   C8   120.19  3.000
 RDY  C10  C9   C8   119.67  3.000
 RDY  H6   C10  C11  119.77  3.000
 RDY  H6   C10  C9   120.02  3.000
 RDY  C11  C10  C9   120.21  3.000
 RDY  H7   C11  C10  119.54  3.000
 RDY  H7   C11  C6   119.98  3.000
 RDY  C10  C11  C6   120.48  3.000
 RDY  C1   N    C3   118.01  3.000
 RDY  C1   N    C4   124.47  3.000
 RDY  C3   N    C4   116.39  3.000
 RDY  H10  C3   H9   107.63  3.000
 RDY  H10  C3   H8   108.40  3.000
 RDY  H9   C3   H8   107.62  3.000
 RDY  H10  C3   N    111.70  3.000
 RDY  H9   C3   N    109.26  3.000
 RDY  H8   C3   N    112.05  3.000
 RDY  H11  C1   C    106.48  3.000
 RDY  H11  C1   C2   105.80  3.000
 RDY  C    C1   C2   113.87  3.000
 RDY  H11  C1   N    107.44  3.000
 RDY  C    C1   N    111.24  3.000
 RDY  C2   C1   N    111.51  3.000
 RDY  O    C2   O1   127.51  3.000
 RDY  O1   C2   C1   115.72  3.000
 RDY  O    C2   C1   116.72  3.000
 RDY  H15  C    H14  107.32  3.000
 RDY  H15  C    H13  107.88  3.000
 RDY  H14  C    H13  108.00  3.000
 RDY  H15  C    C1   109.98  3.000
 RDY  H14  C    C1   112.84  3.000
 RDY  H13  C    C1   110.65  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
 RDY  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 RDY  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 RDY  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 RDY  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 RDY  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 RDY  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 RDY  CONST_07  C8   C7   C6   C5   180.00   0.0  0
 RDY  CONST_08  C10  C11  C6   C5   180.00   0.0  0
 RDY  CONST_09  H4   C8   C7   C6   180.00   0.0  0
 RDY  CONST_10  H6   C10  C11  C6   180.00   0.0  0
 RDY  CONST_11  H7   C11  C6   C7   180.00   0.0  0
 RDY  CONST_12  H5   C9   C8   C7   180.00   0.0  0
 RDY  CONST_13  H3   C7   C8   C9   180.00   0.0  0
 RDY  Var_01    C7   C6   C5   O3   124.81  30.0  2
 RDY  Var_02    C6   C5   O3   C4   175.29  30.0  3
 RDY  Var_03    C3   N    C4   O3  -174.05  30.0  2
 RDY  Var_04    N    C4   O3   C5  -176.25  30.0  1
 RDY  Var_05    H8   C3   N    C4    55.67  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RDY  chir_01  C1  C2  C  N  positiv

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
 RDY  plan-1  C5   0.020
 RDY  plan-1  C6   0.020
 RDY  plan-1  C7   0.020
 RDY  plan-1  C8   0.020
 RDY  plan-1  C9   0.020
 RDY  plan-1  C10  0.020
 RDY  plan-1  C11  0.020
 RDY  plan-1  H3   0.020
 RDY  plan-1  H4   0.020
 RDY  plan-1  H5   0.020
 RDY  plan-1  H6   0.020
 RDY  plan-1  H7   0.020
 RDY  plan-2  C1   0.020
 RDY  plan-2  C2   0.020
 RDY  plan-2  O1   0.020
 RDY  plan-2  O    0.020
 RDY  plan-3  O3   0.020
 RDY  plan-3  C4   0.020
 RDY  plan-3  O2   0.020
 RDY  plan-3  N    0.020

