# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:50:52 2021
#   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  32  17  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.480  51.9030   9.4022  46.3257
 RDY  C4   C  C     0   0.774  51.6645   8.8905  45.1167
 RDY  C5   C  CH2   0  -0.231  51.2354   8.8053  47.4406
 RDY  C6   C  CR6   0   0.076  51.4780   9.6942  48.6228
 RDY  C7   C  CR16  0  -0.281  50.9539  10.9858  48.6465
 RDY  C8   C  CR16  0  -0.241  51.1753  11.8137  49.7359
 RDY  C9   C  CR16  0  -0.263  51.9220  11.3586  50.8174
 RDY  C10  C  CR16  0  -0.241  52.4452  10.0741  50.8018
 RDY  C11  C  CR16  0  -0.304  52.2257   9.2477  49.7056
 RDY  O2   O  O     0  -0.517  50.9869   7.8996  44.9352
 RDY  N    N  NT    0  -0.486  52.2915   9.5973  44.1413
 RDY  C3   C  CH3   0  -0.538  51.9643   9.2825  42.7633
 RDY  C1   C  CH1   0  -0.213  52.8681  10.8929  44.4541
 RDY  C2   C  C     0   0.560  51.7650  11.8907  44.7838
 RDY  O1   O  OH1   0  -0.592  52.2620  13.0208  45.2648
 RDY  O    O  O     0  -0.434  50.5892  11.6862  44.6281
 RDY  C    C  CH3   0  -0.696  53.7722  11.4291  43.3451
 RDY  H1   H  HCH2  0   0.250  50.1664   8.7228  47.2331
 RDY  H2   H  HCH2  0   0.251  51.6231   7.8009  47.6225
 RDY  H3   H  HCR6  0   0.249  50.3658  11.3457  47.8103
 RDY  H4   H  HCR6  0   0.258  50.7626  12.8142  49.7459
 RDY  H5   H  HCR6  0   0.259  52.0934  12.0063  51.6676
 RDY  H6   H  HCR6  0   0.258  53.0274   9.7136  51.6399
 RDY  H7   H  HCR6  0   0.256  52.6417   8.2471  49.6946
 RDY  H8   H  HCH3  0   0.264  51.6692   8.2415  42.6843
 RDY  H9   H  HCH3  0   0.238  51.1490   9.9026  42.3849
 RDY  H10  H  HCH3  0   0.256  52.8317   9.4249  42.1246
 RDY  H11  H  HCH1  0   0.305  53.4958  10.7958  45.3416
 RDY  H12  H  HOH1  0   0.484  51.5494  13.6528  45.4444
 RDY  H13  H  HCH3  0   0.261  54.5423  10.6966  43.1071
 RDY  H14  H  HCH3  0   0.248  53.2289  11.6740  42.4334
 RDY  H15  H  HCH3  0   0.267  54.2729  12.3310  43.6906

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    1.451  0.020  1.451
 RDY  O    C2   double    1.204  0.020  1.204
 RDY  O1   C2   single    1.325  0.020  1.325
 RDY  C2   C1   single    1.524  0.020  1.524
 RDY  C    C1   single    1.528  0.020  1.528
 RDY  N    C1   single    1.452  0.020  1.452
 RDY  N    C4   single    1.358  0.020  1.358
 RDY  O2   C4   double    1.214  0.020  1.214
 RDY  C4   O3   single    1.334  0.020  1.334
 RDY  O3   C5   single    1.430  0.020  1.430
 RDY  C5   C6   single    1.499  0.020  1.499
 RDY  C6   C7   aromatic  1.394  0.020  1.394
 RDY  C6   C11  aromatic  1.390  0.020  1.390
 RDY  C7   C8   aromatic  1.386  0.020  1.386
 RDY  C11  C10  aromatic  1.390  0.020  1.390
 RDY  C8   C9   aromatic  1.391  0.020  1.391
 RDY  C10  C9   aromatic  1.387  0.020  1.387
 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  O1   H12  single    0.850  0.020  0.980
 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   117.58  3.000
 RDY  N    C4   O2   125.11  3.000
 RDY  O2   C4   O3   123.24  3.000
 RDY  N    C4   O3   111.64  3.000
 RDY  H2   C5   H1   108.04  3.000
 RDY  H2   C5   C6   110.89  3.000
 RDY  H1   C5   C6   110.68  3.000
 RDY  H2   C5   O3   110.37  3.000
 RDY  H1   C5   O3   109.90  3.000
 RDY  C6   C5   O3   106.97  3.000
 RDY  C11  C6   C7   119.13  3.000
 RDY  C11  C6   C5   120.74  3.000
 RDY  C7   C6   C5   120.13  3.000
 RDY  H3   C7   C8   119.65  3.000
 RDY  H3   C7   C6   119.91  3.000
 RDY  C8   C7   C6   120.44  3.000
 RDY  H4   C8   C9   120.00  3.000
 RDY  H4   C8   C7   119.90  3.000
 RDY  C9   C8   C7   120.10  3.000
 RDY  H5   C9   C10  120.21  3.000
 RDY  H5   C9   C8   120.00  3.000
 RDY  C10  C9   C8   119.79  3.000
 RDY  H6   C10  C11  119.84  3.000
 RDY  H6   C10  C9   120.18  3.000
 RDY  C11  C10  C9   119.99  3.000
 RDY  H7   C11  C10  119.75  3.000
 RDY  H7   C11  C6   119.69  3.000
 RDY  C10  C11  C6   120.56  3.000
 RDY  C1   N    C3   119.19  3.000
 RDY  C1   N    C4   119.53  3.000
 RDY  C3   N    C4   117.72  3.000
 RDY  H10  C3   H9   108.54  3.000
 RDY  H10  C3   H8   107.46  3.000
 RDY  H9   C3   H8   108.46  3.000
 RDY  H10  C3   N    110.47  3.000
 RDY  H9   C3   N    111.98  3.000
 RDY  H8   C3   N    109.80  3.000
 RDY  H11  C1   C    106.33  3.000
 RDY  H11  C1   C2   107.38  3.000
 RDY  C    C1   C2   110.83  3.000
 RDY  H11  C1   N    108.91  3.000
 RDY  C    C1   N    113.06  3.000
 RDY  C2   C1   N    110.08  3.000
 RDY  O    C2   O1   123.95  3.000
 RDY  O1   C2   C1   111.44  3.000
 RDY  O    C2   C1   124.61  3.000
 RDY  H12  O1   C2   110.34  3.000
 RDY  H15  C    H14  108.00  3.000
 RDY  H15  C    H13  107.55  3.000
 RDY  H14  C    H13  108.72  3.000
 RDY  H15  C    C1   109.44  3.000
 RDY  H14  C    C1   113.03  3.000
 RDY  H13  C    C1   109.94  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  CONST_14  H12  O1   C2   C1   180.00   0.0  0
 RDY  Var_01    C7   C6   C5   O3    65.39  30.0  2
 RDY  Var_02    C6   C5   O3   C4  -170.39  30.0  3
 RDY  Var_03    C3   N    C4   O3  -170.94  30.0  1
 RDY  Var_04    N    C4   O3   C5   176.17  30.0  1
 RDY  Var_05    H8   C3   N    C4   -28.75  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-2  H12  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

