# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 11:23:18 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: methyl L-alpha-aspartyl-L-phenylalaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CC(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
 PME  PME  'methyl L-alpha-aspartyl-L-phenylalaninate'  ligand  39  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PME
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
 PME  N1    N  NH2   0  -0.784  -1.8767   1.5079  -2.3047
 PME  C2    C  CH1   0  -0.238  -0.9418   0.4557  -1.9697
 PME  C3    C  CH2   0  -0.590   0.0216   0.0470  -3.0923
 PME  C4    C  C     0   0.557  -0.6681  -0.6323  -4.2443
 PME  O5    O  O     0  -0.442  -1.8172  -0.9994  -4.2455
 PME  O6    O  OH1   0  -0.591   0.1520  -0.8073  -5.2727
 PME  C7    C  C     0   0.577  -0.0861   0.9149  -0.7985
 PME  O8    O  O     0  -0.485   0.3900   2.0377  -0.7530
 PME  N9    N  NH1   0  -0.632   0.1368  -0.0119   0.1503
 PME  C10   C  CH1   0  -0.178   1.0823   0.1953   1.2114
 PME  C11   C  CH2   0  -0.564   0.8177  -0.7846   2.3647
 PME  C12   C  CR6   0   0.149  -0.5396  -0.5673   2.9738
 PME  C13   C  CR16  0  -0.323  -1.6034  -1.4168   2.6877
 PME  C14   C  CR16  0  -0.240  -2.8598  -1.1918   3.2374
 PME  C15   C  CR16  0  -0.269  -3.0668  -0.1091   4.0806
 PME  C16   C  CR16  0  -0.239  -2.0107   0.7461   4.3721
 PME  C17   C  CR16  0  -0.300  -0.7580   0.5163   3.8226
 PME  C18   C  C     0   0.594   2.5345   0.0759   0.7637
 PME  O19   O  O     0  -0.451   3.4528   0.4410   1.4538
 PME  O20   O  O2    0  -0.438   2.6692  -0.4845  -0.4211
 PME  C21   C  CH3   0  -0.425   3.9966  -0.6603  -0.9221
 PME  HN11  H  HNH2  0   0.355  -2.4849   1.1964  -3.0496
 PME  HN12  H  HNH2  0   0.346  -1.3776   2.3173  -2.6522
 PME  H2    H  HCH1  0   0.267  -1.5186  -0.4230  -1.6701
 PME  H31   H  HCH2  0   0.289   0.5612   0.9242  -3.4610
 PME  H32   H  HCH2  0   0.294   0.7887  -0.6402  -2.7186
 PME  HO6   H  HOH1  0   0.481  -0.3066  -1.2748  -5.9873
 PME  HN9   H  HNH1  0   0.405  -0.2163  -0.9454   0.0064
 PME  H10   H  HCH1  0   0.303   0.9668   1.2129   1.5925
 PME  H111  H  HCH2  0   0.275   0.9144  -1.8116   2.0025
 PME  H112  H  HCH2  0   0.286   1.5929  -0.6410   3.1185
 PME  H13   H  HCR6  0   0.249  -1.4486  -2.2667   2.0327
 PME  H14   H  HCR6  0   0.256  -3.6763  -1.8640   3.0065
 PME  H15   H  HCR6  0   0.256  -4.0441   0.0662   4.5117
 PME  H16   H  HCR6  0   0.256  -2.1620   1.5907   5.0320
 PME  H17   H  HCR6  0   0.251   0.0622   1.1861   4.0573
 PME  H211  H  HCH3  0   0.254   3.8869  -1.1283  -1.8954
 PME  H212  H  HCH3  0   0.244   4.5062   0.2960  -1.0347
 PME  H213  H  HCH3  0   0.244   4.5818  -1.3083  -0.2705

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
 PME  N1   C2    single    1.447  0.020  1.447
 PME  N1   HN11  single    0.890  0.020  1.040
 PME  N1   HN12  single    0.890  0.020  1.040
 PME  C2   C3    single    1.535  0.020  1.535
 PME  C2   C7    single    1.522  0.020  1.522
 PME  C2   H2    single    0.970  0.020  1.090
 PME  C3   C4    single    1.505  0.020  1.505
 PME  C3   H31   single    0.970  0.020  1.090
 PME  C3   H32   single    0.970  0.020  1.090
 PME  C4   O5    double    1.206  0.020  1.206
 PME  C4   O6    single    1.327  0.020  1.327
 PME  O6   HO6   single    0.850  0.020  0.980
 PME  C7   O8    double    1.220  0.020  1.220
 PME  C7   N9    single    1.345  0.020  1.345
 PME  N9   C10   single    1.436  0.020  1.436
 PME  N9   HN9   single    0.860  0.020  1.020
 PME  C10  C11   single    1.536  0.020  1.536
 PME  C10  C18   single    1.524  0.020  1.524
 PME  C10  H10   single    0.970  0.020  1.090
 PME  C11  C12   single    1.504  0.020  1.504
 PME  C11  H111  single    0.970  0.020  1.090
 PME  C11  H112  single    0.970  0.020  1.090
 PME  C12  C13   aromatic  1.391  0.020  1.391
 PME  C12  C17   aromatic  1.394  0.020  1.394
 PME  C13  C14   aromatic  1.390  0.020  1.390
 PME  C13  H13   single    0.930  0.020  1.080
 PME  C14  C15   aromatic  1.388  0.020  1.388
 PME  C14  H14   single    0.930  0.020  1.080
 PME  C15  C16   aromatic  1.390  0.020  1.390
 PME  C15  H15   single    0.930  0.020  1.080
 PME  C16  C17   aromatic  1.387  0.020  1.387
 PME  C16  H16   single    0.930  0.020  1.080
 PME  C17  H17   single    0.930  0.020  1.080
 PME  C18  O19   double    1.205  0.020  1.205
 PME  C18  O20   single    1.318  0.020  1.318
 PME  O20  C21   single    1.430  0.020  1.430
 PME  C21  H211  single    0.970  0.020  1.090
 PME  C21  H212  single    0.970  0.020  1.090
 PME  C21  H213  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
 PME  HN12  N1   HN11  106.86  3.000
 PME  HN12  N1   C2    110.03  3.000
 PME  HN11  N1   C2    109.59  3.000
 PME  H2    C2   C7    109.18  3.000
 PME  H2    C2   C3    108.52  3.000
 PME  C7    C2   C3    106.88  3.000
 PME  H2    C2   N1    107.89  3.000
 PME  C7    C2   N1    108.79  3.000
 PME  C3    C2   N1    115.46  3.000
 PME  H32   C3   H31   105.81  3.000
 PME  H32   C3   C4    107.39  3.000
 PME  H31   C3   C4    109.28  3.000
 PME  H32   C3   C2    110.92  3.000
 PME  H31   C3   C2    110.04  3.000
 PME  C4    C3   C2    113.11  3.000
 PME  O6    C4   O5    123.22  3.000
 PME  O6    C4   C3    111.69  3.000
 PME  O5    C4   C3    125.08  3.000
 PME  HO6   O6   C4    110.04  3.000
 PME  N9    C7   O8    122.90  3.000
 PME  N9    C7   C2    115.35  3.000
 PME  O8    C7   C2    121.72  3.000
 PME  HN9   N9   C10   118.00  3.000
 PME  HN9   N9   C7    118.64  3.000
 PME  C10   N9   C7    122.07  3.000
 PME  H10   C10  C18   106.02  3.000
 PME  H10   C10  C11   108.30  3.000
 PME  C18   C10  C11   109.55  3.000
 PME  H10   C10  N9    108.81  3.000
 PME  C18   C10  N9    113.51  3.000
 PME  C11   C10  N9    110.44  3.000
 PME  H112  C11  H111  106.85  3.000
 PME  H112  C11  C12   110.03  3.000
 PME  H111  C11  C12   110.48  3.000
 PME  H112  C11  C10   108.21  3.000
 PME  H111  C11  C10   109.59  3.000
 PME  C12   C11  C10   111.55  3.000
 PME  C17   C12  C13   118.70  3.000
 PME  C17   C12  C11   120.04  3.000
 PME  C13   C12  C11   121.25  3.000
 PME  H13   C13  C14   119.67  3.000
 PME  H13   C13  C12   119.59  3.000
 PME  C14   C13  C12   120.74  3.000
 PME  H14   C14  C15   120.10  3.000
 PME  H14   C14  C13   119.80  3.000
 PME  C15   C14  C13   120.10  3.000
 PME  H15   C15  C16   120.19  3.000
 PME  H15   C15  C14   120.20  3.000
 PME  C16   C15  C14   119.61  3.000
 PME  H16   C16  C17   119.80  3.000
 PME  H16   C16  C15   120.11  3.000
 PME  C17   C16  C15   120.08  3.000
 PME  H17   C17  C16   119.67  3.000
 PME  H17   C17  C12   119.56  3.000
 PME  C16   C17  C12   120.77  3.000
 PME  O20   C18  O19   124.46  3.000
 PME  O20   C18  C10   113.25  3.000
 PME  O19   C18  C10   122.28  3.000
 PME  C21   O20  C18   117.54  3.000
 PME  H213  C21  H212  109.43  3.000
 PME  H213  C21  H211  109.52  3.000
 PME  H212  C21  H211  109.45  3.000
 PME  H213  C21  O20   111.24  3.000
 PME  H212  C21  O20   111.26  3.000
 PME  H211  C21  O20   105.87  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
 PME  CONST_01  C15   C14  C13  C12     0.00   0.0  0
 PME  CONST_02  C15   C16  C17  C12     0.00   0.0  0
 PME  CONST_03  C16   C17  C12  C13     0.00   0.0  0
 PME  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 PME  CONST_05  C17   C12  C13  C14     0.00   0.0  0
 PME  CONST_06  C17   C16  C15  C14     0.00   0.0  0
 PME  CONST_07  C14   C13  C12  C11   180.00   0.0  0
 PME  CONST_08  C16   C17  C12  C11   180.00   0.0  0
 PME  CONST_09  H14   C14  C13  C12   180.00   0.0  0
 PME  CONST_10  H16   C16  C17  C12   180.00   0.0  0
 PME  CONST_11  H17   C17  C12  C13   180.00   0.0  0
 PME  CONST_12  H15   C15  C14  C13   180.00   0.0  0
 PME  CONST_13  H13   C13  C14  C15   180.00   0.0  0
 PME  CONST_14  C10   N9   C7   C2    180.00   0.0  0
 PME  CONST_15  C10   N9   C7   O8      0.00   0.0  0
 PME  CONST_16  HN9   N9   C7   C2      0.00   0.0  0
 PME  CONST_17  HO6   O6   C4   C3    180.00   0.0  0
 PME  Var_01    C13   C12  C11  C10   102.81  30.0  2
 PME  Var_02    O5    C4   C3   C2     -9.75  30.0  3
 PME  Var_03    H211  C21  O20  C18  -179.85  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
 PME  chir_01  C2   N1  C3   C7   negativ
 PME  chir_02  C10  N9  C11  C18  negativ

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
 PME  plan-1  C11  0.020
 PME  plan-1  C12  0.020
 PME  plan-1  C13  0.020
 PME  plan-1  C14  0.020
 PME  plan-1  C15  0.020
 PME  plan-1  C16  0.020
 PME  plan-1  C17  0.020
 PME  plan-1  H13  0.020
 PME  plan-1  H14  0.020
 PME  plan-1  H15  0.020
 PME  plan-1  H16  0.020
 PME  plan-1  H17  0.020
 PME  plan-2  C2   0.020
 PME  plan-2  C7   0.020
 PME  plan-2  O8   0.020
 PME  plan-2  N9   0.020
 PME  plan-2  C10  0.020
 PME  plan-2  HN9  0.020
 PME  plan-3  C3   0.020
 PME  plan-3  C4   0.020
 PME  plan-3  O5   0.020
 PME  plan-3  O6   0.020
 PME  plan-3  HO6  0.020
 PME  plan-4  C10  0.020
 PME  plan-4  C18  0.020
 PME  plan-4  O19  0.020
 PME  plan-4  O20  0.020

