# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:38:41 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (3S)-3-[(E)-(1-carboxyethylidene)amino]-4-methoxy-4-oxobutanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](CC(O)=O)N=C(C)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
 3A5  3A5  '(3S)-3-[(E)-(1-carboxyethylidene)amino]-4-methoxy-4-oxobutanoic acid (non-preferred name)'  L-peptide  24  15  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3A5
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
 3A5  CA    C  C      0   0.068   0.7660  23.2171  18.5827
 3A5  CB    C  CH3    0  -0.735  -0.6373  22.6955  18.4540
 3A5  C     C  C      0   0.369   1.4046  23.0856  19.9842
 3A5  O     O  O      0  -0.587   2.4254  23.7530  20.2132
 3A5  O1    O  O      0  -0.603   0.1760  26.4631  16.7583
 3A5  O2    O  OC    -1  -0.609   2.1963  27.2437  16.2224
 3A5  C2    C  CH2    0  -0.561   1.6845  25.0031  15.6330
 3A5  C3    C  CH1    0  -0.261   0.9956  23.8163  16.3024
 3A5  N     N  N      0  -0.346   1.4872  23.6900  17.6535
 3A5  C4    C  C      0   0.608   1.2225  22.5624  15.4735
 3A5  O4    O  O      0  -0.457   0.9003  22.4781  14.3130
 3A5  O45   O  O2     0  -0.439   1.7992  21.5761  16.1401
 3A5  C5    C  CH3    0  -0.423   2.0505  20.3644  15.4309
 3A5  OXT   O  OC    -1  -0.588   0.8230  22.2954  20.7529
 3A5  HB1   H  HCH3   0   0.237  -1.1349  22.9980  17.5353
 3A5  HB2   H  HCH3   0   0.248  -0.6261  21.6041  18.4756
 3A5  HB3   H  HCH3   0   0.244  -1.2482  23.0166  19.2959
 3A5  H21C  H  HCH2   0   0.234   1.3827  25.0507  14.5817
 3A5  H22C  H  HCH2   0   0.216   2.7672  24.8559  15.6425
 3A5  H3    H  HCH1   0   0.251  -0.0841  24.0028  16.2510
 3A5  H51   H  HCH3   0   0.248   2.5094  19.6895  16.1478
 3A5  H52   H  HCH3   0   0.236   1.1291  19.9200  15.0557
 3A5  H53   H  HCH3   0   0.236   2.7358  20.5245  14.5985
 3A5  C1    C  C      0   0.414   1.3221  26.3575  16.2784

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
 3A5  CA   CB    single  1.521  0.033  1.521
 3A5  CA   C     single  1.525  0.021  1.525
 3A5  CA   N     double  1.458  0.019  1.458
 3A5  C    O     deloc   1.231  0.020  1.231
 3A5  C    OXT   deloc   1.246  0.020  1.246
 3A5  O1   C1    deloc   1.247  0.020  1.247
 3A5  C1   O2    deloc   1.246  0.020  1.246
 3A5  C1   C2    single  1.544  0.020  1.544
 3A5  C2   C3    single  1.527  0.020  1.527
 3A5  C3   N     single  1.443  0.020  1.443
 3A5  C3   C4    single  1.520  0.020  1.520
 3A5  C4   O4    double  1.207  0.020  1.207
 3A5  C4   O45   single  1.323  0.020  1.323
 3A5  O45  C5    single  1.426  0.020  1.426
 3A5  CB   HB1   single  0.970  0.020  1.090
 3A5  CB   HB2   single  0.970  0.020  1.090
 3A5  CB   HB3   single  0.970  0.020  1.090
 3A5  C2   H21C  single  0.970  0.020  1.090
 3A5  C2   H22C  single  0.970  0.020  1.090
 3A5  C3   H3    single  0.970  0.020  1.090
 3A5  C5   H51   single  0.970  0.020  1.090
 3A5  C5   H52   single  0.970  0.020  1.090
 3A5  C5   H53   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
 3A5  N     CA   C     111.00  2.800
 3A5  N     CA   CB    110.40  1.500
 3A5  C     CA   CB    110.50  1.500
 3A5  HB3   CB   HB2   106.58  3.000
 3A5  HB3   CB   HB1   108.33  3.000
 3A5  HB2   CB   HB1   107.43  3.000
 3A5  HB3   CB   CA    110.82  3.000
 3A5  HB2   CB   CA    109.62  3.000
 3A5  HB1   CB   CA    113.77  3.000
 3A5  OXT   C    O     127.66  3.000
 3A5  OXT   C    CA    120.80  1.700
 3A5  O     C    CA    120.80  1.700
 3A5  H22C  C2   H21C  106.70  3.000
 3A5  H22C  C2   C3    109.79  3.000
 3A5  H21C  C2   C3    109.30  3.000
 3A5  H22C  C2   C1    110.31  3.000
 3A5  H21C  C2   C1    107.37  3.000
 3A5  C3    C2   C1    113.13  3.000
 3A5  H3    C3   C4    105.17  3.000
 3A5  H3    C3   N     113.20  3.000
 3A5  C4    C3   N     112.79  3.000
 3A5  H3    C3   C2    106.95  3.000
 3A5  C4    C3   C2    109.56  3.000
 3A5  N     C3   C2    108.95  3.000
 3A5  C3    N    CA    121.67  3.000
 3A5  O45   C4   O4    123.28  3.000
 3A5  O45   C4   C3    113.92  3.000
 3A5  O4    C4   C3    122.81  3.000
 3A5  C5    O45  C4    117.37  3.000
 3A5  H53   C5   H52   109.19  3.000
 3A5  H53   C5   H51   109.24  3.000
 3A5  H52   C5   H51   109.34  3.000
 3A5  H53   C5   O45   111.44  3.000
 3A5  H52   C5   O45   111.64  3.000
 3A5  H51   C5   O45   105.91  3.000
 3A5  C2    C1   O2    116.14  3.000
 3A5  C2    C1   O1    116.80  3.000
 3A5  O2    C1   O1    127.01  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
 3A5  Var_01  O    C   CA   CB  -164.58  30.0  2
 3A5  Var_02  C3   C2  C1   O1   -32.17  30.0  3
 3A5  Var_03  HB1  CB  CA   C    167.05  30.0  3
 3A5  Var_04  H51  C5  O45  C4  -179.32  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
 3A5  chir_01  C3  C2  N  C4  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
 3A5  plan-1  CA   0.020
 3A5  plan-1  C    0.020
 3A5  plan-1  O    0.020
 3A5  plan-1  OXT  0.020
 3A5  plan-2  O1   0.020
 3A5  plan-2  O2   0.020
 3A5  plan-2  C2   0.020
 3A5  plan-2  C1   0.020
 3A5  plan-3  CA   0.020
 3A5  plan-3  CB   0.020
 3A5  plan-3  C    0.020
 3A5  plan-3  C3   0.020
 3A5  plan-3  N    0.020
 3A5  plan-4  C3   0.020
 3A5  plan-4  C4   0.020
 3A5  plan-4  O4   0.020
 3A5  plan-4  O45  0.020

