# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:43:53 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-2-amino-2-carboxyethyl 1-carboxy-L-prolyl-L-prolinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](COC(=O)[C@@H]1CCCN1C(=O)[C@@H]2CCCN2C(O)=O)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
 A9D  A9D  '(2S)-2-amino-2-carboxyethyl 1-carboxy-L-prolyl-L-prolinate'  L-peptide  43  24  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9D
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
 A9D  C     C  C      0   0.401   5.3224  -1.5086   0.0260
 A9D  N     N  NH2    0  -0.795   3.3387  -1.6478  -1.4639
 A9D  O     O  O      0  -0.594   5.2715  -2.7512   0.0423
 A9D  C1    C  C      0   0.596   1.3780   1.2369   0.5039
 A9D  O2    O  O      0  -0.453   1.3042   1.1252   1.7012
 A9D  C3    C  CH1    0  -0.152   0.3741   2.0055  -0.3333
 A9D  C4    C  CH2    0  -0.475   0.5014   3.5193  -0.1284
 A9D  C5    C  CH2    0  -0.484  -0.9202   4.0087  -0.3764
 A9D  C6    C  CH2    0  -0.267  -1.7794   2.9316   0.2752
 A9D  N7    N  NT     0  -0.486  -0.9786   1.7241   0.1052
 A9D  C8    C  C      0   0.578  -1.3970   0.4484   0.1560
 A9D  O9    O  O      0  -0.512  -0.6513  -0.4656  -0.1788
 A9D  CA    C  CH1    0  -0.253   4.1617  -0.7544  -0.6731
 A9D  CB    C  CH2    0  -0.176   3.3992   0.0006   0.4104
 A9D  OG    O  O2     0  -0.460   2.3705   0.7706  -0.2322
 A9D  C10   C  CH1    0  -0.141  -2.7625   0.1611   0.7614
 A9D  C11   C  CH2    0  -0.478  -2.5947  -0.4726   2.1566
 A9D  C12   C  CH2    0  -0.472  -3.6907  -1.5354   2.2024
 A9D  C13   C  CH2    0  -0.238  -3.7340  -2.0403   0.7654
 A9D  N14   N  NT     0  -0.492  -3.4644  -0.8431   0.0073
 A9D  C15   C  C      0   0.521  -3.6205  -0.7207  -1.3688
 A9D  O16   O  O      0  -0.644  -3.2526   0.3721  -1.8615
 A9D  O17   O  OC    -1  -0.647  -4.1180  -1.6941  -1.9746
 A9D  OXT   O  OC    -1  -0.613   6.1964  -0.7852   0.5425
 A9D  HN    H  HNH2   0   0.330   3.1349  -2.4766  -0.9203
 A9D  HNA   H  HNH2   0   0.334   2.4529  -1.2120  -1.6877
 A9D  H3    H  HCH1   0   0.270   0.5065   1.7507  -1.3893
 A9D  H4    H  HCH2   0   0.248   0.8005   3.7388   0.8991
 A9D  H4A   H  HCH2   0   0.265   1.2384   3.9608  -0.7970
 A9D  H5    H  HCH2   0   0.258  -1.1103   4.9966   0.0408
 A9D  H5A   H  HCH2   0   0.244  -1.1221   4.0524  -1.4484
 A9D  H6    H  HCH2   0   0.238  -1.9477   3.1496   1.3334
 A9D  H6A   H  HCH2   0   0.255  -2.7477   2.8311  -0.2130
 A9D  HA    H  HCH1   0   0.224   4.6136  -0.0109  -1.3409
 A9D  HB    H  HCH2   0   0.227   2.9455  -0.7029   1.1138
 A9D  HBA   H  HCH2   0   0.233   4.0593   0.6700   0.9640
 A9D  H10   H  HCH1   0   0.244  -3.3539   1.0780   0.8366
 A9D  H11   H  HCH2   0   0.238  -1.6164  -0.9496   2.2404
 A9D  H11A  H  HCH2   0   0.247  -2.6707   0.2659   2.9541
 A9D  H12   H  HCH2   0   0.237  -3.4848  -2.3248   2.9256
 A9D  H12A  H  HCH2   0   0.228  -4.6495  -1.0838   2.4678
 A9D  H13   H  HCH2   0   0.195  -2.9762  -2.8197   0.6061
 A9D  H13A  H  HCH2   0   0.220  -4.7020  -2.4697   0.5045

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
 A9D  C    O     deloc   1.231  0.020  1.231
 A9D  C    CA    single  1.525  0.021  1.525
 A9D  C    OXT   deloc   1.247  0.020  1.247
 A9D  N    CA    single  1.458  0.019  1.458
 A9D  N    HN    single  0.890  0.020  1.040
 A9D  N    HNA   single  0.890  0.020  1.040
 A9D  C1   O2    double  1.205  0.020  1.205
 A9D  C1   C3    single  1.516  0.020  1.516
 A9D  C1   OG    single  1.321  0.020  1.321
 A9D  C3   C4    single  1.533  0.020  1.533
 A9D  C3   N7    single  1.450  0.020  1.450
 A9D  C3   H3    single  0.970  0.020  1.090
 A9D  C4   C5    single  1.524  0.020  1.524
 A9D  C4   H4    single  0.970  0.020  1.090
 A9D  C4   H4A   single  0.970  0.020  1.090
 A9D  C5   C6    single  1.524  0.020  1.524
 A9D  C5   H5    single  0.970  0.020  1.090
 A9D  C5   H5A   single  0.970  0.020  1.090
 A9D  C6   N7    single  1.459  0.020  1.459
 A9D  C6   H6    single  0.970  0.020  1.090
 A9D  C6   H6A   single  0.970  0.020  1.090
 A9D  N7   C8    single  1.344  0.020  1.344
 A9D  C8   O9    double  1.226  0.020  1.226
 A9D  C8   C10   single  1.521  0.020  1.521
 A9D  CA   CB    single  1.530  0.020  1.530
 A9D  CA   HA    single  0.970  0.020  0.970
 A9D  CB   OG    single  1.437  0.020  1.437
 A9D  CB   HB    single  0.970  0.020  1.090
 A9D  CB   HBA   single  0.970  0.020  1.090
 A9D  C10  C11   single  1.542  0.020  1.542
 A9D  C10  N14   single  1.439  0.020  1.439
 A9D  C10  H10   single  0.970  0.020  1.090
 A9D  C11  C12   single  1.527  0.020  1.527
 A9D  C11  H11   single  0.970  0.020  1.090
 A9D  C11  H11A  single  0.970  0.020  1.090
 A9D  C12  C13   single  1.524  0.020  1.524
 A9D  C12  H12   single  0.970  0.020  1.090
 A9D  C12  H12A  single  0.970  0.020  1.090
 A9D  C13  N14   single  1.442  0.020  1.442
 A9D  C13  H13   single  0.970  0.020  1.090
 A9D  C13  H13A  single  0.970  0.020  1.090
 A9D  N14  C15   single  1.390  0.020  1.390
 A9D  C15  O16   deloc   1.254  0.020  1.254
 A9D  C15  O17   deloc   1.250  0.020  1.250

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
 A9D  OXT   C    CA   115.42  3.000
 A9D  OXT   C    O    127.09  3.000
 A9D  CA    C    O    120.80  1.700
 A9D  HNA   N    HN   107.16  3.000
 A9D  HNA   N    CA   110.62  3.000
 A9D  HN    N    CA   109.04  3.000
 A9D  OG    C1   C3   111.64  3.000
 A9D  OG    C1   O2   124.55  3.000
 A9D  C3    C1   O2   123.72  3.000
 A9D  H3    C3   N7   111.07  3.000
 A9D  H3    C3   C4   110.42  3.000
 A9D  N7    C3   C4   103.22  3.000
 A9D  H3    C3   C1   109.55  3.000
 A9D  N7    C3   C1   110.63  3.000
 A9D  C4    C3   C1   111.82  3.000
 A9D  H4A   C4   H4   108.11  3.000
 A9D  H4A   C4   C5   113.66  3.000
 A9D  H4    C4   C5   110.12  3.000
 A9D  H4A   C4   C3   112.00  3.000
 A9D  H4    C4   C3   110.30  3.000
 A9D  C5    C4   C3   102.59  3.000
 A9D  H5A   C5   H5   107.91  3.000
 A9D  H5A   C5   C6   110.11  3.000
 A9D  H5    C5   C6   112.26  3.000
 A9D  H5A   C5   C4   110.19  3.000
 A9D  H5    C5   C4   113.07  3.000
 A9D  C6    C5   C4   103.26  3.000
 A9D  H6A   C6   H6   108.38  3.000
 A9D  H6A   C6   N7   111.07  3.000
 A9D  H6    C6   N7   111.24  3.000
 A9D  H6A   C6   C5   112.01  3.000
 A9D  H6    C6   C5   111.07  3.000
 A9D  N7    C6   C5   103.04  3.000
 A9D  C8    N7   C6   127.63  3.000
 A9D  C8    N7   C3   119.10  3.000
 A9D  C6    N7   C3   112.76  3.000
 A9D  C10   C8   O9   120.92  3.000
 A9D  C10   C8   N7   118.29  3.000
 A9D  O9    C8   N7   120.53  3.000
 A9D  HA    CA   CB   109.00  3.000
 A9D  HA    CA   N    110.00  3.000
 A9D  CB    CA   N    110.50  1.700
 A9D  HA    CA   C    109.00  3.000
 A9D  CB    CA   C    110.10  1.900
 A9D  N     CA   C    111.00  2.800
 A9D  HBA   CB   HB   108.63  3.000
 A9D  HBA   CB   OG   109.35  3.000
 A9D  HB    CB   OG   109.59  3.000
 A9D  HBA   CB   CA   111.21  3.000
 A9D  HB    CB   CA   110.25  3.000
 A9D  OG    CB   CA   107.79  3.000
 A9D  CB    OG   C1   118.56  3.000
 A9D  H10   C10  N14  110.94  3.000
 A9D  H10   C10  C11  109.95  3.000
 A9D  N14   C10  C11  103.92  3.000
 A9D  H10   C10  C8   110.76  3.000
 A9D  N14   C10  C8   111.17  3.000
 A9D  C11   C10  C8   109.89  3.000
 A9D  H11A  C11  H11  107.61  3.000
 A9D  H11A  C11  C12  113.56  3.000
 A9D  H11   C11  C12  109.68  3.000
 A9D  H11A  C11  C10  112.10  3.000
 A9D  H11   C11  C10  110.28  3.000
 A9D  C12   C11  C10  103.60  3.000
 A9D  H12A  C12  H12  107.69  3.000
 A9D  H12A  C12  C13  109.94  3.000
 A9D  H12   C12  C13  113.02  3.000
 A9D  H12A  C12  C11  110.45  3.000
 A9D  H12   C12  C11  112.84  3.000
 A9D  C13   C12  C11  102.87  3.000
 A9D  H13A  C13  H13  107.34  3.000
 A9D  H13A  C13  N14  111.53  3.000
 A9D  H13   C13  N14  112.56  3.000
 A9D  H13A  C13  C12  112.41  3.000
 A9D  H13   C13  C12  110.62  3.000
 A9D  N14   C13  C12  102.44  3.000
 A9D  C15   N14  C13  124.91  3.000
 A9D  C15   N14  C10  120.81  3.000
 A9D  C13   N14  C10  113.27  3.000
 A9D  O17   C15  O16  127.24  3.000
 A9D  O17   C15  N14  117.12  3.000
 A9D  O16   C15  N14  115.64  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
 A9D  CONST_01  C10  C8   N7   C3   180.00   0.0  0
 A9D  CONST_03  O9   C8   N7   C3     0.00   0.0  0
 A9D  CONST_04  O9   C8   N7   C6   180.00   0.0  0
 A9D  Var_01    C6   C5   C4   C3    39.06  30.0  1
 A9D  Var_02    C5   C6   N7   C3    11.65  30.0  1
 A9D  Var_03    N7   C6   C5   C4   -31.24  30.0  1
 A9D  Var_04    C13  C12  C11  C10   35.36  30.0  1
 A9D  Var_05    C12  C13  N14  C10   23.20  30.0  1
 A9D  Var_06    N14  C13  C12  C11  -35.47  30.0  1
 A9D  Var_07    O16  C15  N14  C10   -7.85  30.0  2
 A9D  Var_08    CA   CB   OG   C1   163.17  30.0  1

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
 A9D  chir_01  C3   C1  C4   N7   positiv
 A9D  chir_02  CA   N   CB   C    negativ
 A9D  chir_03  C10  C8  C11  N14  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
 A9D  plan-1  C3   0.020
 A9D  plan-1  C6   0.020
 A9D  plan-1  N7   0.020
 A9D  plan-1  C8   0.020
 A9D  plan-1  O9   0.020
 A9D  plan-1  C10  0.020
 A9D  plan-2  C    0.020
 A9D  plan-2  O    0.020
 A9D  plan-2  CA   0.020
 A9D  plan-2  OXT  0.020
 A9D  plan-3  N14  0.020
 A9D  plan-3  C15  0.020
 A9D  plan-3  O16  0.020
 A9D  plan-3  O17  0.020
 A9D  plan-4  C1   0.020
 A9D  plan-4  O2   0.020
 A9D  plan-4  C3   0.020
 A9D  plan-4  OG   0.020

