# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:14:39 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]glycyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN1C(=O)CNC(=O)OCc2ccccc2
#
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
 P0H  P0H  N-[(benzyloxy)carbonyl]glycyl-L-proline  peptide  39  22  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P0H
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
 P0H  C1    C  C      0   0.744  42.5131  37.8703  85.9190
 P0H  O1    O  O      0  -0.502  43.1107  37.3519  85.0008
 P0H  O2    O  O2     0  -0.482  43.0903  38.6216  86.8667
 P0H  C2    C  CH2    0  -0.246  44.5157  38.6596  86.8838
 P0H  C3    C  CR6    0   0.064  45.1051  37.3828  87.4154
 P0H  C4    C  CR16   0  -0.294  46.0886  36.7049  86.7047
 P0H  C5    C  CR16   0  -0.241  46.6522  35.5404  87.2117
 P0H  C6    C  CR16   0  -0.263  46.2239  35.0354  88.4312
 P0H  C7    C  CR16   0  -0.241  45.2355  35.7037  89.1444
 P0H  C8    C  CR16   0  -0.281  44.6831  36.8723  88.6415
 P0H  N1    N  NH1    0  -0.642  41.1904  37.7474  86.1453
 P0H  CA1   C  CH2    0  -0.426  40.3291  37.1950  85.1434
 P0H  C9    C  C      0   0.526  40.0656  38.1661  83.9932
 P0H  O3    O  O      0  -0.503  40.4727  39.3195  84.0379
 P0H  N     N  NR5    0  -0.447  39.3749  37.6690  82.9625
 P0H  CA    C  CR15   0  -0.206  38.8829  38.5245  81.8958
 P0H  C     C  C      0   0.415  37.6811  39.4015  82.3385
 P0H  O     O  O      0  -0.591  37.1662  39.1627  83.4446
 P0H  CB    C  CH2    0  -0.463  38.4614  37.5044  80.8371
 P0H  CG    C  CH2    0  -0.482  37.9032  36.3595  81.6757
 P0H  CD    C  CH2    0  -0.269  38.8358  36.3151  82.8854
 P0H  OXT   O  OC    -1  -0.609  37.3289  40.2561  81.5017
 P0H  H2    H  HCH2   0   0.252  44.9165  38.8892  85.8950
 P0H  H2A   H  HCH2   0   0.262  44.7564  39.4943  87.5425
 P0H  H4    H  HCR6   0   0.252  46.4159  37.0901  85.7463
 P0H  H5    H  HCR6   0   0.254  47.4177  35.0231  86.6479
 P0H  H6    H  HCR6   0   0.255  46.6567  34.1248  88.8251
 P0H  H7    H  HCR6   0   0.254  44.8985  35.3152  90.0969
 P0H  H8    H  HCR6   0   0.253  43.9200  37.3892  89.2112
 P0H  HN1   H  HNH1   0   0.401  40.7727  38.3252  86.8571
 P0H  HA1   H  HCH2   0   0.275  40.7425  36.2558  84.7713
 P0H  HA1A  H  HCH2   0   0.291  39.3782  36.9419  85.6174
 P0H  HA    H  HCR5   0   0.244  39.6820  39.1701  81.5259
 P0H  HB    H  HCH2   0   0.242  37.7440  37.9153  80.1288
 P0H  HBA   H  HCH2   0   0.235  39.3330  37.1683  80.2698
 P0H  HG    H  HCH2   0   0.238  36.8839  36.5840  81.9926
 P0H  HGA   H  HCH2   0   0.246  37.8815  35.4075  81.1469
 P0H  HD    H  HCH2   0   0.239  39.6392  35.5886  82.7344
 P0H  HDA   H  HCH2   0   0.244  38.3024  36.0324  83.7951

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
 P0H  CA   C     single    1.525  0.021  1.525
 P0H  O    C     deloc     1.231  0.020  1.231
 P0H  C    OXT   deloc     1.247  0.020  1.247
 P0H  CA   N     single    1.458  0.019  1.458
 P0H  CD   N     single    1.473  0.014  1.473
 P0H  N    C9    single    1.337  0.020  1.337
 P0H  O1   C1    double    1.212  0.020  1.212
 P0H  C1   N1    single    1.348  0.020  1.348
 P0H  C1   O2    single    1.340  0.020  1.340
 P0H  CA1  N1    single    1.432  0.020  1.432
 P0H  N1   HN1   single    0.890  0.020  1.040
 P0H  C2   O2    single    1.426  0.020  1.426
 P0H  C2   C3    single    1.503  0.020  1.503
 P0H  C2   H2    single    0.970  0.020  1.090
 P0H  C2   H2A   single    0.970  0.020  1.090
 P0H  C4   C3    aromatic  1.390  0.020  1.390
 P0H  C3   C8    aromatic  1.394  0.020  1.394
 P0H  C9   O3    double    1.224  0.020  1.224
 P0H  C4   C5    aromatic  1.389  0.020  1.389
 P0H  C4   H4    single    0.930  0.020  1.080
 P0H  C5   C6    aromatic  1.388  0.020  1.388
 P0H  C5   H5    single    0.930  0.020  1.080
 P0H  C6   C7    aromatic  1.390  0.020  1.390
 P0H  C6   H6    single    0.930  0.020  1.080
 P0H  C8   C7    aromatic  1.387  0.020  1.387
 P0H  C7   H7    single    0.930  0.020  1.080
 P0H  C8   H8    single    0.930  0.020  1.080
 P0H  C9   CA1   single    1.528  0.020  1.528
 P0H  CB   CA    single    1.521  0.033  1.521
 P0H  CA   HA    single    0.970  0.020  0.970
 P0H  CB   CG    single    1.525  0.020  1.525
 P0H  CB   HB    single    0.970  0.020  1.090
 P0H  CB   HBA   single    0.970  0.020  1.090
 P0H  CG   CD    single    1.528  0.020  1.528
 P0H  CD   HD    single    0.970  0.020  1.090
 P0H  CD   HDA   single    0.970  0.020  1.090
 P0H  CG   HG    single    0.970  0.020  1.090
 P0H  CG   HGA   single    0.970  0.020  1.090
 P0H  CA1  HA1   single    0.970  0.020  1.090
 P0H  CA1  HA1A  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
 P0H  N1    C1   O2   110.81  3.000
 P0H  O2    C1   O1   124.27  3.000
 P0H  N1    C1   O1   124.91  3.000
 P0H  C2    O2   C1   117.00  3.000
 P0H  H2A   C2   H2   107.77  3.000
 P0H  H2A   C2   C3   110.49  3.000
 P0H  H2    C2   C3   110.80  3.000
 P0H  H2A   C2   O2   104.38  3.000
 P0H  H2    C2   O2   111.21  3.000
 P0H  C3    C2   O2   111.93  3.000
 P0H  C8    C3   C4   119.05  3.000
 P0H  C8    C3   C2   120.23  3.000
 P0H  C4    C3   C2   120.72  3.000
 P0H  H4    C4   C5   119.88  3.000
 P0H  H4    C4   C3   119.51  3.000
 P0H  C5    C4   C3   120.61  3.000
 P0H  H5    C5   C6   120.14  3.000
 P0H  H5    C5   C4   119.82  3.000
 P0H  C6    C5   C4   120.03  3.000
 P0H  H6    C6   C7   120.14  3.000
 P0H  H6    C6   C5   120.17  3.000
 P0H  C7    C6   C5   119.70  3.000
 P0H  H7    C7   C8   119.83  3.000
 P0H  H7    C7   C6   120.02  3.000
 P0H  C8    C7   C6   120.15  3.000
 P0H  H8    C8   C7   119.46  3.000
 P0H  H8    C8   C3   120.07  3.000
 P0H  C7    C8   C3   120.47  3.000
 P0H  HN1   N1   CA1  117.79  3.000
 P0H  HN1   N1   C1   118.25  3.000
 P0H  CA1   N1   C1   120.54  3.000
 P0H  HA1A  CA1  HA1  106.16  3.000
 P0H  HA1A  CA1  C9   108.89  3.000
 P0H  HA1   CA1  C9   110.82  3.000
 P0H  HA1A  CA1  N1   108.02  3.000
 P0H  HA1   CA1  N1   110.03  3.000
 P0H  C9    CA1  N1   112.66  3.000
 P0H  N     C9   O3   123.40  3.000
 P0H  O3    C9   CA1  120.93  3.000
 P0H  N     C9   CA1  115.67  3.000
 P0H  CD    N    CA   112.48  3.000
 P0H  CD    N    C9   125.22  3.000
 P0H  CA    N    C9   121.47  3.000
 P0H  HA    CA   CB   109.00  3.000
 P0H  HA    CA   C    110.00  3.000
 P0H  CB    CA   C    110.50  1.500
 P0H  HA    CA   N    110.00  3.000
 P0H  CB    CA   N    110.40  1.500
 P0H  C     CA   N    111.00  2.800
 P0H  OXT   C    O    127.71  3.000
 P0H  OXT   C    CA   120.80  1.700
 P0H  O     C    CA   120.80  1.700
 P0H  HBA   CB   HB   107.69  3.000
 P0H  HBA   CB   CG   110.27  3.000
 P0H  HB    CB   CG   113.57  3.000
 P0H  HBA   CB   CA   110.16  3.000
 P0H  HB    CB   CA   112.35  3.000
 P0H  CG    CB   CA   102.77  3.000
 P0H  HGA   CG   HG   107.60  3.000
 P0H  HGA   CG   CD   111.78  3.000
 P0H  HG    CG   CD   110.26  3.000
 P0H  HGA   CG   CB   113.36  3.000
 P0H  HG    CG   CB   110.32  3.000
 P0H  CD    CG   CB   103.51  3.000
 P0H  HDA   CD   HD   107.58  3.000
 P0H  HDA   CD   CG   111.65  3.000
 P0H  HD    CD   CG   111.00  3.000
 P0H  HDA   CD   N    112.13  3.000
 P0H  HD    CD   N    110.62  3.000
 P0H  CG    CD   N    103.20  1.500

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
 P0H  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 P0H  CONST_02  C6   C7   C8   C3     0.00   0.0  0
 P0H  CONST_03  C7   C8   C3   C4     0.00   0.0  0
 P0H  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 P0H  CONST_05  C8   C3   C4   C5     0.00   0.0  0
 P0H  CONST_06  C8   C7   C6   C5     0.00   0.0  0
 P0H  CONST_07  C5   C4   C3   C2   180.00   0.0  0
 P0H  CONST_08  C7   C8   C3   C2   180.00   0.0  0
 P0H  CONST_09  H5   C5   C4   C3   180.00   0.0  0
 P0H  CONST_10  H7   C7   C8   C3   180.00   0.0  0
 P0H  CONST_11  H8   C8   C3   C4   180.00   0.0  0
 P0H  CONST_12  H6   C6   C5   C4   180.00   0.0  0
 P0H  CONST_13  H4   C4   C5   C6   180.00   0.0  0
 P0H  CONST_14  CA   N    C9   CA1  180.00   0.0  0
 P0H  CONST_15  CD   N    C9   CA1    0.00   0.0  0
 P0H  CONST_16  CA   N    C9   O3     0.00   0.0  0
 P0H  CONST_17  CD   N    C9   O3   180.00   0.0  0
 P0H  Var_01    CB   CG   CD   N     24.50  30.0  1
 P0H  Var_02    CG   CD   N    CA    -1.35  30.0  1
 P0H  Var_03    CD   CG   CB   CA   -37.88  30.0  1
 P0H  Var_04    C4   C3   C2   O2   128.59  30.0  2
 P0H  Var_05    C3   C2   O2   C1   -74.07  30.0  1
 P0H  Var_06    N    C9   CA1  N1   173.81  30.0  1
 P0H  Var_07    C9   CA1  N1   C1   -74.62  30.0  1
 P0H  Var_08    CA1  N1   C1   O1   -12.68  30.0  2
 P0H  Var_09    N1   C1   O2   C2   170.02  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
 P0H  chir_01  CA  C  N  CB  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
 P0H  plan-1  C2   0.020
 P0H  plan-1  C3   0.020
 P0H  plan-1  C4   0.020
 P0H  plan-1  C5   0.020
 P0H  plan-1  C6   0.020
 P0H  plan-1  C7   0.020
 P0H  plan-1  C8   0.020
 P0H  plan-1  H4   0.020
 P0H  plan-1  H5   0.020
 P0H  plan-1  H6   0.020
 P0H  plan-1  H7   0.020
 P0H  plan-1  H8   0.020
 P0H  plan-2  CA1  0.020
 P0H  plan-2  C9   0.020
 P0H  plan-2  O3   0.020
 P0H  plan-2  N    0.020
 P0H  plan-2  CA   0.020
 P0H  plan-2  CD   0.020
 P0H  plan-3  CA   0.020
 P0H  plan-3  C    0.020
 P0H  plan-3  O    0.020
 P0H  plan-3  OXT  0.020
 P0H  plan-4  C1   0.020
 P0H  plan-4  O1   0.020
 P0H  plan-4  O2   0.020
 P0H  plan-4  N1   0.020

