# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:30:51 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: glycyl-L-alanyl-N-naphthalen-2-yl-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)CN)C(=O)N1CCC[C@H]1C(=O)Nc2ccc3ccccc3c2
#
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
 GA0  GA0  glycyl-L-alanyl-N-naphthalen-2-yl-L-prolinamide  ligand  51  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GA0
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
 GA0  N1    N  NH2   0  -0.774   0.9178  -3.9961   6.8081
 GA0  CA1   C  CH2   0  -0.422  -0.2753  -3.7232   6.0481
 GA0  C1    C  C     0   0.504  -0.1839  -3.9936   4.5496
 GA0  O1    O  O     0  -0.491   0.8393  -4.3853   4.0088
 GA0  N2    N  NH1   0  -0.625  -1.3192  -3.7803   3.8621
 GA0  CA2   C  CH1   0  -0.195  -1.3621  -3.9017   2.4276
 GA0  CB2   C  CH3   0  -0.686  -2.7863  -3.6630   1.9363
 GA0  C2    C  C     0   0.571  -0.4297  -2.8733   1.7858
 GA0  O2    O  O     0  -0.498  -0.2584  -1.7741   2.2929
 GA0  N3    N  NR5   0  -0.464   0.1459  -3.2102   0.6223
 GA0  CD3   C  CH2   0  -0.280  -0.0225  -4.4557  -0.1222
 GA0  CA3   C  CR15  0  -0.226   0.9552  -2.2372  -0.0767
 GA0  CB3   C  CH2   0  -0.473   1.5135  -3.0279  -1.2705
 GA0  CG3   C  CH2   0  -0.472   0.4544  -4.0945  -1.5227
 GA0  C3    C  C     0   0.562   0.0905  -1.0710  -0.5472
 GA0  O3    O  O     0  -0.455  -1.0702  -1.2233  -0.8721
 GA0  NN    N  NH1   0  -0.749   0.7676   0.1020  -0.6146
 GA0  C4    C  CR6   0   0.392   0.3242   1.3540  -1.0524
 GA0  C5    C  CR16  0  -0.436   1.0719   2.4543  -0.7025
 GA0  C6    C  CR66  0   0.141   0.7123   3.7497  -1.1272
 GA0  C7    C  CR66  0   0.099  -0.4457   3.9202  -1.9279
 GA0  C8    C  CR16  0  -0.306  -0.8109   5.2193  -2.3508
 GA0  C9    C  CR16  0  -0.264  -0.0580   6.3046  -1.9940
 GA0  C10   C  CR16  0  -0.256   1.0951   6.1364  -1.1968
 GA0  C11   C  CR16  0  -0.317   1.4716   4.8915  -0.7727
 GA0  C12   C  CR16  0  -0.303  -1.1916   2.7727  -2.2770
 GA0  C13   C  CR16  0  -0.309  -0.8291   1.5226  -1.8597
 GA0  HN11  H  HNH2  0   0.347   1.1811  -4.9670   6.7010
 GA0  HN12  H  HNH2  0   0.346   1.6910  -3.4584   6.4381
 GA0  HA11  H  HCH2  0   0.262  -0.5597  -2.6754   6.1843
 GA0  HA12  H  HCH2  0   0.262  -1.1066  -4.3078   6.4520
 GA0  HN2   H  HNH1  0   0.402  -2.1090  -3.3648   4.3307
 GA0  HA2   H  HCH1  0   0.276  -1.0543  -4.9135   2.1534
 GA0  HB21  H  HCH3  0   0.253  -2.8546  -3.7724   0.8550
 GA0  HB22  H  HCH3  0   0.259  -3.4674  -4.3842   2.3876
 GA0  HB23  H  HCH3  0   0.245  -3.1250  -2.6585   2.1937
 GA0  HD31  H  HCH2  0   0.257  -1.0589  -4.7912  -0.1207
 GA0  HD32  H  HCH2  0   0.249   0.5912  -5.2485   0.3138
 GA0  HA3   H  HCR5  0   0.290   1.7649  -1.8721   0.5602
 GA0  HB31  H  HCH2  0   0.263   2.4588  -3.4875  -0.9770
 GA0  HB32  H  HCH2  0   0.267   1.7109  -2.3980  -2.1375
 GA0  HG31  H  HCH2  0   0.248  -0.3712  -3.6869  -2.1075
 GA0  HG32  H  HCH2  0   0.259   0.8448  -4.9602  -2.0554
 GA0  HNN   H  HNH1  0   0.417   1.6954   0.0985  -0.2178
 GA0  H5    H  HCR6  0   0.266   1.9566   2.3338  -0.0863
 GA0  H8    H  HCR6  0   0.255  -1.6968   5.3429  -2.9625
 GA0  H9    H  HCR6  0   0.258  -0.3430   7.2962  -2.3202
 GA0  H10   H  HCR6  0   0.258   1.6834   7.0022  -0.9213
 GA0  H11   H  HCR6  0   0.254   2.3554   4.7665  -0.1587
 GA0  H12   H  HCR6  0   0.259  -2.0720   2.8880  -2.8975
 GA0  H13   H  HCR6  0   0.279  -1.4223   0.6724  -2.1533

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
 GA0  N1   CA1   single    1.441  0.020  1.441
 GA0  N1   HN11  single    0.890  0.020  1.040
 GA0  N1   HN12  single    0.890  0.020  1.040
 GA0  CA1  C1    single    1.525  0.020  1.525
 GA0  CA1  HA11  single    0.970  0.020  1.090
 GA0  CA1  HA12  single    0.970  0.020  1.090
 GA0  C1   O1    double    1.222  0.020  1.222
 GA0  C1   N2    single    1.344  0.020  1.344
 GA0  N2   CA2   single    1.440  0.020  1.440
 GA0  N2   HN2   single    0.860  0.020  1.020
 GA0  CA2  CB2   single    1.525  0.020  1.525
 GA0  CA2  C2    single    1.529  0.020  1.529
 GA0  CA2  HA2   single    0.970  0.020  1.090
 GA0  CB2  HB21  single    0.970  0.020  1.090
 GA0  CB2  HB22  single    0.970  0.020  1.090
 GA0  CB2  HB23  single    0.970  0.020  1.090
 GA0  C2   O2    double    1.223  0.020  1.223
 GA0  C2   N3    single    1.341  0.020  1.341
 GA0  N3   CD3   single    1.461  0.020  1.461
 GA0  N3   CA3   single    1.446  0.020  1.446
 GA0  CD3  CG3   single    1.523  0.020  1.523
 GA0  CD3  HD31  single    0.970  0.020  1.090
 GA0  CD3  HD32  single    0.970  0.020  1.090
 GA0  CA3  CB3   single    1.537  0.020  1.537
 GA0  CA3  C3    single    1.526  0.020  1.526
 GA0  CA3  HA3   single    0.970  0.020  1.090
 GA0  CB3  CG3   single    1.524  0.020  1.524
 GA0  CB3  HB31  single    0.970  0.020  1.090
 GA0  CB3  HB32  single    0.970  0.020  1.090
 GA0  CG3  HG31  single    0.970  0.020  1.090
 GA0  CG3  HG32  single    0.970  0.020  1.090
 GA0  C3   O3    double    1.215  0.020  1.215
 GA0  C3   NN    single    1.356  0.020  1.356
 GA0  NN   C4    single    1.398  0.020  1.398
 GA0  NN   HNN   single    0.860  0.020  1.020
 GA0  C4   C5    aromatic  1.376  0.020  1.376
 GA0  C4   C13   aromatic  1.418  0.020  1.418
 GA0  C5   C6    aromatic  1.410  0.020  1.410
 GA0  C5   H5    single    0.930  0.020  1.080
 GA0  C6   C7    aromatic  1.418  0.020  1.418
 GA0  C6   C11   aromatic  1.416  0.020  1.416
 GA0  C7   C8    aromatic  1.414  0.020  1.414
 GA0  C7   C12   aromatic  1.412  0.020  1.412
 GA0  C8   C9    aromatic  1.368  0.020  1.368
 GA0  C8   H8    single    0.930  0.020  1.080
 GA0  C9   C10   aromatic  1.412  0.020  1.412
 GA0  C9   H9    single    0.930  0.020  1.080
 GA0  C10  C11   aromatic  1.368  0.020  1.368
 GA0  C10  H10   single    0.930  0.020  1.080
 GA0  C11  H11   single    0.930  0.020  1.080
 GA0  C12  C13   aromatic  1.367  0.020  1.367
 GA0  C12  H12   single    0.930  0.020  1.080
 GA0  C13  H13   single    0.930  0.020  1.080

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
 GA0  HN12  N1   HN11  105.81  3.000
 GA0  HN12  N1   CA1   109.83  3.000
 GA0  HN11  N1   CA1   109.96  3.000
 GA0  HA12  CA1  HA11  105.57  3.000
 GA0  HA12  CA1  C1    108.28  3.000
 GA0  HA11  CA1  C1    107.91  3.000
 GA0  HA12  CA1  N1    109.48  3.000
 GA0  HA11  CA1  N1    109.33  3.000
 GA0  C1    CA1  N1    115.78  3.000
 GA0  N2    C1   O1    122.12  3.000
 GA0  N2    C1   CA1   115.06  3.000
 GA0  O1    C1   CA1   122.81  3.000
 GA0  HN2   N2   CA2   118.33  3.000
 GA0  HN2   N2   C1    119.30  3.000
 GA0  CA2   N2   C1    121.41  3.000
 GA0  HA2   CA2  C2    110.22  3.000
 GA0  HA2   CA2  CB2   109.09  3.000
 GA0  C2    CA2  CB2   109.20  3.000
 GA0  HA2   CA2  N2    108.64  3.000
 GA0  C2    CA2  N2    110.07  3.000
 GA0  CB2   CA2  N2    109.59  3.000
 GA0  HB23  CB2  HB22  108.52  3.000
 GA0  HB23  CB2  HB21  107.89  3.000
 GA0  HB22  CB2  HB21  107.79  3.000
 GA0  HB23  CB2  CA2   110.98  3.000
 GA0  HB22  CB2  CA2   110.28  3.000
 GA0  HB21  CB2  CA2   111.26  3.000
 GA0  N3    C2   O2    121.70  3.000
 GA0  N3    C2   CA2   117.18  3.000
 GA0  O2    C2   CA2   121.06  3.000
 GA0  CA3   N3   CD3   113.08  3.000
 GA0  CA3   N3   C2    119.38  3.000
 GA0  CD3   N3   C2    127.36  3.000
 GA0  HD32  CD3  HD31  108.07  3.000
 GA0  HD32  CD3  CG3   111.28  3.000
 GA0  HD31  CD3  CG3   111.85  3.000
 GA0  HD32  CD3  N3    110.51  3.000
 GA0  HD31  CD3  N3    111.82  3.000
 GA0  CG3   CD3  N3    103.32  3.000
 GA0  HA3   CA3  C3    110.13  3.000
 GA0  HA3   CA3  CB3   110.82  3.000
 GA0  C3    CA3  CB3   111.07  3.000
 GA0  HA3   CA3  N3    110.96  3.000
 GA0  C3    CA3  N3    110.25  3.000
 GA0  CB3   CA3  N3    103.45  3.000
 GA0  HB32  CB3  HB31  107.48  3.000
 GA0  HB32  CB3  CG3   113.50  3.000
 GA0  HB31  CB3  CG3   110.59  3.000
 GA0  HB32  CB3  CA3   112.73  3.000
 GA0  HB31  CB3  CA3   108.81  3.000
 GA0  CG3   CB3  CA3   103.66  3.000
 GA0  HG32  CG3  HG31  107.83  3.000
 GA0  HG32  CG3  CB3   112.84  3.000
 GA0  HG31  CG3  CB3   110.68  3.000
 GA0  HG32  CG3  CD3   111.94  3.000
 GA0  HG31  CG3  CD3   110.16  3.000
 GA0  CB3   CG3  CD3   103.38  3.000
 GA0  NN    C3   O3    124.90  3.000
 GA0  NN    C3   CA3   113.17  3.000
 GA0  O3    C3   CA3   121.87  3.000
 GA0  HNN   NN   C4    114.69  3.000
 GA0  HNN   NN   C3    115.89  3.000
 GA0  C4    NN   C3    129.17  3.000
 GA0  C13   C4   C5    119.46  3.000
 GA0  C13   C4   NN    122.86  3.000
 GA0  C5    C4   NN    117.66  3.000
 GA0  H5    C5   C6    118.76  3.000
 GA0  H5    C5   C4    119.93  3.000
 GA0  C6    C5   C4    121.31  3.000
 GA0  C11   C6   C7    118.83  3.000
 GA0  C11   C6   C5    121.91  3.000
 GA0  C7    C6   C5    119.26  3.000
 GA0  C12   C7   C8    122.41  3.000
 GA0  C12   C7   C6    118.23  3.000
 GA0  C8    C7   C6    119.35  3.000
 GA0  H8    C8   C9    120.43  3.000
 GA0  H8    C8   C7    119.00  3.000
 GA0  C9    C8   C7    120.57  3.000
 GA0  H9    C9   C10   119.63  3.000
 GA0  H9    C9   C8    120.23  3.000
 GA0  C10   C9   C8    120.14  3.000
 GA0  H10   C10  C11   119.96  3.000
 GA0  H10   C10  C9    119.49  3.000
 GA0  C11   C10  C9    120.54  3.000
 GA0  H11   C11  C10   120.35  3.000
 GA0  H11   C11  C6    119.09  3.000
 GA0  C10   C11  C6    120.56  3.000
 GA0  H12   C12  C13   119.20  3.000
 GA0  H12   C12  C7    118.96  3.000
 GA0  C13   C12  C7    121.84  3.000
 GA0  H13   C13  C12   119.51  3.000
 GA0  H13   C13  C4    120.60  3.000
 GA0  C12   C13  C4    119.89  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
 GA0  CONST_01  C7    C6   C5   C4     0.00   0.0  0
 GA0  CONST_02  C11   C6   C5   C4   180.00   0.0  0
 GA0  CONST_03  C7    C12  C13  C4     0.00   0.0  0
 GA0  CONST_04  C12   C13  C4   C5     0.00   0.0  0
 GA0  CONST_05  C8    C7   C6   C5   180.00   0.0  0
 GA0  CONST_06  C12   C7   C6   C5     0.00   0.0  0
 GA0  CONST_07  C10   C11  C6   C5   180.00   0.0  0
 GA0  CONST_08  C13   C4   C5   C6     0.00   0.0  0
 GA0  CONST_09  C9    C8   C7   C6     0.00   0.0  0
 GA0  CONST_10  C13   C12  C7   C6     0.00   0.0  0
 GA0  CONST_11  C9    C10  C11  C6     0.00   0.0  0
 GA0  CONST_12  C10   C11  C6   C7     0.00   0.0  0
 GA0  CONST_13  C10   C9   C8   C7     0.00   0.0  0
 GA0  CONST_14  C11   C6   C7   C8     0.00   0.0  0
 GA0  CONST_15  C13   C12  C7   C8   180.00   0.0  0
 GA0  CONST_16  C11   C10  C9   C8     0.00   0.0  0
 GA0  CONST_17  C12   C7   C8   C9   180.00   0.0  0
 GA0  CONST_18  C12   C7   C6   C11  180.00   0.0  0
 GA0  CONST_19  C6    C5   C4   NN   180.00   0.0  0
 GA0  CONST_20  C12   C13  C4   NN   180.00   0.0  0
 GA0  CONST_21  H12   C12  C13  C4   180.00   0.0  0
 GA0  CONST_22  H13   C13  C4   C5   180.00   0.0  0
 GA0  CONST_23  H11   C11  C6   C5     0.00   0.0  0
 GA0  CONST_24  H8    C8   C7   C6   180.00   0.0  0
 GA0  CONST_25  H10   C10  C11  C6   180.00   0.0  0
 GA0  CONST_26  H5    C5   C6   C7   180.00   0.0  0
 GA0  CONST_27  H9    C9   C8   C7   180.00   0.0  0
 GA0  CONST_28  CD3   N3   C2   CA2    0.00   0.0  0
 GA0  CONST_29  CA3   N3   C2   CA2  180.00   0.0  0
 GA0  CONST_30  CD3   N3   C2   O2   180.00   0.0  0
 GA0  CONST_31  CA3   N3   C2   O2     0.00   0.0  0
 GA0  CONST_32  C4    NN   C3   CA3  180.00   0.0  0
 GA0  CONST_35  HNN   NN   C4   C5     0.00   0.0  0
 GA0  CONST_36  C4    NN   C3   O3     0.00   0.0  0
 GA0  CONST_37  CA2   N2   C1   CA1  180.00   0.0  0
 GA0  CONST_38  CA2   N2   C1   O1     0.00   0.0  0
 GA0  CONST_39  HN2   N2   C1   CA1    0.00   0.0  0
 GA0  Var_01    CB3   CG3  CD3  N3    30.65  30.0  1
 GA0  Var_02    CA3   CB3  CG3  CD3  -36.42  30.0  1
 GA0  Var_03    CG3   CD3  N3   CA3  -13.69  30.0  1
 GA0  Var_04    O1    C1   CA1  N1    -1.75  30.0  3
 GA0  Var_05    HN11  N1   CA1  C1   -58.81  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
 GA0  chir_01  CA2  N2  CB2  C2  negativ
 GA0  chir_02  CA3  N3  CB3  C3  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
 GA0  plan-1  NN   0.020
 GA0  plan-1  C4   0.020
 GA0  plan-1  C5   0.020
 GA0  plan-1  C6   0.020
 GA0  plan-1  C7   0.020
 GA0  plan-1  C8   0.020
 GA0  plan-1  C9   0.020
 GA0  plan-1  C10  0.020
 GA0  plan-1  C11  0.020
 GA0  plan-1  C12  0.020
 GA0  plan-1  C13  0.020
 GA0  plan-1  H5   0.020
 GA0  plan-1  H8   0.020
 GA0  plan-1  H9   0.020
 GA0  plan-1  H10  0.020
 GA0  plan-1  H11  0.020
 GA0  plan-1  H12  0.020
 GA0  plan-1  H13  0.020
 GA0  plan-2  CA2  0.020
 GA0  plan-2  C2   0.020
 GA0  plan-2  O2   0.020
 GA0  plan-2  N3   0.020
 GA0  plan-2  CD3  0.020
 GA0  plan-2  CA3  0.020
 GA0  plan-3  CA3  0.020
 GA0  plan-3  C3   0.020
 GA0  plan-3  O3   0.020
 GA0  plan-3  NN   0.020
 GA0  plan-3  C4   0.020
 GA0  plan-3  HNN  0.020
 GA0  plan-4  CA1  0.020
 GA0  plan-4  C1   0.020
 GA0  plan-4  O1   0.020
 GA0  plan-4  N2   0.020
 GA0  plan-4  CA2  0.020
 GA0  plan-4  HN2  0.020

