# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:51:07 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: D-phenylalanyl-N-(pyridin-2-ylmethyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccccn3
#
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
 B03  B03  D-phenylalanyl-N-(pyridin-2-ylmethyl)-L-prolinamide  peptide  50  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_B03
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
 B03  N10   N  NH2   0  -0.780  -2.7812   1.7024  -1.1030
 B03  C8    C  CH1   0  -0.224  -2.5804   0.4458  -0.4195
 B03  C9    C  C     0   0.562  -1.1114   0.3125  -0.0413
 B03  O12   O  O     0  -0.498  -0.4141   1.3013   0.1469
 B03  C7    C  CH2   0  -0.541  -3.4260   0.2526   0.8648
 B03  C4    C  CR6   0   0.136  -4.8967   0.3256   0.5760
 B03  C3    C  CR16  0  -0.302  -5.5804  -0.7984   0.1144
 B03  C5    C  CR16  0  -0.319  -5.6000   1.5204   0.7127
 B03  C2    C  CR16  0  -0.241  -6.9306  -0.7334  -0.1985
 B03  C6    C  CR16  0  -0.241  -6.9521   1.5906   0.4007
 B03  C1    C  CR16  0  -0.270  -7.6217   0.4640  -0.0568
 B03  N11   N  NT    0  -0.460  -0.6296  -0.9286   0.1455
 B03  C13   C  CH1   0  -0.222   0.7531  -1.1055   0.5358
 B03  C17   C  C     0   0.582   1.6851  -0.7076  -0.6056
 B03  O28   O  O     0  -0.496   1.3444  -0.7758  -1.7772
 B03  C15   C  CH2   0  -0.466   0.8451  -2.6094   0.8238
 B03  C16   C  CH2   0  -0.475  -0.1684  -3.2154  -0.1395
 B03  C14   C  CH2   0  -0.278  -1.2996  -2.1930  -0.1513
 B03  N18   N  NH1   0  -0.657   2.9108  -0.3406  -0.2191
 B03  C19   C  CH2   0  -0.284   3.9519  -0.0115  -1.1541
 B03  C20   C  CR6   0   0.224   5.2450   0.2822  -0.4376
 B03  C22   C  CR16  0  -0.327   6.3918   0.5715  -1.1729
 B03  C23   C  CR16  0  -0.146   7.5641   0.8469  -0.4941
 B03  C24   C  CR16  0  -0.335   7.5580   0.8255   0.8957
 B03  C25   C  CR16  0  -0.061   6.3693   0.5278   1.5366
 B03  N21   N  N     0  -0.453   5.2390   0.2625   0.8866
 B03  HN10  H  HNH2  0   0.355  -3.7499   1.7798  -1.3856
 B03  HN1A  H  HNH2  0   0.342  -2.6014   2.4755  -0.4741
 B03  H8    H  HCH1  0   0.264  -2.8476  -0.3503  -1.1198
 B03  H7    H  HCH2  0   0.260  -3.1457   1.0247   1.5867
 B03  H7A   H  HCH2  0   0.259  -3.1900  -0.7117   1.3214
 B03  H3    H  HCR6  0   0.245  -5.0496  -1.7376   0.0032
 B03  H5    H  HCR6  0   0.251  -5.0886   2.4032   1.0782
 B03  H2    H  HCR6  0   0.254  -7.4443  -1.6190  -0.5500
 B03  H6    H  HCR6  0   0.254  -7.4825   2.5272   0.5176
 B03  H1    H  HCR6  0   0.254  -8.6756   0.5172  -0.2971
 B03  H13   H  HCH1  0   0.285   0.9883  -0.5186   1.4272
 B03  H15   H  HCH2  0   0.263   1.8551  -2.9981   0.6970
 B03  H15A  H  HCH2  0   0.259   0.5477  -2.7916   1.8580
 B03  H16   H  HCH2  0   0.258  -0.5153  -4.1985   0.1748
 B03  H16A  H  HCH2  0   0.247   0.2609  -3.3157  -1.1367
 B03  H14   H  HCH2  0   0.242  -2.0438  -2.4244   0.6159
 B03  H14A  H  HCH2  0   0.259  -1.8096  -2.1624  -1.1138
 B03  HN18  H  HNH1  0   0.403   3.1461  -0.2634   0.7606
 B03  H19   H  HCH2  0   0.264   4.1088  -0.8313  -1.8613
 B03  H19A  H  HCH2  0   0.265   3.6754   0.8610  -1.7551
 B03  H22   H  HCR6  0   0.271   6.3593   0.5797  -2.2548
 B03  H23   H  HCR6  0   0.277   8.4707   1.0766  -1.0382
 B03  H24   H  HCR6  0   0.273   8.4510   1.0356   1.4674
 B03  H25   H  HCR6  0   0.267   6.3193   0.5018   2.6190

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
 B03  C1   C2    aromatic  1.390  0.020  1.390
 B03  C1   C6    aromatic  1.388  0.020  1.388
 B03  C2   C3    aromatic  1.388  0.020  1.388
 B03  C3   C4    aromatic  1.394  0.020  1.394
 B03  C4   C5    aromatic  1.393  0.020  1.393
 B03  C4   C7    single    1.501  0.020  1.501
 B03  C5   C6    aromatic  1.389  0.020  1.389
 B03  C7   C8    single    1.550  0.020  1.550
 B03  C8   C9    single    1.523  0.020  1.523
 B03  C8   N10   single    1.445  0.020  1.445
 B03  C9   N11   single    1.344  0.020  1.344
 B03  C9   O12   double    1.224  0.020  1.224
 B03  N11  C13   single    1.448  0.020  1.448
 B03  N11  C14   single    1.461  0.020  1.461
 B03  C13  C15   single    1.534  0.020  1.534
 B03  C13  C17   single    1.526  0.020  1.526
 B03  C14  C16   single    1.525  0.020  1.525
 B03  C15  C16   single    1.524  0.020  1.524
 B03  C17  N18   single    1.337  0.020  1.337
 B03  C17  O28   double    1.222  0.020  1.222
 B03  N18  C19   single    1.438  0.020  1.438
 B03  C19  C20   single    1.507  0.020  1.507
 B03  C20  N21   aromatic  1.324  0.020  1.324
 B03  C20  C22   aromatic  1.393  0.020  1.393
 B03  N21  C25   aromatic  1.331  0.020  1.331
 B03  C22  C23   aromatic  1.382  0.020  1.382
 B03  C23  C24   aromatic  1.390  0.020  1.390
 B03  C24  C25   aromatic  1.383  0.020  1.383
 B03  C1   H1    single    0.930  0.020  1.080
 B03  C2   H2    single    0.930  0.020  1.080
 B03  C3   H3    single    0.930  0.020  1.080
 B03  C5   H5    single    0.930  0.020  1.080
 B03  C6   H6    single    0.930  0.020  1.080
 B03  C7   H7    single    0.970  0.020  1.090
 B03  C7   H7A   single    0.970  0.020  1.090
 B03  C8   H8    single    0.970  0.020  1.090
 B03  N10  HN10  single    0.890  0.020  1.040
 B03  N10  HN1A  single    0.890  0.020  1.040
 B03  C13  H13   single    0.970  0.020  1.090
 B03  C14  H14   single    0.970  0.020  1.090
 B03  C14  H14A  single    0.970  0.020  1.090
 B03  C15  H15   single    0.970  0.020  1.090
 B03  C15  H15A  single    0.970  0.020  1.090
 B03  C16  H16   single    0.970  0.020  1.090
 B03  C16  H16A  single    0.970  0.020  1.090
 B03  N18  HN18  single    0.860  0.020  1.020
 B03  C19  H19   single    0.970  0.020  1.090
 B03  C19  H19A  single    0.970  0.020  1.090
 B03  C22  H22   single    0.930  0.020  1.080
 B03  C23  H23   single    0.930  0.020  1.080
 B03  C24  H24   single    0.930  0.020  1.080
 B03  C25  H25   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
 B03  HN1A  N10  HN10  106.55  3.000
 B03  HN1A  N10  C8    110.21  3.000
 B03  HN10  N10  C8    109.37  3.000
 B03  H8    C8   C7    107.86  3.000
 B03  H8    C8   C9    109.33  3.000
 B03  C7    C8   C9    108.04  3.000
 B03  H8    C8   N10   107.23  3.000
 B03  C9    C8   N10   109.13  3.000
 B03  C7    C8   N10   115.14  3.000
 B03  N11   C9   O12   121.34  3.000
 B03  O12   C9   C8    121.12  3.000
 B03  N11   C9   C8    117.45  3.000
 B03  H7A   C7   H7    106.97  3.000
 B03  H7A   C7   C4    109.57  3.000
 B03  H7    C7   C4    110.11  3.000
 B03  H7A   C7   C8    109.79  3.000
 B03  H7    C7   C8    108.61  3.000
 B03  C4    C7   C8    111.66  3.000
 B03  C5    C4   C3    118.44  3.000
 B03  C5    C4   C7    121.18  3.000
 B03  C3    C4   C7    120.34  3.000
 B03  H3    C3   C2    119.58  3.000
 B03  H3    C3   C4    119.48  3.000
 B03  C2    C3   C4    120.94  3.000
 B03  H5    C5   C6    119.59  3.000
 B03  H5    C5   C4    119.57  3.000
 B03  C6    C5   C4    120.84  3.000
 B03  H2    C2   C1    120.14  3.000
 B03  H2    C2   C3    119.79  3.000
 B03  C1    C2   C3    120.08  3.000
 B03  H6    C6   C1    120.10  3.000
 B03  H6    C6   C5    119.75  3.000
 B03  C1    C6   C5    120.16  3.000
 B03  H1    C1   C6    120.20  3.000
 B03  H1    C1   C2    120.26  3.000
 B03  C6    C1   C2    119.54  3.000
 B03  C14   N11  C13   112.76  3.000
 B03  C14   N11  C9    127.32  3.000
 B03  C13   N11  C9    119.51  3.000
 B03  H13   C13  C15   111.13  3.000
 B03  H13   C13  C17   109.79  3.000
 B03  C15   C13  C17   111.06  3.000
 B03  H13   C13  N11   111.09  3.000
 B03  C17   C13  N11   110.47  3.000
 B03  C15   C13  N11   103.16  3.000
 B03  N18   C17  O28   123.25  3.000
 B03  O28   C17  C13   122.15  3.000
 B03  N18   C17  C13   114.53  3.000
 B03  H15A  C15  H15   107.66  3.000
 B03  H15A  C15  C16   110.57  3.000
 B03  H15   C15  C16   113.64  3.000
 B03  H15A  C15  C13   108.97  3.000
 B03  H15   C15  C13   112.55  3.000
 B03  C16   C15  C13   103.37  3.000
 B03  H16A  C16  H16   107.84  3.000
 B03  H16A  C16  C14   110.29  3.000
 B03  H16   C16  C14   111.80  3.000
 B03  H16A  C16  C15   110.66  3.000
 B03  H16   C16  C15   112.86  3.000
 B03  C14   C16  C15   103.39  3.000
 B03  H14A  C14  H14   107.88  3.000
 B03  H14A  C14  C16   111.89  3.000
 B03  H14   C14  C16   110.95  3.000
 B03  H14A  C14  N11   111.69  3.000
 B03  H14   C14  N11   110.65  3.000
 B03  C16   C14  N11   103.80  3.000
 B03  HN18  N18  C19   116.40  3.000
 B03  HN18  N18  C17   120.99  3.000
 B03  C19   N18  C17   122.61  3.000
 B03  H19A  C19  H19   106.17  3.000
 B03  H19A  C19  C20   108.81  3.000
 B03  H19   C19  C20   109.29  3.000
 B03  H19A  C19  N18   110.89  3.000
 B03  H19   C19  N18   110.66  3.000
 B03  C20   C19  N18   110.90  3.000
 B03  N21   C20  C22   122.33  3.000
 B03  C22   C20  C19   119.73  3.000
 B03  N21   C20  C19   117.94  3.000
 B03  H22   C22  C23   120.98  3.000
 B03  H22   C22  C20   120.31  3.000
 B03  C23   C22  C20   118.71  3.000
 B03  H23   C23  C24   120.65  3.000
 B03  H23   C23  C22   120.40  3.000
 B03  C24   C23  C22   118.96  3.000
 B03  H24   C24  C25   120.45  3.000
 B03  H24   C24  C23   121.48  3.000
 B03  C25   C24  C23   118.07  3.000
 B03  H25   C25  N21   116.35  3.000
 B03  H25   C25  C24   120.51  3.000
 B03  N21   C25  C24   123.14  3.000
 B03  C25   N21  C20   118.79  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
 B03  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 B03  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 B03  CONST_03  C6    C1   C2   C3      0.00   0.0  0
 B03  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 B03  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 B03  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 B03  CONST_07  C24   C25  N21  C20     0.00   0.0  0
 B03  CONST_08  C24   C23  C22  C20     0.00   0.0  0
 B03  CONST_09  C25   N21  C20  C22     0.00   0.0  0
 B03  CONST_10  C25   C24  C23  C22     0.00   0.0  0
 B03  CONST_11  N21   C20  C22  C23     0.00   0.0  0
 B03  CONST_12  N21   C25  C24  C23     0.00   0.0  0
 B03  CONST_13  C2    C3   C4   C7    180.00   0.0  0
 B03  CONST_14  C6    C5   C4   C7    180.00   0.0  0
 B03  CONST_15  C25   N21  C20  C19   180.00   0.0  0
 B03  CONST_16  C23   C22  C20  C19   180.00   0.0  0
 B03  CONST_17  H2    C2   C3   C4    180.00   0.0  0
 B03  CONST_18  H6    C6   C5   C4    180.00   0.0  0
 B03  CONST_19  H1    C1   C2   C3    180.00   0.0  0
 B03  CONST_20  H5    C5   C4   C3    180.00   0.0  0
 B03  CONST_21  H3    C3   C4   C5    180.00   0.0  0
 B03  CONST_22  H25   C25  N21  C20   180.00   0.0  0
 B03  CONST_23  H23   C23  C22  C20   180.00   0.0  0
 B03  CONST_24  H24   C24  C23  C22   180.00   0.0  0
 B03  CONST_25  H22   C22  C23  C24   180.00   0.0  0
 B03  CONST_26  C13   N11  C9   C8    180.00   0.0  0
 B03  CONST_27  C14   N11  C9   C8      0.00   0.0  0
 B03  CONST_28  C13   N11  C9   O12     0.00   0.0  0
 B03  CONST_29  C14   N11  C9   O12   180.00   0.0  0
 B03  CONST_30  C19   N18  C17  C13   180.00   0.0  0
 B03  CONST_31  HN18  N18  C17  C13     0.00   0.0  0
 B03  CONST_32  C19   N18  C17  O28     0.00   0.0  0
 B03  Var_01    C15   C16  C14  N11    28.21  30.0  1
 B03  Var_02    C16   C14  N11  C13    -8.83  30.0  1
 B03  Var_03    C14   C16  C15  C13   -36.89  30.0  1
 B03  Var_04    C3    C4   C7   C8     83.36  30.0  2
 B03  Var_05    N21   C20  C19  N18    -2.98  30.0  2
 B03  Var_06    C20   C19  N18  C17  -176.53  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
 B03  chir_01  C8   C7   C9   N10  positiv
 B03  chir_02  C13  N11  C17  C15  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
 B03  plan-1  C7    0.020
 B03  plan-1  C4    0.020
 B03  plan-1  C3    0.020
 B03  plan-1  C5    0.020
 B03  plan-1  C2    0.020
 B03  plan-1  C6    0.020
 B03  plan-1  C1    0.020
 B03  plan-1  H3    0.020
 B03  plan-1  H5    0.020
 B03  plan-1  H2    0.020
 B03  plan-1  H6    0.020
 B03  plan-1  H1    0.020
 B03  plan-2  C19   0.020
 B03  plan-2  C20   0.020
 B03  plan-2  C22   0.020
 B03  plan-2  C23   0.020
 B03  plan-2  C24   0.020
 B03  plan-2  C25   0.020
 B03  plan-2  N21   0.020
 B03  plan-2  H22   0.020
 B03  plan-2  H23   0.020
 B03  plan-2  H24   0.020
 B03  plan-2  H25   0.020
 B03  plan-3  C13   0.020
 B03  plan-3  C17   0.020
 B03  plan-3  O28   0.020
 B03  plan-3  N18   0.020
 B03  plan-3  C19   0.020
 B03  plan-3  HN18  0.020
 B03  plan-4  C8    0.020
 B03  plan-4  C9    0.020
 B03  plan-4  O12   0.020
 B03  plan-4  N11   0.020
 B03  plan-4  C13   0.020
 B03  plan-4  C14   0.020

