# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 17:13:39 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-(1,10-phenanthrolin-2-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc2ccc3cccnc3c2n1)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
 PYA  PYA  3-(1,10-phenanthrolin-2-yl)-L-alanine  L-peptide  32  20  .  2012-08-28  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_PYA
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
 PYA  C1   C  C1     0  -0.187  -0.8557   1.0025  -7.2132
 PYA  C2   C  C1     0  -0.318  -1.7384  -0.0314  -7.0396
 PYA  C3   C  C1     0  -0.084  -2.6439   0.0415  -5.9716
 PYA  N4   N  N      0  -0.403  -2.6967   1.0444  -5.1270
 PYA  C4A  C  CR6    0   0.150  -1.8406   2.0660  -5.2877
 PYA  C4B  C  CR66   0   0.144  -1.9013   3.1817  -4.3647
 PYA  N5   N  N      0  -0.425  -2.8058   3.1549  -3.3766
 PYA  C6   C  CR6    0   0.237  -2.8812   4.1646  -2.5336
 PYA  C7   C  CR16   0  -0.329  -2.0374   5.2879  -2.6416
 PYA  C8   C  CR16   0  -0.186  -1.1009   5.3276  -3.6383
 PYA  C8A  C  CR66   0   0.064  -1.0071   4.2555  -4.5413
 PYA  C9   C  CR16   0  -0.316  -0.0515   4.2392  -5.6019
 PYA  C10  C  CR16   0  -0.320   0.0078   3.1978  -6.4620
 PYA  C1A  C  CR6    0   0.062  -0.8866   2.0921  -6.3265
 PYA  CB   C  CH2    0  -0.477  -3.9312   4.0987  -1.4657
 PYA  CA   C  CH1    0  -0.220  -5.3295   4.3674  -2.0300
 PYA  N    N  NH2    0  -0.814  -5.3650   5.6616  -2.6970
 PYA  C    C  C      0   0.423  -6.4286   4.2985  -0.9348
 PYA  O    O  O      0  -0.596  -6.2111   3.5631   0.0458
 PYA  OXT  O  OC    -1  -0.601  -7.4609   4.9637  -1.1560
 PYA  H1   H  H      0   0.273  -0.1371   0.9913  -8.0237
 PYA  HC2  H  H      0   0.272  -1.7468  -0.8865  -7.7012
 PYA  H3   H  H      0   0.261  -3.3523  -0.7647  -5.8120
 PYA  H7   H  HCR6   0   0.263  -2.1338   6.1012  -1.9352
 PYA  H8   H  HCR6   0   0.268  -0.4330   6.1744  -3.7411
 PYA  H9   H  HCR6   0   0.262   0.6242   5.0794  -5.7055
 PYA  H10  H  HCR6   0   0.262   0.7311   3.1850  -7.2679
 PYA  HB3  H  HCH2   0   0.236  -3.9149   3.1097  -1.0078
 PYA  HB2  H  HCH2   0   0.225  -3.7092   4.8295  -0.6850
 PYA  HA   H  HCH1   0   0.204  -5.5531   3.5409  -2.7268
 PYA  H    H  HNH2   0   0.335  -6.3359   5.9396  -2.7640
 PYA  H2   H  HNH2   0   0.333  -5.0200   5.5795  -3.6445

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
 PYA  C1   C2   aromatic  1.371  0.020  1.371
 PYA  C1   C1A  aromatic  1.405  0.020  1.405
 PYA  C1   H1   single    0.930  0.020  1.080
 PYA  C2   C3   aromatic  1.402  0.020  1.402
 PYA  C2   HC2  single    0.930  0.020  1.080
 PYA  C3   N4   aromatic  1.312  0.020  1.312
 PYA  C3   H3   single    0.930  0.020  1.080
 PYA  N4   C4A  aromatic  1.343  0.020  1.343
 PYA  C4A  C4B  aromatic  1.449  0.020  1.449
 PYA  C4A  C1A  aromatic  1.411  0.020  1.411
 PYA  C4B  N5   aromatic  1.340  0.020  1.340
 PYA  C4B  C8A  aromatic  1.408  0.020  1.408
 PYA  N5   C6   aromatic  1.317  0.020  1.317
 PYA  C6   C7   aromatic  1.409  0.020  1.409
 PYA  C6   CB   single    1.499  0.020  1.499
 PYA  C7   C8   aromatic  1.368  0.020  1.368
 PYA  C7   H7   single    0.930  0.020  1.080
 PYA  C8   C8A  aromatic  1.405  0.020  1.405
 PYA  C8   H8   single    0.930  0.020  1.080
 PYA  C8A  C9   aromatic  1.428  0.020  1.428
 PYA  C9   C10  aromatic  1.352  0.020  1.352
 PYA  C9   H9   single    0.930  0.020  1.080
 PYA  C10  C1A  aromatic  1.429  0.020  1.429
 PYA  C10  H10  single    0.930  0.020  1.080
 PYA  CB   CA   single    1.521  0.033  1.521
 PYA  CB   HB3  single    0.970  0.020  1.090
 PYA  CB   HB2  single    0.970  0.020  1.090
 PYA  CA   N    single    1.458  0.019  1.458
 PYA  CA   C    single    1.525  0.021  1.525
 PYA  CA   HA   single    0.970  0.020  0.970
 PYA  N    H    single    0.860  0.020  0.860
 PYA  N    H2   single    0.890  0.020  1.040
 PYA  C    O    deloc     1.231  0.020  1.231
 PYA  C    OXT  deloc     1.248  0.020  1.248

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
 PYA  H1   C1   C1A  119.66  3.000
 PYA  H1   C1   C2   120.94  3.000
 PYA  C1A  C1   C2   119.40  3.000
 PYA  HC2  C2   C3   120.15  3.000
 PYA  HC2  C2   C1   121.61  3.000
 PYA  C3   C2   C1   118.24  3.000
 PYA  H3   C3   N4   116.55  3.000
 PYA  H3   C3   C2   119.67  3.000
 PYA  N4   C3   C2   123.78  3.000
 PYA  C4A  N4   C3   118.61  3.000
 PYA  C1A  C4A  C4B  118.89  3.000
 PYA  C1A  C4A  N4   122.24  3.000
 PYA  C4B  C4A  N4   118.87  3.000
 PYA  C8A  C4B  N5   122.43  3.000
 PYA  C8A  C4B  C4A  118.71  3.000
 PYA  N5   C4B  C4A  118.85  3.000
 PYA  C6   N5   C4B  119.69  3.000
 PYA  CB   C6   C7   120.60  3.000
 PYA  CB   C6   N5   117.53  3.000
 PYA  C7   C6   N5   121.84  3.000
 PYA  H7   C7   C8   120.99  3.000
 PYA  H7   C7   C6   119.74  3.000
 PYA  C8   C7   C6   119.26  3.000
 PYA  H8   C8   C8A  119.63  3.000
 PYA  H8   C8   C7   120.91  3.000
 PYA  C8A  C8   C7   119.46  3.000
 PYA  C9   C8A  C8   122.06  3.000
 PYA  C9   C8A  C4B  120.63  3.000
 PYA  C8   C8A  C4B  117.31  3.000
 PYA  H9   C9   C10  120.62  3.000
 PYA  H9   C9   C8A  118.67  3.000
 PYA  C10  C9   C8A  120.71  3.000
 PYA  H10  C10  C1A  118.66  3.000
 PYA  H10  C10  C9   120.78  3.000
 PYA  C1A  C10  C9   120.56  3.000
 PYA  C10  C1A  C4A  120.50  3.000
 PYA  C10  C1A  C1   121.77  3.000
 PYA  C4A  C1A  C1   117.73  3.000
 PYA  HB2  CB   HB3  107.69  3.000
 PYA  HB2  CB   CA   109.36  3.000
 PYA  HB3  CB   CA   109.13  3.000
 PYA  HB2  CB   C6   109.72  3.000
 PYA  HB3  CB   C6   109.18  3.000
 PYA  CA   CB   C6   111.67  3.000
 PYA  HA   CA   C    109.00  3.000
 PYA  HA   CA   N    110.00  3.000
 PYA  C    CA   N    111.00  2.800
 PYA  HA   CA   CB   109.00  3.000
 PYA  C    CA   CB   110.50  1.500
 PYA  N    CA   CB   110.40  1.500
 PYA  H2   N    H    106.71  3.000
 PYA  H2   N    CA   110.40  3.000
 PYA  H    N    CA   114.00  3.000
 PYA  OXT  C    O    126.80  3.000
 PYA  OXT  C    CA   115.90  3.000
 PYA  O    C    CA   120.80  1.700

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
 PYA  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 PYA  CONST_02  N4   C4A  C1A  C1     0.00   0.0  0
 PYA  CONST_03  C4B  C4A  C1A  C1   180.00   0.0  0
 PYA  CONST_04  C9   C10  C1A  C1   180.00   0.0  0
 PYA  CONST_05  C4A  C1A  C1   C2     0.00   0.0  0
 PYA  CONST_06  C10  C1A  C1   C2   180.00   0.0  0
 PYA  CONST_07  C4A  N4   C3   C2     0.00   0.0  0
 PYA  CONST_08  C1A  C1   C2   C3     0.00   0.0  0
 PYA  CONST_09  C4B  C4A  N4   C3   180.00   0.0  0
 PYA  CONST_10  C1A  C4A  N4   C3     0.00   0.0  0
 PYA  CONST_11  N5   C4B  C4A  N4     0.00   0.0  0
 PYA  CONST_12  C8A  C4B  C4A  N4   180.00   0.0  0
 PYA  CONST_13  C10  C1A  C4A  N4   180.00   0.0  0
 PYA  CONST_14  C6   N5   C4B  C4A  180.00   0.0  0
 PYA  CONST_15  C8   C8A  C4B  C4A  180.00   0.0  0
 PYA  CONST_16  C9   C8A  C4B  C4A    0.00   0.0  0
 PYA  CONST_17  C9   C10  C1A  C4A    0.00   0.0  0
 PYA  CONST_18  C10  C1A  C4A  C4B    0.00   0.0  0
 PYA  CONST_19  C7   C6   N5   C4B    0.00   0.0  0
 PYA  CONST_20  C7   C8   C8A  C4B    0.00   0.0  0
 PYA  CONST_21  C10  C9   C8A  C4B    0.00   0.0  0
 PYA  CONST_22  C1A  C4A  C4B  N5   180.00   0.0  0
 PYA  CONST_23  C8   C8A  C4B  N5     0.00   0.0  0
 PYA  CONST_24  C9   C8A  C4B  N5   180.00   0.0  0
 PYA  CONST_25  C8   C7   C6   N5     0.00   0.0  0
 PYA  CONST_26  C8A  C4B  N5   C6     0.00   0.0  0
 PYA  CONST_27  C8A  C8   C7   C6     0.00   0.0  0
 PYA  CONST_28  C9   C8A  C8   C7   180.00   0.0  0
 PYA  CONST_29  C10  C9   C8A  C8   180.00   0.0  0
 PYA  CONST_30  C1A  C4A  C4B  C8A    0.00   0.0  0
 PYA  CONST_31  C1A  C10  C9   C8A    0.00   0.0  0
 PYA  CONST_32  CB   C6   N5   C4B  180.00   0.0  0
 PYA  CONST_33  CB   C6   C7   C8   180.00   0.0  0
 PYA  CONST_34  H3   C3   C2   C1   180.00   0.0  0
 PYA  CONST_35  H10  C10  C1A  C1     0.00   0.0  0
 PYA  CONST_36  H1   C1   C2   C3   180.00   0.0  0
 PYA  CONST_37  HC2  C2   C3   N4   180.00   0.0  0
 PYA  CONST_38  H8   C8   C8A  C4B  180.00   0.0  0
 PYA  CONST_39  H9   C9   C8A  C4B  180.00   0.0  0
 PYA  CONST_40  H7   C7   C6   N5   180.00   0.0  0
 PYA  Var_01    CA   CB   C6   N5   -74.53  30.0  2

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
 PYA  chir_01  CA  CB  N  C  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
 PYA  plan-1  C1   0.020
 PYA  plan-1  C2   0.020
 PYA  plan-1  C3   0.020
 PYA  plan-1  N4   0.020
 PYA  plan-1  C4A  0.020
 PYA  plan-1  C4B  0.020
 PYA  plan-1  N5   0.020
 PYA  plan-1  C6   0.020
 PYA  plan-1  C7   0.020
 PYA  plan-1  C8   0.020
 PYA  plan-1  C8A  0.020
 PYA  plan-1  C9   0.020
 PYA  plan-1  C10  0.020
 PYA  plan-1  C1A  0.020
 PYA  plan-1  CB   0.020
 PYA  plan-1  H1   0.020
 PYA  plan-1  HC2  0.020
 PYA  plan-1  H3   0.020
 PYA  plan-1  H7   0.020
 PYA  plan-1  H8   0.020
 PYA  plan-1  H9   0.020
 PYA  plan-1  H10  0.020
 PYA  plan-2  CA   0.020
 PYA  plan-2  C    0.020
 PYA  plan-2  O    0.020
 PYA  plan-2  OXT  0.020

