# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 05:14:42 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1[nH]cc(CCC(O)=O)c1CC(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
 PBG  PBG  '3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid'  ligand  30  16  .  2021-08-19  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PBG
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
 PBG  CHA   C  CH2   0  -0.363  -0.0177  -0.1652   3.5860
 PBG  C1A   C  CR5   0   0.310  -0.6558  -0.2308   2.2371
 PBG  C2A   C  CR5   0  -0.021  -0.1535  -0.6073   1.0112
 PBG  C3A   C  CR5   0   0.022  -1.2214  -0.5170   0.0695
 PBG  C4A   C  CR15  0  -0.121  -2.3245  -0.0840   0.7636
 PBG  NA    N  NR15  0  -0.617  -1.9656   0.0799   2.0658
 PBG  C5A   C  CH2   0  -0.739   1.2417  -1.0547   0.7351
 PBG  C6A   C  C     0   0.556   2.2199   0.0695   0.4896
 PBG  O1A   O  O     0  -0.437   1.9459   1.2414   0.4420
 PBG  O2A   O  OH1   0  -0.596   3.4567  -0.3937   0.3262
 PBG  C7A   C  CH2   0  -0.535  -1.1474  -0.7844  -1.3999
 PBG  C8A   C  CH2   0  -0.576  -0.6106   0.4217  -2.1662
 PBG  C9A   C  C     0   0.551  -0.4278   0.1718  -3.6369
 PBG  O3A   O  O     0  -0.447  -0.6831  -0.8611  -4.2053
 PBG  O4A   O  OH1   0  -0.598   0.0594   1.2395  -4.2640
 PBG  N1    N  NH2   0  -0.801  -0.5745   0.9339   4.3610
 PBG  HHA2  H  HCH2  0   0.215   1.0710  -0.1198   3.4587
 PBG  HHA1  H  HCH2  0   0.241  -0.2164  -1.0899   4.1371
 PBG  H4A1  H  HCR5  0   0.262  -3.3271   0.1236   0.4252
 PBG  HA    H  HNR5  0   0.397  -2.5599   0.4159   2.8063
 PBG  H5A2  H  HCH2  0   0.295   1.6386  -1.6646   1.5520
 PBG  H5A1  H  HCH2  0   0.297   1.2737  -1.7131  -0.1395
 PBG  H2AO  H  HOH1  0   0.479   4.0668   0.3406   0.1613
 PBG  H7A2  H  HCH2  0   0.238  -0.5077  -1.6500  -1.5919
 PBG  H7A1  H  HCH2  0   0.249  -2.1371  -1.0468  -1.7793
 PBG  H8A2  H  HCH2  0   0.281  -1.2853   1.2747  -2.0456
 PBG  H8A1  H  HCH2  0   0.279   0.3453   0.7494  -1.7490
 PBG  H4AO  H  HOH1  0   0.477   0.1638   1.0479  -5.2081
 PBG  H12   H  HNH2  0   0.356  -0.2500   0.8703   5.3168
 PBG  H11   H  HNH2  0   0.346  -0.2276   1.8147   4.0027

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
 PBG  CHA  C1A   single    1.494  0.020  1.494
 PBG  CHA  N1    single    1.456  0.020  1.456
 PBG  CHA  HHA2  single    0.970  0.020  1.090
 PBG  CHA  HHA1  single    0.970  0.020  1.090
 PBG  C1A  C2A   aromatic  1.377  0.020  1.377
 PBG  C1A  NA    aromatic  1.357  0.020  1.357
 PBG  C2A  C3A   aromatic  1.427  0.020  1.427
 PBG  C2A  C5A   single    1.491  0.020  1.491
 PBG  C3A  C4A   aromatic  1.373  0.020  1.373
 PBG  C3A  C7A   single    1.495  0.020  1.495
 PBG  C4A  NA    aromatic  1.361  0.020  1.361
 PBG  C4A  H4A1  single    0.930  0.020  1.080
 PBG  NA   HA    single    0.860  0.020  1.020
 PBG  C5A  C6A   single    1.510  0.020  1.510
 PBG  C5A  H5A2  single    0.970  0.020  1.090
 PBG  C5A  H5A1  single    0.970  0.020  1.090
 PBG  C6A  O1A   double    1.205  0.020  1.205
 PBG  C6A  O2A   single    1.331  0.020  1.331
 PBG  O2A  H2AO  single    0.850  0.020  0.980
 PBG  C7A  C8A   single    1.526  0.020  1.526
 PBG  C7A  H7A2  single    0.970  0.020  1.090
 PBG  C7A  H7A1  single    0.970  0.020  1.090
 PBG  C8A  C9A   single    1.503  0.020  1.503
 PBG  C8A  H8A2  single    0.970  0.020  1.090
 PBG  C8A  H8A1  single    0.970  0.020  1.090
 PBG  C9A  O3A   double    1.206  0.020  1.206
 PBG  C9A  O4A   single    1.331  0.020  1.331
 PBG  O4A  H4AO  single    0.850  0.020  0.980
 PBG  N1   H12   single    0.890  0.020  1.040
 PBG  N1   H11   single    0.890  0.020  1.040

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
 PBG  HHA1  CHA  HHA2  105.88  3.000
 PBG  HHA1  CHA  N1    107.48  3.000
 PBG  HHA2  CHA  N1    114.21  3.000
 PBG  HHA1  CHA  C1A   109.88  3.000
 PBG  HHA2  CHA  C1A   108.72  3.000
 PBG  N1    CHA  C1A   110.52  3.000
 PBG  NA    C1A  C2A   107.59  3.000
 PBG  NA    C1A  CHA   121.08  3.000
 PBG  C2A   C1A  CHA   131.30  3.000
 PBG  C5A   C2A  C3A   126.68  3.000
 PBG  C5A   C2A  C1A   126.02  3.000
 PBG  C3A   C2A  C1A   107.29  3.000
 PBG  C7A   C3A  C4A   126.36  3.000
 PBG  C7A   C3A  C2A   126.88  3.000
 PBG  C4A   C3A  C2A   106.72  3.000
 PBG  H4A1  C4A  NA    121.49  3.000
 PBG  H4A1  C4A  C3A   130.45  3.000
 PBG  NA    C4A  C3A   108.05  3.000
 PBG  HA    NA   C4A   126.03  3.000
 PBG  HA    NA   C1A   123.58  3.000
 PBG  C4A   NA   C1A   110.35  3.000
 PBG  H5A1  C5A  H5A2  104.51  3.000
 PBG  H5A1  C5A  C6A   107.38  3.000
 PBG  H5A2  C5A  C6A   107.54  3.000
 PBG  H5A1  C5A  C2A   110.83  3.000
 PBG  H5A2  C5A  C2A   111.63  3.000
 PBG  C6A   C5A  C2A   114.39  3.000
 PBG  O2A   C6A  O1A   123.04  3.000
 PBG  O2A   C6A  C5A   111.28  3.000
 PBG  O1A   C6A  C5A   125.68  3.000
 PBG  H2AO  O2A  C6A   110.02  3.000
 PBG  H7A1  C7A  H7A2  106.21  3.000
 PBG  H7A1  C7A  C8A   109.52  3.000
 PBG  H7A2  C7A  C8A   109.37  3.000
 PBG  H7A1  C7A  C3A   109.85  3.000
 PBG  H7A2  C7A  C3A   110.07  3.000
 PBG  C8A   C7A  C3A   111.68  3.000
 PBG  H8A1  C8A  H8A2  105.27  3.000
 PBG  H8A1  C8A  C9A   108.48  3.000
 PBG  H8A2  C8A  C9A   108.21  3.000
 PBG  H8A1  C8A  C7A   110.65  3.000
 PBG  H8A2  C8A  C7A   110.11  3.000
 PBG  C9A   C8A  C7A   113.74  3.000
 PBG  O4A   C9A  O3A   122.85  3.000
 PBG  O4A   C9A  C8A   111.85  3.000
 PBG  O3A   C9A  C8A   125.30  3.000
 PBG  H4AO  O4A  C9A   109.87  3.000
 PBG  H11   N1   H12   106.22  3.000
 PBG  H11   N1   CHA   109.73  3.000
 PBG  H12   N1   CHA   109.45  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
 PBG  CONST_01  C4A   C3A  C2A  C1A    0.00   0.0  0
 PBG  CONST_02  C3A   C4A  NA   C1A    0.00   0.0  0
 PBG  CONST_03  C4A   NA   C1A  C2A    0.00   0.0  0
 PBG  CONST_04  NA    C4A  C3A  C2A    0.00   0.0  0
 PBG  CONST_05  NA    C1A  C2A  C3A    0.00   0.0  0
 PBG  CONST_06  C3A   C2A  C1A  CHA  180.00   0.0  0
 PBG  CONST_07  C4A   NA   C1A  CHA  180.00   0.0  0
 PBG  CONST_08  C7A   C3A  C2A  C1A  180.00   0.0  0
 PBG  CONST_09  C5A   C2A  C3A  C4A  180.00   0.0  0
 PBG  CONST_10  C5A   C2A  C1A  NA   180.00   0.0  0
 PBG  CONST_11  C7A   C3A  C4A  NA   180.00   0.0  0
 PBG  CONST_12  H4A1  C4A  NA   C1A  180.00   0.0  0
 PBG  CONST_13  HA    NA   C1A  C2A  180.00   0.0  0
 PBG  CONST_14  H2AO  O2A  C6A  C5A  180.00   0.0  0
 PBG  CONST_15  H4AO  O4A  C9A  C8A  180.00   0.0  0
 PBG  Var_01    C6A   C5A  C2A  C1A  -84.91  30.0  2
 PBG  Var_02    N1    CHA  C1A  C2A  146.76  30.0  1
 PBG  Var_03    C8A   C7A  C3A  C2A  -81.99  30.0  2
 PBG  Var_04    O1A   C6A  C5A  C2A   -3.59  30.0  3
 PBG  Var_05    C9A   C8A  C7A  C3A  176.03  30.0  3
 PBG  Var_06    H12   N1   CHA  C1A  170.52  30.0  3
 PBG  Var_07    O3A   C9A  C8A  C7A    0.90  30.0  3

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
 PBG  plan-1  CHA   0.020
 PBG  plan-1  C1A   0.020
 PBG  plan-1  C2A   0.020
 PBG  plan-1  C3A   0.020
 PBG  plan-1  C4A   0.020
 PBG  plan-1  NA    0.020
 PBG  plan-1  C5A   0.020
 PBG  plan-1  C7A   0.020
 PBG  plan-1  H4A1  0.020
 PBG  plan-1  HA    0.020
 PBG  plan-2  C5A   0.020
 PBG  plan-2  C6A   0.020
 PBG  plan-2  O1A   0.020
 PBG  plan-2  O2A   0.020
 PBG  plan-2  H2AO  0.020
 PBG  plan-3  C8A   0.020
 PBG  plan-3  C9A   0.020
 PBG  plan-3  O3A   0.020
 PBG  plan-3  O4A   0.020
 PBG  plan-3  H4AO  0.020

