# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:15:51 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  28  16  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.372  -0.2630  -0.2267   3.6928
 PBG  C1A   C  CR5    0   0.283  -0.8555  -0.3512   2.3316
 PBG  C2A   C  CR5    0  -0.025  -0.2446  -0.6044   1.1219
 PBG  C3A   C  CR5    0   0.033  -1.2591  -0.5600   0.1171
 PBG  C4A   C  CR15   0  -0.141  -2.4390  -0.2695   0.7596
 PBG  NA    N  NR15   0  -0.627  -2.1806  -0.1416   2.0900
 PBG  C5A   C  CH2    0  -0.685   1.2076  -0.8723   0.8959
 PBG  C6A   C  C      0   0.428   2.0885   0.3781   0.6745
 PBG  O1A   O  O      0  -0.591   1.9165   1.3462   1.4461
 PBG  O2A   O  OC    -1  -0.618   2.9374   0.3171  -0.2369
 PBG  C7A   C  CH2    0  -0.516  -1.0904  -0.7720  -1.3553
 PBG  C8A   C  CH2    0  -0.581  -0.4181   0.4012  -2.0629
 PBG  C9A   C  C      0   0.409  -0.3274   0.2995  -3.5938
 PBG  O3A   O  O      0  -0.612  -0.6707  -0.7721  -4.1326
 PBG  O4A   O  OC    -1  -0.634   0.1012   1.3155  -4.1823
 PBG  N1    N  NH2    0  -0.824   0.1354   1.1539   3.9600
 PBG  HHA2  H  HCH2   0   0.202   0.5687  -0.9405   3.7683
 PBG  HHA1  H  HCH2   0   0.223  -0.9957  -0.5360   4.4448
 PBG  H4A1  H  HCR5   0   0.252  -3.4388  -0.1598   0.3692
 PBG  HA    H  HNR5   0   0.394  -2.8691   0.0616   2.7947
 PBG  H5A2  H  HCH2   0   0.233   1.6222  -1.3935   1.7680
 PBG  H5A1  H  HCH2   0   0.215   1.3333  -1.5550   0.0525
 PBG  H7A2  H  HCH2   0   0.209  -0.5089  -1.6805  -1.5390
 PBG  H7A1  H  HCH2   0   0.215  -2.0702  -0.9535  -1.8045
 PBG  H8A2  H  HCH2   0   0.212  -0.9383   1.3295  -1.8039
 PBG  H8A1  H  HCH2   0   0.233   0.5996   0.5280  -1.6776
 PBG  H12   H  HNH2   0   0.333   0.6349   1.1860   4.8413
 PBG  H11   H  HNH2   0   0.349   0.8054   1.4026   3.2364

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    1.490  0.020  1.490
 PBG  CHA  N1    single    1.462  0.020  1.462
 PBG  CHA  HHA2  single    0.970  0.020  1.090
 PBG  CHA  HHA1  single    0.970  0.020  1.090
 PBG  C1A  C2A   aromatic  1.379  0.020  1.379
 PBG  C1A  NA    aromatic  1.363  0.020  1.363
 PBG  C2A  C3A   aromatic  1.429  0.020  1.429
 PBG  C2A  C5A   single    1.494  0.020  1.494
 PBG  C3A  C4A   aromatic  1.374  0.020  1.374
 PBG  C3A  C7A   single    1.497  0.020  1.497
 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    1.545  0.020  1.545
 PBG  C5A  H5A2  single    0.970  0.020  1.090
 PBG  C5A  H5A1  single    0.970  0.020  1.090
 PBG  C6A  O1A   deloc     1.250  0.020  1.250
 PBG  C6A  O2A   deloc     1.247  0.020  1.247
 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    1.537  0.020  1.537
 PBG  C8A  H8A2  single    0.970  0.020  1.090
 PBG  C8A  H8A1  single    0.970  0.020  1.090
 PBG  C9A  O3A   deloc     1.248  0.020  1.248
 PBG  C9A  O4A   deloc     1.250  0.020  1.250
 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  106.02  3.000
 PBG  HHA1  CHA  N1    108.90  3.000
 PBG  HHA2  CHA  N1    113.26  3.000
 PBG  HHA1  CHA  C1A   109.75  3.000
 PBG  HHA2  CHA  C1A   108.03  3.000
 PBG  N1    CHA  C1A   110.75  3.000
 PBG  NA    C1A  C2A   107.67  3.000
 PBG  NA    C1A  CHA   122.39  3.000
 PBG  C2A   C1A  CHA   129.85  3.000
 PBG  C5A   C2A  C3A   126.13  3.000
 PBG  C5A   C2A  C1A   126.61  3.000
 PBG  C3A   C2A  C1A   107.26  3.000
 PBG  C7A   C3A  C4A   125.90  3.000
 PBG  C7A   C3A  C2A   127.39  3.000
 PBG  C4A   C3A  C2A   106.71  3.000
 PBG  H4A1  C4A  NA    121.33  3.000
 PBG  H4A1  C4A  C3A   130.38  3.000
 PBG  NA    C4A  C3A   108.29  3.000
 PBG  HA    NA   C4A   125.01  3.000
 PBG  HA    NA   C1A   124.91  3.000
 PBG  C4A   NA   C1A   110.07  3.000
 PBG  H5A1  C5A  H5A2  105.86  3.000
 PBG  H5A1  C5A  C6A   109.24  3.000
 PBG  H5A2  C5A  C6A   106.43  3.000
 PBG  H5A1  C5A  C2A   109.92  3.000
 PBG  H5A2  C5A  C2A   109.41  3.000
 PBG  C6A   C5A  C2A   115.51  3.000
 PBG  O2A   C6A  O1A   125.65  3.000
 PBG  O2A   C6A  C5A   116.95  3.000
 PBG  O1A   C6A  C5A   117.37  3.000
 PBG  H7A1  C7A  H7A2  105.63  3.000
 PBG  H7A1  C7A  C8A   109.39  3.000
 PBG  H7A2  C7A  C8A   109.04  3.000
 PBG  H7A1  C7A  C3A   109.07  3.000
 PBG  H7A2  C7A  C3A   110.04  3.000
 PBG  C8A   C7A  C3A   113.38  3.000
 PBG  H8A1  C8A  H8A2  105.07  3.000
 PBG  H8A1  C8A  C9A   107.65  3.000
 PBG  H8A2  C8A  C9A   108.64  3.000
 PBG  H8A1  C8A  C7A   109.57  3.000
 PBG  H8A2  C8A  C7A   109.43  3.000
 PBG  C9A   C8A  C7A   115.91  3.000
 PBG  O4A   C9A  O3A   126.10  3.000
 PBG  O4A   C9A  C8A   115.81  3.000
 PBG  O3A   C9A  C8A   118.08  3.000
 PBG  H11   N1   H12   106.64  3.000
 PBG  H11   N1   CHA   106.29  3.000
 PBG  H12   N1   CHA   108.85  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  Var_01    C6A   C5A  C2A  C1A   -87.85  30.0  2
 PBG  Var_02    N1    CHA  C1A  C2A    88.88  30.0  1
 PBG  Var_03    C8A   C7A  C3A  C2A   -73.77  30.0  2
 PBG  Var_04    O1A   C6A  C5A  C2A    45.27  30.0  3
 PBG  Var_05    C9A   C8A  C7A  C3A  -174.80  30.0  3
 PBG  Var_06    H12   N1   CHA  C1A  -173.16  30.0  3
 PBG  Var_07    O3A   C9A  C8A  C7A    -7.39  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-3  C8A   0.020
 PBG  plan-3  C9A   0.020
 PBG  plan-3  O3A   0.020
 PBG  plan-3  O4A   0.020

