# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 00:24:03 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 4-amino-1-methyl-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(N)cc1C(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
 PYB  PYB  '4-amino-1-methyl-1H-pyrrole-2-carboxylic acid'  ligand  18  10  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PYB
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
 PYB  N    N  NH2   0  -0.864   0.0398  -0.3573  -0.3098
 PYB  CA   C  CR5   0   0.160   0.3690  -0.1733   1.0342
 PYB  CB1  C  CR15  0  -0.391   1.5961   0.2740   1.5472
 PYB  CB   C  CR15  0  -0.095  -0.4285  -0.4631   2.1295
 PYB  CG1  C  CR5   0   0.214   1.5070   0.2420   2.9339
 PYB  NG2  N  NR5   0  -0.455   0.2640  -0.2143   3.2688
 PYB  CD   C  CH3   0  -0.508  -0.2944  -0.4076   4.5916
 PYB  C    C  C     0   0.479   2.5160   0.6073   3.9095
 PYB  O    O  O     0  -0.460   2.3943   0.5396   5.1144
 PYB  OXT  O  OH1   0  -0.602   3.6323   1.0404   3.3229
 PYB  H    H  HNH2  0   0.366  -0.9568  -0.3509  -0.4694
 PYB  HN2  H  HNH2  0   0.367   0.4636   0.3356  -0.9089
 PYB  HB1  H  HCR5  0   0.261   2.4551   0.5877   0.9742
 PYB  HB   H  HCR5  0   0.284  -1.4424  -0.8303   2.1656
 PYB  HD1  H  HCH3  0   0.254   0.2648  -1.1527   5.1522
 PYB  HD2  H  HCH3  0   0.254  -0.3079   0.5220   5.1551
 PYB  HD3  H  HCH3  0   0.253  -1.3169  -0.7558   4.4755
 PYB  HXT  H  HOH1  0   0.482   4.2837   1.2672   4.0019

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
 PYB  N    CA   single    1.396  0.020  1.396
 PYB  N    H    single    0.860  0.020  1.020
 PYB  N    HN2  single    0.890  0.020  1.040
 PYB  CA   CB1  aromatic  1.403  0.020  1.403
 PYB  CA   CB   aromatic  1.385  0.020  1.385
 PYB  CB1  CG1  aromatic  1.390  0.020  1.390
 PYB  CB1  HB1  single    0.930  0.020  1.080
 PYB  CB   NG2  aromatic  1.356  0.020  1.356
 PYB  CB   HB   single    0.930  0.020  1.080
 PYB  CG1  NG2  aromatic  1.366  0.020  1.366
 PYB  CG1  C    single    1.450  0.020  1.450
 PYB  NG2  CD   single    1.449  0.020  1.449
 PYB  CD   HD1  single    0.970  0.020  1.090
 PYB  CD   HD2  single    0.970  0.020  1.090
 PYB  CD   HD3  single    0.970  0.020  1.090
 PYB  C    O    double    1.213  0.020  1.213
 PYB  C    OXT  single    1.333  0.020  1.333
 PYB  OXT  HXT  single    0.850  0.020  0.980

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
 PYB  HN2  N    H    108.45  3.000
 PYB  HN2  N    CA   112.46  3.000
 PYB  H    N    CA   112.60  3.000
 PYB  CB   CA   CB1  106.33  3.000
 PYB  CB   CA   N    126.71  3.000
 PYB  CB1  CA   N    126.89  3.000
 PYB  HB1  CB1  CG1  125.97  3.000
 PYB  HB1  CB1  CA   126.49  3.000
 PYB  CG1  CB1  CA   107.53  3.000
 PYB  HB   CB   NG2  120.94  3.000
 PYB  HB   CB   CA   129.69  3.000
 PYB  NG2  CB   CA   109.37  3.000
 PYB  C    CG1  NG2  123.53  3.000
 PYB  C    CG1  CB1  128.37  3.000
 PYB  NG2  CG1  CB1  108.10  3.000
 PYB  CD   NG2  CG1  128.26  3.000
 PYB  CD   NG2  CB   123.07  3.000
 PYB  CG1  NG2  CB   108.66  3.000
 PYB  HD3  CD   HD2  108.53  3.000
 PYB  HD3  CD   HD1  108.64  3.000
 PYB  HD2  CD   HD1  108.97  3.000
 PYB  HD3  CD   NG2  107.94  3.000
 PYB  HD2  CD   NG2  111.34  3.000
 PYB  HD1  CD   NG2  111.34  3.000
 PYB  OXT  C    O    122.63  3.000
 PYB  OXT  C    CG1  111.61  3.000
 PYB  O    C    CG1  125.76  3.000
 PYB  HXT  OXT  C    109.33  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
 PYB  CONST_01  NG2  CG1  CB1  CA      0.00   0.0  0
 PYB  CONST_02  CG1  NG2  CB   CA      0.00   0.0  0
 PYB  CONST_03  NG2  CB   CA   CB1     0.00   0.0  0
 PYB  CONST_04  CB   NG2  CG1  CB1     0.00   0.0  0
 PYB  CONST_05  CG1  CB1  CA   CB      0.00   0.0  0
 PYB  CONST_06  CG1  CB1  CA   N     180.00   0.0  0
 PYB  CONST_07  NG2  CB   CA   N     180.00   0.0  0
 PYB  CONST_08  C    CG1  CB1  CA    180.00   0.0  0
 PYB  CONST_09  CD   NG2  CB   CA    180.00   0.0  0
 PYB  CONST_10  CD   NG2  CG1  CB1   180.00   0.0  0
 PYB  CONST_11  C    CG1  NG2  CB    180.00   0.0  0
 PYB  CONST_12  HB   CB   CA   CB1   180.00   0.0  0
 PYB  CONST_13  HB1  CB1  CA   CB    180.00   0.0  0
 PYB  CONST_16  HXT  OXT  C    CG1   180.00   0.0  0
 PYB  Var_01    O    C    CG1  CB1  -178.69  30.0  2
 PYB  Var_02    HD1  CD   NG2  CB    118.42  30.0  2

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
 PYB  plan-1  N    0.020
 PYB  plan-1  CA   0.020
 PYB  plan-1  CB1  0.020
 PYB  plan-1  CB   0.020
 PYB  plan-1  CG1  0.020
 PYB  plan-1  NG2  0.020
 PYB  plan-1  CD   0.020
 PYB  plan-1  C    0.020
 PYB  plan-1  HB1  0.020
 PYB  plan-1  HB   0.020
 PYB  plan-2  N    0.020
 PYB  plan-2  CA   0.020
 PYB  plan-2  H    0.020
 PYB  plan-2  HN2  0.020
 PYB  plan-3  CG1  0.020
 PYB  plan-3  C    0.020
 PYB  plan-3  O    0.020
 PYB  plan-3  OXT  0.020
 PYB  plan-3  HXT  0.020

