# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:14:20 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: 3-[(5S)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(C[C@@H]2NC(=O)C(=C2CC(O)=O)CCC(O)=O)c(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
 29P  29P  '3-[(5S)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid'  ligand  51  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_29P
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
 29P  O4A  O  O      0  -0.612   2.0418   4.0793   0.0862
 29P  C9A  C  C      0   0.406   2.3814   3.5161   1.1466
 29P  O3A  O  OC    -1  -0.635   2.6175   4.0831   2.2356
 29P  C8A  C  CH2    0  -0.582   2.5369   1.9875   1.1335
 29P  C7A  C  CH2    0  -0.519   2.1110   1.2847  -0.1514
 29P  C3A  C  CR5    0  -0.033   2.3790  -0.1877  -0.1136
 29P  C2A  C  CR5    0   0.039   3.5934  -0.8395  -0.4881
 29P  C5A  C  CH2    0  -0.739   4.8092  -0.1882  -1.0505
 29P  C6A  C  C      0   0.423   5.9028   0.2381  -0.0433
 29P  O1A  O  OC    -1  -0.637   6.9261   0.7442  -0.5544
 29P  O2A  O  O      0  -0.594   5.6991   0.0533   1.1694
 29P  C1A  C  CR5    0   0.246   3.4213  -2.1848  -0.2556
 29P  CHA  C  CH3    0  -0.737   4.3644  -3.3233  -0.4282
 29P  NA   N  NR15   0  -0.680   2.1654  -2.3588   0.2511
 29P  C4A  C  CR5    0   0.286   1.5180  -1.1584   0.3455
 29P  CHB  C  CH2    0  -0.543   0.1036  -1.0542   0.7998
 29P  C1B  C  CR15   0  -0.078  -0.8997  -1.4796  -0.2857
 29P  C2B  C  CR5    0   0.155  -2.3324  -1.2333   0.0987
 29P  C5B  C  CH2    0  -0.725  -2.9395  -1.8668   1.2955
 29P  C6B  C  C      0   0.431  -3.2119  -3.3891   1.1595
 29P  O1B  O  O      0  -0.593  -2.8969  -3.9391   0.0889
 29P  O2B  O  OC    -1  -0.617  -3.7346  -3.9246   2.1545
 29P  NB   N  NR15   0  -0.661  -0.7660  -0.6949  -1.4844
 29P  C4B  C  CR5    0   0.510  -1.8883  -0.0059  -1.7861
 29P  O5B  O  O      0  -0.503  -2.0340   0.7670  -2.7251
 29P  C3B  C  CR5    0  -0.102  -2.8960  -0.3793  -0.7675
 29P  C7B  C  CH2    0  -0.507  -4.2630   0.2154  -0.7688
 29P  C8B  C  CH2    0  -0.578  -4.2681   1.6246  -0.1810
 29P  C9B  C  C      0   0.412  -5.6337   2.3322  -0.1617
 29P  O3B  O  OC    -1  -0.632  -5.6622   3.4445   0.4073
 29P  O4B  O  O      0  -0.608  -6.5957   1.7595  -0.7100
 29P  H2   H  HCH2   0   0.238   3.5809   1.7333   1.3446
 29P  H3   H  HCH2   0   0.211   1.9712   1.5714   1.9754
 29P  H4   H  HCH2   0   0.208   1.0492   1.4671  -0.3375
 29P  H5   H  HCH2   0   0.213   2.6360   1.7337  -0.9976
 29P  H6   H  HCH2   0   0.228   5.2836  -0.8420  -1.7909
 29P  H7   H  HCH2   0   0.232   4.5205   0.7059  -1.6149
 29P  H9   H  HCH3   0   0.237   4.7585  -3.6810   0.5265
 29P  H10  H  HCH3   0   0.236   3.8982  -4.1759  -0.9260
 29P  H11  H  HCH3   0   0.242   5.2183  -3.0202  -1.0337
 29P  H12  H  HNR5   0   0.389   1.7704  -3.2479   0.5090
 29P  H13  H  HCH2   0   0.253  -0.0622  -1.6739   1.6861
 29P  H14  H  HCH2   0   0.254  -0.1090  -0.0235   1.0923
 29P  H15  H  HCR5   0   0.264  -0.7574  -2.5431  -0.5036
 29P  H16  H  HCH2   0   0.253  -2.2858  -1.7225   2.1631
 29P  H17  H  HCH2   0   0.253  -3.8788  -1.3693   1.5519
 29P  H19  H  HNR5   0   0.392   0.1149  -0.5585  -1.9548
 29P  H20  H  HCH2   0   0.226  -4.6437   0.2485  -1.7921
 29P  H21  H  HCH2   0   0.225  -4.9488  -0.4220  -0.2083
 29P  H22  H  HCH2   0   0.224  -3.8731   1.5944   0.8397
 29P  H23  H  HCH2   0   0.230  -3.5668   2.2538  -0.7400

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
 29P  O1B  C6B  deloc     1.244  0.020  1.244
 29P  O2B  C6B  deloc     1.245  0.020  1.245
 29P  C6B  C5B  single    1.552  0.020  1.552
 29P  O4A  C9A  deloc     1.248  0.020  1.248
 29P  C5B  C2B  single    1.484  0.020  1.484
 29P  C9A  O3A  deloc     1.250  0.020  1.250
 29P  C9A  C8A  single    1.536  0.020  1.536
 29P  O4B  C9B  deloc     1.247  0.020  1.247
 29P  C9B  O3B  deloc     1.250  0.020  1.250
 29P  C9B  C8B  single    1.538  0.020  1.538
 29P  C7B  C8B  single    1.527  0.020  1.527
 29P  C7B  C3B  single    1.491  0.020  1.491
 29P  C8A  C7A  single    1.525  0.020  1.525
 29P  C2B  C3B  double    1.341  0.020  1.341
 29P  C2B  C1B  single    1.504  0.020  1.504
 29P  C3B  C4B  single    1.481  0.020  1.481
 29P  C1B  CHB  single    1.538  0.020  1.538
 29P  C1B  NB   single    1.439  0.020  1.439
 29P  C7A  C3A  single    1.497  0.020  1.497
 29P  CHB  C4A  single    1.489  0.020  1.489
 29P  C4B  NB   single    1.351  0.020  1.351
 29P  C4B  O5B  double    1.225  0.020  1.225
 29P  C3A  C4A  aromatic  1.376  0.020  1.376
 29P  C3A  C2A  aromatic  1.428  0.020  1.428
 29P  C4A  NA   aromatic  1.367  0.020  1.367
 29P  C2A  C5A  single    1.490  0.020  1.490
 29P  C2A  C1A  aromatic  1.376  0.020  1.376
 29P  NA   C1A  aromatic  1.365  0.020  1.365
 29P  C5A  C6A  single    1.547  0.020  1.547
 29P  C1A  CHA  single    1.488  0.020  1.488
 29P  C6A  O2A  deloc     1.243  0.020  1.243
 29P  C6A  O1A  deloc     1.251  0.020  1.251
 29P  C8A  H2   single    0.970  0.020  1.090
 29P  C8A  H3   single    0.970  0.020  1.090
 29P  C7A  H4   single    0.970  0.020  1.090
 29P  C7A  H5   single    0.970  0.020  1.090
 29P  C5A  H6   single    0.970  0.020  1.090
 29P  C5A  H7   single    0.970  0.020  1.090
 29P  CHA  H9   single    0.970  0.020  1.090
 29P  CHA  H10  single    0.970  0.020  1.090
 29P  CHA  H11  single    0.970  0.020  1.090
 29P  NA   H12  single    0.860  0.020  1.020
 29P  CHB  H13  single    0.970  0.020  1.090
 29P  CHB  H14  single    0.970  0.020  1.090
 29P  C1B  H15  single    0.970  0.020  1.090
 29P  C5B  H16  single    0.970  0.020  1.090
 29P  C5B  H17  single    0.970  0.020  1.090
 29P  NB   H19  single    0.860  0.020  1.020
 29P  C7B  H20  single    0.970  0.020  1.090
 29P  C7B  H21  single    0.970  0.020  1.090
 29P  C8B  H22  single    0.970  0.020  1.090
 29P  C8B  H23  single    0.970  0.020  1.090

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
 29P  C8A  C9A  O3A  116.08  3.000
 29P  C8A  C9A  O4A  117.99  3.000
 29P  O3A  C9A  O4A  125.93  3.000
 29P  H3   C8A  H2   104.82  3.000
 29P  H3   C8A  C7A  109.14  3.000
 29P  H2   C8A  C7A  108.76  3.000
 29P  H3   C8A  C9A  108.59  3.000
 29P  H2   C8A  C9A  109.01  3.000
 29P  C7A  C8A  C9A  115.94  3.000
 29P  H5   C7A  H4   105.44  3.000
 29P  H5   C7A  C3A  109.74  3.000
 29P  H4   C7A  C3A  110.01  3.000
 29P  H5   C7A  C8A  109.21  3.000
 29P  H4   C7A  C8A  109.74  3.000
 29P  C3A  C7A  C8A  112.46  3.000
 29P  C4A  C3A  C2A  107.31  3.000
 29P  C2A  C3A  C7A  126.47  3.000
 29P  C4A  C3A  C7A  126.16  3.000
 29P  C1A  C2A  C5A  126.39  3.000
 29P  C1A  C2A  C3A  107.18  3.000
 29P  C5A  C2A  C3A  126.41  3.000
 29P  H7   C5A  H6   104.65  3.000
 29P  H7   C5A  C6A  107.26  3.000
 29P  H6   C5A  C6A  107.37  3.000
 29P  H7   C5A  C2A  109.63  3.000
 29P  H6   C5A  C2A  110.34  3.000
 29P  C6A  C5A  C2A  116.86  3.000
 29P  O2A  C6A  O1A  126.35  3.000
 29P  O1A  C6A  C5A  115.07  3.000
 29P  O2A  C6A  C5A  118.57  3.000
 29P  NA   C1A  CHA  121.89  3.000
 29P  CHA  C1A  C2A  130.46  3.000
 29P  NA   C1A  C2A  107.60  3.000
 29P  H11  CHA  H10  107.37  3.000
 29P  H11  CHA  H9   107.09  3.000
 29P  H10  CHA  H9   107.26  3.000
 29P  H11  CHA  C1A  110.37  3.000
 29P  H10  CHA  C1A  112.31  3.000
 29P  H9   CHA  C1A  112.18  3.000
 29P  H12  NA   C4A  124.90  3.000
 29P  H12  NA   C1A  124.66  3.000
 29P  C4A  NA   C1A  110.44  3.000
 29P  CHB  C4A  NA   122.16  3.000
 29P  NA   C4A  C3A  107.46  3.000
 29P  CHB  C4A  C3A  130.28  3.000
 29P  H14  CHB  H13  106.74  3.000
 29P  H14  CHB  C1B  108.85  3.000
 29P  H13  CHB  C1B  108.43  3.000
 29P  H14  CHB  C4A  109.42  3.000
 29P  H13  CHB  C4A  110.57  3.000
 29P  C1B  CHB  C4A  112.64  3.000
 29P  H15  C1B  NB   110.60  3.000
 29P  H15  C1B  C2B  109.50  3.000
 29P  NB   C1B  C2B  102.24  3.000
 29P  H15  C1B  CHB  108.93  3.000
 29P  NB   C1B  CHB  112.12  3.000
 29P  C2B  C1B  CHB  113.31  3.000
 29P  C3B  C2B  C5B  128.39  3.000
 29P  C3B  C2B  C1B  109.86  3.000
 29P  C5B  C2B  C1B  121.73  3.000
 29P  H17  C5B  H16  105.47  3.000
 29P  H17  C5B  C6B  108.42  3.000
 29P  H16  C5B  C6B  107.65  3.000
 29P  H17  C5B  C2B  110.26  3.000
 29P  H16  C5B  C2B  109.77  3.000
 29P  C6B  C5B  C2B  114.82  3.000
 29P  O2B  C6B  O1B  127.15  3.000
 29P  O2B  C6B  C5B  115.18  3.000
 29P  O1B  C6B  C5B  117.67  3.000
 29P  H19  NB   C4B  123.56  3.000
 29P  H19  NB   C1B  122.94  3.000
 29P  C4B  NB   C1B  112.77  3.000
 29P  C3B  C4B  O5B  127.27  3.000
 29P  O5B  C4B  NB   126.28  3.000
 29P  C3B  C4B  NB   106.45  3.000
 29P  C7B  C3B  C4B  121.52  3.000
 29P  C4B  C3B  C2B  108.60  3.000
 29P  C7B  C3B  C2B  129.81  3.000
 29P  H21  C7B  H20  106.25  3.000
 29P  H21  C7B  C8B  109.83  3.000
 29P  H20  C7B  C8B  109.36  3.000
 29P  H21  C7B  C3B  110.05  3.000
 29P  H20  C7B  C3B  109.43  3.000
 29P  C8B  C7B  C3B  111.77  3.000
 29P  H23  C8B  H22  105.11  3.000
 29P  H23  C8B  C9B  108.09  3.000
 29P  H22  C8B  C9B  108.74  3.000
 29P  H23  C8B  C7B  109.36  3.000
 29P  H22  C8B  C7B  109.40  3.000
 29P  C9B  C8B  C7B  115.62  3.000
 29P  O4B  C9B  O3B  126.26  3.000
 29P  O3B  C9B  C8B  115.82  3.000
 29P  O4B  C9B  C8B  117.92  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
 29P  CONST_01  C1A  NA   C4A  C3A    0.00   0.0  0
 29P  CONST_02  NA   C1A  C2A  C3A    0.00   0.0  0
 29P  CONST_03  NA   C4A  C3A  C2A    0.00   0.0  0
 29P  CONST_04  C4A  NA   C1A  C2A    0.00   0.0  0
 29P  CONST_05  C4A  C3A  C2A  C1A    0.00   0.0  0
 29P  CONST_06  C3B  C4B  NB   C1B    0.00   0.0  0
 29P  CONST_07  NA   C4A  C3A  C7A  180.00   0.0  0
 29P  CONST_08  C1A  C2A  C3A  C7A  180.00   0.0  0
 29P  CONST_09  CHA  C1A  C2A  C3A  180.00   0.0  0
 29P  CONST_10  CHB  C4A  C3A  C2A  180.00   0.0  0
 29P  CONST_11  C4A  C3A  C2A  C5A  180.00   0.0  0
 29P  CONST_12  NA   C1A  C2A  C5A  180.00   0.0  0
 29P  CONST_13  CHB  C4A  NA   C1A  180.00   0.0  0
 29P  CONST_14  C4A  NA   C1A  CHA  180.00   0.0  0
 29P  CONST_15  O5B  C4B  NB   C1B  180.00   0.0  0
 29P  CONST_16  H12  NA   C4A  C3A  180.00   0.0  0
 29P  CONST_17  H19  NB   C4B  C3B  180.00   0.0  0
 29P  Var_01    C4B  C3B  C2B  C1B    0.32  30.0  1
 29P  Var_02    NB   C4B  C3B  C2B    1.42  30.0  1
 29P  Var_03    C1B  CHB  C4A  C3A   99.72  30.0  2
 29P  Var_04    C4A  C3A  C7A  C8A   89.49  30.0  2
 29P  Var_05    C6A  C5A  C2A  C3A   92.91  30.0  2
 29P  Var_06    C6B  C5B  C2B  C1B  -72.15  30.0  2
 29P  Var_07    C8B  C7B  C3B  C2B   98.31  30.0  1
 29P  Var_08    H9   CHA  C1A  C2A  104.59  30.0  2
 29P  Var_09    C3A  C7A  C8A  C9A  176.21  30.0  3
 29P  Var_10    O2A  C6A  C5A  C2A   -1.98  30.0  3
 29P  Var_11    O1B  C6B  C5B  C2B    0.53  30.0  2
 29P  Var_12    C9B  C8B  C7B  C3B  178.99  30.0  3
 29P  Var_13    C7A  C8A  C9A  O4A   -6.38  30.0  3
 29P  Var_14    O4B  C9B  C8B  C7B   -5.40  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
 29P  chir_01  C1B  C2B  CHB  NB  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
 29P  plan-1  C7A  0.020
 29P  plan-1  C3A  0.020
 29P  plan-1  C2A  0.020
 29P  plan-1  C5A  0.020
 29P  plan-1  C1A  0.020
 29P  plan-1  CHA  0.020
 29P  plan-1  NA   0.020
 29P  plan-1  C4A  0.020
 29P  plan-1  CHB  0.020
 29P  plan-1  H12  0.020
 29P  plan-2  C1B  0.020
 29P  plan-2  NB   0.020
 29P  plan-2  C4B  0.020
 29P  plan-2  O5B  0.020
 29P  plan-2  C3B  0.020
 29P  plan-2  H19  0.020
 29P  plan-3  O4A  0.020
 29P  plan-3  C9A  0.020
 29P  plan-3  O3A  0.020
 29P  plan-3  C8A  0.020
 29P  plan-4  C5A  0.020
 29P  plan-4  C6A  0.020
 29P  plan-4  O1A  0.020
 29P  plan-4  O2A  0.020
 29P  plan-5  C5B  0.020
 29P  plan-5  C6B  0.020
 29P  plan-5  O1B  0.020
 29P  plan-5  O2B  0.020
 29P  plan-6  C8B  0.020
 29P  plan-6  C9B  0.020
 29P  plan-6  O3B  0.020
 29P  plan-6  O4B  0.020

