# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:01:51 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(Cc2[nH]cc(CCC(O)=O)c2CC(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
 DPM  DPM  '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid'  ligand  50  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DPM
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
 DPM  C1A   C  CR5    0   0.254   2.7106   2.5817   0.1911
 DPM  C2A   C  CR5    0   0.001   3.4554   1.4573  -0.0769
 DPM  C3A   C  CR5    0  -0.030   2.6479   0.5995  -0.8839
 DPM  C4A   C  CR5    0   0.305   1.4407   1.2272  -1.0777
 DPM  C5A   C  CH2    0  -0.679   4.8373   1.1504   0.3966
 DPM  C6A   C  C      0   0.414   4.9093   0.5348   1.8116
 DPM  C7A   C  CH2    0  -0.546   2.9893  -0.7728  -1.3583
 DPM  C8A   C  CH2    0  -0.553   2.9051  -1.8352  -0.2489
 DPM  C9A   C  C      0   0.421   2.5815  -3.2319  -0.7897
 DPM  CHA   C  CH3    0  -0.734   3.0406   3.7944   0.9865
 DPM  NA    N  NR15   0  -0.680   1.4966   2.4228  -0.4191
 DPM  O1A   O  O      0  -0.602   4.2115   1.0727   2.6922
 DPM  O2A   O  OC    -1  -0.628   5.6895  -0.4285   1.9706
 DPM  O3A   O  O      0  -0.606   1.5047  -3.3290  -1.4387
 DPM  O4A   O  OC    -1  -0.599   3.3657  -4.1678  -0.5593
 DPM  C1B   C  CR5    0   0.328  -0.7101  -0.0752  -0.9692
 DPM  C2B   C  CR5    0  -0.044  -1.8477   0.2909  -0.2806
 DPM  C3B   C  CR5    0   0.034  -2.3452  -0.8829   0.3622
 DPM  C4B   C  CR15   0  -0.166  -1.4828  -1.9032   0.0360
 DPM  C5B   C  CH2    0  -0.691  -2.4558   1.6539  -0.2049
 DPM  C6B   C  C      0   0.416  -3.3576   2.0512  -1.3942
 DPM  C7B   C  CH2    0  -0.516  -3.5816  -1.0020   1.1984
 DPM  C8B   C  CH2    0  -0.584  -4.8707  -0.8684   0.3920
 DPM  C9B   C  C      0   0.409  -6.1806  -1.0412   1.1783
 DPM  CHB   C  CH2    0  -0.667   0.2112   0.7674  -1.7965
 DPM  NB    N  NR15   0  -0.667  -0.5044  -1.4078  -0.7710
 DPM  O1B   O  O      0  -0.600  -2.9709   1.7257  -2.5339
 DPM  O2B   O  OC    -1  -0.627  -4.3865   2.7063  -1.1242
 DPM  O3B   O  O      0  -0.612  -6.1061  -1.3151   2.3931
 DPM  O4B   O  OC    -1  -0.635  -7.2348  -0.8932   0.5224
 DPM  H5A1  H  HCH2   0   0.210   5.3378   0.4899  -0.3157
 DPM  H5A2  H  HCH2   0   0.226   5.4348   2.0703   0.4204
 DPM  H7A1  H  HCH2   0   0.225   2.3118  -1.0505  -2.1688
 DPM  H7A2  H  HCH2   0   0.222   3.9948  -0.7920  -1.7918
 DPM  H8A1  H  HCH2   0   0.218   3.8247  -1.8269   0.3405
 DPM  H8A2  H  HCH2   0   0.220   2.0971  -1.5557   0.4347
 DPM  HCA1  H  HCH3   0   0.225   2.9943   4.7098   0.3912
 DPM  HCA2  H  HCH3   0   0.232   2.3626   3.9248   1.8332
 DPM  HCA3  H  HCH3   0   0.244   4.0453   3.7097   1.3949
 DPM  H10   H  HNR5   0   0.388   0.7574   3.1056  -0.4125
 DPM  H4B1  H  HCR5   0   0.240  -1.5009  -2.9450   0.3183
 DPM  H5B1  H  HCH2   0   0.216  -3.0194   1.7549   0.7261
 DPM  H5B2  H  HCH2   0   0.223  -1.6662   2.4145  -0.1480
 DPM  H7B1  H  HCH2   0   0.212  -3.5752  -1.9662   1.7136
 DPM  H7B2  H  HCH2   0   0.204  -3.5775  -0.2456   1.9903
 DPM  H8B1  H  HCH2   0   0.232  -4.9001   0.1072  -0.1043
 DPM  H8B2  H  HCH2   0   0.215  -4.8614  -1.5994  -0.4250
 DPM  HCB1  H  HCH2   0   0.266  -0.3566   1.6242  -2.1636
 DPM  HCB2  H  HCH2   0   0.255   0.5096   0.2124  -2.6909
 DPM  H22   H  HNR5   0   0.413   0.2798  -1.9783  -1.1127

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
 DPM  C1A  C2A   aromatic  1.375  0.020  1.375
 DPM  C1A  CHA   single    1.487  0.020  1.487
 DPM  C1A  NA    aromatic  1.368  0.020  1.368
 DPM  C2A  C3A   aromatic  1.428  0.020  1.428
 DPM  C2A  C5A   single    1.493  0.020  1.493
 DPM  C3A  C4A   aromatic  1.374  0.020  1.374
 DPM  C3A  C7A   single    1.492  0.020  1.492
 DPM  C4A  NA    aromatic  1.366  0.020  1.366
 DPM  C4A  CHB   single    1.497  0.020  1.497
 DPM  C5A  C6A   single    1.545  0.020  1.545
 DPM  C6A  O1A   deloc     1.246  0.020  1.246
 DPM  C6A  O2A   deloc     1.250  0.020  1.250
 DPM  C7A  C8A   single    1.538  0.020  1.538
 DPM  C8A  C9A   single    1.532  0.020  1.532
 DPM  C9A  O3A   deloc     1.261  0.020  1.261
 DPM  C9A  O4A   deloc     1.243  0.020  1.243
 DPM  C1B  C2B   aromatic  1.379  0.020  1.379
 DPM  C1B  CHB   single    1.498  0.020  1.498
 DPM  C1B  NB    aromatic  1.363  0.020  1.363
 DPM  C2B  C3B   aromatic  1.428  0.020  1.428
 DPM  C2B  C5B   single    1.494  0.020  1.494
 DPM  C3B  C4B   aromatic  1.375  0.020  1.375
 DPM  C3B  C7B   single    1.497  0.020  1.497
 DPM  C4B  NB    aromatic  1.362  0.020  1.362
 DPM  C5B  C6B   single    1.545  0.020  1.545
 DPM  C6B  O1B   deloc     1.247  0.020  1.247
 DPM  C6B  O2B   deloc     1.249  0.020  1.249
 DPM  C7B  C8B   single    1.526  0.020  1.526
 DPM  C8B  C9B   single    1.538  0.020  1.538
 DPM  C9B  O3B   deloc     1.248  0.020  1.248
 DPM  C9B  O4B   deloc     1.250  0.020  1.250
 DPM  C5A  H5A1  single    0.970  0.020  1.090
 DPM  C5A  H5A2  single    0.970  0.020  1.090
 DPM  C7A  H7A1  single    0.970  0.020  1.090
 DPM  C7A  H7A2  single    0.970  0.020  1.090
 DPM  C8A  H8A1  single    0.970  0.020  1.090
 DPM  C8A  H8A2  single    0.970  0.020  1.090
 DPM  CHA  HCA1  single    0.970  0.020  1.090
 DPM  CHA  HCA2  single    0.970  0.020  1.090
 DPM  CHA  HCA3  single    0.970  0.020  1.090
 DPM  NA   H10   single    0.860  0.020  1.020
 DPM  C4B  H4B1  single    0.930  0.020  1.080
 DPM  C5B  H5B1  single    0.970  0.020  1.090
 DPM  C5B  H5B2  single    0.970  0.020  1.090
 DPM  C7B  H7B1  single    0.970  0.020  1.090
 DPM  C7B  H7B2  single    0.970  0.020  1.090
 DPM  C8B  H8B1  single    0.970  0.020  1.090
 DPM  C8B  H8B2  single    0.970  0.020  1.090
 DPM  CHB  HCB1  single    0.970  0.020  1.090
 DPM  CHB  HCB2  single    0.970  0.020  1.090
 DPM  NB   H22   single    0.860  0.020  1.020

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
 DPM  NA    C1A  CHA   122.01  3.000
 DPM  NA    C1A  C2A   107.38  3.000
 DPM  CHA   C1A  C2A   130.60  3.000
 DPM  C5A   C2A  C3A   125.40  3.000
 DPM  C5A   C2A  C1A   127.43  3.000
 DPM  C3A   C2A  C1A   107.16  3.000
 DPM  C7A   C3A  C4A   125.20  3.000
 DPM  C7A   C3A  C2A   127.08  3.000
 DPM  C4A   C3A  C2A   107.58  3.000
 DPM  CHB   C4A  NA    122.28  3.000
 DPM  CHB   C4A  C3A   130.47  3.000
 DPM  NA    C4A  C3A   107.21  3.000
 DPM  H5A2  C5A  H5A1  105.75  3.000
 DPM  H5A2  C5A  C6A   106.79  3.000
 DPM  H5A1  C5A  C6A   109.56  3.000
 DPM  H5A2  C5A  C2A   109.80  3.000
 DPM  H5A1  C5A  C2A   109.97  3.000
 DPM  C6A   C5A  C2A   114.56  3.000
 DPM  O2A   C6A  O1A   126.34  3.000
 DPM  O2A   C6A  C5A   116.92  3.000
 DPM  O1A   C6A  C5A   116.70  3.000
 DPM  H7A2  C7A  H7A1  105.74  3.000
 DPM  H7A2  C7A  C8A   108.88  3.000
 DPM  H7A1  C7A  C8A   109.00  3.000
 DPM  H7A2  C7A  C3A   110.62  3.000
 DPM  H7A1  C7A  C3A   109.14  3.000
 DPM  C8A   C7A  C3A   113.17  3.000
 DPM  H8A2  C8A  H8A1  106.41  3.000
 DPM  H8A2  C8A  C9A   107.29  3.000
 DPM  H8A1  C8A  C9A   112.04  3.000
 DPM  H8A2  C8A  C7A   108.32  3.000
 DPM  H8A1  C8A  C7A   109.74  3.000
 DPM  C9A   C8A  C7A   112.74  3.000
 DPM  O4A   C9A  O3A   125.19  3.000
 DPM  O4A   C9A  C8A   119.20  3.000
 DPM  O3A   C9A  C8A   115.61  3.000
 DPM  HCA3  CHA  HCA2  106.95  3.000
 DPM  HCA3  CHA  HCA1  107.99  3.000
 DPM  HCA2  CHA  HCA1  107.21  3.000
 DPM  HCA3  CHA  C1A   110.01  3.000
 DPM  HCA2  CHA  C1A   111.97  3.000
 DPM  HCA1  CHA  C1A   112.47  3.000
 DPM  H10   NA   C4A   124.54  3.000
 DPM  H10   NA   C1A   124.76  3.000
 DPM  C4A   NA   C1A   110.67  3.000
 DPM  NB    C1B  CHB   122.52  3.000
 DPM  NB    C1B  C2B   108.15  3.000
 DPM  CHB   C1B  C2B   129.33  3.000
 DPM  C5B   C2B  C3B   125.82  3.000
 DPM  C5B   C2B  C1B   127.09  3.000
 DPM  C3B   C2B  C1B   107.09  3.000
 DPM  C7B   C3B  C4B   126.25  3.000
 DPM  C7B   C3B  C2B   127.19  3.000
 DPM  C4B   C3B  C2B   106.54  3.000
 DPM  H4B1  C4B  NB    121.20  3.000
 DPM  H4B1  C4B  C3B   130.06  3.000
 DPM  NB    C4B  C3B   108.74  3.000
 DPM  H5B2  C5B  H5B1  105.23  3.000
 DPM  H5B2  C5B  C6B   106.36  3.000
 DPM  H5B1  C5B  C6B   109.33  3.000
 DPM  H5B2  C5B  C2B   109.99  3.000
 DPM  H5B1  C5B  C2B   109.71  3.000
 DPM  C6B   C5B  C2B   115.67  3.000
 DPM  O2B   C6B  O1B   126.15  3.000
 DPM  O2B   C6B  C5B   116.70  3.000
 DPM  O1B   C6B  C5B   117.10  3.000
 DPM  H7B2  C7B  H7B1  105.57  3.000
 DPM  H7B2  C7B  C8B   108.95  3.000
 DPM  H7B1  C7B  C8B   109.34  3.000
 DPM  H7B2  C7B  C3B   110.23  3.000
 DPM  H7B1  C7B  C3B   109.18  3.000
 DPM  C8B   C7B  C3B   113.29  3.000
 DPM  H8B2  C8B  H8B1  104.87  3.000
 DPM  H8B2  C8B  C9B   108.26  3.000
 DPM  H8B1  C8B  C9B   108.00  3.000
 DPM  H8B2  C8B  C7B   109.15  3.000
 DPM  H8B1  C8B  C7B   109.89  3.000
 DPM  C9B   C8B  C7B   116.07  3.000
 DPM  O4B   C9B  O3B   125.95  3.000
 DPM  O4B   C9B  C8B   115.89  3.000
 DPM  O3B   C9B  C8B   118.16  3.000
 DPM  HCB2  CHB  HCB1  105.37  3.000
 DPM  HCB2  CHB  C1B   109.51  3.000
 DPM  HCB1  CHB  C1B   107.90  3.000
 DPM  HCB2  CHB  C4A   108.93  3.000
 DPM  HCB1  CHB  C4A   110.35  3.000
 DPM  C1B   CHB  C4A   114.39  3.000
 DPM  H22   NB   C4B   122.90  3.000
 DPM  H22   NB   C1B   127.54  3.000
 DPM  C4B   NB   C1B   109.48  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
 DPM  CONST_01  C4A   C3A  C2A  C1A    0.00   0.0  0
 DPM  CONST_02  C3A   C4A  NA   C1A    0.00   0.0  0
 DPM  CONST_03  C4A   NA   C1A  C2A    0.00   0.0  0
 DPM  CONST_04  NA    C4A  C3A  C2A    0.00   0.0  0
 DPM  CONST_05  NA    C1A  C2A  C3A    0.00   0.0  0
 DPM  CONST_06  C4B   C3B  C2B  C1B    0.00   0.0  0
 DPM  CONST_07  C3B   C4B  NB   C1B    0.00   0.0  0
 DPM  CONST_08  C4B   NB   C1B  C2B    0.00   0.0  0
 DPM  CONST_09  NB    C4B  C3B  C2B    0.00   0.0  0
 DPM  CONST_10  NB    C1B  C2B  C3B    0.00   0.0  0
 DPM  CONST_11  C7A   C3A  C2A  C1A  180.00   0.0  0
 DPM  CONST_12  CHB   C4A  NA   C1A  180.00   0.0  0
 DPM  CONST_13  CHB   C4A  C3A  C2A  180.00   0.0  0
 DPM  CONST_14  CHA   C1A  C2A  C3A  180.00   0.0  0
 DPM  CONST_15  C5A   C2A  C3A  C4A  180.00   0.0  0
 DPM  CONST_16  CHA   C1A  NA   C4A  180.00   0.0  0
 DPM  CONST_17  NA    C1A  C2A  C5A  180.00   0.0  0
 DPM  CONST_18  NA    C4A  C3A  C7A  180.00   0.0  0
 DPM  CONST_19  C7B   C3B  C2B  C1B  180.00   0.0  0
 DPM  CONST_20  CHB   C1B  C2B  C3B  180.00   0.0  0
 DPM  CONST_21  C5B   C2B  C3B  C4B  180.00   0.0  0
 DPM  CONST_22  CHB   C1B  NB   C4B  180.00   0.0  0
 DPM  CONST_23  NB    C1B  C2B  C5B  180.00   0.0  0
 DPM  CONST_24  NB    C4B  C3B  C7B  180.00   0.0  0
 DPM  CONST_25  H10   NA   C1A  C2A  180.00   0.0  0
 DPM  CONST_26  H4B1  C4B  NB   C1B  180.00   0.0  0
 DPM  CONST_27  H22   NB   C1B  C2B  180.00   0.0  0
 DPM  Var_01    C1B   CHB  C4A  C3A   84.82  30.0  2
 DPM  Var_02    C2B   C1B  CHB  C4A   97.71  30.0  1
 DPM  Var_03    C6A   C5A  C2A  C1A   83.63  30.0  2
 DPM  Var_04    C8A   C7A  C3A  C2A   74.26  30.0  2
 DPM  Var_05    C6B   C5B  C2B  C1B   82.34  30.0  2
 DPM  Var_06    C8B   C7B  C3B  C2B   69.64  30.0  2
 DPM  Var_07    HCA1  CHA  C1A  C2A  120.20  30.0  2
 DPM  Var_08    O1A   C6A  C5A  C2A  -45.46  30.0  3
 DPM  Var_09    C9A   C8A  C7A  C3A  152.26  30.0  3
 DPM  Var_10    O1B   C6B  C5B  C2B  -40.73  30.0  3
 DPM  Var_11    C9B   C8B  C7B  C3B  177.46  30.0  3
 DPM  Var_12    O3A   C9A  C8A  C7A  -58.20  30.0  3
 DPM  Var_13    O3B   C9B  C8B  C7B   -2.13  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
 DPM  plan-1  C1A   0.020
 DPM  plan-1  C2A   0.020
 DPM  plan-1  C3A   0.020
 DPM  plan-1  C4A   0.020
 DPM  plan-1  C5A   0.020
 DPM  plan-1  C7A   0.020
 DPM  plan-1  CHA   0.020
 DPM  plan-1  NA    0.020
 DPM  plan-1  CHB   0.020
 DPM  plan-1  H10   0.020
 DPM  plan-2  C1B   0.020
 DPM  plan-2  C2B   0.020
 DPM  plan-2  C3B   0.020
 DPM  plan-2  C4B   0.020
 DPM  plan-2  C5B   0.020
 DPM  plan-2  C7B   0.020
 DPM  plan-2  CHB   0.020
 DPM  plan-2  NB    0.020
 DPM  plan-2  H4B1  0.020
 DPM  plan-2  H22   0.020
 DPM  plan-3  C5A   0.020
 DPM  plan-3  C6A   0.020
 DPM  plan-3  O1A   0.020
 DPM  plan-3  O2A   0.020
 DPM  plan-4  C8A   0.020
 DPM  plan-4  C9A   0.020
 DPM  plan-4  O3A   0.020
 DPM  plan-4  O4A   0.020
 DPM  plan-5  C5B   0.020
 DPM  plan-5  C6B   0.020
 DPM  plan-5  O1B   0.020
 DPM  plan-5  O2B   0.020
 DPM  plan-6  C8B   0.020
 DPM  plan-6  C9B   0.020
 DPM  plan-6  O3B   0.020
 DPM  plan-6  O4B   0.020

