# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 05:37:52 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}-[[2,8-bis(oxidanyl)naphthalen-1-yl]methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c([nH]c(C)c1C(C)=O)C(=O)NCc2c(O)ccc3cccc(O)c23
#
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
 99E  99E  ~{N}-[[2,8-bis(oxidanyl)naphthalen-1-yl]methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide  ligand  49  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_99E
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
 99E  O1   O  OH1   0  -0.627   1.7365  -0.4897   2.0335
 99E  C11  C  CR6   0  -0.093   2.8096   0.9183  -0.2501
 99E  C21  C  CR16  0  -0.338   5.1874  -1.9645   0.2801
 99E  C7   C  CH2   0  -0.499  -3.5336   0.8702   2.0160
 99E  C8   C  CH3   0  -0.663  -4.3825   2.1353   1.9143
 99E  C10  C  CH3   0  -0.794  -5.8093  -2.1532  -0.7713
 99E  C1   C  C     0   0.514  -0.8026   1.3697   0.4466
 99E  C2   C  CR5   0   0.154  -1.9650   0.5748   0.0204
 99E  N3   N  NR15  0  -0.684  -1.9866  -0.1220  -1.1657
 99E  C4   C  CR5   0   0.356  -3.1351  -0.7953  -1.3136
 99E  C5   C  CR5   0  -0.190  -3.9050  -0.5506  -0.1714
 99E  C6   C  CR5   0   0.080  -3.1501   0.3304   0.6730
 99E  C9   C  C     0   0.307  -5.2305  -1.0879   0.1268
 99E  C12  C  CH3   0  -0.760  -3.3734  -1.5792  -2.5574
 99E  N13  N  NH1   0  -0.646   0.3810   1.0020  -0.0813
 99E  O15  O  O     0  -0.495  -0.9101   2.3137   1.2214
 99E  O16  O  O     0  -0.425  -5.8743  -0.6967   1.0869
 99E  C3   C  CH2   0  -0.308   1.6201   1.6407   0.3318
 99E  C13  C  CR6   0   0.349   3.3652   1.4358  -1.4056
 99E  C14  C  CR16  0  -0.374   4.5185   0.8705  -1.9895
 99E  C15  C  CR16  0  -0.308   5.1004  -0.2203  -1.4230
 99E  C16  C  CR66  0   0.086   4.5604  -0.8197  -0.2636
 99E  C17  C  CR66  0   0.038   3.3909  -0.2577   0.3267
 99E  C18  C  CR6   0   0.286   2.8715  -0.9459   1.4706
 99E  C19  C  CR16  0  -0.397   3.5026  -2.0580   1.9762
 99E  C20  C  CR16  0  -0.257   4.6687  -2.5698   1.3870
 99E  H1   H  HOH1  0   0.477   1.4797  -1.0589   2.7679
 99E  H2   H  HCR6  0   0.251   6.0773  -2.3495  -0.2017
 99E  H3   H  HCH2  0   0.232  -2.6314   1.0966   2.5833
 99E  H4   H  HCH2  0   0.233  -4.0772   0.1122   2.5773
 99E  H5   H  HCH3  0   0.220  -3.8356   2.9243   1.3985
 99E  H6   H  HCH3  0   0.224  -5.3065   1.9467   1.3696
 99E  H7   H  HCH3  0   0.222  -4.6478   2.5038   2.9063
 99E  H8   H  HCH3  0   0.256  -5.1185  -2.9834  -0.9137
 99E  H9   H  HCH3  0   0.266  -6.7338  -2.5339  -0.3419
 99E  H10  H  HCH3  0   0.260  -6.0358  -1.7488  -1.7589
 99E  H11  H  HNR5  0   0.415  -1.2830  -0.0598  -1.8856
 99E  H12  H  HCH3  0   0.264  -3.4154  -2.6501  -2.3570
 99E  H13  H  HCH3  0   0.262  -4.3085  -1.2992  -3.0405
 99E  H14  H  HCH3  0   0.272  -2.5696  -1.4125  -3.2729
 99E  H15  H  HNH1  0   0.399   0.4621   0.0918  -0.5054
 99E  H16  H  HCH2  0   0.257   1.6832   1.6823   1.4168
 99E  H17  H  HCH2  0   0.261   1.6179   2.6747  -0.0103
 99E  H18  H  HCR6  0   0.277   4.9388   1.3105  -2.8869
 99E  H19  H  HCR6  0   0.264   5.9899  -0.6486  -1.8681
 99E  H20  H  HCR6  0   0.268   3.0841  -2.5572   2.8436
 99E  H21  H  HCR6  0   0.258   5.1397  -3.4458   1.8132
 99E  H22  H  HOH1  0   0.479   3.3009   2.8057  -2.7368
 99E  O22  O  OH1   0  -0.628   2.7870   2.5117  -1.9766

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
 99E  O22  C13  single    1.348  0.020  1.348
 99E  C14  C13  aromatic  1.411  0.020  1.411
 99E  C14  C15  aromatic  1.360  0.020  1.360
 99E  C13  C11  aromatic  1.383  0.020  1.383
 99E  C15  C16  aromatic  1.412  0.020  1.412
 99E  C11  C3   single    1.508  0.020  1.508
 99E  C11  C17  aromatic  1.433  0.020  1.433
 99E  C16  C17  aromatic  1.425  0.020  1.425
 99E  C16  C21  aromatic  1.414  0.020  1.414
 99E  C3   N13  single    1.454  0.020  1.454
 99E  C17  C18  aromatic  1.432  0.020  1.432
 99E  C21  C20  aromatic  1.364  0.020  1.364
 99E  O15  C1   double    1.226  0.020  1.226
 99E  C18  C19  aromatic  1.375  0.020  1.375
 99E  C18  O1   single    1.347  0.020  1.347
 99E  C20  C19  aromatic  1.403  0.020  1.403
 99E  N13  C1   single    1.347  0.020  1.347
 99E  C1   C2   single    1.471  0.020  1.471
 99E  C2   N3   aromatic  1.376  0.020  1.376
 99E  C2   C6   aromatic  1.375  0.020  1.375
 99E  N3   C4   aromatic  1.339  0.020  1.339
 99E  C7   C6   single    1.497  0.020  1.497
 99E  C7   C8   single    1.527  0.020  1.527
 99E  C6   C5   aromatic  1.435  0.020  1.435
 99E  C4   C5   aromatic  1.399  0.020  1.399
 99E  C4   C12  single    1.489  0.020  1.489
 99E  C5   C9   single    1.461  0.020  1.461
 99E  C10  C9   single    1.509  0.020  1.509
 99E  C9   O16  double    1.220  0.020  1.220
 99E  O1   H1   single    0.850  0.020  0.980
 99E  C21  H2   single    0.930  0.020  1.080
 99E  C7   H3   single    0.970  0.020  1.090
 99E  C7   H4   single    0.970  0.020  1.090
 99E  C8   H5   single    0.970  0.020  1.090
 99E  C8   H6   single    0.970  0.020  1.090
 99E  C8   H7   single    0.970  0.020  1.090
 99E  C10  H8   single    0.970  0.020  1.090
 99E  C10  H9   single    0.970  0.020  1.090
 99E  C10  H10  single    0.970  0.020  1.090
 99E  N3   H11  single    0.860  0.020  1.020
 99E  C12  H12  single    0.970  0.020  1.090
 99E  C12  H13  single    0.970  0.020  1.090
 99E  C12  H14  single    0.970  0.020  1.090
 99E  N13  H15  single    0.890  0.020  1.040
 99E  C3   H16  single    0.970  0.020  1.090
 99E  C3   H17  single    0.970  0.020  1.090
 99E  C14  H18  single    0.930  0.020  1.080
 99E  C15  H19  single    0.930  0.020  1.080
 99E  C19  H20  single    0.930  0.020  1.080
 99E  C20  H21  single    0.930  0.020  1.080
 99E  O22  H22  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
 99E  H1   O1   C18  110.06  3.000
 99E  C17  C11  C13  118.72  3.000
 99E  C17  C11  C3   123.89  3.000
 99E  C13  C11  C3   117.39  3.000
 99E  H2   C21  C20  121.05  3.000
 99E  H2   C21  C16  118.77  3.000
 99E  C20  C21  C16  120.18  3.000
 99E  H4   C7   H3   106.84  3.000
 99E  H4   C7   C6   109.84  3.000
 99E  H3   C7   C6   109.26  3.000
 99E  H4   C7   C8   109.49  3.000
 99E  H3   C7   C8   108.84  3.000
 99E  C6   C7   C8   112.42  3.000
 99E  H7   C8   H6   107.87  3.000
 99E  H7   C8   H5   107.93  3.000
 99E  H6   C8   H5   108.33  3.000
 99E  H7   C8   C7   110.76  3.000
 99E  H6   C8   C7   111.20  3.000
 99E  H5   C8   C7   110.63  3.000
 99E  H10  C10  H9   108.09  3.000
 99E  H10  C10  H8   107.21  3.000
 99E  H9   C10  H8   108.89  3.000
 99E  H10  C10  C9   110.90  3.000
 99E  H9   C10  C9   109.75  3.000
 99E  H8   C10  C9   111.88  3.000
 99E  O15  C1   N13  122.34  3.000
 99E  N13  C1   C2   115.67  3.000
 99E  O15  C1   C2   121.99  3.000
 99E  C6   C2   N3   107.80  3.000
 99E  C6   C2   C1   129.76  3.000
 99E  N3   C2   C1   122.39  3.000
 99E  H11  N3   C4   123.39  3.000
 99E  H11  N3   C2   124.97  3.000
 99E  C4   N3   C2   111.30  3.000
 99E  C12  C4   C5   133.29  3.000
 99E  C12  C4   N3   119.61  3.000
 99E  C5   C4   N3   107.08  3.000
 99E  C9   C5   C6   125.66  3.000
 99E  C9   C5   C4   126.98  3.000
 99E  C6   C5   C4   107.35  3.000
 99E  C5   C6   C2   106.46  3.000
 99E  C5   C6   C7   127.91  3.000
 99E  C2   C6   C7   125.62  3.000
 99E  O16  C9   C5   121.42  3.000
 99E  O16  C9   C10  119.49  3.000
 99E  C5   C9   C10  119.09  3.000
 99E  H14  C12  H13  107.63  3.000
 99E  H14  C12  H12  107.43  3.000
 99E  H13  C12  H12  107.52  3.000
 99E  H14  C12  C4   110.49  3.000
 99E  H13  C12  C4   111.87  3.000
 99E  H12  C12  C4   111.70  3.000
 99E  H15  N13  C3   116.61  3.000
 99E  H15  N13  C1   118.84  3.000
 99E  C3   N13  C1   121.17  3.000
 99E  H17  C3   H16  106.09  3.000
 99E  H17  C3   N13  109.04  3.000
 99E  H16  C3   N13  110.47  3.000
 99E  H17  C3   C11  109.57  3.000
 99E  H16  C3   C11  110.94  3.000
 99E  N13  C3   C11  110.61  3.000
 99E  O22  C13  C14  119.67  3.000
 99E  C14  C13  C11  121.63  3.000
 99E  O22  C13  C11  118.70  3.000
 99E  H18  C14  C15  120.29  3.000
 99E  H18  C14  C13  119.79  3.000
 99E  C15  C14  C13  119.92  3.000
 99E  H19  C15  C16  118.92  3.000
 99E  H19  C15  C14  119.83  3.000
 99E  C16  C15  C14  121.25  3.000
 99E  C17  C16  C15  119.09  3.000
 99E  C17  C16  C21  121.59  3.000
 99E  C15  C16  C21  119.32  3.000
 99E  C18  C17  C16  116.02  3.000
 99E  C18  C17  C11  124.65  3.000
 99E  C16  C17  C11  119.32  3.000
 99E  C19  C18  C17  121.05  3.000
 99E  C19  C18  O1   120.47  3.000
 99E  C17  C18  O1   118.47  3.000
 99E  H20  C19  C20  119.24  3.000
 99E  H20  C19  C18  119.28  3.000
 99E  C20  C19  C18  121.47  3.000
 99E  H21  C20  C19  119.45  3.000
 99E  H21  C20  C21  120.89  3.000
 99E  C19  C20  C21  119.66  3.000
 99E  H22  O22  C13  110.42  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
 99E  CONST_01  C15  C14  C13  C11     0.00   0.0  0
 99E  CONST_02  C15  C16  C17  C11     0.00   0.0  0
 99E  CONST_03  C21  C16  C17  C11   180.00   0.0  0
 99E  CONST_04  C19  C18  C17  C11   180.00   0.0  0
 99E  CONST_05  C14  C15  C16  C21   180.00   0.0  0
 99E  CONST_06  C18  C17  C16  C21     0.00   0.0  0
 99E  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 99E  CONST_08  C5   C4   N3   C2      0.00   0.0  0
 99E  CONST_09  C4   C5   C6   C2      0.00   0.0  0
 99E  CONST_10  C5   C6   C2   N3      0.00   0.0  0
 99E  CONST_11  C6   C5   C4   N3      0.00   0.0  0
 99E  CONST_12  C6   C2   N3   C4      0.00   0.0  0
 99E  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 99E  CONST_14  C16  C17  C11  C13     0.00   0.0  0
 99E  CONST_15  C18  C17  C11  C13   180.00   0.0  0
 99E  CONST_16  C17  C11  C13  C14     0.00   0.0  0
 99E  CONST_17  C17  C16  C15  C14     0.00   0.0  0
 99E  CONST_18  C18  C17  C16  C15   180.00   0.0  0
 99E  CONST_19  C20  C21  C16  C15   180.00   0.0  0
 99E  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 99E  CONST_21  C19  C20  C21  C16     0.00   0.0  0
 99E  CONST_22  C20  C21  C16  C17     0.00   0.0  0
 99E  CONST_23  C20  C19  C18  C17     0.00   0.0  0
 99E  CONST_24  C11  C17  C18  O1      0.00   0.0  0
 99E  CONST_25  C16  C17  C18  O1    180.00   0.0  0
 99E  CONST_26  C20  C19  C18  O1    180.00   0.0  0
 99E  CONST_27  N3   C2   C6   C7    180.00   0.0  0
 99E  CONST_28  C4   C5   C6   C7    180.00   0.0  0
 99E  CONST_29  C4   N3   C2   C1    180.00   0.0  0
 99E  CONST_30  C5   C6   C2   C1    180.00   0.0  0
 99E  CONST_31  C12  C4   N3   C2    180.00   0.0  0
 99E  CONST_32  C9   C5   C6   C2    180.00   0.0  0
 99E  CONST_33  C9   C5   C4   N3    180.00   0.0  0
 99E  CONST_34  C12  C4   C5   C6    180.00   0.0  0
 99E  CONST_35  C14  C13  C11  C3    180.00   0.0  0
 99E  CONST_36  C16  C17  C11  C3    180.00   0.0  0
 99E  CONST_37  C18  C17  C11  C3      0.00   0.0  0
 99E  CONST_38  O22  C13  C14  C15   180.00   0.0  0
 99E  CONST_39  O22  C13  C11  C17   180.00   0.0  0
 99E  CONST_40  H18  C14  C13  C11   180.00   0.0  0
 99E  CONST_41  H19  C15  C16  C21     0.00   0.0  0
 99E  CONST_42  H20  C19  C20  C21   180.00   0.0  0
 99E  CONST_43  H11  N3   C4   C5    180.00   0.0  0
 99E  CONST_44  H2   C21  C16  C15     0.00   0.0  0
 99E  CONST_45  H21  C20  C21  C16   180.00   0.0  0
 99E  CONST_46  C3   N13  C1   C2    180.00   0.0  0
 99E  CONST_48  C3   N13  C1   O15     0.00   0.0  0
 99E  Var_01    C2   C6   C7   C8     95.98  30.0  2
 99E  Var_02    C6   C5   C9   C10  -171.47  30.0  2
 99E  Var_03    O15  C1   C2   N3    155.11  30.0  2
 99E  Var_04    C13  C11  C3   N13    97.43  30.0  2
 99E  Var_05    H12  C12  C4   N3    113.63  30.0  2
 99E  Var_06    C1   N13  C3   C11   171.71  30.0  3
 99E  Var_07    H8   C10  C9   C5     51.67  30.0  3
 99E  Var_08    H5   C8   C7   C6    -60.48  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
 99E  plan-1  C7   0.020
 99E  plan-1  C1   0.020
 99E  plan-1  C2   0.020
 99E  plan-1  N3   0.020
 99E  plan-1  C4   0.020
 99E  plan-1  C5   0.020
 99E  plan-1  C6   0.020
 99E  plan-1  C9   0.020
 99E  plan-1  C12  0.020
 99E  plan-1  H11  0.020
 99E  plan-2  O1   0.020
 99E  plan-2  C11  0.020
 99E  plan-2  C21  0.020
 99E  plan-2  C3   0.020
 99E  plan-2  C13  0.020
 99E  plan-2  C14  0.020
 99E  plan-2  C15  0.020
 99E  plan-2  C16  0.020
 99E  plan-2  C17  0.020
 99E  plan-2  C18  0.020
 99E  plan-2  C19  0.020
 99E  plan-2  C20  0.020
 99E  plan-2  H2   0.020
 99E  plan-2  H18  0.020
 99E  plan-2  H19  0.020
 99E  plan-2  H20  0.020
 99E  plan-2  H21  0.020
 99E  plan-2  O22  0.020
 99E  plan-3  C1   0.020
 99E  plan-3  C2   0.020
 99E  plan-3  N13  0.020
 99E  plan-3  O15  0.020
 99E  plan-3  C3   0.020
 99E  plan-3  H15  0.020
 99E  plan-4  C10  0.020
 99E  plan-4  C5   0.020
 99E  plan-4  C9   0.020
 99E  plan-4  O16  0.020

