# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:33:21 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(c1)c2c[nH]cc2CN(C)CCN
#
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
 O3S  O3S  N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide  ligand  46  22  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O3S
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
 O3S  C    C  CH3   0  -0.657   7.3620  -0.3696  -0.3884
 O3S  O    O  O     0  -0.469   4.9011  -1.5843   0.1898
 O3S  N    N  NH1   0  -0.749   3.7036   0.3401  -0.0140
 O3S  C2   C  C     0   0.547   4.8531  -0.3865  -0.0216
 O3S  C1   C  CH2   0  -0.587   6.0844   0.4462  -0.3178
 O3S  C3   C  CR6   0   0.405   2.3839  -0.0727   0.1943
 O3S  C8   C  CR16  0  -0.338   2.0126  -1.3645   0.5716
 O3S  C7   C  CR16  0  -0.235   0.6651  -1.6509   0.7439
 O3S  C6   C  CR16  0  -0.365  -0.3168  -0.6931   0.5553
 O3S  C5   C  CR6   0   0.068   0.0411   0.6036   0.1750
 O3S  C4   C  CR16  0  -0.454   1.3931   0.8908  -0.0041
 O3S  C9   C  CR5   0  -0.015  -0.9663   1.6482  -0.0321
 O3S  C12  C  CR5   0  -0.007  -2.2785   1.5172  -0.5937
 O3S  C11  C  CR15  0  -0.079  -2.8193   2.7791  -0.6240
 O3S  N1   N  NR15  0  -0.581  -1.9145   3.6492  -0.1058
 O3S  C10  C  CR15  0  -0.084  -0.7895   2.9859   0.2535
 O3S  C13  C  CH2   0  -0.396  -2.9349   0.2813  -1.1194
 O3S  N2   N  NT    0  -0.410  -3.5196  -0.5607  -0.0809
 O3S  C14  C  CH3   0  -0.530  -4.6692   0.0668   0.5344
 O3S  C15  C  CH2   0  -0.266  -3.8195  -1.8884  -0.5839
 O3S  C16  C  CH2   0  -0.300  -4.1145  -2.8912   0.5238
 O3S  N3   N  NH2   0  -0.802  -4.2515  -4.2243  -0.0431
 O3S  H1   H  HCH3  0   0.229   7.3195  -1.1152  -1.1813
 O3S  H2   H  HCH3  0   0.235   8.2084   0.2852  -0.5929
 O3S  H3   H  HCH3  0   0.229   7.5625  -0.8859   0.5496
 O3S  H4   H  HNH1  0   0.414   3.8091   1.3223  -0.2192
 O3S  H5   H  HCH2  0   0.272   6.1686   1.2197   0.4514
 O3S  H6   H  HCH2  0   0.269   5.9244   0.9835  -1.2572
 O3S  H7   H  HCR6  0   0.273   2.7480  -2.1355   0.7272
 O3S  H8   H  HCR6  0   0.250   0.3803  -2.6525   1.0410
 O3S  H9   H  HCR6  0   0.275  -1.3610  -0.9336   0.7142
 O3S  H10  H  HCR6  0   0.255   1.6847   1.8843  -0.3279
 O3S  H11  H  HCR5  0   0.275  -3.7789   3.1126  -0.9855
 O3S  H12  H  HNR5  0   0.411  -2.0614   4.6382   0.0063
 O3S  H13  H  HCR5  0   0.273   0.0463   3.4993   0.7011
 O3S  H14  H  HCH2  0   0.216  -3.6894   0.5636  -1.8727
 O3S  H15  H  HCH2  0   0.238  -2.1892  -0.3181  -1.6491
 O3S  H17  H  HCH3  0   0.187  -5.5225   0.1665  -0.1557
 O3S  H18  H  HCH3  0   0.237  -5.0043  -0.5018   1.4014
 O3S  H19  H  HCH3  0   0.242  -4.4082   1.0636   0.8882
 O3S  H20  H  HCH2  0   0.194  -4.6574  -1.8832  -1.3022
 O3S  H21  H  HCH2  0   0.221  -2.9404  -2.2429  -1.1324
 O3S  H22  H  HCH2  0   0.195  -3.3262  -2.8053   1.2857
 O3S  H23  H  HCH2  0   0.221  -5.0553  -2.6437   1.0195
 O3S  H24  H  HNH2  0   0.339  -3.3474  -4.5508  -0.3614
 O3S  H25  H  HNH2  0   0.350  -4.5332  -4.8707   0.6822

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
 O3S  C1   C2   single    1.516  0.020  1.516
 O3S  C1   C    single    1.517  0.020  1.517
 O3S  O    C2   double    1.217  0.020  1.217
 O3S  C2   N    single    1.360  0.020  1.360
 O3S  N    C3   single    1.398  0.020  1.398
 O3S  C8   C3   aromatic  1.396  0.020  1.396
 O3S  C8   C7   aromatic  1.388  0.020  1.388
 O3S  C3   C4   aromatic  1.396  0.020  1.396
 O3S  C7   C6   aromatic  1.385  0.020  1.385
 O3S  C4   C5   aromatic  1.394  0.020  1.394
 O3S  N3   C16  single    1.455  0.020  1.455
 O3S  C16  C15  single    1.523  0.020  1.523
 O3S  C6   C5   aromatic  1.398  0.020  1.398
 O3S  C5   C9   single    1.466  0.020  1.466
 O3S  C14  N2   single    1.447  0.020  1.447
 O3S  C15  N2   single    1.451  0.020  1.451
 O3S  C13  N2   single    1.459  0.020  1.459
 O3S  C13  C12  single    1.495  0.020  1.495
 O3S  C9   C12  aromatic  1.433  0.020  1.433
 O3S  C9   C10  aromatic  1.379  0.020  1.379
 O3S  C12  C11  aromatic  1.373  0.020  1.373
 O3S  C10  N1   aromatic  1.355  0.020  1.355
 O3S  C11  N1   aromatic  1.358  0.020  1.358
 O3S  C    H1   single    0.970  0.020  1.090
 O3S  C    H2   single    0.970  0.020  1.090
 O3S  C    H3   single    0.970  0.020  1.090
 O3S  N    H4   single    0.860  0.020  1.020
 O3S  C1   H5   single    0.970  0.020  1.090
 O3S  C1   H6   single    0.970  0.020  1.090
 O3S  C8   H7   single    0.930  0.020  1.080
 O3S  C7   H8   single    0.930  0.020  1.080
 O3S  C6   H9   single    0.930  0.020  1.080
 O3S  C4   H10  single    0.930  0.020  1.080
 O3S  C11  H11  single    0.930  0.020  1.080
 O3S  N1   H12  single    0.860  0.020  1.020
 O3S  C10  H13  single    0.930  0.020  1.080
 O3S  C13  H14  single    0.970  0.020  1.090
 O3S  C13  H15  single    0.970  0.020  1.090
 O3S  C14  H17  single    0.970  0.020  1.090
 O3S  C14  H18  single    0.970  0.020  1.090
 O3S  C14  H19  single    0.970  0.020  1.090
 O3S  C15  H20  single    0.970  0.020  1.090
 O3S  C15  H21  single    0.970  0.020  1.090
 O3S  C16  H22  single    0.970  0.020  1.090
 O3S  C16  H23  single    0.970  0.020  1.090
 O3S  N3   H24  single    0.890  0.020  1.040
 O3S  N3   H25  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
 O3S  H3   C    H2   107.66  3.000
 O3S  H3   C    H1   108.03  3.000
 O3S  H2   C    H1   107.76  3.000
 O3S  H3   C    C1   111.70  3.000
 O3S  H2   C    C1   109.86  3.000
 O3S  H1   C    C1   111.65  3.000
 O3S  H4   N    C3   114.60  3.000
 O3S  H4   N    C2   115.50  3.000
 O3S  C3   N    C2   129.86  3.000
 O3S  C1   C2   N    113.22  3.000
 O3S  N    C2   O    123.92  3.000
 O3S  C1   C2   O    122.86  3.000
 O3S  H6   C1   H5   105.53  3.000
 O3S  H6   C1   C2   108.59  3.000
 O3S  H5   C1   C2   108.27  3.000
 O3S  H6   C1   C    110.32  3.000
 O3S  H5   C1   C    110.37  3.000
 O3S  C2   C1   C    113.44  3.000
 O3S  C4   C3   C8   119.22  3.000
 O3S  C4   C3   N    116.42  3.000
 O3S  C8   C3   N    124.36  3.000
 O3S  H7   C8   C7   119.81  3.000
 O3S  H7   C8   C3   121.33  3.000
 O3S  C7   C8   C3   118.86  3.000
 O3S  H8   C7   C6   119.39  3.000
 O3S  H8   C7   C8   118.70  3.000
 O3S  C6   C7   C8   121.92  3.000
 O3S  H9   C6   C5   119.52  3.000
 O3S  H9   C6   C7   120.67  3.000
 O3S  C5   C6   C7   119.81  3.000
 O3S  C9   C5   C4   120.11  3.000
 O3S  C9   C5   C6   121.57  3.000
 O3S  C4   C5   C6   118.32  3.000
 O3S  H10  C4   C5   119.20  3.000
 O3S  H10  C4   C3   118.92  3.000
 O3S  C5   C4   C3   121.87  3.000
 O3S  C10  C9   C12  106.69  3.000
 O3S  C10  C9   C5   125.01  3.000
 O3S  C12  C9   C5   128.27  3.000
 O3S  C13  C12  C11  125.38  3.000
 O3S  C11  C12  C9   106.57  3.000
 O3S  C13  C12  C9   127.98  3.000
 O3S  H11  C11  N1   121.51  3.000
 O3S  H11  C11  C12  129.95  3.000
 O3S  N1   C11  C12  108.54  3.000
 O3S  H12  N1   C10  124.97  3.000
 O3S  H12  N1   C11  125.10  3.000
 O3S  C10  N1   C11  109.93  3.000
 O3S  H13  C10  N1   121.38  3.000
 O3S  H13  C10  C9   130.33  3.000
 O3S  N1   C10  C9   108.28  3.000
 O3S  H15  C13  H14  106.02  3.000
 O3S  H15  C13  N2   107.56  3.000
 O3S  H14  C13  N2   111.08  3.000
 O3S  H15  C13  C12  108.91  3.000
 O3S  H14  C13  C12  109.21  3.000
 O3S  N2   C13  C12  113.75  3.000
 O3S  C15  N2   C14  112.33  3.000
 O3S  C15  N2   C13  111.35  3.000
 O3S  C14  N2   C13  111.76  3.000
 O3S  H19  C14  H18  107.02  3.000
 O3S  H19  C14  H17  107.82  3.000
 O3S  H18  C14  H17  107.90  3.000
 O3S  H19  C14  N2   110.16  3.000
 O3S  H18  C14  N2   110.88  3.000
 O3S  H17  C14  N2   112.83  3.000
 O3S  H21  C15  H20  106.56  3.000
 O3S  H21  C15  C16  107.86  3.000
 O3S  H20  C15  C16  109.23  3.000
 O3S  H21  C15  N2   107.69  3.000
 O3S  H20  C15  N2   112.22  3.000
 O3S  C16  C15  N2   112.97  3.000
 O3S  H23  C16  H22  106.58  3.000
 O3S  H23  C16  N3   107.67  3.000
 O3S  H22  C16  N3   114.14  3.000
 O3S  H23  C16  C15  110.36  3.000
 O3S  H22  C16  C15  108.28  3.000
 O3S  N3   C16  C15  109.76  3.000
 O3S  H25  N3   H24  105.54  3.000
 O3S  H25  N3   C16  109.41  3.000
 O3S  H24  N3   C16  109.50  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
 O3S  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 O3S  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 O3S  CONST_03  C9   C5   C4   C3    180.00   0.0  0
 O3S  CONST_04  C5   C4   C3   C8      0.00   0.0  0
 O3S  CONST_05  C5   C6   C7   C8      0.00   0.0  0
 O3S  CONST_06  C4   C3   C8   C7      0.00   0.0  0
 O3S  CONST_07  C4   C5   C6   C7      0.00   0.0  0
 O3S  CONST_08  C9   C5   C6   C7    180.00   0.0  0
 O3S  CONST_11  C11  C12  C9   C5    180.00   0.0  0
 O3S  CONST_12  N1   C10  C9   C5    180.00   0.0  0
 O3S  CONST_15  N1   C11  C12  C9      0.00   0.0  0
 O3S  CONST_16  C11  N1   C10  C9      0.00   0.0  0
 O3S  CONST_17  N1   C10  C9   C12     0.00   0.0  0
 O3S  CONST_18  C10  N1   C11  C12     0.00   0.0  0
 O3S  CONST_19  C10  C9   C12  C11     0.00   0.0  0
 O3S  CONST_20  C7   C8   C3   N     180.00   0.0  0
 O3S  CONST_21  C5   C4   C3   N     180.00   0.0  0
 O3S  CONST_22  C13  C12  C9   C5      0.00   0.0  0
 O3S  CONST_23  C13  C12  C11  N1    180.00   0.0  0
 O3S  CONST_24  C13  C12  C9   C10   180.00   0.0  0
 O3S  CONST_25  H8   C7   C8   C3    180.00   0.0  0
 O3S  CONST_26  H10  C4   C3   C8    180.00   0.0  0
 O3S  CONST_27  H9   C6   C7   C8    180.00   0.0  0
 O3S  CONST_28  H7   C8   C7   C6    180.00   0.0  0
 O3S  CONST_29  H13  C10  C9   C5      0.00   0.0  0
 O3S  CONST_30  H11  C11  C12  C9    180.00   0.0  0
 O3S  CONST_31  H12  N1   C10  C9    180.00   0.0  0
 O3S  CONST_32  C8   C3   N    C2      0.00   0.0  0
 O3S  CONST_33  C4   C3   N    C2    180.00   0.0  0
 O3S  CONST_34  H4   N    C3   C8    180.00   0.0  0
 O3S  CONST_35  C3   N    C2   O       0.00   0.0  0
 O3S  CONST_36  C3   N    C2   C1    180.00   0.0  0
 O3S  Var_01    N2   C13  C12  C9     81.46  30.0  1
 O3S  Var_02    C14  N2   C13  C12    68.72  30.0  3
 O3S  Var_03    O    C2   C1   C       2.72  30.0  3
 O3S  Var_04    C16  C15  N2   C13   166.28  30.0  1
 O3S  Var_05    N3   C16  C15  N2   -173.44  30.0  2
 O3S  Var_06    H1   C    C1   C2     61.09  30.0  3
 O3S  Var_07    H17  C14  N2   C13    67.21  30.0  3
 O3S  Var_08    H24  N3   C16  C15    70.09  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
 O3S  plan-1  C5   0.020
 O3S  plan-1  C9   0.020
 O3S  plan-1  C12  0.020
 O3S  plan-1  C11  0.020
 O3S  plan-1  N1   0.020
 O3S  plan-1  C10  0.020
 O3S  plan-1  C13  0.020
 O3S  plan-1  H11  0.020
 O3S  plan-1  H12  0.020
 O3S  plan-1  H13  0.020
 O3S  plan-2  N    0.020
 O3S  plan-2  C3   0.020
 O3S  plan-2  C8   0.020
 O3S  plan-2  C7   0.020
 O3S  plan-2  C6   0.020
 O3S  plan-2  C5   0.020
 O3S  plan-2  C4   0.020
 O3S  plan-2  C9   0.020
 O3S  plan-2  H7   0.020
 O3S  plan-2  H8   0.020
 O3S  plan-2  H9   0.020
 O3S  plan-2  H10  0.020
 O3S  plan-3  O    0.020
 O3S  plan-3  N    0.020
 O3S  plan-3  C2   0.020
 O3S  plan-3  C1   0.020
 O3S  plan-3  C3   0.020
 O3S  plan-3  H4   0.020

