# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 07:08:55 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2Cn3cnc[n+]3C2)[C@@H]1C)C([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
 BMG  BMG  (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylate  ligand  44  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BMG
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
 BMG  C1    C  CR15   0  -0.209  -0.3849  -1.1656   0.1509
 BMG  C3    C  CR5    0   0.219  -0.9190   1.0007   0.8025
 BMG  C5    C  CR15   0  -0.120  -1.8080  -1.1135   0.7507
 BMG  C6    C  CH1    0  -0.389  -2.9283  -1.1539  -0.3121
 BMG  C7    C  C1     0   0.199  -2.9610   0.0793  -1.1814
 BMG  C8    C  CH1    0   0.048  -4.3351  -1.3733   0.2815
 BMG  C11   C  C      0   0.375  -0.9977   2.4914   1.0606
 BMG  C17   C  CR15   0  -0.426   2.5002   1.5307  -0.0268
 BMG  C18   C  CH2    0  -0.287   2.5062   0.8837   1.3503
 BMG  C20   C  CR15   0   0.166   3.3066  -1.6113   1.5122
 BMG  C22   C  CR15   0   0.177   4.4460  -1.4806  -0.2605
 BMG  C9    C  CH3    0  -0.697  -4.4853  -2.7432   0.9260
 BMG  O14   O  O      0  -0.392  -2.9341   0.0489  -2.3901
 BMG  O15   O  OH1    0  -0.669  -4.5990  -0.3252   1.1924
 BMG  C10   C  CH3    0  -0.681  -0.1790  -2.0534  -1.0621
 BMG  N4    N  NR15   0  -0.620  -1.7628   0.1555   1.4742
 BMG  O13   O  OC    -1  -0.560   0.0515   3.1384   0.9139
 BMG  O12   O  O      0  -0.586  -2.1224   2.9077   1.3941
 BMG  C2    C  CR5    0  -0.281  -0.1061   0.3140  -0.0333
 BMG  S16   S  S2     0   0.025   1.1168   0.9399  -1.0921
 BMG  C24   C  CH2    0  -0.289   3.8054   1.0330  -0.6555
 BMG  N23   N  N      0  -0.184   3.8933  -0.2984  -0.0655
 BMG  N19   N  N      1  -0.190   3.1731  -0.3807   1.0540
 BMG  N21   N  N      0  -0.434   4.0947  -2.3162   0.7096
 BMG  H1    H  HCR5   0   0.237   0.2704  -1.5460   0.9505
 BMG  H5    H  HCR5   0   0.259  -1.9548  -1.9445   1.4415
 BMG  H6    H  HCH1   0   0.275  -2.7525  -2.0080  -0.9715
 BMG  H7    H  H      0   0.196  -3.0900   1.0390  -0.6539
 BMG  H8    H  HCH1   0   0.226  -5.0445  -1.3296  -0.5579
 BMG  H17   H  HCR5   0   0.335   2.4712   2.6128   0.0493
 BMG  H18A  H  HCH2   0   0.332   1.5211   0.7044   1.7708
 BMG  H20   H  HCR5   0   0.353   2.8269  -1.9607   2.4122
 BMG  H22   H  HCR5   0   0.350   5.0832  -1.7022  -1.1013
 BMG  H9    H  HCH3   0   0.245  -5.5031  -2.8740   1.2984
 BMG  H9A   H  HCH3   0   0.235  -4.3017  -3.5320   0.1960
 BMG  H9B   H  HCH3   0   0.235  -3.8025  -2.8857   1.7636
 BMG  HO15  H  HOH1   0   0.459  -5.4786  -0.4521   1.5620
 BMG  H10   H  HCH3   0   0.228  -0.7233  -1.6999  -1.9379
 BMG  H10A  H  HCH3   0   0.237   0.8776  -2.0808  -1.3287
 BMG  H10B  H  HCH3   0   0.238  -0.4920  -3.0782  -0.8566
 BMG  HN4   H  HNR5   0   0.376  -2.6357   0.5485   1.7955
 BMG  H24   H  HCH2   0   0.328   3.7963   0.9631  -1.7399
 BMG  H24A  H  HCH2   0   0.328   4.6664   1.6191  -0.3329
 BMG  H18   H  HCH2   0   0.335   3.1140   1.4478   2.0576

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
 BMG  C9   C8    single    1.521  0.020  1.521
 BMG  C10  C1    single    1.517  0.020  1.517
 BMG  O15  C8    single    1.413  0.020  1.413
 BMG  C8   C6    single    1.543  0.020  1.543
 BMG  C6   C5    single    1.545  0.020  1.545
 BMG  C6   C7    single    1.509  0.020  1.509
 BMG  C1   C5    single    1.545  0.020  1.545
 BMG  C1   C2    single    1.517  0.020  1.517
 BMG  S16  C2    single    1.734  0.020  1.734
 BMG  S16  C17   single    1.843  0.020  1.843
 BMG  C18  C17   single    1.522  0.020  1.522
 BMG  C18  N19   single    1.460  0.020  1.460
 BMG  O14  C7    double    1.209  0.020  1.209
 BMG  C5   N4    single    1.461  0.020  1.461
 BMG  C2   C3    double    1.353  0.020  1.353
 BMG  C17  C24   single    1.532  0.020  1.532
 BMG  N19  C20   aromatic  1.320  0.020  1.320
 BMG  N19  N23   aromatic  1.334  0.020  1.334
 BMG  C20  N21   aromatic  1.328  0.020  1.328
 BMG  C3   N4    single    1.370  0.020  1.370
 BMG  C3   C11   single    1.515  0.020  1.515
 BMG  C24  N23   single    1.459  0.020  1.459
 BMG  N23  C22   aromatic  1.320  0.020  1.320
 BMG  O12  C11   deloc     1.245  0.020  1.245
 BMG  N21  C22   aromatic  1.328  0.020  1.328
 BMG  C11  O13   deloc     1.241  0.020  1.241
 BMG  C1   H1    single    0.970  0.020  1.090
 BMG  C5   H5    single    0.970  0.020  1.090
 BMG  C6   H6    single    0.970  0.020  1.090
 BMG  C7   H7    single    0.930  0.020  1.080
 BMG  C8   H8    single    0.970  0.020  1.090
 BMG  C17  H17   single    0.970  0.020  1.090
 BMG  C18  H18   single    0.970  0.020  1.090
 BMG  C18  H18A  single    0.970  0.020  1.090
 BMG  C20  H20   single    0.930  0.020  1.080
 BMG  C22  H22   single    0.930  0.020  1.080
 BMG  C9   H9    single    0.970  0.020  1.090
 BMG  C9   H9A   single    0.970  0.020  1.090
 BMG  C9   H9B   single    0.970  0.020  1.090
 BMG  O15  HO15  single    0.850  0.020  0.980
 BMG  C10  H10   single    0.970  0.020  1.090
 BMG  C10  H10A  single    0.970  0.020  1.090
 BMG  C10  H10B  single    0.970  0.020  1.090
 BMG  N4   HN4   single    0.890  0.020  1.040
 BMG  C24  H24   single    0.970  0.020  1.090
 BMG  C24  H24A  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
 BMG  H1    C1   C2    108.40  3.000
 BMG  H1    C1   C10   107.31  3.000
 BMG  C2    C1   C10   116.66  3.000
 BMG  H1    C1   C5    106.13  3.000
 BMG  C2    C1   C5    100.57  3.000
 BMG  C10   C1   C5    117.07  3.000
 BMG  C2    C3   N4    111.08  3.000
 BMG  N4    C3   C11   119.43  3.000
 BMG  C2    C3   C11   129.49  3.000
 BMG  H5    C5   N4    110.62  3.000
 BMG  H5    C5   C6    108.55  3.000
 BMG  N4    C5   C6    112.69  3.000
 BMG  H5    C5   C1    110.13  3.000
 BMG  N4    C5   C1    101.13  3.000
 BMG  C6    C5   C1    113.58  3.000
 BMG  H6    C6   C8    105.52  3.000
 BMG  H6    C6   C7    107.12  3.000
 BMG  C8    C6   C7    108.54  3.000
 BMG  H6    C6   C5    108.59  3.000
 BMG  C7    C6   C5    112.99  3.000
 BMG  C8    C6   C5    113.61  3.000
 BMG  H7    C7   O14   120.17  3.000
 BMG  H7    C7   C6    115.99  3.000
 BMG  O14   C7   C6    123.69  3.000
 BMG  H8    C8   O15   110.00  3.000
 BMG  H8    C8   C9    107.18  3.000
 BMG  O15   C8   C9    112.10  3.000
 BMG  H8    C8   C6    106.79  3.000
 BMG  O15   C8   C6    108.23  3.000
 BMG  C9    C8   C6    112.40  3.000
 BMG  O12   C11  O13   128.39  3.000
 BMG  O13   C11  C3    116.67  3.000
 BMG  O12   C11  C3    114.94  3.000
 BMG  H17   C17  C24   112.05  3.000
 BMG  H17   C17  S16   109.89  3.000
 BMG  C24   C17  S16   107.35  3.000
 BMG  H17   C17  C18   111.14  3.000
 BMG  C24   C17  C18   103.29  3.000
 BMG  S16   C17  C18   112.94  3.000
 BMG  H18A  C18  H18   109.88  3.000
 BMG  H18A  C18  N19   110.49  3.000
 BMG  H18   C18  N19   108.98  3.000
 BMG  H18A  C18  C17   114.65  3.000
 BMG  H18   C18  C17   111.68  3.000
 BMG  N19   C18  C17   100.74  3.000
 BMG  H20   C20  N21   126.64  3.000
 BMG  H20   C20  N19   123.16  3.000
 BMG  N21   C20  N19   110.19  3.000
 BMG  H22   C22  N21   126.65  3.000
 BMG  H22   C22  N23   123.16  3.000
 BMG  N21   C22  N23   110.18  3.000
 BMG  H9B   C9   H9A   108.32  3.000
 BMG  H9B   C9   H9    107.83  3.000
 BMG  H9A   C9   H9    107.38  3.000
 BMG  H9B   C9   C8    112.43  3.000
 BMG  H9A   C9   C8    110.56  3.000
 BMG  H9    C9   C8    110.15  3.000
 BMG  HO15  O15  C8    108.68  3.000
 BMG  H10B  C10  H10A  107.49  3.000
 BMG  H10B  C10  H10   108.22  3.000
 BMG  H10A  C10  H10   107.20  3.000
 BMG  H10B  C10  C1    111.10  3.000
 BMG  H10A  C10  C1    109.98  3.000
 BMG  H10   C10  C1    112.63  3.000
 BMG  HN4   N4   C5    117.95  3.000
 BMG  HN4   N4   C3    116.63  3.000
 BMG  C5    N4   C3    108.18  3.000
 BMG  S16   C2   C3    128.13  3.000
 BMG  C3    C2   C1    108.04  3.000
 BMG  S16   C2   C1    123.76  3.000
 BMG  C2    S16  C17   106.98  3.000
 BMG  H24A  C24  H24   109.66  3.000
 BMG  H24A  C24  N23   108.87  3.000
 BMG  H24   C24  N23   110.20  3.000
 BMG  H24A  C24  C17   112.13  3.000
 BMG  H24   C24  C17   115.04  3.000
 BMG  N23   C24  C17   100.48  3.000
 BMG  N19   N23  C24   111.30  3.000
 BMG  C24   N23  C22   141.54  3.000
 BMG  N19   N23  C22   107.16  3.000
 BMG  N23   N19  C20   107.12  3.000
 BMG  N23   N19  C18   111.32  3.000
 BMG  C20   N19  C18   141.56  3.000
 BMG  C22   N21  C20   105.35  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
 BMG  CONST_01  C22  N23  N19  C20     0.00   0.0  0
 BMG  CONST_02  N23  C22  N21  C20     0.00   0.0  0
 BMG  CONST_03  N19  C20  N21  C22     0.00   0.0  0
 BMG  CONST_04  N21  C20  N19  N23     0.00   0.0  0
 BMG  CONST_05  N21  C22  N23  N19     0.00   0.0  0
 BMG  CONST_06  H20  C20  N19  C18     0.00   0.0  0
 BMG  CONST_07  H22  C22  N21  C20   180.00   0.0  0
 BMG  Var_01    N4   C3   C2   C1     -3.29  30.0  1
 BMG  Var_02    C2   C3   N4   C5    -18.62  30.0  1
 BMG  Var_03    C20  N19  C18  C17  -157.68  30.0  1
 BMG  Var_04    N19  N23  C24  C17   -21.80  30.0  1
 BMG  Var_05    O12  C11  C3   N4    -29.30  30.0  2

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
 BMG  chir_01  C1   C10  C5   C2   positiv
 BMG  chir_02  C5   N4   C6   C1   negativ
 BMG  chir_03  C6   C8   C5   C7   positiv
 BMG  chir_04  C8   O15  C6   C9   negativ
 BMG  chir_05  C17  S16  C24  C18  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
 BMG  plan-1  C3   0.020
 BMG  plan-1  C5   0.020
 BMG  plan-1  N4   0.020
 BMG  plan-1  HN4  0.020
 BMG  plan-2  C18  0.020
 BMG  plan-2  C20  0.020
 BMG  plan-2  C22  0.020
 BMG  plan-2  C24  0.020
 BMG  plan-2  N23  0.020
 BMG  plan-2  N19  0.020
 BMG  plan-2  N21  0.020
 BMG  plan-2  H20  0.020
 BMG  plan-2  H22  0.020
 BMG  plan-3  C3   0.020
 BMG  plan-3  C11  0.020
 BMG  plan-3  O13  0.020
 BMG  plan-3  O12  0.020
 BMG  plan-4  C6   0.020
 BMG  plan-4  C7   0.020
 BMG  plan-4  O14  0.020
 BMG  plan-4  H7   0.020

