# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:03:09 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(3E,5R,6R,7S,8R,8aR)-5,6,7,8-tetrahydroxyhexahydroimidazo[1,5-a]pyridin-3(2H)-ylidene]octan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC[NH+]=C1NC[C@@H]2[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)N12
#
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
 MT5  MT5  N-[(3E,5R,6R,7S,8R,8aR)-5,6,7,8-tetrahydroxyhexahydroimidazo[1,5-a]pyridin-3(2H)-ylidene]octan-1-aminium  ligand  52  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MT5
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
 MT5  C1    C  CH3   0  -0.663  10.1280  -0.8402   0.1050
 MT5  C2    C  CH2   0  -0.419   8.9482   0.1218   0.1324
 MT5  C3    C  CH2   0  -0.407   7.6029  -0.5928   0.0858
 MT5  C4    C  CH2   0  -0.413   6.4144   0.3603   0.1101
 MT5  C5    C  CH2   0  -0.414   5.0701  -0.3548   0.0611
 MT5  C6    C  CH2   0  -0.420   3.8875   0.6052   0.0864
 MT5  C7    C  CH2   0  -0.478   2.5447  -0.1113   0.0283
 MT5  C8    C  CH2   0  -0.275   1.3906   0.8748   0.0526
 MT5  N9    N  NC1   1  -0.683   0.1170   0.1680  -0.0085
 MT5  C10   C  C     0   0.974  -1.0439   0.7766  -0.0840
 MT5  N11   N  NH1   0  -0.680  -1.1967   2.0921  -0.1698
 MT5  C12   C  CH2   0  -0.260  -2.6013   2.4622  -0.0717
 MT5  C13   C  CH1   0  -0.127  -3.2828   1.1397  -0.4211
 MT5  N14   N  NT    0  -0.555  -2.2417   0.1676  -0.0887
 MT5  C15   C  CH1   0   0.132  -2.4897  -1.2332  -0.2522
 MT5  O16   O  OH1   0  -0.645  -2.5527  -1.5197  -1.6182
 MT5  C17   C  CH1   0  -0.030  -3.7998  -1.5723   0.4781
 MT5  O18   O  OH1   0  -0.663  -4.1997  -2.8795   0.1461
 MT5  C19   C  CH1   0   0.008  -4.9372  -0.6272   0.0904
 MT5  O20   O  OH1   0  -0.670  -6.0919  -0.8876   0.8468
 MT5  C21   C  CH1   0   0.047  -4.5403   0.8210   0.3609
 MT5  O22   O  OH1   0  -0.667  -5.5183   1.7336  -0.0558
 MT5  H11   H  HNH1  0   0.442  -0.4551   2.7466   0.0231
 MT5  H121  H  HCH2  0   0.272  -2.8405   2.7962   0.9411
 MT5  H122  H  HCH2  0   0.286  -2.8448   3.2554  -0.7730
 MT5  H13   H  HCH1  0   0.294  -3.4989   1.0959  -1.4950
 MT5  H21   H  HCH1  0   0.226  -4.3218   0.9286   1.4350
 MT5  H17   H  HCH1  0   0.250  -3.6124  -1.4694   1.5543
 MT5  H18   H  HOH1  0   0.469  -3.7542  -3.5047   0.7268
 MT5  H19   H  HCH1  0   0.224  -5.1371  -0.7348  -0.9864
 MT5  H20   H  HOH1  0   0.459  -6.4527  -1.7386   0.5786
 MT5  H22   H  HOH1  0   0.459  -6.3279   1.5581   0.4351
 MT5  H1    H  HCH3  0   0.226  11.0809  -0.3107   0.1371
 MT5  H2    H  HCH3  0   0.216  10.0991  -1.5212   0.9575
 MT5  H3    H  HCH3  0   0.216  10.1185  -1.4477  -0.8020
 MT5  H9    H  HNC1  0   0.436   0.1370  -0.8401   0.0067
 MT5  H23   H  HCH2  0   0.210   8.9982   0.7398   1.0346
 MT5  H24   H  HCH2  0   0.210   9.0192   0.8144  -0.7122
 MT5  H31   H  HCH2  0   0.206   7.5532  -1.2120  -0.8171
 MT5  H32   H  HCH2  0   0.207   7.5304  -1.2854   0.9316
 MT5  H41   H  HCH2  0   0.208   6.4640   0.9807   1.0120
 MT5  H42   H  HCH2  0   0.209   6.4884   1.0519  -0.7365
 MT5  H51   H  HCH2  0   0.212   5.0184  -0.9709  -0.8434
 MT5  H52   H  HCH2  0   0.212   4.9936  -1.0477   0.9060
 MT5  H61   H  HCH2  0   0.221   3.9359   1.2179   0.9928
 MT5  H62   H  HCH2  0   0.221   3.9667   1.2994  -0.7565
 MT5  H71   H  HCH2  0   0.242   2.4877  -0.7159  -0.8820
 MT5  H72   H  HCH2  0   0.242   2.4550  -0.7984   0.8753
 MT5  H81   H  HCH2  0   0.262   1.4323   1.4758   0.9647
 MT5  H82   H  HCH2  0   0.260   1.4680   1.5537  -0.8001
 MT5  H15   H  HCH1  0   0.255  -1.6807  -1.7902   0.2386
 MT5  H16   H  HOH1  0   0.459  -2.9840  -2.3779  -1.7199

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
 MT5  C3   H32   single  0.970  0.020  1.090
 MT5  C4   H41   single  0.970  0.020  1.090
 MT5  C4   H42   single  0.970  0.020  1.090
 MT5  C5   H51   single  0.970  0.020  1.090
 MT5  C5   H52   single  0.970  0.020  1.090
 MT5  C6   H61   single  0.970  0.020  1.090
 MT5  C6   H62   single  0.970  0.020  1.090
 MT5  C7   H71   single  0.970  0.020  1.090
 MT5  C7   H72   single  0.970  0.020  1.090
 MT5  C8   H81   single  0.970  0.020  1.090
 MT5  C8   H82   single  0.970  0.020  1.090
 MT5  C15  H15   single  0.970  0.020  1.090
 MT5  O16  H16   single  0.850  0.020  0.980
 MT5  C1   C2    single  1.523  0.020  1.523
 MT5  C2   C3    single  1.524  0.020  1.524
 MT5  C3   C4    single  1.524  0.020  1.524
 MT5  C4   C5    single  1.524  0.020  1.524
 MT5  C5   C6    single  1.523  0.020  1.523
 MT5  C6   C7    single  1.523  0.020  1.523
 MT5  C7   C8    single  1.518  0.020  1.518
 MT5  C8   N9    single  1.458  0.020  1.458
 MT5  N9   C10   double  1.313  0.020  1.313
 MT5  C10  N11   single  1.327  0.020  1.327
 MT5  N11  C12   single  1.456  0.020  1.456
 MT5  C12  C13   single  1.528  0.020  1.528
 MT5  C10  N14   single  1.344  0.020  1.344
 MT5  C13  N14   single  1.463  0.020  1.463
 MT5  N14  C15   single  1.432  0.020  1.432
 MT5  C15  O16   single  1.397  0.020  1.397
 MT5  C15  C17   single  1.538  0.020  1.538
 MT5  C17  O18   single  1.407  0.020  1.407
 MT5  C17  C19   single  1.529  0.020  1.529
 MT5  C19  O20   single  1.405  0.020  1.405
 MT5  C13  C21   single  1.515  0.020  1.515
 MT5  C19  C21   single  1.526  0.020  1.526
 MT5  C21  O22   single  1.401  0.020  1.401
 MT5  N11  H11   single  0.890  0.020  1.040
 MT5  C12  H121  single  0.970  0.020  1.090
 MT5  C12  H122  single  0.970  0.020  1.090
 MT5  C13  H13   single  0.970  0.020  1.090
 MT5  C21  H21   single  0.970  0.020  1.090
 MT5  C17  H17   single  0.970  0.020  1.090
 MT5  O18  H18   single  0.850  0.020  0.980
 MT5  C19  H19   single  0.970  0.020  1.090
 MT5  O20  H20   single  0.850  0.020  0.980
 MT5  O22  H22   single  0.850  0.020  0.980
 MT5  C1   H1    single  0.970  0.020  1.090
 MT5  C1   H2    single  0.970  0.020  1.090
 MT5  C1   H3    single  0.970  0.020  1.090
 MT5  N9   H9    single  0.860  0.020  1.020
 MT5  C2   H23   single  0.970  0.020  1.090
 MT5  C2   H24   single  0.970  0.020  1.090
 MT5  C3   H31   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
 MT5  H3    C1   H2    107.55  3.000
 MT5  H3    C1   H1    107.60  3.000
 MT5  H2    C1   H1    107.64  3.000
 MT5  H3    C1   C2    111.09  3.000
 MT5  H2    C1   C2    111.07  3.000
 MT5  H1    C1   C2    111.70  3.000
 MT5  H24   C2   H23   106.01  3.000
 MT5  H24   C2   C3    109.28  3.000
 MT5  H23   C2   C3    109.28  3.000
 MT5  H24   C2   C1    109.61  3.000
 MT5  H23   C2   C1    109.64  3.000
 MT5  C3    C2   C1    112.78  3.000
 MT5  H32   C3   H31   106.01  3.000
 MT5  H31   C3   C4    109.34  3.000
 MT5  H32   C3   C4    109.36  3.000
 MT5  H31   C3   C2    109.27  3.000
 MT5  C4    C3   C2    113.25  3.000
 MT5  H32   C3   C2    109.34  3.000
 MT5  H42   C4   H41   105.99  3.000
 MT5  H42   C4   C5    109.33  3.000
 MT5  H41   C4   C5    109.40  3.000
 MT5  C5    C4   C3    113.22  3.000
 MT5  H42   C4   C3    109.26  3.000
 MT5  H41   C4   C3    109.39  3.000
 MT5  H52   C5   H51   106.13  3.000
 MT5  H52   C5   C6    109.36  3.000
 MT5  H51   C5   C6    109.36  3.000
 MT5  C6    C5   C4    112.87  3.000
 MT5  H52   C5   C4    109.49  3.000
 MT5  H51   C5   C4    109.40  3.000
 MT5  H62   C6   H61   106.22  3.000
 MT5  H62   C6   C7    109.43  3.000
 MT5  H61   C6   C7    109.50  3.000
 MT5  C7    C6   C5    112.78  3.000
 MT5  H62   C6   C5    109.30  3.000
 MT5  H61   C6   C5    109.39  3.000
 MT5  H72   C7   H71   107.02  3.000
 MT5  H72   C7   C8    109.46  3.000
 MT5  H71   C7   C8    109.42  3.000
 MT5  C8    C7   C6    111.35  3.000
 MT5  H72   C7   C6    109.76  3.000
 MT5  H71   C7   C6    109.73  3.000
 MT5  H82   C8   H81   107.87  3.000
 MT5  H82   C8   N9    109.29  3.000
 MT5  H81   C8   N9    109.56  3.000
 MT5  N9    C8   C7    110.40  3.000
 MT5  H82   C8   C7    109.71  3.000
 MT5  H81   C8   C7    109.97  3.000
 MT5  H9    N9   C10   118.81  3.000
 MT5  H9    N9   C8    117.82  3.000
 MT5  C10   N9   C8    123.37  3.000
 MT5  N14   C10  N11   110.27  3.000
 MT5  N14   C10  N9    125.33  3.000
 MT5  N11   C10  N9    124.40  3.000
 MT5  H11   N11  C12   122.14  3.000
 MT5  H11   N11  C10   123.14  3.000
 MT5  C12   N11  C10   111.02  3.000
 MT5  H122  C12  H121  109.03  3.000
 MT5  H122  C12  C13   112.59  3.000
 MT5  H121  C12  C13   112.25  3.000
 MT5  H122  C12  N11   111.00  3.000
 MT5  H121  C12  N11   110.57  3.000
 MT5  C13   C12  N11   101.23  3.000
 MT5  H13   C13  C21   109.50  3.000
 MT5  H13   C13  N14   109.65  3.000
 MT5  C21   C13  N14   109.50  3.000
 MT5  H13   C13  C12   110.27  3.000
 MT5  C21   C13  C12   115.74  3.000
 MT5  N14   C13  C12   101.87  3.000
 MT5  C15   N14  C13   120.06  3.000
 MT5  C15   N14  C10   126.74  3.000
 MT5  C13   N14  C10   109.52  3.000
 MT5  H15   C15  C17   107.68  3.000
 MT5  C17   C15  O16   112.37  3.000
 MT5  H15   C15  O16   111.48  3.000
 MT5  C17   C15  N14   108.01  3.000
 MT5  O16   C15  N14   108.66  3.000
 MT5  H15   C15  N14   108.52  3.000
 MT5  H16   O16  C15   107.78  3.000
 MT5  H17   C17  C19   108.53  3.000
 MT5  H17   C17  O18   111.54  3.000
 MT5  C19   C17  O18   107.64  3.000
 MT5  H17   C17  C15   107.43  3.000
 MT5  C19   C17  C15   112.15  3.000
 MT5  O18   C17  C15   109.57  3.000
 MT5  H18   O18  C17   109.24  3.000
 MT5  H19   C19  C21   108.27  3.000
 MT5  H19   C19  O20   111.07  3.000
 MT5  C21   C19  O20   107.11  3.000
 MT5  H19   C19  C17   108.84  3.000
 MT5  C21   C19  C17   110.38  3.000
 MT5  O20   C19  C17   111.13  3.000
 MT5  H20   O20  C19   108.78  3.000
 MT5  H21   C21  O22   111.41  3.000
 MT5  H21   C21  C19   108.49  3.000
 MT5  O22   C21  C19   112.58  3.000
 MT5  H21   C21  C13   108.56  3.000
 MT5  O22   C21  C13   106.79  3.000
 MT5  C19   C21  C13   108.91  3.000
 MT5  H22   O22  C21   108.46  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
 MT5  CONST_02  C13   N14  C10  N11     0.00   0.0  0
 MT5  CONST_03  C15   N14  C10  N11   180.00   0.0  0
 MT5  CONST_04  N14   C10  N11  C12     0.00   0.0  0
 MT5  CONST_05  C12   N11  C10  N9    180.00   0.0  0
 MT5  CONST_06  C13   N14  C10  N9    180.00   0.0  0
 MT5  CONST_07  C15   N14  C10  N9      0.00   0.0  0
 MT5  CONST_08  H11   N11  C12  C13   180.00   0.0  0
 MT5  CONST_09  N11   C10  N9   C8      0.00   0.0  0
 MT5  CONST_10  N14   C10  N9   C8    180.00   0.0  0
 MT5  CONST_11  H9    N9   C10  N11   180.00   0.0  0
 MT5  Var_01    H121  C12  N11  C10    99.36  30.0  1
 MT5  Var_02    C10   N9   C8   C7   -175.76  30.0  3
 MT5  Var_03    C4    C3   C2   C1   -179.89  30.0  3
 MT5  Var_04    C5    C4   C3   C2    179.90  30.0  3
 MT5  Var_05    C6    C5   C4   C3    179.97  30.0  3
 MT5  Var_06    C7    C6   C5   C4    179.63  30.0  3
 MT5  Var_07    C8    C7   C6   C5   -179.89  30.0  3
 MT5  Var_08    N9    C8   C7   C6    179.80  30.0  3
 MT5  Var_09    H1    C1   C2   C3    179.89  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
 MT5  chir_01  C13  C12  N14  C21  negativ
 MT5  chir_02  C15  O16  N14  C17  negativ
 MT5  chir_03  C17  O18  C15  C19  negativ
 MT5  chir_04  C19  O20  C17  C21  positiv
 MT5  chir_05  C21  O22  C19  C13  negativ

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
 MT5  plan-1  C8   0.020
 MT5  plan-1  N9   0.020
 MT5  plan-1  C10  0.020
 MT5  plan-1  N11  0.020
 MT5  plan-1  C12  0.020
 MT5  plan-1  C13  0.020
 MT5  plan-1  N14  0.020
 MT5  plan-1  C15  0.020
 MT5  plan-1  H11  0.020
 MT5  plan-1  H9   0.020

