# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:46:03 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 1-amino-3-({[4-({[4-(formylamino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)propan-1-iminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(NC=O)nc1C(=O)Nc2cn(C)c(n2)C(=O)NCCC(N)=[NH2+]
#
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
 DIM  DIM  1-amino-3-({[4-({[4-(formylamino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)propan-1-iminium  ligand  46  26  .  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_DIM
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
 DIM  O1    O  O     0  -0.469   7.2043  -2.7796  -0.4984
 DIM  C1    C  C1    0   0.237   6.1326  -3.3350  -0.6451
 DIM  N1    N  NH1   0  -0.682   4.9337  -2.7285  -0.5656
 DIM  C2    C  CR5   0   0.360   4.7237  -1.3818  -0.3091
 DIM  N2    N  N     0  -0.485   3.4671  -0.9065  -0.2603
 DIM  C3    C  CR5   0   0.372   3.5808   0.3829  -0.0051
 DIM  N3    N  NR5   0  -0.439   4.8727   0.7500   0.1124
 DIM  C4    C  CR15  0  -0.125   5.6270  -0.3682  -0.0798
 DIM  C5    C  CH3   0  -0.513   5.4304   2.0633   0.3840
 DIM  C6    C  C     0   0.500   2.4281   1.2886   0.1330
 DIM  O2    O  O     0  -0.461   2.5384   2.4787   0.3819
 DIM  N4    N  NH1   0  -0.728   1.2453   0.6631  -0.0424
 DIM  C7    C  CR5   0   0.362   0.0011   1.2653   0.0358
 DIM  N5    N  N     0  -0.486  -1.0978   0.5229  -0.1921
 DIM  C8    C  CR5   0   0.375  -2.1217   1.3412  -0.0467
 DIM  N6    N  NR5   0  -0.442  -1.7143   2.5880   0.2660
 DIM  C9    C  CR15  0  -0.124  -0.3529   2.5642   0.3250
 DIM  C10   C  CH3   0  -0.511  -2.5112   3.7787   0.5043
 DIM  C11   C  C     0   0.507  -3.5285   0.9235  -0.2062
 DIM  O3    O  O     0  -0.476  -4.4685   1.6774   0.0032
 DIM  N7    N  NH1   0  -0.644  -3.6684  -0.3512  -0.6066
 DIM  C12   C  CH2   0  -0.289  -4.9537  -0.9665  -0.7867
 DIM  C13   C  CH2   0  -0.565  -5.5312  -1.4779   0.5450
 DIM  C14   C  C     0   0.609  -6.8648  -2.1125   0.3229
 DIM  N9    N  NC2   1  -0.748  -6.9158  -3.3656  -0.0506
 DIM  N8    N  NH2   0  -0.748  -7.9450  -1.3873   0.4570
 DIM  H1    H  H     0   0.224   6.0341  -4.4075  -0.8583
 DIM  HN1   H  HNH1  0   0.418   4.1073  -3.2905  -0.7051
 DIM  H4    H  HCR5  0   0.311   6.7003  -0.3430  -0.0395
 DIM  H51   H  HCH3  0   0.266   5.1524   2.7685  -0.3937
 DIM  H52   H  HCH3  0   0.267   5.0907   2.4361   1.3459
 DIM  H53   H  HCH3  0   0.264   6.5117   1.9694   0.4030
 DIM  HN4   H  HNH1  0   0.417   1.2558  -0.3275  -0.2440
 DIM  H9    H  HCR5  0   0.307   0.2202   3.4426   0.5581
 DIM  H101  H  HCH3  0   0.266  -3.1409   3.9982  -0.3528
 DIM  H102  H  HCH3  0   0.265  -3.1344   3.6563   1.3855
 DIM  H103  H  HCH3  0   0.262  -1.8316   4.6101   0.6646
 DIM  HN7   H  HNH1  0   0.414  -2.8389  -0.9145  -0.7151
 DIM  H121  H  HCH2  0   0.270  -5.6418  -0.2547  -1.2426
 DIM  H122  H  HCH2  0   0.284  -4.8321  -1.7940  -1.4843
 DIM  H131  H  HCH2  0   0.306  -4.8535  -2.2090   0.9864
 DIM  H132  H  HCH2  0   0.304  -5.6361  -0.6538   1.2505
 DIM  HN91  H  HNC2  0   0.446  -6.0704  -3.9043  -0.1473
 DIM  HN92  H  HNC2  0   0.438  -7.7833  -3.8357  -0.2614
 DIM  HN81  H  HNH2  0   0.438  -8.8694  -1.7512   0.2803
 DIM  HN82  H  HNH2  0   0.445  -7.8825  -0.4263   0.7513

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
 DIM  O1   C1    double    1.216  0.020  1.216
 DIM  C1   N1    single    1.346  0.020  1.346
 DIM  C1   H1    single    0.930  0.020  1.080
 DIM  N1   C2    single    1.387  0.020  1.387
 DIM  N1   HN1   single    0.860  0.020  1.020
 DIM  C2   N2    aromatic  1.344  0.020  1.344
 DIM  C2   C4    aromatic  1.377  0.020  1.377
 DIM  N2   C3    aromatic  1.319  0.020  1.319
 DIM  C3   N3    aromatic  1.348  0.020  1.348
 DIM  C3   C6    single    1.472  0.020  1.472
 DIM  N3   C4    aromatic  1.362  0.020  1.362
 DIM  N3   C5    single    1.452  0.020  1.452
 DIM  C4   H4    single    0.930  0.020  1.080
 DIM  C5   H51   single    0.970  0.020  1.090
 DIM  C5   H52   single    0.970  0.020  1.090
 DIM  C5   H53   single    0.970  0.020  1.090
 DIM  C6   O2    double    1.221  0.020  1.221
 DIM  C6   N4    single    1.349  0.020  1.349
 DIM  N4   C7    single    1.384  0.020  1.384
 DIM  N4   HN4   single    0.860  0.020  1.020
 DIM  C7   N5    aromatic  1.346  0.020  1.346
 DIM  C7   C9    aromatic  1.377  0.020  1.377
 DIM  N5   C8    aromatic  1.319  0.020  1.319
 DIM  C8   N6    aromatic  1.348  0.020  1.348
 DIM  C8   C11   single    1.476  0.020  1.476
 DIM  N6   C9    aromatic  1.363  0.020  1.363
 DIM  N6   C10   single    1.452  0.020  1.452
 DIM  C9   H9    single    0.930  0.020  1.080
 DIM  C10  H101  single    0.970  0.020  1.090
 DIM  C10  H102  single    0.970  0.020  1.090
 DIM  C10  H103  single    0.970  0.020  1.090
 DIM  C11  O3    double    1.223  0.020  1.223
 DIM  C11  N7    single    1.343  0.020  1.343
 DIM  N7   C12   single    1.436  0.020  1.436
 DIM  N7   HN7   single    0.860  0.020  1.020
 DIM  C12  C13   single    1.539  0.020  1.539
 DIM  C12  H121  single    0.970  0.020  1.090
 DIM  C12  H122  single    0.970  0.020  1.090
 DIM  C13  C14   single    1.494  0.020  1.494
 DIM  C13  H131  single    0.970  0.020  1.090
 DIM  C13  H132  single    0.970  0.020  1.090
 DIM  C14  N9    double    1.308  0.020  1.308
 DIM  C14  N8    single    1.308  0.020  1.308
 DIM  N9   HN91  single    0.860  0.020  1.020
 DIM  N9   HN92  single    0.860  0.020  1.020
 DIM  N8   HN81  single    0.860  0.020  1.020
 DIM  N8   HN82  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
 DIM  H1    C1   N1    111.82  3.000
 DIM  H1    C1   O1    123.28  3.000
 DIM  N1    C1   O1    124.90  3.000
 DIM  HN1   N1   C2    116.26  3.000
 DIM  HN1   N1   C1    118.06  3.000
 DIM  C2    N1   C1    125.69  3.000
 DIM  C4    C2   N2    110.30  3.000
 DIM  C4    C2   N1    130.26  3.000
 DIM  N2    C2   N1    119.44  3.000
 DIM  C3    N2   C2    105.78  3.000
 DIM  C6    C3   N3    125.07  3.000
 DIM  C6    C3   N2    123.49  3.000
 DIM  N3    C3   N2    111.44  3.000
 DIM  C5    N3   C4    123.77  3.000
 DIM  C5    N3   C3    129.08  3.000
 DIM  C4    N3   C3    107.14  3.000
 DIM  H4    C4   N3    121.90  3.000
 DIM  H4    C4   C2    132.76  3.000
 DIM  N3    C4   C2    105.33  3.000
 DIM  H53   C5   H52   109.01  3.000
 DIM  H53   C5   H51   108.88  3.000
 DIM  H52   C5   H51   109.34  3.000
 DIM  H53   C5   N3    107.91  3.000
 DIM  H52   C5   N3    110.85  3.000
 DIM  H51   C5   N3    110.79  3.000
 DIM  N4    C6   O2    123.89  3.000
 DIM  N4    C6   C3    112.89  3.000
 DIM  O2    C6   C3    123.23  3.000
 DIM  HN4   N4   C7    116.54  3.000
 DIM  HN4   N4   C6    118.10  3.000
 DIM  C7    N4   C6    125.36  3.000
 DIM  C9    C7   N5    110.25  3.000
 DIM  C9    C7   N4    130.78  3.000
 DIM  N5    C7   N4    118.97  3.000
 DIM  C8    N5   C7    105.85  3.000
 DIM  C11   C8   N6    125.07  3.000
 DIM  C11   C8   N5    123.54  3.000
 DIM  N6    C8   N5    111.39  3.000
 DIM  C10   N6   C9    123.73  3.000
 DIM  C10   N6   C8    129.07  3.000
 DIM  C9    N6   C8    107.20  3.000
 DIM  H9    C9   N6    121.87  3.000
 DIM  H9    C9   C7    132.81  3.000
 DIM  N6    C9   C7    105.32  3.000
 DIM  H103  C10  H102  109.01  3.000
 DIM  H103  C10  H101  108.95  3.000
 DIM  H102  C10  H101  109.30  3.000
 DIM  H103  C10  N6    107.97  3.000
 DIM  H102  C10  N6    110.82  3.000
 DIM  H101  C10  N6    110.75  3.000
 DIM  N7    C11  O3    123.77  3.000
 DIM  N7    C11  C8    113.57  3.000
 DIM  O3    C11  C8    122.65  3.000
 DIM  HN7   N7   C12   118.90  3.000
 DIM  HN7   N7   C11   118.45  3.000
 DIM  C12   N7   C11   122.48  3.000
 DIM  H122  C12  H121  107.38  3.000
 DIM  H122  C12  C13   110.10  3.000
 DIM  H121  C12  C13   110.01  3.000
 DIM  H122  C12  N7    107.81  3.000
 DIM  H121  C12  N7    109.73  3.000
 DIM  C13   C12  N7    111.69  3.000
 DIM  H132  C13  H131  107.75  3.000
 DIM  H132  C13  C14   109.36  3.000
 DIM  H131  C13  C14   109.29  3.000
 DIM  H132  C13  C12   110.18  3.000
 DIM  H131  C13  C12   109.88  3.000
 DIM  C14   C13  C12   110.34  3.000
 DIM  N8    C14  N9    121.88  3.000
 DIM  N8    C14  C13   119.12  3.000
 DIM  N9    C14  C13   118.95  3.000
 DIM  HN92  N9   HN91  116.90  3.000
 DIM  HN92  N9   C14   122.64  3.000
 DIM  HN91  N9   C14   120.46  3.000
 DIM  HN82  N8   HN81  116.88  3.000
 DIM  HN82  N8   C14   120.52  3.000
 DIM  HN81  N8   C14   122.59  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
 DIM  CONST_01  N3    C3   N2   C2      0.00   0.0  0
 DIM  CONST_02  C3    N3   C4   C2      0.00   0.0  0
 DIM  CONST_03  N3    C4   C2   N2      0.00   0.0  0
 DIM  CONST_04  C4    N3   C3   N2      0.00   0.0  0
 DIM  CONST_05  C4    C2   N2   C3      0.00   0.0  0
 DIM  CONST_06  N6    C8   N5   C7      0.00   0.0  0
 DIM  CONST_07  C8    N6   C9   C7      0.00   0.0  0
 DIM  CONST_08  N6    C9   C7   N5      0.00   0.0  0
 DIM  CONST_09  C9    N6   C8   N5      0.00   0.0  0
 DIM  CONST_10  C9    C7   N5   C8      0.00   0.0  0
 DIM  CONST_11  C3    N2   C2   N1    180.00   0.0  0
 DIM  CONST_12  N3    C4   C2   N1    180.00   0.0  0
 DIM  CONST_13  C6    C3   N2   C2    180.00   0.0  0
 DIM  CONST_14  C5    N3   C4   C2    180.00   0.0  0
 DIM  CONST_15  C5    N3   C3   N2    180.00   0.0  0
 DIM  CONST_16  C6    C3   N3   C4    180.00   0.0  0
 DIM  CONST_17  C8    N5   C7   N4    180.00   0.0  0
 DIM  CONST_18  N6    C9   C7   N4    180.00   0.0  0
 DIM  CONST_19  C11   C8   N5   C7    180.00   0.0  0
 DIM  CONST_20  C10   N6   C9   C7    180.00   0.0  0
 DIM  CONST_21  C10   N6   C8   N5    180.00   0.0  0
 DIM  CONST_22  C11   C8   N6   C9    180.00   0.0  0
 DIM  CONST_23  H4    C4   C2   N2    180.00   0.0  0
 DIM  CONST_24  H9    C9   C7   N5    180.00   0.0  0
 DIM  CONST_25  C7    N4   C6   C3    180.00   0.0  0
 DIM  CONST_26  N2    C2   N1   C1    180.00   0.0  0
 DIM  CONST_27  C4    C2   N1   C1      0.00   0.0  0
 DIM  CONST_28  N5    C7   N4   C6    180.00   0.0  0
 DIM  CONST_29  C9    C7   N4   C6      0.00   0.0  0
 DIM  CONST_30  HN1   N1   C2   N2      0.00   0.0  0
 DIM  CONST_31  HN4   N4   C7   N5      0.00   0.0  0
 DIM  CONST_32  C2    N1   C1   O1      0.00   0.0  0
 DIM  CONST_33  C7    N4   C6   O2      0.00   0.0  0
 DIM  CONST_34  C12   N7   C11  C8    180.00   0.0  0
 DIM  CONST_35  HN7   N7   C11  C8      0.00   0.0  0
 DIM  CONST_36  H1    C1   N1   C2    180.00   0.0  0
 DIM  CONST_37  C12   N7   C11  O3      0.00   0.0  0
 DIM  CONST_38  HN91  N9   C14  C13     0.00   0.0  0
 DIM  CONST_39  HN92  N9   C14  C13   180.00   0.0  0
 DIM  CONST_40  HN81  N8   C14  C13   180.00   0.0  0
 DIM  CONST_41  HN82  N8   C14  C13     0.00   0.0  0
 DIM  Var_01    O2    C6   C3   N2    179.27  30.0  2
 DIM  Var_02    O3    C11  C8   N5    175.91  30.0  2
 DIM  Var_03    H51   C5   N3   C3    -60.74  30.0  2
 DIM  Var_04    H101  C10  N6   C8    -57.07  30.0  2
 DIM  Var_05    C13   C12  N7   C11   -82.52  30.0  3
 DIM  Var_06    C14   C13  C12  N7   -179.93  30.0  3
 DIM  Var_07    N9    C14  C13  C12    84.24  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
 DIM  plan-1  N1    0.020
 DIM  plan-1  C2    0.020
 DIM  plan-1  N2    0.020
 DIM  plan-1  C3    0.020
 DIM  plan-1  N3    0.020
 DIM  plan-1  C4    0.020
 DIM  plan-1  C5    0.020
 DIM  plan-1  C6    0.020
 DIM  plan-1  H4    0.020
 DIM  plan-2  C13   0.020
 DIM  plan-2  C14   0.020
 DIM  plan-2  N9    0.020
 DIM  plan-2  N8    0.020
 DIM  plan-2  HN91  0.020
 DIM  plan-2  HN92  0.020
 DIM  plan-2  HN81  0.020
 DIM  plan-2  HN82  0.020
 DIM  plan-3  N4    0.020
 DIM  plan-3  C7    0.020
 DIM  plan-3  N5    0.020
 DIM  plan-3  C8    0.020
 DIM  plan-3  N6    0.020
 DIM  plan-3  C9    0.020
 DIM  plan-3  C10   0.020
 DIM  plan-3  C11   0.020
 DIM  plan-3  H9    0.020
 DIM  plan-4  O1    0.020
 DIM  plan-4  C1    0.020
 DIM  plan-4  N1    0.020
 DIM  plan-4  C2    0.020
 DIM  plan-4  H1    0.020
 DIM  plan-4  HN1   0.020
 DIM  plan-5  C3    0.020
 DIM  plan-5  C6    0.020
 DIM  plan-5  O2    0.020
 DIM  plan-5  N4    0.020
 DIM  plan-5  C7    0.020
 DIM  plan-5  HN4   0.020
 DIM  plan-6  C8    0.020
 DIM  plan-6  C11   0.020
 DIM  plan-6  O3    0.020
 DIM  plan-6  N7    0.020
 DIM  plan-6  C12   0.020
 DIM  plan-6  HN7   0.020

