# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 08:01:01 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 3-(2-amino-2-oxoethyl)-2-[(1S)-1,5-diaminopentyl]-5-[(4-hydroxyphenyl)methyl]-4-oxo-4H-imidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)C1=[N+](CC(N)=O)C(=O)C(=N1)Cc2ccc(O)cc2
#
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
 CIV  CIV  "2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-yl]ethanamide"
  ligand  49  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CIV
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
 CIV  N1    N  NH2   0  -0.742   5.4072  10.8868  40.3344
 CIV  CA1   C  CH1   0  -0.229   6.0663  12.1169  39.9518
 CIV  CB1   C  CH2   0  -0.417   5.0882  13.2445  39.6365
 CIV  CG1   C  CH2   0  -0.412   4.2741  12.9661  38.3799
 CIV  C1    C  CR5   0   0.683   6.9187  12.4396  41.1200
 CIV  N2    N  N     0  -0.377   6.3284  12.7901  42.3252
 CIV  N3    N  NR5   1  -0.563   8.2321  12.3412  41.1965
 CIV  C2    C  CR5   0   0.578   8.6070  12.6534  42.5347
 CIV  O2    O  O     0  -0.270   9.7120  12.7004  42.9572
 CIV  CA2   C  CR5   0   0.199   7.2670  12.9328  43.1875
 CIV  CA3   C  CH2   0  -0.454   9.1810  11.9437  40.1726
 CIV  C3    C  C     0   0.528   9.6533  13.0157  39.1938
 CIV  O3    O  O     0  -0.464  10.4399  12.6668  38.3339
 CIV  CB2   C  CH2   0  -0.589   7.1197  13.2232  44.6207
 CIV  CG2   C  CR6   0   0.032   7.5205  11.9481  45.3338
 CIV  CD1   C  CR16  0  -0.272   8.6822  11.8829  46.0957
 CIV  CD2   C  CR16  0  -0.246   6.7441  10.7972  45.2000
 CIV  CE1   C  CR16  0  -0.364   9.0537  10.7084  46.7264
 CIV  CE2   C  CR16  0  -0.320   7.1051   9.6165  45.8228
 CIV  CZ    C  CR6   0   0.358   8.2669   9.5638  46.5923
 CIV  OH    O  OH1   0  -0.619   8.5767   8.3960  47.1766
 CIV  CD    C  CH2   0  -0.436   3.3078  14.1046  38.0763
 CIV  CE    C  CH2   0  -0.287   2.4075  13.8441  36.8775
 CIV  NZ    N  NH2   0  -0.794   3.1805  13.6440  35.6599
 CIV  H1    H  HNH2  0   0.394   6.0368  10.1067  40.4692
 CIV  HN11  H  HNH2  0   0.386   4.7925  10.9846  41.1328
 CIV  HA1   H  HCH1  0   0.309   6.6850  11.9260  39.0733
 CIV  HB11  H  HCH2  0   0.254   5.6620  14.1665  39.5056
 CIV  HB12  H  HCH2  0   0.247   4.4254  13.4031  40.4914
 CIV  HG12  H  HCH2  0   0.223   3.7128  12.0355  38.4962
 CIV  HG11  H  HCH2  0   0.226   4.9489  12.8188  37.5335
 CIV  HA32  H  HCH2  0   0.340   8.7584  11.1183  39.6009
 CIV  HA31  H  HCH2  0   0.338  10.0614  11.5518  40.6813
 CIV  HB2   H  HCH2  0   0.319   7.7846  14.0421  44.9042
 CIV  H5    H  HCH2  0   0.315   6.0926  13.5166  44.8349
 CIV  HD1   H  HCR6  0   0.267   9.3054  12.7616  46.2063
 CIV  HD2   H  HCR6  0   0.267   5.8388  10.8199  44.6042
 CIV  HE1   H  HCR6  0   0.278   9.9581  10.6835  47.3237
 CIV  HE2   H  HCR6  0   0.270   6.4903   8.7319  45.7159
 CIV  HOH   H  HOH1  0   0.477   9.3934   8.4717  47.6843
 CIV  HD2A  H  HCH2  0   0.216   3.8705  15.0306  37.9131
 CIV  HD1A  H  HCH2  0   0.221   2.6733  14.2875  38.9489
 CIV  HE2A  H  HCH2  0   0.201   1.6824  14.6666  36.8020
 CIV  HE1A  H  HCH2  0   0.211   1.8227  12.9382  37.0621
 CIV  N4    N  NH2   0  -0.800   9.1802  14.2561  39.3280
 CIV  H2    H  HNH2  0   0.417   9.5029  14.9716  38.6951
 CIV  H3    H  HNH2  0   0.345   2.5542  13.4419  34.8912
 CIV  H4    H  HNH2  0   0.335   3.6439  14.5104  35.4138
 CIV  H6    H  HNH2  0   0.420   8.5666  14.5611  40.0631

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
 CIV  NZ   CE    single    1.456  0.020  1.456
 CIV  CE   CD    single    1.522  0.020  1.522
 CIV  CD   CG1   single    1.524  0.020  1.524
 CIV  CG1  CB1   single    1.523  0.020  1.523
 CIV  O3   C3    double    1.216  0.020  1.216
 CIV  N1   CA1   single    1.447  0.020  1.447
 CIV  C3   CA3   single    1.527  0.020  1.527
 CIV  CA1  CB1   single    1.526  0.020  1.526
 CIV  CA1  C1    single    1.482  0.020  1.482
 CIV  CA3  N3    single    1.451  0.020  1.451
 CIV  C1   N3    double    1.319  0.020  1.319
 CIV  C1   N2    single    1.387  0.020  1.387
 CIV  N3   C2    single    1.424  0.020  1.424
 CIV  N2   CA2   double    1.283  0.020  1.283
 CIV  C2   O2    double    1.184  0.020  1.184
 CIV  C2   CA2   single    1.517  0.020  1.517
 CIV  CA2  CB2   single    1.470  0.020  1.470
 CIV  CB2  CG2   single    1.515  0.020  1.515
 CIV  CD2  CG2   aromatic  1.395  0.020  1.395
 CIV  CD2  CE2   aromatic  1.383  0.020  1.383
 CIV  CG2  CD1   aromatic  1.391  0.020  1.391
 CIV  CE2  CZ    aromatic  1.395  0.020  1.395
 CIV  CD1  CE1   aromatic  1.384  0.020  1.384
 CIV  CZ   CE1   aromatic  1.395  0.020  1.395
 CIV  CZ   OH    single    1.342  0.020  1.342
 CIV  N1   H1    single    0.890  0.020  1.040
 CIV  N1   HN11  single    0.890  0.020  1.040
 CIV  CA1  HA1   single    0.970  0.020  1.090
 CIV  CB1  HB11  single    0.970  0.020  1.090
 CIV  CB1  HB12  single    0.970  0.020  1.090
 CIV  CG1  HG12  single    0.970  0.020  1.090
 CIV  CG1  HG11  single    0.970  0.020  1.090
 CIV  CA3  HA32  single    0.970  0.020  1.090
 CIV  CA3  HA31  single    0.970  0.020  1.090
 CIV  CB2  HB2   single    0.970  0.020  1.090
 CIV  CB2  H5    single    0.970  0.020  1.090
 CIV  CD1  HD1   single    0.930  0.020  1.080
 CIV  CD2  HD2   single    0.930  0.020  1.080
 CIV  CE1  HE1   single    0.930  0.020  1.080
 CIV  CE2  HE2   single    0.930  0.020  1.080
 CIV  OH   HOH   single    0.850  0.020  0.980
 CIV  CD   HD2A  single    0.970  0.020  1.090
 CIV  CD   HD1A  single    0.970  0.020  1.090
 CIV  CE   HE2A  single    0.970  0.020  1.090
 CIV  CE   HE1A  single    0.970  0.020  1.090
 CIV  C3   N4    single    1.334  0.020  1.334
 CIV  N4   H2    single    0.860  0.020  1.020
 CIV  NZ   H3    single    0.890  0.020  1.040
 CIV  NZ   H4    single    0.890  0.020  1.040
 CIV  N4   H6    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
 CIV  HN11  N1   H1    110.32  3.000
 CIV  HN11  N1   CA1   113.76  3.000
 CIV  H1    N1   CA1   114.04  3.000
 CIV  HA1   CA1  C1    110.28  3.000
 CIV  HA1   CA1  CB1   109.05  3.000
 CIV  C1    CA1  CB1   111.76  3.000
 CIV  HA1   CA1  N1    108.81  3.000
 CIV  C1    CA1  N1    103.81  3.000
 CIV  CB1   CA1  N1    113.01  3.000
 CIV  HB12  CB1  HB11  106.81  3.000
 CIV  HB12  CB1  CG1   110.35  3.000
 CIV  HB11  CB1  CG1   109.62  3.000
 CIV  HB12  CB1  CA1   109.53  3.000
 CIV  HB11  CB1  CA1   108.14  3.000
 CIV  CG1   CB1  CA1   112.22  3.000
 CIV  HG11  CG1  HG12  106.56  3.000
 CIV  HG11  CG1  CD    109.76  3.000
 CIV  HG12  CG1  CD    109.37  3.000
 CIV  HG11  CG1  CB1   109.50  3.000
 CIV  HG12  CG1  CB1   110.02  3.000
 CIV  CD    CG1  CB1   111.52  3.000
 CIV  N3    C1   N2    113.08  3.000
 CIV  N2    C1   CA1   119.69  3.000
 CIV  N3    C1   CA1   127.03  3.000
 CIV  CA2   N2   C1    107.51  3.000
 CIV  CA3   N3   C2    123.42  3.000
 CIV  C2    N3   C1    107.47  3.000
 CIV  CA3   N3   C1    129.07  3.000
 CIV  CA2   C2   O2    131.58  3.000
 CIV  CA2   C2   N3    102.26  3.000
 CIV  O2    C2   N3    126.13  3.000
 CIV  CB2   CA2  C2    123.01  3.000
 CIV  CB2   CA2  N2    127.18  3.000
 CIV  C2    CA2  N2    109.67  3.000
 CIV  HA31  CA3  HA32  106.61  3.000
 CIV  HA31  CA3  C3    107.57  3.000
 CIV  HA32  CA3  C3    108.40  3.000
 CIV  HA31  CA3  N3    107.30  3.000
 CIV  HA32  CA3  N3    108.91  3.000
 CIV  C3    CA3  N3    117.53  3.000
 CIV  N4    C3   O3    124.54  3.000
 CIV  N4    C3   CA3   118.59  3.000
 CIV  O3    C3   CA3   116.87  3.000
 CIV  H5    CB2  HB2   108.72  3.000
 CIV  H5    CB2  CG2   112.55  3.000
 CIV  HB2   CB2  CG2   110.35  3.000
 CIV  H5    CB2  CA2   109.84  3.000
 CIV  HB2   CB2  CA2   109.90  3.000
 CIV  CG2   CB2  CA2   105.43  3.000
 CIV  CD2   CG2  CD1   118.61  3.000
 CIV  CD1   CG2  CB2   121.22  3.000
 CIV  CD2   CG2  CB2   120.14  3.000
 CIV  HD1   CD1  CE1   119.18  3.000
 CIV  HD1   CD1  CG2   119.91  3.000
 CIV  CE1   CD1  CG2   120.91  3.000
 CIV  HD2   CD2  CE2   118.90  3.000
 CIV  HD2   CD2  CG2   120.03  3.000
 CIV  CE2   CD2  CG2   121.07  3.000
 CIV  HE1   CE1  CZ    120.30  3.000
 CIV  HE1   CE1  CD1   119.64  3.000
 CIV  CZ    CE1  CD1   120.07  3.000
 CIV  HE2   CE2  CZ    119.78  3.000
 CIV  HE2   CE2  CD2   120.33  3.000
 CIV  CZ    CE2  CD2   119.89  3.000
 CIV  OH    CZ   CE2   117.74  3.000
 CIV  OH    CZ   CE1   122.80  3.000
 CIV  CE2   CZ   CE1   119.46  3.000
 CIV  HOH   OH   CZ    110.87  3.000
 CIV  HD1A  CD   HD2A  105.97  3.000
 CIV  HD1A  CD   CE    108.29  3.000
 CIV  HD2A  CD   CE    109.34  3.000
 CIV  HD1A  CD   CG1   109.50  3.000
 CIV  HD2A  CD   CG1   109.59  3.000
 CIV  CE    CD   CG1   113.85  3.000
 CIV  HE1A  CE   HE2A  106.18  3.000
 CIV  HE1A  CE   NZ    108.13  3.000
 CIV  HE2A  CE   NZ    113.31  3.000
 CIV  HE1A  CE   CD    108.97  3.000
 CIV  HE2A  CE   CD    108.44  3.000
 CIV  NZ    CE   CD    111.60  3.000
 CIV  H4    NZ   H3    105.62  3.000
 CIV  H4    NZ   CE    109.18  3.000
 CIV  H3    NZ   CE    109.52  3.000
 CIV  H6    N4   H2    116.06  3.000
 CIV  H6    N4   C3    124.90  3.000
 CIV  H2    N4   C3    118.88  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
 CIV  CONST_01  CZ    CE2  CD2  CG2      0.00   0.0  0
 CIV  CONST_02  CZ    CE1  CD1  CG2      0.00   0.0  0
 CIV  CONST_03  CE2   CD2  CG2  CD1      0.00   0.0  0
 CIV  CONST_04  CE2   CZ   CE1  CD1      0.00   0.0  0
 CIV  CONST_05  CE1   CD1  CG2  CD2      0.00   0.0  0
 CIV  CONST_06  CE1   CZ   CE2  CD2      0.00   0.0  0
 CIV  CONST_07  CA2   C2   N3   C1       0.00   0.0  0
 CIV  CONST_08  C2    CA2  N2   C1       0.00   0.0  0
 CIV  CONST_09  C2    N3   C1   N2       0.00   0.0  0
 CIV  CONST_10  N3    C2   CA2  N2       0.00   0.0  0
 CIV  CONST_11  CA2   N2   C1   N3       0.00   0.0  0
 CIV  CONST_12  CE2   CD2  CG2  CB2    180.00   0.0  0
 CIV  CONST_13  CE1   CD1  CG2  CB2    180.00   0.0  0
 CIV  CONST_14  OH    CZ   CE1  CD1    180.00   0.0  0
 CIV  CONST_15  OH    CZ   CE2  CD2    180.00   0.0  0
 CIV  CONST_16  C2    N3   C1   CA1    180.00   0.0  0
 CIV  CONST_17  CA2   N2   C1   CA1    180.00   0.0  0
 CIV  CONST_18  O2    C2   N3   C1     180.00   0.0  0
 CIV  CONST_19  CA3   N3   C1   N2     180.00   0.0  0
 CIV  CONST_20  CA3   N3   C2   CA2    180.00   0.0  0
 CIV  CONST_21  HE2   CE2  CD2  CG2    180.00   0.0  0
 CIV  CONST_22  HE1   CE1  CD1  CG2    180.00   0.0  0
 CIV  CONST_23  HD2   CD2  CG2  CD1    180.00   0.0  0
 CIV  CONST_24  HD1   CD1  CG2  CD2    180.00   0.0  0
 CIV  CONST_25  HE2   CE2  CZ   CE1    180.00   0.0  0
 CIV  CONST_26  HE1   CE1  CZ   CE2    180.00   0.0  0
 CIV  CONST_27  HD2   CD2  CE2  CZ     180.00   0.0  0
 CIV  CONST_28  HD1   CD1  CE1  CZ     180.00   0.0  0
 CIV  CONST_29  CA3   N3   C1   CA1      0.00   0.0  0
 CIV  CONST_30  CA3   N3   C2   O2       0.00   0.0  0
 CIV  CONST_31  H2    N4   C3   CA3    180.00   0.0  0
 CIV  CONST_32  H6    N4   C3   CA3      0.00   0.0  0
 CIV  CONST_33  H2    N4   C3   O3       0.00   0.0  0
 CIV  CONST_34  H6    N4   C3   O3     180.00   0.0  0
 CIV  Var_01    CB2   CA2  N2   C1    -176.10  30.0  1
 CIV  Var_02    CG2   CB2  CA2  N2     109.44  30.0  3
 CIV  Var_03    CB2   CA2  C2   N3     175.97  30.0  1
 CIV  Var_04    CG2   CB2  CA2  C2     -65.82  30.0  3
 CIV  Var_05    CD2   CG2  CB2  CA2    -66.35  30.0  2
 CIV  Var_06    CD1   CG2  CB2  CA2    111.59  30.0  2
 CIV  Var_07    C3    CA3  N3   C1      83.93  30.0  3
 CIV  Var_08    C3    CA3  N3   C2     -98.74  30.0  3
 CIV  Var_09    CB2   CA2  C2   O2      -5.95  30.0  1
 CIV  Var_10    HA32  CA3  N3   C1     -39.78  30.0  3
 CIV  Var_11    HA31  CA3  N3   C1    -154.82  30.0  3
 CIV  Var_12    HB2   CB2  CA2  N2    -131.64  30.0  3
 CIV  Var_13    H5    CB2  CA2  N2     -12.07  30.0  3
 CIV  Var_14    HA32  CA3  N3   C2     137.56  30.0  3
 CIV  Var_15    HA31  CA3  N3   C2      22.52  30.0  3
 CIV  Var_16    HB2   CB2  CA2  C2      53.10  30.0  3
 CIV  Var_17    H5    CB2  CA2  C2     172.68  30.0  3
 CIV  Var_18    HB2   CB2  CG2  CD1     -7.03  30.0  3
 CIV  Var_19    H5    CB2  CG2  CD1   -128.68  30.0  3
 CIV  Var_20    HB2   CB2  CG2  CD2    175.04  30.0  3
 CIV  Var_21    H5    CB2  CG2  CD2     53.39  30.0  3
 CIV  Var_22    O3    C3   CA3  N3    -179.41  30.0  1
 CIV  Var_23    N4    C3   CA3  N3       0.26  30.0  1
 CIV  Var_24    CD    CG1  CB1  CA1   -179.73  30.0  1
 CIV  Var_25    CE    CD   CG1  CB1   -176.52  30.0  1
 CIV  Var_26    NZ    CE   CD   CG1    -60.28  30.0  1
 CIV  Var_27    HG12  CG1  CB1  CA1     58.74  30.0  1
 CIV  Var_28    HG11  CG1  CB1  CA1    -58.05  30.0  1
 CIV  Var_29    HD2A  CD   CG1  CB1     60.68  30.0  1
 CIV  Var_30    HD1A  CD   CG1  CB1    -55.16  30.0  1
 CIV  Var_31    HE2A  CE   CD   CG1    174.22  30.0  1
 CIV  Var_32    HE1A  CE   CD   CG1     59.06  30.0  1
 CIV  Var_33    HA32  CA3  C3   O3     -55.45  30.0  3
 CIV  Var_34    HA31  CA3  C3   O3      59.47  30.0  3
 CIV  Var_35    H3    NZ   CE   CD     178.04  30.0  3
 CIV  Var_36    H4    NZ   CE   CD     -66.75  30.0  3
 CIV  Var_37    HB11  CB1  CG1  CD     -59.55  30.0  3
 CIV  Var_38    HB12  CB1  CG1  CD      57.82  30.0  3
 CIV  Var_39    HG12  CG1  CD   CE     -54.60  30.0  3
 CIV  Var_40    HG11  CG1  CD   CE      61.96  30.0  3
 CIV  Var_41    HD2A  CD   CE   NZ      62.66  30.0  3
 CIV  Var_42    HD1A  CD   CE   NZ     177.69  30.0  3
 CIV  Var_43    N4    C3   CA3  HA32   124.22  30.0  1
 CIV  Var_44    N4    C3   CA3  HA31  -120.86  30.0  1

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
 CIV  chir_01  CA1  N1  CB1  C1  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
 CIV  plan-1  CB2  0.020
 CIV  plan-1  CG2  0.020
 CIV  plan-1  CD1  0.020
 CIV  plan-1  CD2  0.020
 CIV  plan-1  CE1  0.020
 CIV  plan-1  CE2  0.020
 CIV  plan-1  CZ   0.020
 CIV  plan-1  OH   0.020
 CIV  plan-1  HD1  0.020
 CIV  plan-1  HD2  0.020
 CIV  plan-1  HE1  0.020
 CIV  plan-1  HE2  0.020
 CIV  plan-2  CA3  0.020
 CIV  plan-2  C3   0.020
 CIV  plan-2  O3   0.020
 CIV  plan-2  N4   0.020
 CIV  plan-2  H2   0.020
 CIV  plan-2  H6   0.020
 CIV  plan-3  CA1  0.020
 CIV  plan-3  C1   0.020
 CIV  plan-3  N2   0.020
 CIV  plan-3  N3   0.020
 CIV  plan-3  C2   0.020
 CIV  plan-3  O2   0.020
 CIV  plan-3  CA2  0.020
 CIV  plan-3  CA3  0.020

