# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 07:19:17 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-[(2-aminoethyl)amino]-2-{[(2-aminoethyl)amino]methyl}propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNCC(CNCCN)C=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
 CH4  CH4  3-[(2-aminoethyl)amino]-2-{[(2-aminoethyl)amino]methyl}propanal  ligand  33  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CH4
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
 CH4  CA    C  CH1   0  -0.394  -0.0117   0.2546   0.0566
 CH4  CB1   C  CH2   0  -0.253   1.2479  -0.5164   0.4637
 CH4  NG1   N  NH1   0  -0.606   2.4457   0.0816  -0.0872
 CH4  CD1   C  CH2   0  -0.264   3.6357  -0.7134   0.1496
 CH4  CE1   C  CH2   0  -0.299   4.8488  -0.0788  -0.5101
 CH4  NZ1   N  NH2   0  -0.803   6.0346  -0.8862  -0.2706
 CH4  CB2   C  CH2   0  -0.254  -1.2657  -0.5241   0.4662
 CH4  NG2   N  NH1   0  -0.606  -2.4688   0.0732  -0.0745
 CH4  CD2   C  CH2   0  -0.264  -3.6536  -0.7314   0.1567
 CH4  CE2   C  CH2   0  -0.299  -4.8714  -0.0999  -0.4975
 CH4  NZ2   N  NH2   0  -0.803  -6.0517  -0.9167  -0.2612
 CH4  C     C  C1    0   0.175  -0.0149   1.5875   0.7458
 CH4  O     O  O     0  -0.369  -0.0120   2.6653   0.2048
 CH4  HA    H  HCH1  0   0.256  -0.0129   0.3974  -1.0265
 CH4  HB12  H  HCH2  0   0.242   1.1605  -1.5310   0.0661
 CH4  HB13  H  HCH2  0   0.203   1.2789  -0.6215   1.5606
 CH4  HG1   H  HNH1  0   0.343   2.5899   1.0012   0.3154
 CH4  HD12  H  HCH2  0   0.221   3.4792  -1.7084  -0.2777
 CH4  HD13  H  HCH2  0   0.190   3.8395  -0.8645   1.2228
 CH4  HE12  H  HCH2  0   0.192   4.9451   0.9604  -0.1606
 CH4  HE13  H  HCH2  0   0.220   4.6745  -0.0276  -1.5873
 CH4  HZ11  H  HNH2  0   0.350   6.8140  -0.5030  -0.7888
 CH4  HZ12  H  HNH2  0   0.340   6.2963  -0.8202   0.7053
 CH4  HB22  H  HCH2  0   0.242  -1.1763  -1.5359   0.0620
 CH4  HB23  H  HCH2  0   0.203  -1.2899  -0.6353   1.5624
 CH4  HG2   H  HNH1  0   0.343  -2.6171   0.9863   0.3413
 CH4  HD22  H  HCH2  0   0.221  -3.4907  -1.7215  -0.2789
 CH4  HD23  H  HCH2  0   0.190  -3.8560  -0.8926   1.2286
 CH4  HE22  H  HCH2  0   0.192  -4.9745   0.9362  -0.1411
 CH4  HE23  H  HCH2  0   0.220  -4.6990  -0.0407  -1.5746
 CH4  HZ21  H  HNH2  0   0.339  -6.3149  -0.8551   0.7145
 CH4  HZ22  H  HNH2  0   0.350  -6.8333  -0.5379  -0.7795
 CH4  H     H  H     0   0.183  -0.0193   1.5094   1.8519

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
 CH4  CA   CB1   single  1.532  0.020  1.532
 CH4  CA   CB2   single  1.532  0.020  1.532
 CH4  CA   C     single  1.501  0.020  1.501
 CH4  CA   HA    single  0.970  0.020  1.090
 CH4  CB1  NG1   single  1.448  0.020  1.448
 CH4  CB1  HB12  single  0.970  0.020  1.090
 CH4  CB1  HB13  single  0.970  0.020  1.090
 CH4  NG1  CD1   single  1.451  0.020  1.451
 CH4  NG1  HG1   single  0.890  0.020  1.040
 CH4  CD1  CE1   single  1.520  0.020  1.520
 CH4  CD1  HD12  single  0.970  0.020  1.090
 CH4  CD1  HD13  single  0.970  0.020  1.090
 CH4  CE1  NZ1   single  1.454  0.020  1.454
 CH4  CE1  HE12  single  0.970  0.020  1.090
 CH4  CE1  HE13  single  0.970  0.020  1.090
 CH4  NZ1  HZ11  single  0.890  0.020  1.040
 CH4  NZ1  HZ12  single  0.890  0.020  1.040
 CH4  CB2  NG2   single  1.448  0.020  1.448
 CH4  CB2  HB22  single  0.970  0.020  1.090
 CH4  CB2  HB23  single  0.970  0.020  1.090
 CH4  NG2  CD2   single  1.451  0.020  1.451
 CH4  NG2  HG2   single  0.890  0.020  1.040
 CH4  CD2  CE2   single  1.520  0.020  1.520
 CH4  CD2  HD22  single  0.970  0.020  1.090
 CH4  CD2  HD23  single  0.970  0.020  1.090
 CH4  CE2  NZ2   single  1.455  0.020  1.455
 CH4  CE2  HE22  single  0.970  0.020  1.090
 CH4  CE2  HE23  single  0.970  0.020  1.090
 CH4  NZ2  HZ21  single  0.890  0.020  1.040
 CH4  NZ2  HZ22  single  0.890  0.020  1.040
 CH4  C    O     double  1.206  0.020  1.206
 CH4  C    H     single  0.930  0.020  1.080

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
 CH4  HA    CA   C     109.83  3.000
 CH4  HA    CA   CB2   109.31  3.000
 CH4  C     CA   CB2   109.09  3.000
 CH4  HA    CA   CB1   109.28  3.000
 CH4  C     CA   CB1   109.07  3.000
 CH4  CB2   CA   CB1   110.25  3.000
 CH4  HB13  CB1  HB12  106.00  3.000
 CH4  HB13  CB1  NG1   113.25  3.000
 CH4  HB12  CB1  NG1   108.13  3.000
 CH4  HB13  CB1  CA    109.60  3.000
 CH4  HB12  CB1  CA    107.74  3.000
 CH4  NG1   CB1  CA    111.79  3.000
 CH4  HG1   NG1  CD1   108.39  3.000
 CH4  HG1   NG1  CB1   109.94  3.000
 CH4  CD1   NG1  CB1   112.97  3.000
 CH4  HD13  CD1  HD12  106.38  3.000
 CH4  HD13  CD1  CE1   109.40  3.000
 CH4  HD12  CD1  CE1   108.93  3.000
 CH4  HD13  CD1  NG1   112.68  3.000
 CH4  HD12  CD1  NG1   108.50  3.000
 CH4  CE1   CD1  NG1   110.80  3.000
 CH4  HE13  CE1  HE12  106.43  3.000
 CH4  HE13  CE1  NZ1   108.57  3.000
 CH4  HE12  CE1  NZ1   113.61  3.000
 CH4  HE13  CE1  CD1   108.68  3.000
 CH4  HE12  CE1  CD1   109.05  3.000
 CH4  NZ1   CE1  CD1   110.33  3.000
 CH4  HZ12  NZ1  HZ11  105.65  3.000
 CH4  HZ12  NZ1  CE1   109.47  3.000
 CH4  HZ11  NZ1  CE1   109.49  3.000
 CH4  HB23  CB2  HB22  106.04  3.000
 CH4  HB23  CB2  NG2   113.25  3.000
 CH4  HB22  CB2  NG2   108.16  3.000
 CH4  HB23  CB2  CA    109.59  3.000
 CH4  HB22  CB2  CA    107.74  3.000
 CH4  NG2   CB2  CA    111.75  3.000
 CH4  HG2   NG2  CD2   108.33  3.000
 CH4  HG2   NG2  CB2   109.87  3.000
 CH4  CD2   NG2  CB2   112.98  3.000
 CH4  HD23  CD2  HD22  106.39  3.000
 CH4  HD23  CD2  CE2   109.39  3.000
 CH4  HD22  CD2  CE2   108.90  3.000
 CH4  HD23  CD2  NG2   112.70  3.000
 CH4  HD22  CD2  NG2   108.48  3.000
 CH4  CE2   CD2  NG2   110.82  3.000
 CH4  HE23  CE2  HE22  106.44  3.000
 CH4  HE23  CE2  NZ2   108.58  3.000
 CH4  HE22  CE2  NZ2   113.58  3.000
 CH4  HE23  CE2  CD2   108.69  3.000
 CH4  HE22  CE2  CD2   109.07  3.000
 CH4  NZ2   CE2  CD2   110.30  3.000
 CH4  HZ22  NZ2  HZ21  105.67  3.000
 CH4  HZ22  NZ2  CE2   109.48  3.000
 CH4  HZ21  NZ2  CE2   109.47  3.000
 CH4  H     C    O     120.69  3.000
 CH4  H     C    CA    113.30  3.000
 CH4  O     C    CA    126.00  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
 CH4  Var_01  CD1   NG1  CB1  CA   -173.18  30.0  3
 CH4  Var_02  CD2   NG2  CB2  CA    172.83  30.0  3
 CH4  Var_03  NG2   CB2  CA   CB1  -171.48  30.0  3
 CH4  Var_04  O     C    CA   CB1   119.37  30.0  3
 CH4  Var_05  CE1   CD1  NG1  CB1   177.04  30.0  3
 CH4  Var_06  CB2   CA   CB1  NG1   171.04  30.0  1
 CH4  Var_07  NZ1   CE1  CD1  NG1  -179.79  30.0  3
 CH4  Var_08  CE2   CD2  NG2  CB2  -176.78  30.0  3
 CH4  Var_09  NZ2   CE2  CD2  NG2   179.88  30.0  3
 CH4  Var_10  HZ11  NZ1  CE1  CD1   174.49  30.0  3
 CH4  Var_11  HZ21  NZ2  CE2  CD2    70.39  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
 CH4  plan-1  CA  0.020
 CH4  plan-1  C   0.020
 CH4  plan-1  O   0.020
 CH4  plan-1  H   0.020

