# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 01:09:36 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: [(1R)-6,10-dioxooctahydro-6H-pyridazino[1,2-a][1,2]diazepin-1-yl]acetaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CC[C@H]1CCCN2N1C(=O)CCCC2=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
 RNG  RNG  '[(1R)-6,10-dioxooctahydro-6H-pyridazino[1,2-a][1,2]diazepin-1-yl]acetaldehyde'  ligand  32  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RNG
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
 RNG  O    O  O     0  -0.370   6.4225   1.3323  -0.4675
 RNG  C    C  C1    0   0.185   5.8115   0.6774  -1.2738
 RNG  CA   C  CH2   0  -0.566   4.4564   0.0793  -1.0421
 RNG  CH   C  CH1   0  -0.112   4.3797  -1.3561  -1.5711
 RNG  CG   C  CH2   0  -0.449   5.3253  -2.3236  -0.8562
 RNG  CF   C  CH2   0  -0.459   4.8595  -2.6286   0.5623
 RNG  CE   C  CH2   0  -0.288   3.4065  -3.0807   0.5531
 RNG  N1   N  NT    0  -0.328   2.5949  -2.1133  -0.1701
 RNG  C1   C  C     0   0.527   1.5460  -1.4321   0.3735
 RNG  O1   O  O     0  -0.467   1.2176  -1.5932   1.5352
 RNG  CD   C  CH2   0  -0.596   0.7763  -0.5692  -0.5944
 RNG  CC   C  CH2   0  -0.431   0.0091  -1.4300  -1.6107
 RNG  CB   C  CH2   0  -0.593   0.8260  -2.6018  -2.1826
 RNG  C2   C  C     0   0.533   2.2291  -2.1739  -2.5306
 RNG  O2   O  O     0  -0.466   2.6237  -2.0257  -3.6728
 RNG  N2   N  NT    0  -0.331   3.0173  -1.8649  -1.4591
 RNG  H    H  H     0   0.194   6.2263   0.4955  -2.2826
 RNG  HA1  H  HCH2  0   0.294   3.7532   0.6969  -1.6139
 RNG  HA2  H  HCH2  0   0.267   4.1886   0.1624   0.0127
 RNG  HH   H  HCH1  0   0.288   4.6200  -1.3450  -2.6336
 RNG  HG1  H  HCH2  0   0.254   6.3409  -1.9210  -0.8505
 RNG  HG2  H  HCH2  0   0.253   5.3626  -3.2504  -1.4342
 RNG  HF1  H  HCH2  0   0.259   5.4780  -3.4135   0.9994
 RNG  HF2  H  HCH2  0   0.240   4.9632  -1.7500   1.2034
 RNG  HE1  H  HCH2  0   0.252   3.3088  -4.0527   0.0609
 RNG  HE2  H  HCH2  0   0.273   3.0128  -3.1755   1.5610
 RNG  HD1  H  HCH2  0   0.284   0.0772   0.0411  -0.0251
 RNG  HD2  H  HCH2  0   0.273   1.4481   0.1175  -1.1129
 RNG  HC1  H  HCH2  0   0.261  -0.8882  -1.8363  -1.1431
 RNG  HC2  H  HCH2  0   0.261  -0.3252  -0.7855  -2.4244
 RNG  HB1  H  HCH2  0   0.283   0.3501  -2.9727  -3.0887
 RNG  HB2  H  HCH2  0   0.274   0.8480  -3.4300  -1.4711

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
 RNG  O   C    double  1.205  0.020  1.205
 RNG  C   CA   single  1.499  0.020  1.499
 RNG  C   H    single  0.930  0.020  1.080
 RNG  CA  CH   single  1.532  0.020  1.532
 RNG  CA  HA1  single  0.970  0.020  1.090
 RNG  CA  HA2  single  0.970  0.020  1.090
 RNG  CH  CG   single  1.530  0.020  1.530
 RNG  CH  N2   single  1.459  0.020  1.459
 RNG  CH  HH   single  0.970  0.020  1.090
 RNG  CG  CF   single  1.524  0.020  1.524
 RNG  CG  HG1  single  0.970  0.020  1.090
 RNG  CG  HG2  single  0.970  0.020  1.090
 RNG  CF  CE   single  1.522  0.020  1.522
 RNG  CF  HF1  single  0.970  0.020  1.090
 RNG  CF  HF2  single  0.970  0.020  1.090
 RNG  CE  N1   single  1.455  0.020  1.455
 RNG  CE  HE1  single  0.970  0.020  1.090
 RNG  CE  HE2  single  0.970  0.020  1.090
 RNG  N1  C1   single  1.364  0.020  1.364
 RNG  N1  N2   single  1.379  0.020  1.379
 RNG  C1  O1   double  1.218  0.020  1.218
 RNG  C1  CD   single  1.508  0.020  1.508
 RNG  CD  CC   single  1.537  0.020  1.537
 RNG  CD  HD1  single  0.970  0.020  1.090
 RNG  CD  HD2  single  0.970  0.020  1.090
 RNG  CC  CB   single  1.539  0.020  1.539
 RNG  CC  HC1  single  0.970  0.020  1.090
 RNG  CC  HC2  single  0.970  0.020  1.090
 RNG  CB  C2   single  1.508  0.020  1.508
 RNG  CB  HB1  single  0.970  0.020  1.090
 RNG  CB  HB2  single  0.970  0.020  1.090
 RNG  C2  O2   double  1.217  0.020  1.217
 RNG  C2  N2   single  1.366  0.020  1.366

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
 RNG  H    C   CA   114.48  3.000
 RNG  H    C   O    120.64  3.000
 RNG  CA   C   O    124.87  3.000
 RNG  HA2  CA  HA1  107.68  3.000
 RNG  HA2  CA  CH   113.13  3.000
 RNG  HA1  CA  CH   108.40  3.000
 RNG  HA2  CA  C    109.92  3.000
 RNG  HA1  CA  C    105.92  3.000
 RNG  CH   CA  C    111.45  3.000
 RNG  HH   CH  N2   106.53  3.000
 RNG  HH   CH  CG   109.01  3.000
 RNG  N2   CH  CG   108.71  3.000
 RNG  HH   CH  CA   108.43  3.000
 RNG  N2   CH  CA   110.31  3.000
 RNG  CG   CH  CA   113.59  3.000
 RNG  HG2  CG  HG1  106.48  3.000
 RNG  HG2  CG  CF   109.45  3.000
 RNG  HG1  CG  CF   110.68  3.000
 RNG  HG2  CG  CH   108.07  3.000
 RNG  HG1  CG  CH   110.12  3.000
 RNG  CF   CG  CH   111.87  3.000
 RNG  HF2  CF  HF1  106.84  3.000
 RNG  HF2  CF  CE   109.45  3.000
 RNG  HF1  CF  CE   109.28  3.000
 RNG  HF2  CF  CG   110.87  3.000
 RNG  HF1  CF  CG   110.10  3.000
 RNG  CE   CF  CG   110.23  3.000
 RNG  HE2  CE  HE1  107.92  3.000
 RNG  HE2  CE  N1   108.48  3.000
 RNG  HE1  CE  N1   108.50  3.000
 RNG  HE2  CE  CF   111.50  3.000
 RNG  HE1  CE  CF   110.61  3.000
 RNG  N1   CE  CF   109.76  3.000
 RNG  N2   N1  C1   121.22  3.000
 RNG  N2   N1  CE   114.42  3.000
 RNG  C1   N1  CE   124.26  3.000
 RNG  CD   C1  O1   123.39  3.000
 RNG  CD   C1  N1   114.99  3.000
 RNG  O1   C1  N1   121.43  3.000
 RNG  HD2  CD  HD1  106.91  3.000
 RNG  HD2  CD  CC   110.21  3.000
 RNG  HD1  CD  CC   109.83  3.000
 RNG  HD2  CD  C1   110.53  3.000
 RNG  HD1  CD  C1   108.23  3.000
 RNG  CC   CD  C1   111.02  3.000
 RNG  HC2  CC  HC1  106.74  3.000
 RNG  HC2  CC  CB   109.60  3.000
 RNG  HC1  CC  CB   108.21  3.000
 RNG  HC2  CC  CD   108.38  3.000
 RNG  HC1  CC  CD   109.63  3.000
 RNG  CB   CC  CD   114.03  3.000
 RNG  HB2  CB  HB1  107.02  3.000
 RNG  HB2  CB  C2   110.30  3.000
 RNG  HB1  CB  C2   108.14  3.000
 RNG  HB2  CB  CC   110.25  3.000
 RNG  HB1  CB  CC   109.68  3.000
 RNG  C2   CB  CC   111.33  3.000
 RNG  N2   C2  O2   121.43  3.000
 RNG  N2   C2  CB   114.85  3.000
 RNG  O2   C2  CB   123.56  3.000
 RNG  C2   N2  N1   121.05  3.000
 RNG  C2   N2  CH   123.90  3.000
 RNG  N1   N2  CH   114.88  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
 RNG  Var_01  CE  CF  CG  CH    52.18  30.0  1
 RNG  Var_02  N1  CE  CF  CG   -52.13  30.0  1
 RNG  Var_03  CH  CA  C   O   -136.79  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
 RNG  chir_01  CH  CA  CG  N2  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
 RNG  plan-1  CE  0.020
 RNG  plan-1  N1  0.020
 RNG  plan-1  C1  0.020
 RNG  plan-1  O1  0.020
 RNG  plan-1  CD  0.020
 RNG  plan-1  N2  0.020
 RNG  plan-2  CH  0.020
 RNG  plan-2  N1  0.020
 RNG  plan-2  CB  0.020
 RNG  plan-2  C2  0.020
 RNG  plan-2  O2  0.020
 RNG  plan-2  N2  0.020
 RNG  plan-3  O   0.020
 RNG  plan-3  C   0.020
 RNG  plan-3  CA  0.020
 RNG  plan-3  H   0.020

