# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 11:23:40 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: N~5~-carbamoyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=O)C(O)=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
 CIR  CIR  N~5~-carbamoyl-L-ornithine  L-peptide  24  12  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CIR
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
 CIR  C1    C  C      0   0.386   3.5282   0.3250  -0.0890
 CIR  O1    O  O      0  -0.539   4.2608  -0.0199   0.8586
 CIR  O2    O  OC    -1  -0.776   3.6820   1.3260  -0.8192
 CIR  C2    C  CH1    0  -0.184   2.2697  -0.5281  -0.3647
 CIR  N2    N  NH2    0  -0.805   2.4204  -1.8625   0.1943
 CIR  C3    C  CH2    0  -0.434   1.0346   0.2386   0.1379
 CIR  C4    C  CH2    0  -0.487  -0.2831  -0.3775  -0.3138
 CIR  C5    C  CH2    0  -0.202  -1.4881   0.4015   0.1896
 CIR  N6    N  NH1    0  -0.668  -2.7105  -0.2147  -0.2784
 CIR  C7    C  C      0   0.653  -3.9315   0.1988   0.1357
 CIR  O7    O  O      0  -0.641  -4.0775   1.0506   1.0077
 CIR  N8    N  NH2    0  -0.737  -4.9903  -0.3781  -0.5087
 CIR  H2    H  HCH1   0   0.276   2.1691  -0.6201  -1.4536
 CIR  HN21  H  HNH2   0   0.315   2.7788  -1.7692   1.1366
 CIR  HN22  H  HNH2   0   0.352   1.5218  -2.3222   0.2704
 CIR  H31   H  HCH2   0   0.201   1.0669   0.2892   1.2324
 CIR  H32   H  HCH2   0   0.257   1.0839   1.2689  -0.2250
 CIR  H41   H  HCH2   0   0.208  -0.3021  -0.4123  -1.4087
 CIR  H42   H  HCH2   0   0.216  -0.3695  -1.4122   0.0324
 CIR  H51   H  HCH2   0   0.238  -1.4818   0.4156   1.2817
 CIR  H52   H  HCH2   0   0.174  -1.4147   1.4439  -0.1408
 CIR  HN6   H  HNH1   0   0.378  -2.6456  -0.7968  -1.0978
 CIR  HN81  H  HNH2   0   0.411  -4.8582  -1.2553  -0.9856
 CIR  HN82  H  HNH2   0   0.408  -5.8829  -0.2920  -0.0516

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
 CIR  C1  O1    deloc   1.246  0.020  1.246
 CIR  C1  O2    deloc   1.249  0.020  1.249
 CIR  C1  C2    single  1.545  0.020  1.545
 CIR  C2  N2    single  1.455  0.020  1.455
 CIR  C2  C3    single  1.538  0.020  1.538
 CIR  C2  H2    single  0.970  0.020  1.090
 CIR  N2  HN21  single  0.890  0.020  1.040
 CIR  N2  HN22  single  0.890  0.020  1.040
 CIR  C3  C4    single  1.523  0.020  1.523
 CIR  C3  H31   single  0.970  0.020  1.090
 CIR  C3  H32   single  0.970  0.020  1.090
 CIR  C4  C5    single  1.521  0.020  1.521
 CIR  C4  H41   single  0.970  0.020  1.090
 CIR  C4  H42   single  0.970  0.020  1.090
 CIR  C5  N6    single  1.447  0.020  1.447
 CIR  C5  H51   single  0.970  0.020  1.090
 CIR  C5  H52   single  0.970  0.020  1.090
 CIR  N6  C7    single  1.354  0.020  1.354
 CIR  N6  HN6   single  0.860  0.020  1.020
 CIR  C7  O7    double  1.228  0.020  1.228
 CIR  C7  N8    single  1.367  0.020  1.367
 CIR  N8  HN81  single  0.890  0.020  1.040
 CIR  N8  HN82  single  0.890  0.020  1.040

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
 CIR  C2    C1  O2    116.01  3.000
 CIR  C2    C1  O1    117.49  3.000
 CIR  O2    C1  O1    126.45  3.000
 CIR  H2    C2  C3    107.00  3.000
 CIR  H2    C2  N2    108.30  3.000
 CIR  C3    C2  N2    114.51  3.000
 CIR  H2    C2  C1    107.34  3.000
 CIR  C3    C2  C1    108.69  3.000
 CIR  N2    C2  C1    110.70  3.000
 CIR  HN22  N2  HN21  106.63  3.000
 CIR  HN22  N2  C2    110.70  3.000
 CIR  HN21  N2  C2    108.05  3.000
 CIR  H32   C3  H31   106.65  3.000
 CIR  H32   C3  C4    108.77  3.000
 CIR  H31   C3  C4    109.90  3.000
 CIR  H32   C3  C2    108.97  3.000
 CIR  H31   C3  C2    108.99  3.000
 CIR  C4    C3  C2    113.34  3.000
 CIR  H42   C4  H41   106.55  3.000
 CIR  H42   C4  C5    108.48  3.000
 CIR  H41   C4  C5    109.47  3.000
 CIR  H42   C4  C3    110.91  3.000
 CIR  H41   C4  C3    108.92  3.000
 CIR  C5    C4  C3    112.34  3.000
 CIR  H52   C5  H51   106.78  3.000
 CIR  H52   C5  N6    111.36  3.000
 CIR  H51   C5  N6    109.50  3.000
 CIR  H52   C5  C4    109.54  3.000
 CIR  H51   C5  C4    109.46  3.000
 CIR  N6    C5  C4    110.14  3.000
 CIR  HN6   N6  C7    118.90  3.000
 CIR  HN6   N6  C5    117.06  3.000
 CIR  C7    N6  C5    122.21  3.000
 CIR  N8    C7  O7    122.37  3.000
 CIR  N8    C7  N6    115.18  3.000
 CIR  O7    C7  N6    122.44  3.000
 CIR  HN82  N8  HN81  113.95  3.000
 CIR  HN82  N8  C7    115.89  3.000
 CIR  HN81  N8  C7    119.28  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
 CIR  CONST_01  O7   C7  N6  C5     0.00   0.0  0
 CIR  CONST_02  N8   C7  N6  C5   180.00   0.0  0
 CIR  CONST_03  HN6  N6  C7  O7   180.00   0.0  0
 CIR  Var_01    C5   C4  C3  C2  -179.73  30.0  3
 CIR  Var_02    N6   C5  C4  C3   179.36  30.0  3
 CIR  Var_03    C7   N6  C5  C4   173.19  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
 CIR  chir_01  C2  C1  N2  C3  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
 CIR  plan-1  C5    0.020
 CIR  plan-1  N6    0.020
 CIR  plan-1  C7    0.020
 CIR  plan-1  O7    0.020
 CIR  plan-1  N8    0.020
 CIR  plan-1  HN6   0.020
 CIR  plan-1  HN81  0.020
 CIR  plan-1  HN82  0.020
 CIR  plan-2  C1    0.020
 CIR  plan-2  O1    0.020
 CIR  plan-2  O2    0.020
 CIR  plan-2  C2    0.020

