# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:03:39 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (3R,4S)-3-(ethylamino)-4-(methylamino)cyclobutane-1,2-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN[C@@H]1[C@H](NC)C(=O)C1=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
 SQ  SQ  (3R,4S)-3-(ethylamino)-4-(methylamino)cyclobutane-1,2-dione  ligand  23  11  .  2022-07-22  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_SQ
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
 SQ  O1   O  O     0  -0.322   2.4836   0.4601   0.4736
 SQ  O2   O  O     0  -0.319   1.1475  -0.8068  -2.1840
 SQ  N1   N  NH1   0  -0.571  -0.5996   0.0354   1.4002
 SQ  N2   N  NH1   0  -0.583  -1.8065   0.1403  -1.2257
 SQ  C1   C  C     0  -0.229  -0.0083   0.9313   0.4374
 SQ  C2   C  C     0   0.299   1.3885   0.4713  -0.0049
 SQ  C3   C  C     0   0.279   0.7800  -0.0481  -1.3382
 SQ  C4   C  C     0  -0.193  -0.5164   0.7133  -1.0181
 SQ  C6   C  CH2   0  -0.277  -0.1276   0.2150   2.7650
 SQ  C7   C  CH3   0  -0.678  -0.8834  -0.6985   3.7120
 SQ  H1   H  HNH1  0   0.353  -0.4961  -0.9370   1.1262
 SQ  H3   H  HNH1  0   0.355  -1.8660  -0.7849  -0.8228
 SQ  H2   H  H     0   0.295  -0.0811   1.9583   0.7964
 SQ  H4   H  H     0   0.309  -0.4607   1.6789  -1.5380
 SQ  H10  H  HCH3  0   0.239  -3.2295  -0.3108  -2.6759
 SQ  H11  H  HCH3  0   0.229  -2.2720   1.1280  -3.0045
 SQ  H12  H  HCH3  0   0.211  -1.5779  -0.4728  -3.2788
 SQ  H5   H  HCH2  0   0.231  -0.3019   1.2585   3.0400
 SQ  H6   H  HCH2  0   0.210   0.9513   0.0409   2.8730
 SQ  H7   H  HCH3  0   0.235  -0.5638  -0.5287   4.7399
 SQ  H8   H  HCH3  0   0.227  -1.9572  -0.5197   3.6552
 SQ  H9   H  HCH3  0   0.227  -0.7006  -1.7494   3.4808
 SQ  C5   C  CH3   0  -0.526  -2.2265   0.1094  -2.6152

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
 SQ  O1  C2   double  1.195  0.020  1.195
 SQ  O2  C3   double  1.194  0.020  1.194
 SQ  N1  C1   single  1.442  0.020  1.442
 SQ  N1  C6   single  1.455  0.020  1.455
 SQ  N1  H1   single  0.890  0.020  1.040
 SQ  N2  C4   single  1.427  0.020  1.427
 SQ  N2  C5   single  1.452  0.020  1.452
 SQ  N2  H3   single  0.890  0.020  1.040
 SQ  C1  C2   single  1.536  0.020  1.536
 SQ  C1  C4   single  1.557  0.020  1.557
 SQ  C1  H2   single  0.970  0.020  1.090
 SQ  C2  C3   single  1.555  0.020  1.555
 SQ  C3  C4   single  1.537  0.020  1.537
 SQ  C4  H4   single  0.970  0.020  1.090
 SQ  C5  H10  single  0.970  0.020  1.090
 SQ  C5  H11  single  0.970  0.020  1.090
 SQ  C5  H12  single  0.970  0.020  1.090
 SQ  C6  C7   single  1.517  0.020  1.517
 SQ  C6  H5   single  0.970  0.020  1.090
 SQ  C6  H6   single  0.970  0.020  1.090
 SQ  C7  H7   single  0.970  0.020  1.090
 SQ  C7  H8   single  0.970  0.020  1.090
 SQ  C7  H9   single  0.970  0.020  1.090

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
 SQ  H1   N1  C6   109.76  3.000
 SQ  H1   N1  C1   111.90  3.000
 SQ  C6   N1  C1   114.61  3.000
 SQ  H3   N2  C5   110.18  3.000
 SQ  H3   N2  C4   111.28  3.000
 SQ  C5   N2  C4   114.16  3.000
 SQ  H2   C1  C4   114.71  3.000
 SQ  H2   C1  C2   115.96  3.000
 SQ  C4   C1  C2    89.18  3.000
 SQ  H2   C1  N1   109.75  3.000
 SQ  C4   C1  N1   113.79  3.000
 SQ  C2   C1  N1   112.28  3.000
 SQ  C3   C2  C1    89.49  3.000
 SQ  C3   C2  O1   134.33  3.000
 SQ  C1   C2  O1   136.14  3.000
 SQ  C4   C3  C2    89.20  3.000
 SQ  C4   C3  O2   136.20  3.000
 SQ  C2   C3  O2   134.36  3.000
 SQ  H4   C4  C3   107.11  3.000
 SQ  H4   C4  C1   107.63  3.000
 SQ  C3   C4  C1    89.36  3.000
 SQ  H4   C4  N2   109.28  3.000
 SQ  C3   C4  N2   122.23  3.000
 SQ  C1   C4  N2   119.16  3.000
 SQ  H6   C6  H5   106.45  3.000
 SQ  H6   C6  C7   109.43  3.000
 SQ  H5   C6  C7   109.77  3.000
 SQ  H6   C6  N1   113.03  3.000
 SQ  H5   C6  N1   107.58  3.000
 SQ  C7   C6  N1   110.46  3.000
 SQ  H9   C7  H8   108.17  3.000
 SQ  H9   C7  H7   107.50  3.000
 SQ  H8   C7  H7   108.21  3.000
 SQ  H9   C7  C6   111.35  3.000
 SQ  H8   C7  C6   111.06  3.000
 SQ  H7   C7  C6   110.42  3.000
 SQ  H12  C5  H11  107.74  3.000
 SQ  H12  C5  H10  107.84  3.000
 SQ  H11  C5  H10  107.56  3.000
 SQ  H12  C5  N2   114.82  3.000
 SQ  H11  C5  N2   109.49  3.000
 SQ  H10  C5  N2   109.14  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
 SQ  Var_01  C4   C3  C2  C1    12.65  30.0  1
 SQ  Var_02  C7   C6  N1  C1   175.72  30.0  3
 SQ  Var_03  H10  C5  N2  C4  -178.13  30.0  3
 SQ  Var_04  H7   C7  C6  N1  -177.24  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
 SQ  chir_01  C1  N1  C2  C4  negativ
 SQ  chir_02  C4  N2  C3  C1  positiv

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
 SQ  plan-1  O1  0.020
 SQ  plan-1  C1  0.020
 SQ  plan-1  C2  0.020
 SQ  plan-1  C3  0.020
 SQ  plan-2  O2  0.020
 SQ  plan-2  C2  0.020
 SQ  plan-2  C3  0.020
 SQ  plan-2  C4  0.020

