# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:41:34 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: N-[(1S,2R,5R,6R)-2-amino-5,6-dihydroxy-4-(hydroxymethyl)cyclohex-3-en-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](N)C=C(CO)[C@@H](O)[C@@H]1O
#
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
 BEU  BEU  N-[(1S,2R,5R,6R)-2-amino-5,6-dihydroxy-4-(hydroxymethyl)cyclohex-3-en-1-yl]acetamide  ligand  31  15  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BEU
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
 BEU  C'    C  CH2   0  -0.184  -3.5610  -0.3241  -0.2486
 BEU  O1'   O  OH1   0  -0.666  -4.0519  -1.6195  -0.0232
 BEU  C1    C  C     0   0.013  -2.0831  -0.2601  -0.0014
 BEU  C2    C  C1    0  -0.290  -1.3770  -1.2733   0.4937
 BEU  C3    C  CH1   0  -0.113   0.1137  -1.2688   0.7129
 BEU  N3    N  NH2   0  -0.779   0.7663  -2.4940   0.2752
 BEU  C4    C  CH1   0  -0.106   0.7716  -0.0694   0.0282
 BEU  N4    N  NH1   0  -0.617   2.1260   0.1038   0.4839
 BEU  C4'   C  C     0   0.520   3.1976   0.1913  -0.3199
 BEU  O4'   O  O     0  -0.511   3.1410   0.0897  -1.5388
 BEU  CM4   C  CH3   0  -0.781   4.5092   0.4333   0.3866
 BEU  C5    C  CH1   0   0.064  -0.0598   1.1873   0.2641
 BEU  O5    O  OH1   0  -0.665   0.6380   2.2918  -0.2475
 BEU  C6    C  CH1   0  -0.048  -1.4195   1.0347  -0.4044
 BEU  O4    O  OH1   0  -0.673  -2.1963   2.1644  -0.0418
 BEU  H'C1  H  HCH2  0   0.207  -3.7511   0.0040  -1.2829
 BEU  H'C2  H  HCH2  0   0.219  -4.0593   0.4108   0.3963
 BEU  H1'   H  HOH1  0   0.460  -5.0110  -1.5855  -0.0738
 BEU  H2    H  H     0   0.246  -1.8774  -2.1968   0.7665
 BEU  H6    H  HCH1  0   0.239  -1.2648   1.0251  -1.4934
 BEU  H3    H  HCH1  0   0.241   0.2943  -1.1854   1.7927
 BEU  H3N1  H  HNH2  0   0.351   0.3968  -3.2771   0.8006
 BEU  H3N2  H  HNH2  0   0.338   0.5264  -2.6733  -0.6933
 BEU  H4    H  HCH1  0   0.255   0.8133  -0.2610  -1.0484
 BEU  HA    H  HNH1  0   0.394   2.2657   0.2159   1.4756
 BEU  H5    H  HCH1  0   0.205  -0.2270   1.2969   1.3491
 BEU  HM41  H  HCH3  0   0.246   4.4384   0.3925   1.4718
 BEU  HM42  H  HCH3  0   0.262   5.2411  -0.3040   0.0585
 BEU  HM43  H  HCH3  0   0.265   4.8914   1.4156   0.1058
 BEU  HB    H  HOH1  0   0.448   0.0800   3.0679  -0.1270
 BEU  HC    H  HOH1  0   0.463  -2.7150   2.4453  -0.7999

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
 BEU  C'   O1'   single  1.404  0.020  1.404
 BEU  C'   C1    single  1.500  0.020  1.500
 BEU  C'   H'C1  single  0.970  0.020  1.090
 BEU  C'   H'C2  single  0.970  0.020  1.090
 BEU  O1'  H1'   single  0.850  0.020  0.980
 BEU  C1   C2    double  1.331  0.020  1.331
 BEU  C1   C6    single  1.510  0.020  1.510
 BEU  C2   C3    single  1.507  0.020  1.507
 BEU  C2   H2    single  0.930  0.020  1.080
 BEU  C3   N3    single  1.455  0.020  1.455
 BEU  C3   C4    single  1.530  0.020  1.530
 BEU  C3   H3    single  0.970  0.020  1.090
 BEU  N3   H3N1  single  0.890  0.020  1.040
 BEU  N3   H3N2  single  0.890  0.020  1.040
 BEU  C4   N4    single  1.439  0.020  1.439
 BEU  C4   C5    single  1.525  0.020  1.525
 BEU  C4   H4    single  0.970  0.020  1.090
 BEU  N4   C4'   single  1.342  0.020  1.342
 BEU  N4   HA    single  0.860  0.020  1.020
 BEU  C4'  O4'   double  1.224  0.020  1.224
 BEU  C4'  CM4   single  1.509  0.020  1.509
 BEU  CM4  HM41  single  0.970  0.020  1.090
 BEU  CM4  HM42  single  0.970  0.020  1.090
 BEU  CM4  HM43  single  0.970  0.020  1.090
 BEU  C5   O5    single  1.403  0.020  1.403
 BEU  C5   C6    single  1.523  0.020  1.523
 BEU  C5   H5    single  0.970  0.020  1.090
 BEU  O5   HB    single  0.850  0.020  0.980
 BEU  C6   O4    single  1.418  0.020  1.418
 BEU  C6   H6    single  0.970  0.020  1.090
 BEU  O4   HC    single  0.850  0.020  0.980

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
 BEU  H'C2  C'   H'C1  105.90  3.000
 BEU  H'C2  C'   C1    108.79  3.000
 BEU  H'C1  C'   C1    108.19  3.000
 BEU  H'C2  C'   O1'   111.39  3.000
 BEU  H'C1  C'   O1'   111.43  3.000
 BEU  C1    C'   O1'   110.95  3.000
 BEU  H1'   O1'  C'    107.94  3.000
 BEU  C6    C1   C2    121.28  3.000
 BEU  C6    C1   C'    115.20  3.000
 BEU  C2    C1   C'    123.49  3.000
 BEU  H2    C2   C3    114.97  3.000
 BEU  H2    C2   C1    119.80  3.000
 BEU  C3    C2   C1    125.23  3.000
 BEU  H3    C3   C4    108.05  3.000
 BEU  H3    C3   N3    106.61  3.000
 BEU  C4    C3   N3    109.42  3.000
 BEU  H3    C3   C2    107.82  3.000
 BEU  C4    C3   C2    111.27  3.000
 BEU  N3    C3   C2    113.41  3.000
 BEU  H3N2  N3   H3N1  105.81  3.000
 BEU  H3N2  N3   C3    109.27  3.000
 BEU  H3N1  N3   C3    109.35  3.000
 BEU  H4    C4   C5    108.50  3.000
 BEU  H4    C4   N4    107.26  3.000
 BEU  C5    C4   N4    111.39  3.000
 BEU  H4    C4   C3    108.63  3.000
 BEU  C5    C4   C3    110.02  3.000
 BEU  N4    C4   C3    110.94  3.000
 BEU  HA    N4   C4'   118.12  3.000
 BEU  HA    N4   C4    117.08  3.000
 BEU  C4'   N4   C4    124.71  3.000
 BEU  CM4   C4'  O4'   121.29  3.000
 BEU  CM4   C4'  N4    115.08  3.000
 BEU  O4'   C4'  N4    123.62  3.000
 BEU  HM43  CM4  HM42  107.25  3.000
 BEU  HM43  CM4  HM41  108.26  3.000
 BEU  HM42  CM4  HM41  108.58  3.000
 BEU  HM43  CM4  C4'   109.18  3.000
 BEU  HM42  CM4  C4'   109.53  3.000
 BEU  HM41  CM4  C4'   113.84  3.000
 BEU  H5    C5   C6    107.84  3.000
 BEU  H5    C5   O5    110.85  3.000
 BEU  C6    C5   O5    111.28  3.000
 BEU  H5    C5   C4    108.46  3.000
 BEU  C6    C5   C4    109.65  3.000
 BEU  O5    C5   C4    108.73  3.000
 BEU  HB    O5   C5    107.48  3.000
 BEU  H6    C6   O4    109.70  3.000
 BEU  H6    C6   C5    108.05  3.000
 BEU  O4    C6   C5    107.28  3.000
 BEU  H6    C6   C1    108.58  3.000
 BEU  O4    C6   C1    111.98  3.000
 BEU  C5    C6   C1    111.18  3.000
 BEU  HC    O4   C6    109.08  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
 BEU  CONST_01  O4'   C4'  N4   C4     0.00   0.0  0
 BEU  CONST_02  CM4   C4'  N4   C4   180.00   0.0  0
 BEU  CONST_03  HA    N4   C4'  O4'  180.00   0.0  0
 BEU  Var_01    C6    C1   C2   C3     0.09  30.0  1
 BEU  Var_02    C2    C1   C'   O1'   -6.20  30.0  3
 BEU  Var_03    HM41  CM4  C4'  N4     6.69  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
 BEU  chir_01  C3  C2  N3  C4  negativ
 BEU  chir_02  C4  N4  C5  C3  positiv
 BEU  chir_03  C5  O5  C6  C4  negativ
 BEU  chir_04  C6  O4  C5  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
 BEU  plan-1  C4   0.020
 BEU  plan-1  N4   0.020
 BEU  plan-1  C4'  0.020
 BEU  plan-1  O4'  0.020
 BEU  plan-1  CM4  0.020
 BEU  plan-1  HA   0.020

