# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:54:07 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CC12CC3CC(CC(C3)C1)C2
#
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
 AXM  AXM  N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide  ligand  34  15  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AXM
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
 AXM  O28  O  O     0  -0.478   2.7653  -0.2669   1.5310
 AXM  C27  C  C     0   0.511   2.4758   0.4097   0.5581
 AXM  N29  N  NH1   0  -0.367   3.1918   0.3900  -0.5840
 AXM  O30  O  OH1   0  -0.545   4.3723  -0.2856  -0.6470
 AXM  C26  C  CH2   0  -0.555   1.2721   1.3204   0.4946
 AXM  C5   C  C     0  -0.095  -0.0712   0.6087   0.2575
 AXM  C4   C  C     0  -0.400  -0.4277  -0.3610   1.3932
 AXM  C3   C  CR16  0  -0.247  -1.7993  -0.9949   1.1426
 AXM  C9   C  C     0  -0.398  -1.1630   1.6880   0.1881
 AXM  C1   C  C     0  -0.247  -2.5362   1.0617  -0.0594
 AXM  C8   C  C     0  -0.419  -2.5069   0.3002  -1.3863
 AXM  C2   C  C     0  -0.417  -2.8679   0.0966   1.0795
 AXM  C6   C  C     0  -0.410  -0.0694  -0.1636  -1.0692
 AXM  C7   C  CR16  0  -0.243  -1.4412  -0.7946  -1.3217
 AXM  C10  C  CH2   0  -0.419  -1.7721  -1.7608  -0.1823
 AXM  H1   H  HNH1  0   0.413   3.0370   1.0474  -1.3337
 AXM  H2   H  HOH1  0   0.476   4.1678  -1.1534  -1.0183
 AXM  H3   H  HCH2  0   0.264   1.2279   1.8642   1.4427
 AXM  H4   H  HCH2  0   0.250   1.4065   2.0718  -0.2899
 AXM  H5   H  H     0   0.229   0.3276  -1.1466   1.4798
 AXM  H6   H  H     0   0.217  -0.4311   0.1765   2.3483
 AXM  H7   H  HCR6  0   0.222  -2.0249  -1.6866   1.9600
 AXM  H8   H  H     0   0.223  -1.1707   2.2621   1.1218
 AXM  H9   H  H     0   0.222  -0.9316   2.3980  -0.6141
 AXM  H10  H  H     0   0.223  -3.2897   1.8539  -0.1050
 AXM  H11  H  H     0   0.221  -3.4891  -0.1376  -1.5925
 AXM  H12  H  H     0   0.220  -2.2922   0.9906  -2.2087
 AXM  H13  H  H     0   0.220  -3.8563  -0.3482   0.9241
 AXM  H14  H  H     0   0.219  -2.9103   0.6376   2.0305
 AXM  H15  H  H     0   0.220   0.1870   0.5131  -1.8926
 AXM  H16  H  H     0   0.227   0.6938  -0.9488  -1.0549
 AXM  H17  H  HCR6  0   0.222  -1.4157  -1.3395  -2.2705
 AXM  H18  H  HCH2  0   0.220  -1.0277  -2.5630  -0.1393
 AXM  H19  H  HCH2  0   0.221  -2.7407  -2.2384  -0.3623

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
 AXM  C10  C7   single  1.530  0.020  1.530
 AXM  C10  C3   single  1.531  0.020  1.531
 AXM  C7   C8   single  1.529  0.020  1.529
 AXM  C7   C6   single  1.531  0.020  1.531
 AXM  C8   C1   single  1.530  0.020  1.530
 AXM  C6   C5   single  1.535  0.020  1.535
 AXM  C3   C2   single  1.529  0.020  1.529
 AXM  C3   C4   single  1.532  0.020  1.532
 AXM  C2   C1   single  1.529  0.020  1.529
 AXM  C1   C9   single  1.529  0.020  1.529
 AXM  C4   C5   single  1.535  0.020  1.535
 AXM  C5   C9   single  1.537  0.020  1.537
 AXM  C5   C26  single  1.539  0.020  1.539
 AXM  O28  C27  double  1.220  0.020  1.220
 AXM  C26  C27  single  1.511  0.020  1.511
 AXM  C27  N29  single  1.348  0.020  1.348
 AXM  N29  O30  single  1.362  0.020  1.362
 AXM  N29  H1   single  0.860  0.020  1.020
 AXM  O30  H2   single  0.850  0.020  0.980
 AXM  C26  H3   single  0.970  0.020  1.090
 AXM  C26  H4   single  0.970  0.020  1.090
 AXM  C4   H5   single  0.970  0.020  1.090
 AXM  C4   H6   single  0.970  0.020  1.090
 AXM  C3   H7   single  0.970  0.020  1.090
 AXM  C9   H8   single  0.970  0.020  1.090
 AXM  C9   H9   single  0.970  0.020  1.090
 AXM  C1   H10  single  0.970  0.020  1.090
 AXM  C8   H11  single  0.970  0.020  1.090
 AXM  C8   H12  single  0.970  0.020  1.090
 AXM  C2   H13  single  0.970  0.020  1.090
 AXM  C2   H14  single  0.970  0.020  1.090
 AXM  C6   H15  single  0.970  0.020  1.090
 AXM  C6   H16  single  0.970  0.020  1.090
 AXM  C7   H17  single  0.970  0.020  1.090
 AXM  C10  H18  single  0.970  0.020  1.090
 AXM  C10  H19  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
 AXM  C26  C27  N29  113.35  3.000
 AXM  N29  C27  O28  122.78  3.000
 AXM  C26  C27  O28  123.85  3.000
 AXM  H1   N29  O30  114.96  3.000
 AXM  H1   N29  C27  122.57  3.000
 AXM  O30  N29  C27  120.46  3.000
 AXM  H2   O30  N29  106.27  3.000
 AXM  H4   C26  H3   106.55  3.000
 AXM  H4   C26  C5   108.31  3.000
 AXM  H3   C26  C5   109.16  3.000
 AXM  H4   C26  C27  110.25  3.000
 AXM  H3   C26  C27  107.19  3.000
 AXM  C5   C26  C27  115.04  3.000
 AXM  C6   C5   C9   108.37  3.000
 AXM  C9   C5   C4   108.18  3.000
 AXM  C6   C5   C4   108.77  3.000
 AXM  C9   C5   C26  107.60  3.000
 AXM  C4   C5   C26  112.39  3.000
 AXM  C6   C5   C26  111.40  3.000
 AXM  H6   C4   H5   106.59  3.000
 AXM  H6   C4   C3   110.05  3.000
 AXM  H5   C4   C3   109.53  3.000
 AXM  H6   C4   C5   109.60  3.000
 AXM  H5   C4   C5   110.61  3.000
 AXM  C3   C4   C5   110.39  3.000
 AXM  H7   C3   C10  109.51  3.000
 AXM  H7   C3   C2   109.76  3.000
 AXM  C10  C3   C2   109.51  3.000
 AXM  H7   C3   C4   108.91  3.000
 AXM  C2   C3   C4   109.71  3.000
 AXM  C10  C3   C4   109.44  3.000
 AXM  H9   C9   H8   106.60  3.000
 AXM  H9   C9   C1   109.66  3.000
 AXM  H8   C9   C1   110.24  3.000
 AXM  H9   C9   C5   109.76  3.000
 AXM  H8   C9   C5   109.54  3.000
 AXM  C1   C9   C5   110.95  3.000
 AXM  H10  C1   C2   109.79  3.000
 AXM  H10  C1   C8   109.72  3.000
 AXM  C2   C1   C8   109.63  3.000
 AXM  H10  C1   C9   109.18  3.000
 AXM  C2   C1   C9   109.43  3.000
 AXM  C8   C1   C9   109.08  3.000
 AXM  H12  C8   H11  106.64  3.000
 AXM  H12  C8   C7   110.27  3.000
 AXM  H11  C8   C7   110.29  3.000
 AXM  H12  C8   C1   109.96  3.000
 AXM  H11  C8   C1   110.19  3.000
 AXM  C7   C8   C1   109.45  3.000
 AXM  H14  C2   H13  106.80  3.000
 AXM  H14  C2   C1   110.09  3.000
 AXM  H13  C2   C1   110.28  3.000
 AXM  H14  C2   C3   110.12  3.000
 AXM  H13  C2   C3   110.29  3.000
 AXM  C1   C2   C3   109.25  3.000
 AXM  H16  C6   H15  106.82  3.000
 AXM  H16  C6   C7   109.34  3.000
 AXM  H15  C6   C7   109.89  3.000
 AXM  H16  C6   C5   110.50  3.000
 AXM  H15  C6   C5   109.81  3.000
 AXM  C7   C6   C5   110.42  3.000
 AXM  H17  C7   C10  109.65  3.000
 AXM  H17  C7   C6   109.10  3.000
 AXM  C10  C7   C6   109.34  3.000
 AXM  H17  C7   C8   109.64  3.000
 AXM  C6   C7   C8   109.66  3.000
 AXM  C10  C7   C8   109.44  3.000
 AXM  H19  C10  H18  106.75  3.000
 AXM  H19  C10  C7   110.14  3.000
 AXM  H18  C10  C7   110.16  3.000
 AXM  H19  C10  C3   110.18  3.000
 AXM  H18  C10  C3   110.16  3.000
 AXM  C7   C10  C3   109.42  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
 AXM  CONST_01  O30  N29  C27  O28    0.00   0.0  0
 AXM  CONST_02  C26  C27  N29  O30  180.00   0.0  0
 AXM  CONST_03  H1   N29  C27  O28  180.00   0.0  0
 AXM  Var_01    C5   C26  C27  O28  -77.55  30.0  2

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
 AXM  chir_01  C5  C4   C9  C26  negativ
 AXM  chir_02  C3  C4   C2  C10  negativ
 AXM  chir_03  C1  C8   C2  C9   negativ
 AXM  chir_04  C7  C10  C8  C6   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
 AXM  plan-1  O28  0.020
 AXM  plan-1  C27  0.020
 AXM  plan-1  N29  0.020
 AXM  plan-1  O30  0.020
 AXM  plan-1  C26  0.020
 AXM  plan-1  H1   0.020

