# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:57:50 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-[[[(4~{S})-2,2-dimethyloxan-4-yl]amino]methyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)C[C@H](CCO1)NCc2ccc(O)cc2
#
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
 B0J  B0J  4-[[[(4~{S})-2,2-dimethyloxan-4-yl]amino]methyl]phenol  ligand  38  17  .  2022-07-24  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_B0J
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
 B0J  N1   N  NH1   0  -0.594  -0.1498   0.1049   0.0548
 B0J  C4   C  CH1   0  -0.082  -1.5337  -0.1507  -0.3097
 B0J  C5   C  CH2   0  -0.468  -2.0487  -1.5452   0.0500
 B0J  C6   C  CH2   0  -0.184  -3.5324  -1.6607  -0.2564
 B0J  C7   C  CH2   0  -0.317   0.8225  -0.7088  -0.6495
 B0J  C8   C  CR6   0   0.066   2.2321  -0.3101  -0.2977
 B0J  C10  C  CR16  0  -0.324   3.9061   1.4026   0.0772
 B0J  C13  C  CR16  0  -0.302   3.2093  -1.2691  -0.0608
 B0J  C2   C  CT    0   0.201  -3.9213   0.6782   0.0857
 B0J  C3   C  CH2   0  -0.430  -2.4262   0.8875   0.3634
 B0J  O1   O  O2    0  -0.499  -4.2906  -0.6639   0.3921
 B0J  C9   C  CR16  0  -0.279   2.6055   1.0310  -0.2188
 B0J  C11  C  CR6   0   0.338   4.8757   0.4270   0.3050
 B0J  C12  C  CR16  0  -0.370   4.5199  -0.9155   0.2340
 B0J  O2   O  OH1   0  -0.636   6.1291   0.8369   0.5938
 B0J  C14  C  CH3   0  -0.680  -4.2757   1.0300  -1.3615
 B0J  H1   H  HNH1  0   0.335  -0.0376  -0.0318   1.0542
 B0J  H3   H  HCH1  0   0.222  -1.5982  -0.0292  -1.3984
 B0J  H4   H  HCH2  0   0.237  -1.5150  -2.3236  -0.5010
 B0J  H5   H  HCH2  0   0.217  -1.8727  -1.7266   1.1164
 B0J  H6   H  HCH2  0   0.197  -3.6849  -1.6334  -1.3438
 B0J  H7   H  HCH2  0   0.235  -3.9230  -2.6188   0.0920
 B0J  H8   H  HCH2  0   0.213   0.7104  -1.7886  -0.4759
 B0J  H9   H  HCH2  0   0.233   0.6584  -0.5619  -1.7232
 B0J  H10  H  HCR6  0   0.258   4.1761   2.4501   0.1350
 B0J  H11  H  HCR6  0   0.250   2.9497  -2.3207  -0.1028
 B0J  H12  H  HCH3  0   0.230  -4.5351   1.3132   2.0686
 B0J  H13  H  HCH3  0   0.225  -4.5142   2.6034   0.8665
 B0J  H14  H  HCH3  0   0.231  -5.8148   1.4134   0.8504
 B0J  H15  H  HCH2  0   0.221  -2.2619   0.8347   1.4468
 B0J  H16  H  HCH2  0   0.234  -2.1325   1.8920   0.0481
 B0J  H17  H  HCR6  0   0.245   1.8610   1.7997  -0.3833
 B0J  H18  H  HCR6  0   0.267   5.2588  -1.6886   0.4139
 B0J  H19  H  HOH1  0   0.472   6.7066   0.0771   0.7261
 B0J  H20  H  HCH3  0   0.233  -5.3390   0.8649  -1.5443
 B0J  H21  H  HCH3  0   0.231  -4.0634   2.0827  -1.5515
 B0J  H22  H  HCH3  0   0.233  -3.7188   0.4517  -2.0989
 B0J  C1   C  CH3   0  -0.663  -4.7456   1.5494   1.0241

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
 B0J  C10  C9   aromatic  1.385  0.020  1.385
 B0J  C10  C11  aromatic  1.394  0.020  1.394
 B0J  O2   C11  single    1.350  0.020  1.350
 B0J  C9   C8   aromatic  1.394  0.020  1.394
 B0J  C11  C12  aromatic  1.391  0.020  1.391
 B0J  C8   C7   single    1.507  0.020  1.507
 B0J  C8   C13  aromatic  1.390  0.020  1.390
 B0J  C12  C13  aromatic  1.389  0.020  1.389
 B0J  C7   N1   single    1.450  0.020  1.450
 B0J  N1   C4   single    1.454  0.020  1.454
 B0J  C4   C5   single    1.529  0.020  1.529
 B0J  C4   C3   single    1.526  0.020  1.526
 B0J  C5   C6   single    1.519  0.020  1.519
 B0J  C3   C2   single    1.535  0.020  1.535
 B0J  C6   O1   single    1.410  0.020  1.410
 B0J  C14  C2   single    1.531  0.020  1.531
 B0J  C2   O1   single    1.425  0.020  1.425
 B0J  C2   C1   single    1.523  0.020  1.523
 B0J  N1   H1   single    0.890  0.020  1.040
 B0J  C4   H3   single    0.970  0.020  1.090
 B0J  C5   H4   single    0.970  0.020  1.090
 B0J  C5   H5   single    0.970  0.020  1.090
 B0J  C6   H6   single    0.970  0.020  1.090
 B0J  C6   H7   single    0.970  0.020  1.090
 B0J  C7   H8   single    0.970  0.020  1.090
 B0J  C7   H9   single    0.970  0.020  1.090
 B0J  C10  H10  single    0.930  0.020  1.080
 B0J  C13  H11  single    0.930  0.020  1.080
 B0J  C1   H12  single    0.970  0.020  1.090
 B0J  C1   H13  single    0.970  0.020  1.090
 B0J  C1   H14  single    0.970  0.020  1.090
 B0J  C3   H15  single    0.970  0.020  1.090
 B0J  C3   H16  single    0.970  0.020  1.090
 B0J  C9   H17  single    0.930  0.020  1.080
 B0J  C12  H18  single    0.930  0.020  1.080
 B0J  O2   H19  single    0.850  0.020  0.980
 B0J  C14  H20  single    0.970  0.020  1.090
 B0J  C14  H21  single    0.970  0.020  1.090
 B0J  C14  H22  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
 B0J  H1   N1   C7   109.18  3.000
 B0J  H1   N1   C4   109.18  3.000
 B0J  C7   N1   C4   114.70  3.000
 B0J  H3   C4   C3   109.15  3.000
 B0J  H3   C4   C5   108.33  3.000
 B0J  C3   C4   C5   108.65  3.000
 B0J  H3   C4   N1   106.57  3.000
 B0J  C3   C4   N1   109.07  3.000
 B0J  C5   C4   N1   114.95  3.000
 B0J  H5   C5   H4   107.11  3.000
 B0J  H5   C5   C6   109.90  3.000
 B0J  H4   C5   C6   108.73  3.000
 B0J  H5   C5   C4   109.01  3.000
 B0J  H4   C5   C4   111.50  3.000
 B0J  C6   C5   C4   110.53  3.000
 B0J  H7   C6   H6   106.74  3.000
 B0J  H7   C6   O1   106.34  3.000
 B0J  H6   C6   O1   111.29  3.000
 B0J  H7   C6   C5   110.59  3.000
 B0J  H6   C6   C5   109.47  3.000
 B0J  O1   C6   C5   112.24  3.000
 B0J  H9   C7   H8   105.73  3.000
 B0J  H9   C7   C8   109.47  3.000
 B0J  H8   C7   C8   108.57  3.000
 B0J  H9   C7   N1   107.47  3.000
 B0J  H8   C7   N1   113.95  3.000
 B0J  C8   C7   N1   111.43  3.000
 B0J  C9   C8   C13  117.76  3.000
 B0J  C13  C8   C7   121.01  3.000
 B0J  C9   C8   C7   121.22  3.000
 B0J  H10  C10  C11  119.64  3.000
 B0J  H10  C10  C9   120.33  3.000
 B0J  C11  C10  C9   120.03  3.000
 B0J  H11  C13  C12  118.76  3.000
 B0J  H11  C13  C8   119.64  3.000
 B0J  C12  C13  C8   121.60  3.000
 B0J  C14  C2   O1   111.08  3.000
 B0J  O1   C2   C3   109.99  3.000
 B0J  C14  C2   C3   111.42  3.000
 B0J  O1   C2   C1   105.42  3.000
 B0J  C14  C2   C1   109.01  3.000
 B0J  C3   C2   C1   109.74  3.000
 B0J  H16  C3   H15  106.79  3.000
 B0J  H16  C3   C2   109.56  3.000
 B0J  H15  C3   C2   108.54  3.000
 B0J  H16  C3   C4   109.94  3.000
 B0J  H15  C3   C4   108.39  3.000
 B0J  C2   C3   C4   113.40  3.000
 B0J  C2   O1   C6   115.30  3.000
 B0J  H17  C9   C10  119.20  3.000
 B0J  H17  C9   C8   119.35  3.000
 B0J  C10  C9   C8   121.45  3.000
 B0J  O2   C11  C12  122.79  3.000
 B0J  C12  C11  C10  119.29  3.000
 B0J  O2   C11  C10  117.92  3.000
 B0J  H18  C12  C11  120.36  3.000
 B0J  H18  C12  C13  119.77  3.000
 B0J  C11  C12  C13  119.87  3.000
 B0J  H19  O2   C11  110.27  3.000
 B0J  H22  C14  H21  107.14  3.000
 B0J  H22  C14  H20  107.71  3.000
 B0J  H21  C14  H20  107.85  3.000
 B0J  H22  C14  C2   113.53  3.000
 B0J  H21  C14  C2   109.97  3.000
 B0J  H20  C14  C2   110.43  3.000
 B0J  H14  C1   H13  107.77  3.000
 B0J  H14  C1   H12  108.32  3.000
 B0J  H13  C1   H12  107.85  3.000
 B0J  H14  C1   C2   111.15  3.000
 B0J  H13  C1   C2   110.43  3.000
 B0J  H12  C1   C2   111.19  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
 B0J  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 B0J  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 B0J  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 B0J  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 B0J  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 B0J  CONST_06  C12  C13  C8   C9     0.00   0.0  0
 B0J  CONST_07  C10  C9   C8   C7   180.00   0.0  0
 B0J  CONST_08  C12  C13  C8   C7   180.00   0.0  0
 B0J  CONST_09  O2   C11  C12  C13  180.00   0.0  0
 B0J  CONST_10  O2   C11  C10  C9   180.00   0.0  0
 B0J  CONST_11  H10  C10  C9   C8   180.00   0.0  0
 B0J  CONST_12  H18  C12  C13  C8   180.00   0.0  0
 B0J  CONST_13  H17  C9   C8   C13  180.00   0.0  0
 B0J  CONST_14  H11  C13  C8   C9   180.00   0.0  0
 B0J  Var_01    O1   C6   C5   C4   -55.74  30.0  1
 B0J  Var_02    O1   C2   C3   C4    52.07  30.0  1
 B0J  Var_03    C3   C2   O1   C6   -54.77  30.0  1
 B0J  Var_04    C9   C8   C7   N1   -43.55  30.0  3
 B0J  Var_05    C8   C7   N1   C4   175.50  30.0  1
 B0J  Var_06    H20  C14  C2   C3   179.36  30.0  3
 B0J  Var_07    H12  C1   C2   C3   -58.87  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
 B0J  chir_01  C4  N1  C5  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
 B0J  plan-1  C7   0.020
 B0J  plan-1  C8   0.020
 B0J  plan-1  C10  0.020
 B0J  plan-1  C13  0.020
 B0J  plan-1  C9   0.020
 B0J  plan-1  C11  0.020
 B0J  plan-1  C12  0.020
 B0J  plan-1  O2   0.020
 B0J  plan-1  H10  0.020
 B0J  plan-1  H11  0.020
 B0J  plan-1  H17  0.020
 B0J  plan-1  H18  0.020

