# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 16:39:36 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl hydrogen (R)-phenylphosphonite
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H]2CC[C@H]1CC(C2)O[P](O)(=O)c3ccccc3
#
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
 XOP  XOP  '(3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl hydrogen (R)-phenylphosphonite'  ligand  39  19  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XOP
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
 XOP  C1    C  CR6   0  -0.243  -2.4716   0.0793   0.0012
 XOP  C2    C  CR16  0  -0.270  -2.3897  -0.8563  -1.0305
 XOP  C3    C  CR16  0  -0.235  -3.3996  -1.7911  -1.1988
 XOP  C4    C  CR16  0  -0.251  -4.4939  -1.7968  -0.3425
 XOP  C5    C  CR16  0  -0.234  -4.5765  -0.8698   0.6874
 XOP  C6    C  CR16  0  -0.277  -3.5672   0.0663   0.8617
 XOP  C7    C  CH1   0  -0.014   1.3980   1.1899  -0.2495
 XOP  C8    C  CH2   0  -0.424   2.1442   1.0148   1.0704
 XOP  C9    C  CR15  0  -0.131   2.8697  -0.3257   1.1753
 XOP  N     N  NR5   0  -0.401   3.7879  -0.4163   0.0397
 XOP  O1    O  O     0  -0.702  -1.2390   2.0050   1.5616
 XOP  O2    O  O2    0  -0.596   0.0978   0.5533  -0.1769
 XOP  O3    O  OH1   0  -0.745  -1.4466   2.4642  -0.9014
 XOP  P     P  P     0   1.391  -1.2230   1.3445   0.2351
 XOP  C10   C  CH2   0  -0.461   1.9296  -1.5434   1.0275
 XOP  C11   C  CH2   0  -0.464   1.9201  -1.8107  -0.4912
 XOP  C12   C  CR15  0  -0.132   2.8677  -0.7269  -1.0549
 XOP  C13   C  CH2   0  -0.421   2.1499   0.5709  -1.4231
 XOP  C14   C  CH3   0  -0.527   4.8219  -1.4163   0.2162
 XOP  H2    H  HCR6  0   0.269  -1.5397  -0.8675  -1.7007
 XOP  H3    H  HCR6  0   0.268  -3.3316  -2.5163  -1.9987
 XOP  H4    H  HCR6  0   0.269  -5.2813  -2.5266  -0.4779
 XOP  H5    H  HCR6  0   0.266  -5.4255  -0.8767   1.3578
 XOP  H6    H  HCR6  0   0.271  -3.6338   0.7820   1.6707
 XOP  H7    H  HCH1  0   0.254   1.2531   2.2563  -0.4445
 XOP  H8    H  HCH2  0   0.238   2.8915   1.8097   1.1399
 XOP  H8A   H  HCH2  0   0.246   1.4573   1.1564   1.9074
 XOP  H9    H  HCR5  0   0.237   3.4287  -0.3476   2.1138
 XOP  HO3   H  HOH1  0   0.487  -1.4718   2.1430  -1.8120
 XOP  H10   H  HCH2  0   0.235   2.3361  -2.3996   1.5685
 XOP  H10A  H  HCH2  0   0.239   0.9370  -1.3591   1.4366
 XOP  H11   H  HCH2  0   0.235   2.3064  -2.8065  -0.7135
 XOP  H11A  H  HCH2  0   0.241   0.9235  -1.7577  -0.9274
 XOP  H12   H  HCR5  0   0.237   3.4240  -1.0780  -1.9272
 XOP  H13   H  HCH2  0   0.243   1.4633   0.4182  -2.2589
 XOP  H13A  H  HCH2  0   0.239   2.9028   1.2873  -1.7597
 XOP  H14   H  HCH3  0   0.199   4.4570  -2.4363   0.4003
 XOP  H14A  H  HCH3  0   0.232   5.4505  -1.4491  -0.6747
 XOP  H14B  H  HCH3  0   0.231   5.4592  -1.1398   1.0576

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
 XOP  C2   C1    aromatic  1.395  0.020  1.395
 XOP  C1   C6    aromatic  1.393  0.020  1.393
 XOP  C1   P     single    1.793  0.020  1.793
 XOP  C3   C2    aromatic  1.386  0.020  1.386
 XOP  C2   H2    single    0.930  0.020  1.080
 XOP  C3   C4    aromatic  1.390  0.020  1.390
 XOP  C3   H3    single    0.930  0.020  1.080
 XOP  C4   C5    aromatic  1.388  0.020  1.388
 XOP  C4   H4    single    0.930  0.020  1.080
 XOP  C5   C6    aromatic  1.388  0.020  1.388
 XOP  C5   H5    single    0.930  0.020  1.080
 XOP  C6   H6    single    0.930  0.020  1.080
 XOP  C13  C7    single    1.525  0.020  1.525
 XOP  O2   C7    single    1.450  0.020  1.450
 XOP  C8   C7    single    1.526  0.020  1.526
 XOP  C7   H7    single    0.970  0.020  1.090
 XOP  C9   C8    single    1.528  0.020  1.528
 XOP  C8   H8    single    0.970  0.020  1.090
 XOP  C8   H8A   single    0.970  0.020  1.090
 XOP  C10  C9    single    1.546  0.020  1.546
 XOP  N    C9    single    1.463  0.020  1.463
 XOP  C9   H9    single    0.970  0.020  1.090
 XOP  C14  N     single    1.449  0.020  1.449
 XOP  C12  N     single    1.463  0.020  1.463
 XOP  P    O1    double    1.482  0.020  1.482
 XOP  O3   HO3   single    0.850  0.020  0.980
 XOP  O2   P     single    1.594  0.020  1.594
 XOP  O3   P     single    1.611  0.020  1.611
 XOP  C11  C10   single    1.542  0.020  1.542
 XOP  C10  H10   single    0.970  0.020  1.090
 XOP  C10  H10A  single    0.970  0.020  1.090
 XOP  C11  C12   single    1.546  0.020  1.546
 XOP  C11  H11   single    0.970  0.020  1.090
 XOP  C11  H11A  single    0.970  0.020  1.090
 XOP  C12  C13   single    1.528  0.020  1.528
 XOP  C12  H12   single    0.970  0.020  1.090
 XOP  C13  H13   single    0.970  0.020  1.090
 XOP  C13  H13A  single    0.970  0.020  1.090
 XOP  C14  H14   single    0.970  0.020  1.090
 XOP  C14  H14A  single    0.970  0.020  1.090
 XOP  C14  H14B  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
 XOP  P     C1   C6    118.27  3.000
 XOP  P     C1   C2    121.92  3.000
 XOP  C6    C1   C2    119.78  3.000
 XOP  H2    C2   C3    119.33  3.000
 XOP  H2    C2   C1    120.73  3.000
 XOP  C3    C2   C1    119.94  3.000
 XOP  H3    C3   C4    120.16  3.000
 XOP  H3    C3   C2    119.73  3.000
 XOP  C4    C3   C2    120.11  3.000
 XOP  H4    C4   C5    119.99  3.000
 XOP  H4    C4   C3    119.91  3.000
 XOP  C5    C4   C3    120.09  3.000
 XOP  H5    C5   C6    119.82  3.000
 XOP  H5    C5   C4    120.15  3.000
 XOP  C6    C5   C4    120.03  3.000
 XOP  H6    C6   C5    119.69  3.000
 XOP  H6    C6   C1    120.26  3.000
 XOP  C5    C6   C1    120.05  3.000
 XOP  H7    C7   C13   108.90  3.000
 XOP  H7    C7   O2    108.56  3.000
 XOP  C13   C7   O2    107.61  3.000
 XOP  H7    C7   C8    109.32  3.000
 XOP  O2    C7   C8    110.17  3.000
 XOP  C13   C7   C8    112.21  3.000
 XOP  H8A   C8   H8    106.68  3.000
 XOP  H8A   C8   C9    111.09  3.000
 XOP  H8    C8   C9    108.00  3.000
 XOP  H8A   C8   C7    109.90  3.000
 XOP  H8    C8   C7    107.80  3.000
 XOP  C9    C8   C7    113.09  3.000
 XOP  H9    C9   C10   112.18  3.000
 XOP  H9    C9   N     110.15  3.000
 XOP  C10   C9   N     104.99  3.000
 XOP  H9    C9   C8    108.63  3.000
 XOP  N     C9   C8    107.40  3.000
 XOP  C10   C9   C8    113.32  3.000
 XOP  C14   N    C12   113.16  3.000
 XOP  C12   N    C9    101.49  3.000
 XOP  C14   N    C9    113.33  3.000
 XOP  P     O2   C7    122.57  3.000
 XOP  HO3   O3   P     115.94  3.000
 XOP  O3    P    O2    106.12  3.000
 XOP  O3    P    O1    108.67  3.000
 XOP  O2    P    O1    117.48  3.000
 XOP  O3    P    C1    107.57  3.000
 XOP  O2    P    C1    101.14  3.000
 XOP  O1    P    C1    115.08  3.000
 XOP  H10A  C10  H10   106.62  3.000
 XOP  H10A  C10  C11   113.17  3.000
 XOP  H10   C10  C11   110.77  3.000
 XOP  H10A  C10  C9    112.65  3.000
 XOP  H10   C10  C9    110.13  3.000
 XOP  C11   C10  C9    103.56  3.000
 XOP  H11A  C11  H11   106.67  3.000
 XOP  H11A  C11  C12   112.38  3.000
 XOP  H11   C11  C12   110.40  3.000
 XOP  H11A  C11  C10   113.05  3.000
 XOP  H11   C11  C10   110.90  3.000
 XOP  C12   C11  C10   103.52  3.000
 XOP  H12   C12  C13   108.65  3.000
 XOP  H12   C12  C11   112.20  3.000
 XOP  C13   C12  C11   113.28  3.000
 XOP  H12   C12  N     110.20  3.000
 XOP  C13   C12  N     107.18  3.000
 XOP  C11   C12  N     105.16  3.000
 XOP  H13A  C13  H13   106.80  3.000
 XOP  H13A  C13  C12   107.90  3.000
 XOP  H13   C13  C12   111.16  3.000
 XOP  H13A  C13  C7    108.10  3.000
 XOP  H13   C13  C7    109.62  3.000
 XOP  C12   C13  C7    113.01  3.000
 XOP  H14B  C14  H14A  107.51  3.000
 XOP  H14B  C14  H14   107.46  3.000
 XOP  H14A  C14  H14   107.47  3.000
 XOP  H14B  C14  N     109.62  3.000
 XOP  H14A  C14  N     109.42  3.000
 XOP  H14   C14  N     115.09  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
 XOP  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 XOP  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 XOP  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 XOP  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 XOP  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 XOP  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 XOP  CONST_07  P    C1   C2   C3   180.00   0.0  0
 XOP  CONST_08  P    C1   C6   C5   180.00   0.0  0
 XOP  CONST_09  H3   C3   C2   C1   180.00   0.0  0
 XOP  CONST_10  H5   C5   C6   C1   180.00   0.0  0
 XOP  CONST_11  H6   C6   C1   C2   180.00   0.0  0
 XOP  CONST_12  H4   C4   C3   C2   180.00   0.0  0
 XOP  CONST_13  H2   C2   C3   C4   180.00   0.0  0
 XOP  Var_01    C12  C11  C10  C9     0.56  30.0  3
 XOP  Var_02    O1   P    C1   C2  -163.56  30.0  2
 XOP  Var_03    H14  C14  N    C9    57.34  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
 XOP  chir_01  C7   C13  O2   C8   negativ
 XOP  chir_02  C9   N    C10  C8   positiv
 XOP  chir_04  C12  N    C11  C13  negativ
 XOP  chir_05  P    O1   O2   O3   both

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
 XOP  plan-1  C1  0.020
 XOP  plan-1  C2  0.020
 XOP  plan-1  C3  0.020
 XOP  plan-1  C4  0.020
 XOP  plan-1  C5  0.020
 XOP  plan-1  C6  0.020
 XOP  plan-1  P   0.020
 XOP  plan-1  H2  0.020
 XOP  plan-1  H3  0.020
 XOP  plan-1  H4  0.020
 XOP  plan-1  H5  0.020
 XOP  plan-1  H6  0.020

