# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:50:22 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-hydroxy-1-[(2R)-4-{3-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yloxy]phenyl}but-3-yn-2-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C#Cc1cccc(OC23CC4CC(CC(C4)C2)C3)c1)N(O)C(N)=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
 H10  H10  1-hydroxy-1-[(2R)-4-{3-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yloxy]phenyl}but-3-yn-2-yl]urea  ligand  52  26  .  2022-07-25  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_H10
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
 H10  C1    C  CT    0   0.243   3.3628   0.2548   0.2077
 H10  O2    O  O2    0  -0.524   2.0235   0.6246   0.5848
 H10  C3    C  CR6   0   0.400   0.9919  -0.2270   0.7395
 H10  C4    C  CR16  0  -0.408  -0.2697   0.3394   0.5512
 H10  C5    C  CR6   0  -0.105  -1.4280  -0.4142   0.7264
 H10  C6    C  CSP   0   0.138  -2.7061   0.1932   0.5429
 H10  C7    C  CSP   0   0.113  -3.7882   0.7025   0.3969
 H10  C8    C  CH1   0  -0.271  -5.1014   1.3346   0.2383
 H10  N9    N  NT    0  -0.248  -6.1336   0.3882  -0.1845
 H10  C10   C  C     0   0.679  -5.9489  -0.3651  -1.3367
 H10  O11   O  O     0  -0.517  -5.2033   0.0311  -2.2204
 H10  N12   N  NH2   0  -0.828  -6.6595  -1.5029  -1.4138
 H10  O13   O  OH1   0  -0.558  -6.6658  -0.3196   0.8794
 H10  C14   C  CH3   0  -0.664  -5.0348   2.5843  -0.6368
 H10  C15   C  CR16  0  -0.322  -1.3331  -1.7642   1.0769
 H10  C16   C  CR16  0  -0.239  -0.0810  -2.3220   1.2585
 H10  C17   C  CR16  0  -0.365   1.0783  -1.5718   1.1030
 H10  C18   C  CH2   0  -0.466   3.4011  -0.7426  -0.9515
 H10  C19   C  CH1   0  -0.254   4.8589  -0.9785  -1.3669
 H10  C20   C  CH2   0  -0.419   5.4821   0.3387  -1.8306
 H10  C21   C  CH1   0  -0.259   5.4431   1.3472  -0.6822
 H10  C22   C  CH2   0  -0.421   6.2400   0.8023   0.5040
 H10  C23   C  CH1   0  -0.254   5.6171  -0.5140   0.9697
 H10  C24   C  CH2   0  -0.421   5.6423  -1.5300  -0.1741
 H10  C25   C  CH2   0  -0.458   4.1664  -0.2686   1.4011
 H10  C26   C  CH2   0  -0.442   3.9893   1.5723  -0.2598
 H10  H4    H  HCR6  0   0.261  -0.3441   1.3825   0.2707
 H10  H8    H  HCH1  0   0.295  -5.4299   1.6650   1.2267
 H10  HN12  H  HNH2  0   0.404  -7.2979  -1.7961  -0.6968
 H10  HN1A  H  HNH2  0   0.404  -6.6649  -2.0025  -2.2857
 H10  HO13  H  HOH1  0   0.480  -7.5108   0.1068   1.0705
 H10  H14   H  HCH3  0   0.244  -6.0348   2.9997  -0.7592
 H10  H14A  H  HCH3  0   0.240  -4.4164   3.3329  -0.1430
 H10  H14B  H  HCH3  0   0.248  -4.6143   2.3782  -1.6157
 H10  H15   H  HCR6  0   0.254  -2.2275  -2.3576   1.2076
 H10  H16   H  HCR6  0   0.265   0.0058  -3.3646   1.5351
 H10  H17   H  HCR6  0   0.274   2.0273  -2.0533   1.2827
 H10  H18   H  HCH2  0   0.246   2.9508  -1.6986  -0.6766
 H10  H18A  H  HCH2  0   0.240   2.8243  -0.3496  -1.7956
 H10  H19   H  HCH1  0   0.234   4.8754  -1.7025  -2.1860
 H10  H20   H  HCH2  0   0.227   6.5137   0.1750  -2.1576
 H10  H20A  H  HCH2  0   0.226   4.9340   0.7265  -2.6949
 H10  H21   H  HCH1  0   0.233   5.8685   2.3005  -1.0078
 H10  H22   H  HCH2  0   0.227   7.2843   0.6476   0.2162
 H10  H22A  H  HCH2  0   0.226   6.2421   1.5270   1.3243
 H10  H23   H  HCH1  0   0.233   6.1771  -0.9055   1.8235
 H10  H24   H  HCH2  0   0.226   5.2085  -2.4804   0.1527
 H10  H24A  H  HCH2  0   0.229   6.6749  -1.7399  -0.4684
 H10  H25   H  HCH2  0   0.238   4.1302   0.4633   2.2148
 H10  H25A  H  HCH2  0   0.241   3.7464  -1.1969   1.7946
 H10  H26   H  HCH2  0   0.235   3.4106   1.9719  -1.0986
 H10  H26A  H  HCH2  0   0.236   3.9391   2.3087   0.5489

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
 H10  C1   O2    single    1.440  0.020  1.440
 H10  C1   C18   single    1.530  0.020  1.530
 H10  C1   C25   single    1.531  0.020  1.531
 H10  C1   C26   single    1.532  0.020  1.532
 H10  O2   C3    single    1.347  0.020  1.347
 H10  C3   C4    aromatic  1.396  0.020  1.396
 H10  C3   C17   aromatic  1.396  0.020  1.396
 H10  C4   C5    aromatic  1.393  0.020  1.393
 H10  C5   C6    single    1.427  0.020  1.427
 H10  C5   C15   aromatic  1.398  0.020  1.398
 H10  C6   C7    triple    1.205  0.020  1.205
 H10  C7   C8    single    1.466  0.020  1.466
 H10  C8   N9    single    1.463  0.020  1.463
 H10  C8   C14   single    1.527  0.020  1.527
 H10  N9   C10   single    1.389  0.020  1.389
 H10  N9   O13   single    1.384  0.020  1.384
 H10  C10  O11   double    1.222  0.020  1.222
 H10  C10  N12   single    1.344  0.020  1.344
 H10  C15  C16   aromatic  1.383  0.020  1.383
 H10  C16  C17   aromatic  1.390  0.020  1.390
 H10  C18  C19   single    1.534  0.020  1.534
 H10  C19  C20   single    1.529  0.020  1.529
 H10  C19  C24   single    1.530  0.020  1.530
 H10  C20  C21   single    1.529  0.020  1.529
 H10  C21  C22   single    1.529  0.020  1.529
 H10  C21  C26   single    1.531  0.020  1.531
 H10  C22  C23   single    1.529  0.020  1.529
 H10  C23  C24   single    1.530  0.020  1.530
 H10  C23  C25   single    1.533  0.020  1.533
 H10  C4   H4    single    0.930  0.020  1.080
 H10  C8   H8    single    0.970  0.020  1.090
 H10  N12  HN12  single    0.860  0.020  1.020
 H10  N12  HN1A  single    0.860  0.020  1.020
 H10  O13  HO13  single    0.850  0.020  0.980
 H10  C14  H14   single    0.970  0.020  1.090
 H10  C14  H14A  single    0.970  0.020  1.090
 H10  C14  H14B  single    0.970  0.020  1.090
 H10  C15  H15   single    0.930  0.020  1.080
 H10  C16  H16   single    0.930  0.020  1.080
 H10  C17  H17   single    0.930  0.020  1.080
 H10  C18  H18   single    0.970  0.020  1.090
 H10  C18  H18A  single    0.970  0.020  1.090
 H10  C19  H19   single    0.970  0.020  1.090
 H10  C20  H20   single    0.970  0.020  1.090
 H10  C20  H20A  single    0.970  0.020  1.090
 H10  C21  H21   single    0.970  0.020  1.090
 H10  C22  H22   single    0.970  0.020  1.090
 H10  C22  H22A  single    0.970  0.020  1.090
 H10  C23  H23   single    0.970  0.020  1.090
 H10  C24  H24   single    0.970  0.020  1.090
 H10  C24  H24A  single    0.970  0.020  1.090
 H10  C25  H25   single    0.970  0.020  1.090
 H10  C25  H25A  single    0.970  0.020  1.090
 H10  C26  H26   single    0.970  0.020  1.090
 H10  C26  H26A  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
 H10  C26   C1   C25   108.49  3.000
 H10  C26   C1   C18   108.62  3.000
 H10  C25   C1   C18   110.77  3.000
 H10  C26   C1   O2    103.86  3.000
 H10  C25   C1   O2    111.83  3.000
 H10  C18   C1   O2    112.91  3.000
 H10  C3    O2   C1    125.47  3.000
 H10  C17   C3   C4    118.82  3.000
 H10  C17   C3   O2    126.28  3.000
 H10  C4    C3   O2    114.86  3.000
 H10  H4    C4   C5    119.78  3.000
 H10  H4    C4   C3    119.21  3.000
 H10  C5    C4   C3    121.01  3.000
 H10  C15   C5   C6    120.27  3.000
 H10  C15   C5   C4    119.84  3.000
 H10  C6    C5   C4    119.89  3.000
 H10  C7    C6   C5    180.00  3.000
 H10  C8    C7   C6    180.00  3.000
 H10  H8    C8   C14   106.50  3.000
 H10  H8    C8   N9    104.18  3.000
 H10  C14   C8   N9    113.24  3.000
 H10  H8    C8   C7    107.57  3.000
 H10  C14   C8   C7    112.07  3.000
 H10  N9    C8   C7    112.61  3.000
 H10  O13   N9   C10   114.29  3.000
 H10  O13   N9   C8    112.33  3.000
 H10  C10   N9   C8    119.79  3.000
 H10  N12   C10  O11   123.75  3.000
 H10  N12   C10  N9    115.88  3.000
 H10  O11   C10  N9    120.34  3.000
 H10  HN1A  N12  HN12  118.11  3.000
 H10  HN1A  N12  C10   118.27  3.000
 H10  HN12  N12  C10   122.86  3.000
 H10  HO13  O13  N9    105.24  3.000
 H10  H14B  C14  H14A  108.63  3.000
 H10  H14B  C14  H14   109.07  3.000
 H10  H14A  C14  H14   108.05  3.000
 H10  H14B  C14  C8    112.24  3.000
 H10  H14A  C14  C8    109.11  3.000
 H10  H14   C14  C8    109.65  3.000
 H10  H15   C15  C16   120.78  3.000
 H10  H15   C15  C5    120.27  3.000
 H10  C16   C15  C5    118.95  3.000
 H10  H16   C16  C17   118.80  3.000
 H10  H16   C16  C15   119.67  3.000
 H10  C17   C16  C15   121.53  3.000
 H10  H17   C17  C16   118.30  3.000
 H10  H17   C17  C3    121.85  3.000
 H10  C16   C17  C3    119.85  3.000
 H10  H18A  C18  H18   106.91  3.000
 H10  H18A  C18  C19   110.30  3.000
 H10  H18   C18  C19   108.99  3.000
 H10  H18A  C18  C1    109.68  3.000
 H10  H18   C18  C1    111.70  3.000
 H10  C19   C18  C1    109.23  3.000
 H10  H19   C19  C24   109.73  3.000
 H10  H19   C19  C20   109.70  3.000
 H10  C24   C19  C20   109.77  3.000
 H10  H19   C19  C18   108.61  3.000
 H10  C24   C19  C18   109.32  3.000
 H10  C20   C19  C18   109.69  3.000
 H10  H20A  C20  H20   106.81  3.000
 H10  H20A  C20  C21   110.28  3.000
 H10  H20   C20  C21   110.31  3.000
 H10  H20A  C20  C19   109.91  3.000
 H10  H20   C20  C19   110.24  3.000
 H10  C21   C20  C19   109.27  3.000
 H10  H21   C21  C26   108.88  3.000
 H10  H21   C21  C22   109.81  3.000
 H10  C26   C21  C22   109.47  3.000
 H10  H21   C21  C20   109.96  3.000
 H10  C26   C21  C20   109.18  3.000
 H10  C22   C21  C20   109.52  3.000
 H10  H22A  C22  H22   106.79  3.000
 H10  H22A  C22  C23   110.03  3.000
 H10  H22   C22  C23   110.32  3.000
 H10  H22A  C22  C21   110.26  3.000
 H10  H22   C22  C21   110.10  3.000
 H10  C23   C22  C21   109.31  3.000
 H10  H23   C23  C25   108.79  3.000
 H10  H23   C23  C24   109.73  3.000
 H10  C25   C23  C24   109.40  3.000
 H10  H23   C23  C22   109.72  3.000
 H10  C25   C23  C22   109.47  3.000
 H10  C24   C23  C22   109.71  3.000
 H10  H24A  C24  H24   106.73  3.000
 H10  H24A  C24  C23   110.12  3.000
 H10  H24   C24  C23   110.29  3.000
 H10  H24A  C24  C19   110.04  3.000
 H10  H24   C24  C19   110.05  3.000
 H10  C23   C24  C19   109.57  3.000
 H10  H25A  C25  H25   106.72  3.000
 H10  H25A  C25  C23   109.21  3.000
 H10  H25   C25  C23   110.32  3.000
 H10  H25A  C25  C1    111.69  3.000
 H10  H25   C25  C1    109.48  3.000
 H10  C23   C25  C1    109.39  3.000
 H10  H26A  C26  H26   107.23  3.000
 H10  H26A  C26  C21   110.26  3.000
 H10  H26   C26  C21   110.14  3.000
 H10  H26A  C26  C1    109.52  3.000
 H10  H26   C26  C1    109.37  3.000
 H10  C21   C26  C1    110.26  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
 H10  CONST_01  C15   C5   C4   C3      0.00   0.0  0
 H10  CONST_02  C15   C16  C17  C3      0.00   0.0  0
 H10  CONST_03  C16   C17  C3   C4      0.00   0.0  0
 H10  CONST_04  C16   C15  C5   C4      0.00   0.0  0
 H10  CONST_05  C17   C3   C4   C5      0.00   0.0  0
 H10  CONST_06  C17   C16  C15  C5      0.00   0.0  0
 H10  CONST_07  C5    C4   C3   O2    180.00   0.0  0
 H10  CONST_08  C16   C17  C3   O2    180.00   0.0  0
 H10  CONST_09  C6    C5   C4   C3    180.00   0.0  0
 H10  CONST_10  C16   C15  C5   C6    180.00   0.0  0
 H10  CONST_11  H16   C16  C17  C3    180.00   0.0  0
 H10  CONST_12  H17   C17  C3   C4    180.00   0.0  0
 H10  CONST_13  H15   C15  C5   C4    180.00   0.0  0
 H10  CONST_14  H4    C4   C5   C15   180.00   0.0  0
 H10  CONST_19  HN12  N12  C10  O11   180.00   0.0  0
 H10  CONST_20  HN1A  N12  C10  O11     0.00   0.0  0
 H10  Var_01    C4    C3   O2   C1   -154.30  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
 H10  chir_01  C1   C18  C25  C26  negativ
 H10  chir_02  C8   C7   N9   C14  positiv
 H10  chir_03  C19  C18  C20  C24  negativ
 H10  chir_04  C21  C20  C22  C26  positiv
 H10  chir_05  C23  C22  C24  C25  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
 H10  plan-1  O2    0.020
 H10  plan-1  C3    0.020
 H10  plan-1  C4    0.020
 H10  plan-1  C5    0.020
 H10  plan-1  C6    0.020
 H10  plan-1  C7    0.020
 H10  plan-1  C15   0.020
 H10  plan-1  C16   0.020
 H10  plan-1  C17   0.020
 H10  plan-1  H4    0.020
 H10  plan-1  H15   0.020
 H10  plan-1  H16   0.020
 H10  plan-1  H17   0.020
 H10  plan-2  C8    0.020
 H10  plan-2  N9    0.020
 H10  plan-2  C10   0.020
 H10  plan-2  O11   0.020
 H10  plan-2  N12   0.020
 H10  plan-2  O13   0.020
 H10  plan-2  HN12  0.020
 H10  plan-2  HN1A  0.020

