# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 04:50:14 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-benzylcyclopentyl [(1S)-1-formylpentyl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](NC(=O)OC1(CCCC1)Cc2ccccc2)C=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
 CT2  CT2  '1-benzylcyclopentyl [(1S)-1-formylpentyl]carbamate'  ligand  50  23  .  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_CT2
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
 CT2  C1    C  CH3   0  -0.662   3.7955  -3.7573  -0.4622
 CT2  C2    C  CH2   0  -0.422   4.1772  -2.3178  -0.7792
 CT2  C3    C  CH2   0  -0.407   3.2819  -1.3128  -0.0668
 CT2  C4    C  CH2   0  -0.454   3.6596   0.1342  -0.3576
 CT2  C5    C  CH1   0  -0.198   2.7009   1.1295   0.3033
 CT2  N8    N  NH1   0  -0.646   1.3847   1.0244  -0.2523
 CT2  C9    C  C     0   0.770   0.2656   1.2391   0.4673
 CT2  O10   O  O     0  -0.519   0.2524   1.4826   1.6577
 CT2  O11   O  O2    0  -0.506  -0.8067   1.1196  -0.3141
 CT2  C12   C  CT    0   0.220  -2.1520   1.1479   0.2053
 CT2  C13   C  CH2   0  -0.559  -2.4048  -0.0094   1.1792
 CT2  C14   C  CR6   0   0.157  -1.9128  -1.3475   0.6963
 CT2  C15   C  CR16  0  -0.305  -2.6667  -2.1162  -0.1901
 CT2  C16   C  CR16  0  -0.240  -2.1990  -3.3378  -0.6552
 CT2  C17   C  CR16  0  -0.275  -0.9661  -3.8197  -0.2345
 CT2  C18   C  CR16  0  -0.235  -0.2124  -3.0731   0.6603
 CT2  C19   C  CR16  0  -0.321  -0.6842  -1.8505   1.1208
 CT2  C20   C  CH2   0  -0.454  -2.5037   2.5216   0.7781
 CT2  C21   C  CH2   0  -0.448  -2.5556   3.4492  -0.4392
 CT2  C22   C  CH2   0  -0.440  -2.9304   2.5396  -1.6315
 CT2  C23   C  CH2   0  -0.447  -3.0171   1.1187  -1.0558
 CT2  C6    C  C1    0   0.190   3.2530   2.5331   0.2128
 CT2  O7    O  O     0  -0.363   2.6600   3.4710  -0.2501
 CT2  H11   H  HCH3  0   0.230   4.4413  -4.4678  -0.9789
 CT2  H12   H  HCH3  0   0.217   3.8727  -3.9575   0.6081
 CT2  H13   H  HCH3  0   0.214   2.7673  -3.9662  -0.7632
 CT2  H21   H  HCH2  0   0.215   5.2207  -2.1449  -0.4994
 CT2  H22   H  HCH2  0   0.215   4.1203  -2.1523  -1.8595
 CT2  H31   H  HCH2  0   0.226   2.2422  -1.4868  -0.3584
 CT2  H32   H  HCH2  0   0.216   3.3275  -1.4818   1.0146
 CT2  H41   H  HCH2  0   0.248   4.6722   0.3304   0.0050
 CT2  H42   H  HCH2  0   0.240   3.6800   0.3100  -1.4385
 CT2  H5    H  HCH1  0   0.283   2.6604   0.8915   1.3727
 CT2  HN8   H  HNH1  0   0.399   1.2991   0.8840  -1.2471
 CT2  H131  H  HCH2  0   0.265  -1.9533   0.2228   2.1444
 CT2  H132  H  HCH2  0   0.256  -3.4844  -0.0489   1.3449
 CT2  H15   H  HCR6  0   0.246  -3.6370  -1.7617  -0.5169
 CT2  H16   H  HCR6  0   0.254  -2.8016  -3.9162  -1.3438
 CT2  H17   H  HCR6  0   0.253  -0.6016  -4.7731  -0.5946
 CT2  H18   H  HCR6  0   0.248   0.7447  -3.4424   1.0063
 CT2  H19   H  HCR6  0   0.245  -0.0888  -1.2856   1.8275
 CT2  H201  H  HCH2  0   0.236  -3.4969   2.4376   1.2287
 CT2  H202  H  HCH2  0   0.255  -1.8284   2.8596   1.5614
 CT2  H211  H  HCH2  0   0.233  -3.2729   4.2567  -0.2930
 CT2  H212  H  HCH2  0   0.230  -1.5850   3.9189  -0.6045
 CT2  H221  H  HCH2  0   0.231  -3.8756   2.8326  -2.0888
 CT2  H222  H  HCH2  0   0.232  -2.1734   2.5977  -2.4140
 CT2  H231  H  HCH2  0   0.248  -2.7129   0.3484  -1.7657
 CT2  H232  H  HCH2  0   0.235  -4.0421   0.8919  -0.7536
 CT2  H6    H  H     0   0.197   4.2732   2.6412   0.6237

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
 CT2  C1   C2    single    1.523  0.020  1.523
 CT2  C1   H11   single    0.970  0.020  1.090
 CT2  C1   H12   single    0.970  0.020  1.090
 CT2  C1   H13   single    0.970  0.020  1.090
 CT2  C2   C3    single    1.523  0.020  1.523
 CT2  C2   H21   single    0.970  0.020  1.090
 CT2  C2   H22   single    0.970  0.020  1.090
 CT2  C3   C4    single    1.523  0.020  1.523
 CT2  C3   H31   single    0.970  0.020  1.090
 CT2  C3   H32   single    0.970  0.020  1.090
 CT2  C4   C5    single    1.532  0.020  1.532
 CT2  C4   H41   single    0.970  0.020  1.090
 CT2  C4   H42   single    0.970  0.020  1.090
 CT2  C5   N8    single    1.432  0.020  1.432
 CT2  C5   C6    single    1.511  0.020  1.511
 CT2  C5   H5    single    0.970  0.020  1.090
 CT2  N8   C9    single    1.348  0.020  1.348
 CT2  N8   HN8   single    0.860  0.020  1.020
 CT2  C9   O10   double    1.215  0.020  1.215
 CT2  C9   O11   single    1.332  0.020  1.332
 CT2  O11  C12   single    1.442  0.020  1.442
 CT2  C12  C13   single    1.534  0.020  1.534
 CT2  C12  C20   single    1.529  0.020  1.529
 CT2  C12  C23   single    1.530  0.020  1.530
 CT2  C13  C14   single    1.505  0.020  1.505
 CT2  C13  H131  single    0.970  0.020  1.090
 CT2  C13  H132  single    0.970  0.020  1.090
 CT2  C14  C15   aromatic  1.395  0.020  1.395
 CT2  C14  C19   aromatic  1.394  0.020  1.394
 CT2  C15  C16   aromatic  1.388  0.020  1.388
 CT2  C15  H15   single    0.930  0.020  1.080
 CT2  C16  C17   aromatic  1.389  0.020  1.389
 CT2  C16  H16   single    0.930  0.020  1.080
 CT2  C17  C18   aromatic  1.388  0.020  1.388
 CT2  C17  H17   single    0.930  0.020  1.080
 CT2  C18  C19   aromatic  1.389  0.020  1.389
 CT2  C18  H18   single    0.930  0.020  1.080
 CT2  C19  H19   single    0.930  0.020  1.080
 CT2  C20  C21   single    1.531  0.020  1.531
 CT2  C20  H201  single    0.970  0.020  1.090
 CT2  C20  H202  single    0.970  0.020  1.090
 CT2  C21  C22   single    1.546  0.020  1.546
 CT2  C21  H211  single    0.970  0.020  1.090
 CT2  C21  H212  single    0.970  0.020  1.090
 CT2  C22  C23   single    1.536  0.020  1.536
 CT2  C22  H221  single    0.970  0.020  1.090
 CT2  C22  H222  single    0.970  0.020  1.090
 CT2  C23  H231  single    0.970  0.020  1.090
 CT2  C23  H232  single    0.970  0.020  1.090
 CT2  C6   O7    double    1.202  0.020  1.202
 CT2  C6   H6    single    0.930  0.020  1.080

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
 CT2  H13   C1   H12   107.57  3.000
 CT2  H13   C1   H11   107.61  3.000
 CT2  H12   C1   H11   107.65  3.000
 CT2  H13   C1   C2    111.08  3.000
 CT2  H12   C1   C2    111.09  3.000
 CT2  H11   C1   C2    111.64  3.000
 CT2  H22   C2   H21   106.15  3.000
 CT2  H22   C2   C3    109.35  3.000
 CT2  H21   C2   C3    109.68  3.000
 CT2  H22   C2   C1    109.60  3.000
 CT2  H21   C2   C1    109.59  3.000
 CT2  C3    C2   C1    112.28  3.000
 CT2  H32   C3   H31   106.15  3.000
 CT2  H32   C3   C4    108.94  3.000
 CT2  H31   C3   C4    109.63  3.000
 CT2  H32   C3   C2    109.60  3.000
 CT2  H31   C3   C2    109.22  3.000
 CT2  C4    C3   C2    113.06  3.000
 CT2  H42   C4   H41   106.33  3.000
 CT2  H42   C4   C5    109.46  3.000
 CT2  H41   C4   C5    108.66  3.000
 CT2  H42   C4   C3    110.21  3.000
 CT2  H41   C4   C3    109.68  3.000
 CT2  C5    C4   C3    112.31  3.000
 CT2  H5    C5   C6    105.87  3.000
 CT2  H5    C5   N8    109.17  3.000
 CT2  C6    C5   N8    112.37  3.000
 CT2  H5    C5   C4    107.64  3.000
 CT2  C6    C5   C4    110.43  3.000
 CT2  N8    C5   C4    111.10  3.000
 CT2  HN8   N8   C9    118.58  3.000
 CT2  HN8   N8   C5    118.09  3.000
 CT2  C9    N8   C5    122.97  3.000
 CT2  O11   C9   O10   125.72  3.000
 CT2  O11   C9   N8    109.94  3.000
 CT2  O10   C9   N8    124.33  3.000
 CT2  C12   O11  C9    122.54  3.000
 CT2  C23   C12  C20   101.30  3.000
 CT2  C23   C12  C13   114.58  3.000
 CT2  C20   C12  C13   113.70  3.000
 CT2  C23   C12  O11   103.32  3.000
 CT2  C20   C12  O11   111.53  3.000
 CT2  C13   C12  O11   111.57  3.000
 CT2  H132  C13  H131  106.41  3.000
 CT2  H132  C13  C14   109.84  3.000
 CT2  H131  C13  C14   109.74  3.000
 CT2  H132  C13  C12   106.64  3.000
 CT2  H131  C13  C12   109.46  3.000
 CT2  C14   C13  C12   114.41  3.000
 CT2  C19   C14  C15   118.11  3.000
 CT2  C19   C14  C13   120.75  3.000
 CT2  C15   C14  C13   121.14  3.000
 CT2  H15   C15  C16   119.25  3.000
 CT2  H15   C15  C14   119.70  3.000
 CT2  C16   C15  C14   121.05  3.000
 CT2  H16   C16  C17   120.09  3.000
 CT2  H16   C16  C15   119.72  3.000
 CT2  C17   C16  C15   120.19  3.000
 CT2  H17   C17  C18   120.37  3.000
 CT2  H17   C17  C16   120.25  3.000
 CT2  C18   C17  C16   119.38  3.000
 CT2  H18   C18  C19   119.64  3.000
 CT2  H18   C18  C17   120.17  3.000
 CT2  C19   C18  C17   120.19  3.000
 CT2  H19   C19  C18   119.26  3.000
 CT2  H19   C19  C14   119.67  3.000
 CT2  C18   C19  C14   121.07  3.000
 CT2  H202  C20  H201  106.91  3.000
 CT2  H202  C20  C21   113.90  3.000
 CT2  H201  C20  C21   110.07  3.000
 CT2  H202  C20  C12   113.95  3.000
 CT2  H201  C20  C12   107.10  3.000
 CT2  C21   C20  C12   104.72  3.000
 CT2  H212  C21  H211  106.68  3.000
 CT2  H212  C21  C22   110.62  3.000
 CT2  H211  C21  C22   112.32  3.000
 CT2  H212  C21  C20   110.56  3.000
 CT2  H211  C21  C20   111.37  3.000
 CT2  C22   C21  C20   105.36  3.000
 CT2  H222  C22  H221  106.66  3.000
 CT2  H222  C22  C23   110.95  3.000
 CT2  H221  C22  C23   110.92  3.000
 CT2  H222  C22  C21   110.72  3.000
 CT2  H221  C22  C21   112.06  3.000
 CT2  C23   C22  C21   105.61  3.000
 CT2  H232  C23  H231  107.16  3.000
 CT2  H232  C23  C22   110.41  3.000
 CT2  H231  C23  C22   113.18  3.000
 CT2  H232  C23  C12   107.85  3.000
 CT2  H231  C23  C12   113.10  3.000
 CT2  C22   C23  C12   105.04  3.000
 CT2  H6    C6   O7    121.48  3.000
 CT2  H6    C6   C5    113.95  3.000
 CT2  O7    C6   C5    124.57  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
 CT2  CONST_01  C17  C16  C15  C14    0.00   0.0  0
 CT2  CONST_02  C17  C18  C19  C14    0.00   0.0  0
 CT2  CONST_03  C18  C19  C14  C15    0.00   0.0  0
 CT2  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 CT2  CONST_05  C19  C14  C15  C16    0.00   0.0  0
 CT2  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 CT2  CONST_07  C16  C15  C14  C13  180.00   0.0  0
 CT2  CONST_08  C18  C19  C14  C13  180.00   0.0  0
 CT2  CONST_09  H16  C16  C15  C14  180.00   0.0  0
 CT2  CONST_10  H18  C18  C19  C14  180.00   0.0  0
 CT2  CONST_11  H19  C19  C14  C15  180.00   0.0  0
 CT2  CONST_12  H17  C17  C16  C15  180.00   0.0  0
 CT2  CONST_13  H15  C15  C16  C17  180.00   0.0  0
 CT2  Var_01    C22  C21  C20  C12   27.26  30.0  1
 CT2  Var_02    C21  C22  C23  C12  -23.33  30.0  1
 CT2  Var_03    C23  C22  C21  C20   -2.40  30.0  1
 CT2  Var_04    C15  C14  C13  C12  -81.72  30.0  2
 CT2  Var_05    C4   C3   C2   C1   179.27  30.0  3
 CT2  Var_06    C5   C4   C3   C2   176.78  30.0  3
 CT2  Var_07    O10  C9   N8   C5    -3.35  30.0  2
 CT2  Var_08    H11  C1   C2   C3   179.88  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
 CT2  chir_01  C5   C4   N8   C6   positiv
 CT2  chir_02  C12  C23  C20  C13  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
 CT2  plan-1  C13  0.020
 CT2  plan-1  C14  0.020
 CT2  plan-1  C15  0.020
 CT2  plan-1  C16  0.020
 CT2  plan-1  C17  0.020
 CT2  plan-1  C18  0.020
 CT2  plan-1  C19  0.020
 CT2  plan-1  H15  0.020
 CT2  plan-1  H16  0.020
 CT2  plan-1  H17  0.020
 CT2  plan-1  H18  0.020
 CT2  plan-1  H19  0.020
 CT2  plan-2  N8   0.020
 CT2  plan-2  C9   0.020
 CT2  plan-2  O10  0.020
 CT2  plan-2  O11  0.020
 CT2  plan-3  C5   0.020
 CT2  plan-3  C6   0.020
 CT2  plan-3  O7   0.020
 CT2  plan-3  H6   0.020

