# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:34:42 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: ~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-propan-2-yl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1N(CC[C@@]12C(=O)Nc3ccccc23)C(=O)OC(C)(C)C
#
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
 D43  D43  '~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-propan-2-yl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate'  ligand  50  24  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D43
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
 D43  C10  C  CH1   0  -0.042  11.2710  -10.1184  -35.9407
 D43  C13  C  CH2   0  -0.471  10.0693   -8.2135  -35.0286
 D43  C17  C  CT    0   0.196  11.9058  -13.6562  -33.9065
 D43  C20  C  CH3   0  -0.671  12.3978  -13.3537  -32.4959
 D43  C24  C  CH3   0  -0.681   9.3657   -9.9931  -37.6893
 D43  N11  N  NT    0  -0.483  10.3413  -10.5682  -34.9138
 D43  C14  C  C     0   0.775  10.5044  -11.6713  -34.1446
 D43  O15  O  O     0  -0.527   9.7966  -11.9136  -33.1845
 D43  O16  O  O2    0  -0.493  11.4950  -12.4401  -34.5798
 D43  C18  C  CH3   0  -0.671  10.7898  -14.6940  -33.9109
 D43  C1   C  CR16  0  -0.259  12.4356   -6.3572  -38.5165
 D43  C2   C  CR16  0  -0.268  13.6702   -5.9598  -38.0218
 D43  C3   C  CR16  0  -0.308  14.1281   -6.4135  -36.7874
 D43  C4   C  CR56  0   0.362  13.3127   -7.2781  -36.0820
 D43  C5   C  CR56  0   0.135  12.0770   -7.7066  -36.5679
 D43  C6   C  CR16  0  -0.349  11.6311   -7.2313  -37.7862
 D43  N7   N  NR15  0  -0.739  13.5311   -7.8295  -34.8275
 D43  C8   C  CR5   0   0.587  12.4806   -8.5849  -34.4119
 D43  C9   C  CR5   0  -0.337  11.4526   -8.6208  -35.5545
 D43  C12  C  CH2   0  -0.268   9.4983   -9.4899  -34.4081
 D43  C19  C  CH3   0  -0.657  13.0646  -14.1478  -34.7656
 D43  O21  O  O     0  -0.439  12.3875   -9.1367  -33.3359
 D43  C22  C  CH1   0  -0.233  10.7969  -10.4166  -37.3737
 D43  C23  C  CH3   0  -0.648  10.9567  -11.9038  -37.6869
 D43  H1   H  HCH1  0   0.273  12.2264  -10.6323  -35.8221
 D43  H2   H  HCH2  0   0.275  10.1286   -7.4012  -34.3043
 D43  H3   H  HCH2  0   0.264   9.4485   -7.8585  -35.8495
 D43  H4   H  HCH3  0   0.244  11.5921  -13.0437  -31.8346
 D43  H5   H  HCH3  0   0.232  12.8520  -14.2501  -32.0724
 D43  H6   H  HCH3  0   0.234  13.1579  -12.5709  -32.5091
 D43  H7   H  HCH3  0   0.230   9.1921   -8.9240  -37.5761
 D43  H8   H  HCH3  0   0.239   9.1278  -10.2429  -38.7242
 D43  H9   H  HCH3  0   0.230   8.6483  -10.5186  -37.0566
 D43  H10  H  HCH3  0   0.246   9.9519  -14.4067  -33.2806
 D43  H11  H  HCH3  0   0.233  10.4224  -14.8673  -34.9238
 D43  H12  H  HCH3  0   0.232  11.1804  -15.6414  -33.5371
 D43  H13  H  HCR6  0   0.255  12.0925   -5.9857  -39.4727
 D43  H14  H  HCR6  0   0.261  14.2859   -5.2803  -38.5964
 D43  H15  H  HCR6  0   0.268  15.0836   -6.0923  -36.3942
 D43  H16  H  HCR6  0   0.260  10.6665   -7.5233  -38.1817
 D43  H17  H  HNR5  0   0.411  14.3384   -7.6405  -34.2526
 D43  H18  H  HCH2  0   0.243   8.4522   -9.6329  -34.6851
 D43  H19  H  HCH2  0   0.252   9.5500   -9.4567  -33.3211
 D43  H20  H  HCH3  0   0.228  13.4669  -15.0731  -34.3526
 D43  H21  H  HCH3  0   0.237  12.7382  -14.3500  -35.7870
 D43  H22  H  HCH3  0   0.236  13.8726  -13.4155  -34.8023
 D43  H23  H  HCH1  0   0.235  11.4761   -9.8758  -38.0400
 D43  H24  H  HCH3  0   0.228  11.9748  -12.2518  -37.5078
 D43  H25  H  HCH3  0   0.219  10.2851  -12.5150  -37.0831
 D43  H26  H  HCH3  0   0.227  10.7188  -12.0912  -38.7349

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
 D43  C1   C2   aromatic  1.388  0.020  1.388
 D43  C1   C6   aromatic  1.395  0.020  1.395
 D43  C23  C22  single    1.528  0.020  1.528
 D43  C2   C3   aromatic  1.393  0.020  1.393
 D43  C24  C22  single    1.526  0.020  1.526
 D43  C6   C5   aromatic  1.382  0.020  1.382
 D43  C22  C10  single    1.539  0.020  1.539
 D43  C3   C4   aromatic  1.382  0.020  1.382
 D43  C5   C4   aromatic  1.395  0.020  1.395
 D43  C5   C9   single    1.501  0.020  1.501
 D43  C4   N7   single    1.388  0.020  1.388
 D43  C10  C9   single    1.557  0.020  1.557
 D43  C10  N11  single    1.456  0.020  1.456
 D43  C9   C13  single    1.535  0.020  1.535
 D43  C9   C8   single    1.537  0.020  1.537
 D43  C19  C17  single    1.524  0.020  1.524
 D43  N11  C12  single    1.459  0.020  1.459
 D43  N11  C14  single    1.355  0.020  1.355
 D43  O16  C14  single    1.327  0.020  1.327
 D43  O16  C17  single    1.449  0.020  1.449
 D43  C13  C12  single    1.530  0.020  1.530
 D43  N7   C8   single    1.359  0.020  1.359
 D43  C14  O15  double    1.217  0.020  1.217
 D43  C8   O21  double    1.213  0.020  1.213
 D43  C17  C18  single    1.524  0.020  1.524
 D43  C17  C20  single    1.524  0.020  1.524
 D43  C10  H1   single    0.970  0.020  1.090
 D43  C13  H2   single    0.970  0.020  1.090
 D43  C13  H3   single    0.970  0.020  1.090
 D43  C20  H4   single    0.970  0.020  1.090
 D43  C20  H5   single    0.970  0.020  1.090
 D43  C20  H6   single    0.970  0.020  1.090
 D43  C24  H7   single    0.970  0.020  1.090
 D43  C24  H8   single    0.970  0.020  1.090
 D43  C24  H9   single    0.970  0.020  1.090
 D43  C18  H10  single    0.970  0.020  1.090
 D43  C18  H11  single    0.970  0.020  1.090
 D43  C18  H12  single    0.970  0.020  1.090
 D43  C1   H13  single    0.930  0.020  1.080
 D43  C2   H14  single    0.930  0.020  1.080
 D43  C3   H15  single    0.930  0.020  1.080
 D43  C6   H16  single    0.930  0.020  1.080
 D43  N7   H17  single    0.860  0.020  1.020
 D43  C12  H18  single    0.970  0.020  1.090
 D43  C12  H19  single    0.970  0.020  1.090
 D43  C19  H20  single    0.970  0.020  1.090
 D43  C19  H21  single    0.970  0.020  1.090
 D43  C19  H22  single    0.970  0.020  1.090
 D43  C22  H23  single    0.970  0.020  1.090
 D43  C23  H24  single    0.970  0.020  1.090
 D43  C23  H25  single    0.970  0.020  1.090
 D43  C23  H26  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
 D43  H1   C10  C22  106.24  3.000
 D43  H1   C10  C9   108.89  3.000
 D43  C22  C10  C9   116.95  3.000
 D43  H1   C10  N11  109.68  3.000
 D43  C9   C10  N11  101.34  3.000
 D43  C22  C10  N11  113.59  3.000
 D43  H3   C13  H2   106.81  3.000
 D43  H3   C13  C12  111.41  3.000
 D43  H2   C13  C12  111.88  3.000
 D43  H3   C13  C9   110.00  3.000
 D43  H2   C13  C9   112.11  3.000
 D43  C12  C13  C9   104.71  3.000
 D43  C19  C17  C18  109.60  3.000
 D43  C18  C17  O16  111.25  3.000
 D43  C19  C17  O16  102.96  3.000
 D43  C18  C17  C20  111.98  3.000
 D43  O16  C17  C20  110.78  3.000
 D43  C19  C17  C20  109.89  3.000
 D43  H6   C20  H5   107.71  3.000
 D43  H6   C20  H4   108.60  3.000
 D43  H5   C20  H4   107.86  3.000
 D43  H6   C20  C17  110.86  3.000
 D43  H5   C20  C17  109.31  3.000
 D43  H4   C20  C17  112.35  3.000
 D43  H9   C24  H8   107.24  3.000
 D43  H9   C24  H7   107.92  3.000
 D43  H8   C24  H7   106.78  3.000
 D43  H9   C24  C22  111.29  3.000
 D43  H8   C24  C22  109.71  3.000
 D43  H7   C24  C22  113.61  3.000
 D43  C12  N11  C14  118.33  3.000
 D43  C14  N11  C10  125.10  3.000
 D43  C12  N11  C10  112.64  3.000
 D43  O16  C14  O15  125.26  3.000
 D43  O15  C14  N11  122.68  3.000
 D43  O16  C14  N11  112.05  3.000
 D43  C14  O16  C17  123.04  3.000
 D43  H12  C18  H11  107.50  3.000
 D43  H12  C18  H10  107.87  3.000
 D43  H11  C18  H10  108.70  3.000
 D43  H12  C18  C17  109.16  3.000
 D43  H11  C18  C17  110.94  3.000
 D43  H10  C18  C17  112.50  3.000
 D43  H13  C1   C6   119.69  3.000
 D43  H13  C1   C2   119.92  3.000
 D43  C6   C1   C2   120.39  3.000
 D43  H14  C2   C3   119.23  3.000
 D43  H14  C2   C1   119.77  3.000
 D43  C3   C2   C1   121.00  3.000
 D43  H15  C3   C4   121.42  3.000
 D43  H15  C3   C2   121.05  3.000
 D43  C4   C3   C2   117.53  3.000
 D43  N7   C4   C5   109.40  3.000
 D43  N7   C4   C3   128.11  3.000
 D43  C5   C4   C3   122.47  3.000
 D43  C9   C5   C6   132.11  3.000
 D43  C9   C5   C4   108.69  3.000
 D43  C6   C5   C4   119.16  3.000
 D43  H16  C6   C5   121.13  3.000
 D43  H16  C6   C1   119.45  3.000
 D43  C5   C6   C1   119.42  3.000
 D43  H17  N7   C8   123.26  3.000
 D43  H17  N7   C4   124.51  3.000
 D43  C8   N7   C4   112.07  3.000
 D43  O21  C8   C9   126.69  3.000
 D43  O21  C8   N7   125.70  3.000
 D43  C9   C8   N7   107.61  3.000
 D43  C8   C9   C5   102.09  3.000
 D43  C8   C9   C13  109.98  3.000
 D43  C5   C9   C13  116.40  3.000
 D43  C8   C9   C10  106.54  3.000
 D43  C13  C9   C10  103.59  3.000
 D43  C5   C9   C10  117.83  3.000
 D43  H19  C12  H18  107.63  3.000
 D43  H19  C12  N11  109.95  3.000
 D43  H18  C12  N11  111.65  3.000
 D43  H19  C12  C13  111.21  3.000
 D43  H18  C12  C13  111.35  3.000
 D43  N11  C12  C13  105.09  3.000
 D43  H22  C19  H21  108.32  3.000
 D43  H22  C19  H20  108.00  3.000
 D43  H21  C19  H20  107.92  3.000
 D43  H22  C19  C17  111.44  3.000
 D43  H21  C19  C17  111.10  3.000
 D43  H20  C19  C17  109.93  3.000
 D43  H23  C22  C23  106.93  3.000
 D43  H23  C22  C24  108.61  3.000
 D43  C23  C22  C24  109.02  3.000
 D43  H23  C22  C10  106.26  3.000
 D43  C24  C22  C10  115.34  3.000
 D43  C23  C22  C10  110.32  3.000
 D43  H26  C23  H25  107.54  3.000
 D43  H26  C23  H24  107.85  3.000
 D43  H25  C23  H24  107.77  3.000
 D43  H26  C23  C22  109.96  3.000
 D43  H25  C23  C22  111.56  3.000
 D43  H24  C23  C22  111.98  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
 D43  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D43  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 D43  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 D43  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 D43  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 D43  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 D43  CONST_07  C9   C5   C6   C1    180.00   0.0  0
 D43  CONST_08  C9   C5   C4   C3    180.00   0.0  0
 D43  CONST_09  C9   C5   C4   N7      0.00   0.0  0
 D43  CONST_10  C9   C8   N7   C4      0.00   0.0  0
 D43  CONST_11  O21  C8   N7   C4    180.00   0.0  0
 D43  CONST_12  H15  C3   C2   C1    180.00   0.0  0
 D43  CONST_13  H16  C6   C1   C2    180.00   0.0  0
 D43  CONST_14  H13  C1   C2   C3    180.00   0.0  0
 D43  CONST_15  H14  C2   C3   C4    180.00   0.0  0
 D43  CONST_16  H17  N7   C8   C9    180.00   0.0  0
 D43  Var_01    C13  C12  N11  C10    -8.13  30.0  1
 D43  Var_02    C9   C13  C12  N11   -15.10  30.0  1
 D43  Var_03    O16  C14  N11  C10   -10.95  30.0  2
 D43  Var_04    N11  C14  O16  C17   177.78  30.0  3
 D43  Var_05    H24  C23  C22  C10   -54.19  30.0  3
 D43  Var_06    H7   C24  C22  C10    60.37  30.0  3
 D43  Var_07    C19  C17  O16  C14  -179.19  30.0  3
 D43  Var_08    H20  C19  C17  C20    61.84  30.0  3
 D43  Var_09    H10  C18  C17  C20    55.65  30.0  3
 D43  Var_10    H4   C20  C17  O16    69.60  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
 D43  chir_01  C10  C22  C9   N11  negativ
 D43  chir_02  C9   C10  C13  C8   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
 D43  plan-1  C1   0.020
 D43  plan-1  C2   0.020
 D43  plan-1  C3   0.020
 D43  plan-1  C4   0.020
 D43  plan-1  C5   0.020
 D43  plan-1  C6   0.020
 D43  plan-1  N7   0.020
 D43  plan-1  C8   0.020
 D43  plan-1  C9   0.020
 D43  plan-1  O21  0.020
 D43  plan-1  H13  0.020
 D43  plan-1  H14  0.020
 D43  plan-1  H15  0.020
 D43  plan-1  H16  0.020
 D43  plan-1  H17  0.020
 D43  plan-2  N11  0.020
 D43  plan-2  C14  0.020
 D43  plan-2  O15  0.020
 D43  plan-2  O16  0.020

