# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:43:57 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (4R)-7-chloro-9-methyl-1-oxo-1,2,4,9-tetrahydrospiro[beta-carboline-3,4'-piperidine]-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2cc(Cl)ccc2c3[C@@H](C#N)C4(CCNCC4)NC(=O)c13
#
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
 MB9  MB9  (4R)-7-chloro-9-methyl-1-oxo-1,2,4,9-tetrahydrospiro[beta-carboline-3,4'-piperidine]-4-carbonitrile  ligand  40  23  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MB9
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
 MB9  C1K   C   CH2   0  -0.465  -3.7202  -1.1970   0.3552
 MB9  C1I   C   CH2   0  -0.331  -4.9795  -0.6115  -0.2887
 MB9  N1M   N   NH1   0  -0.569  -4.9007  -0.4726  -1.7299
 MB9  C1J   C   CH2   0  -0.323  -3.7151   0.2659  -2.1260
 MB9  C1L   C   CH2   0  -0.405  -2.4133  -0.3120  -1.5766
 MB9  C1W   C   CT    0   0.083  -2.4478  -0.4448  -0.0438
 MB9  N1N   N   NH1   0  -0.661  -2.4496   0.8669   0.6038
 MB9  C1O   C   C     0   0.508  -1.3874   1.7007   0.6977
 MB9  O1C   O   O     0  -0.465  -1.4781   2.8644   1.0582
 MB9  C1Q   C   CR5   0   0.187  -0.1134   1.0394   0.3868
 MB9  N1V   N   NR5   0  -0.600   1.1068   1.6414   0.2349
 MB9  C1A   C   CH3   0  -0.526   1.3868   3.0616   0.2923
 MB9  C1T   C   CR56  0   0.358   2.0305   0.6600   0.0172
 MB9  C1H   C   CR16  0  -0.273   3.4062   0.7638  -0.2040
 MB9  C1P   C   CR6   0  -0.054   4.0904  -0.4142  -0.3993
 MB9  CL1D  CL  CL    0  -0.125   5.8021  -0.3484  -0.6750
 MB9  C1F   C   CR16  0  -0.229   3.4688  -1.6745  -0.3857
 MB9  C1G   C   CR16  0  -0.374   2.1136  -1.7662  -0.1689
 MB9  C1S   C   CR56  0   0.054   1.3757  -0.5945   0.0335
 MB9  C1R   C   CR5   0   0.106   0.0078  -0.3162   0.2667
 MB9  C1U   C   CH1   0  -0.460  -1.1823  -1.2079   0.4163
 MB9  C1E   C   CSP   0   0.150  -1.2822  -1.6380   1.8131
 MB9  N1B   N   NS    0  -0.254  -1.3339  -1.9607   2.9161
 MB9  H1K   H   HCH2  0   0.260  -3.8331  -1.2053   1.4422
 MB9  H1KA  H   HCH2  0   0.254  -3.6088  -2.2373   0.0363
 MB9  H1I   H   HCH2  0   0.256  -5.8300  -1.2467  -0.0368
 MB9  H1IA  H   HCH2  0   0.224  -5.2064   0.3708   0.1402
 MB9  HN1M  H   HNH1  0   0.344  -4.8700  -1.3955  -2.1479
 MB9  H1J   H   HCH2  0   0.249  -3.6622   0.2932  -3.2154
 MB9  H1JA  H   HCH2  0   0.224  -3.8297   1.3050  -1.8002
 MB9  H1L   H   HCH2  0   0.239  -2.2528  -1.3055  -2.0065
 MB9  H1LA  H   HCH2  0   0.250  -1.5702   0.3055  -1.8930
 MB9  HN1N  H   HNH1  0   0.404  -3.3443   1.2831   0.8195
 MB9  H1A   H   HCH3  0   0.260   1.2777   3.4419   1.3053
 MB9  H1AA  H   HCH3  0   0.263   2.4074   3.2323  -0.0347
 MB9  H1AB  H   HCH3  0   0.264   0.7224   3.6109  -0.3686
 MB9  H1H   H   HCR6  0   0.293   3.9215   1.7142  -0.2222
 MB9  H1F   H   HCR6  0   0.278   4.0582  -2.5661  -0.5477
 MB9  H1G   H   HCR6  0   0.259   1.6320  -2.7356  -0.1584
 MB9  H1U   H   HCH1  0   0.345  -1.0860  -2.1098  -0.1948

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
 MB9  C1K  C1I   single    1.531  0.020  1.531
 MB9  C1K  C1W   single    1.531  0.020  1.531
 MB9  C1I  N1M   single    1.450  0.020  1.450
 MB9  N1M  C1J   single    1.452  0.020  1.452
 MB9  C1J  C1L   single    1.527  0.020  1.527
 MB9  C1L  C1W   single    1.539  0.020  1.539
 MB9  C1W  N1N   single    1.463  0.020  1.463
 MB9  C1W  C1U   single    1.548  0.020  1.548
 MB9  N1N  C1O   single    1.354  0.020  1.354
 MB9  C1O  O1C   double    1.222  0.020  1.222
 MB9  C1O  C1Q   single    1.469  0.020  1.469
 MB9  C1Q  N1V   aromatic  1.369  0.020  1.369
 MB9  C1Q  C1R   aromatic  1.366  0.020  1.366
 MB9  N1V  C1A   single    1.449  0.020  1.449
 MB9  N1V  C1T   aromatic  1.365  0.020  1.365
 MB9  C1T  C1H   aromatic  1.397  0.020  1.397
 MB9  C1T  C1S   aromatic  1.415  0.020  1.415
 MB9  C1H  C1P   aromatic  1.376  0.020  1.376
 MB9  C1P  CL1D  single    1.735  0.020  1.735
 MB9  C1P  C1F   aromatic  1.405  0.020  1.405
 MB9  C1F  C1G   aromatic  1.375  0.020  1.375
 MB9  C1G  C1S   aromatic  1.399  0.020  1.399
 MB9  C1S  C1R   aromatic  1.415  0.020  1.415
 MB9  C1R  C1U   single    1.495  0.020  1.495
 MB9  C1U  C1E   single    1.465  0.020  1.465
 MB9  C1E  N1B   triple    1.150  0.020  1.150
 MB9  C1K  H1K   single    0.970  0.020  1.090
 MB9  C1K  H1KA  single    0.970  0.020  1.090
 MB9  C1I  H1I   single    0.970  0.020  1.090
 MB9  C1I  H1IA  single    0.970  0.020  1.090
 MB9  N1M  HN1M  single    0.890  0.020  1.040
 MB9  C1J  H1J   single    0.970  0.020  1.090
 MB9  C1J  H1JA  single    0.970  0.020  1.090
 MB9  C1L  H1L   single    0.970  0.020  1.090
 MB9  C1L  H1LA  single    0.970  0.020  1.090
 MB9  N1N  HN1N  single    0.860  0.020  1.020
 MB9  C1A  H1A   single    0.970  0.020  1.090
 MB9  C1A  H1AA  single    0.970  0.020  1.090
 MB9  C1A  H1AB  single    0.970  0.020  1.090
 MB9  C1H  H1H   single    0.930  0.020  1.080
 MB9  C1F  H1F   single    0.930  0.020  1.080
 MB9  C1G  H1G   single    0.930  0.020  1.080
 MB9  C1U  H1U   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
 MB9  H1KA  C1K  H1K   107.06  3.000
 MB9  H1KA  C1K  C1W   107.86  3.000
 MB9  H1K   C1K  C1W   110.42  3.000
 MB9  H1KA  C1K  C1I   108.95  3.000
 MB9  H1K   C1K  C1I   109.65  3.000
 MB9  C1W   C1K  C1I   112.71  3.000
 MB9  H1IA  C1I  H1I   105.67  3.000
 MB9  H1IA  C1I  N1M   108.33  3.000
 MB9  H1I   C1I  N1M   109.13  3.000
 MB9  H1IA  C1I  C1K   110.40  3.000
 MB9  H1I   C1I  C1K   108.75  3.000
 MB9  N1M   C1I  C1K   114.21  3.000
 MB9  HN1M  N1M  C1J   109.02  3.000
 MB9  HN1M  N1M  C1I   108.92  3.000
 MB9  C1J   N1M  C1I   111.36  3.000
 MB9  H1JA  C1J  H1J   106.16  3.000
 MB9  H1JA  C1J  C1L   109.96  3.000
 MB9  H1J   C1J  C1L   109.12  3.000
 MB9  H1JA  C1J  N1M   108.42  3.000
 MB9  H1J   C1J  N1M   108.95  3.000
 MB9  C1L   C1J  N1M   113.93  3.000
 MB9  H1LA  C1L  H1L   106.64  3.000
 MB9  H1LA  C1L  C1W   110.78  3.000
 MB9  H1L   C1L  C1W   108.43  3.000
 MB9  H1LA  C1L  C1J   109.88  3.000
 MB9  H1L   C1L  C1J   109.11  3.000
 MB9  C1W   C1L  C1J   111.84  3.000
 MB9  C1U   C1W  N1N   108.15  3.000
 MB9  C1U   C1W  C1L   108.68  3.000
 MB9  N1N   C1W  C1L   111.32  3.000
 MB9  C1U   C1W  C1K   111.09  3.000
 MB9  N1N   C1W  C1K   108.91  3.000
 MB9  C1L   C1W  C1K   108.70  3.000
 MB9  HN1N  N1N  C1O   115.25  3.000
 MB9  HN1N  N1N  C1W   117.71  3.000
 MB9  C1O   N1N  C1W   125.60  3.000
 MB9  C1Q   C1O  O1C   123.77  3.000
 MB9  C1Q   C1O  N1N   112.87  3.000
 MB9  O1C   C1O  N1N   123.29  3.000
 MB9  C1R   C1Q  N1V   110.33  3.000
 MB9  C1R   C1Q  C1O   122.84  3.000
 MB9  N1V   C1Q  C1O   126.77  3.000
 MB9  C1T   N1V  C1A   125.47  3.000
 MB9  C1T   N1V  C1Q   107.74  3.000
 MB9  C1A   N1V  C1Q   126.79  3.000
 MB9  H1AB  C1A  H1AA  108.20  3.000
 MB9  H1AB  C1A  H1A   109.19  3.000
 MB9  H1AA  C1A  H1A   108.66  3.000
 MB9  H1AB  C1A  N1V   110.70  3.000
 MB9  H1AA  C1A  N1V   108.91  3.000
 MB9  H1A   C1A  N1V   111.11  3.000
 MB9  C1S   C1T  C1H   121.55  3.000
 MB9  C1S   C1T  N1V   108.80  3.000
 MB9  C1H   C1T  N1V   129.65  3.000
 MB9  H1H   C1H  C1P   120.87  3.000
 MB9  H1H   C1H  C1T   122.49  3.000
 MB9  C1P   C1H  C1T   116.64  3.000
 MB9  C1F   C1P  CL1D  118.16  3.000
 MB9  C1F   C1P  C1H   123.12  3.000
 MB9  CL1D  C1P  C1H   118.72  3.000
 MB9  H1F   C1F  C1G   120.39  3.000
 MB9  H1F   C1F  C1P   119.80  3.000
 MB9  C1G   C1F  C1P   119.81  3.000
 MB9  H1G   C1G  C1S   120.91  3.000
 MB9  H1G   C1G  C1F   119.98  3.000
 MB9  C1S   C1G  C1F   119.11  3.000
 MB9  C1R   C1S  C1G   134.28  3.000
 MB9  C1R   C1S  C1T   105.95  3.000
 MB9  C1G   C1S  C1T   119.77  3.000
 MB9  C1U   C1R  C1S   131.97  3.000
 MB9  C1U   C1R  C1Q   120.83  3.000
 MB9  C1S   C1R  C1Q   107.18  3.000
 MB9  H1U   C1U  C1E   107.26  3.000
 MB9  H1U   C1U  C1R   111.47  3.000
 MB9  C1E   C1U  C1R   108.96  3.000
 MB9  H1U   C1U  C1W   108.21  3.000
 MB9  C1E   C1U  C1W   111.86  3.000
 MB9  C1R   C1U  C1W   109.10  3.000
 MB9  N1B   C1E  C1U   180.00  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
 MB9  CONST_01  C1H   C1T  N1V  C1Q   180.00   0.0  0
 MB9  CONST_02  C1S   C1T  N1V  C1Q     0.00   0.0  0
 MB9  CONST_03  C1T   C1S  C1R  C1Q     0.00   0.0  0
 MB9  CONST_04  C1G   C1S  C1R  C1Q   180.00   0.0  0
 MB9  CONST_05  C1S   C1R  C1Q  N1V     0.00   0.0  0
 MB9  CONST_06  C1P   C1H  C1T  N1V   180.00   0.0  0
 MB9  CONST_07  C1G   C1S  C1T  N1V   180.00   0.0  0
 MB9  CONST_08  C1R   C1S  C1T  N1V     0.00   0.0  0
 MB9  CONST_09  C1R   C1Q  N1V  C1T     0.00   0.0  0
 MB9  CONST_10  C1F   C1P  C1H  C1T     0.00   0.0  0
 MB9  CONST_11  C1F   C1G  C1S  C1T     0.00   0.0  0
 MB9  CONST_12  C1G   C1S  C1T  C1H     0.00   0.0  0
 MB9  CONST_13  C1R   C1S  C1T  C1H   180.00   0.0  0
 MB9  CONST_14  C1G   C1F  C1P  C1H     0.00   0.0  0
 MB9  CONST_15  C1S   C1T  C1H  C1P     0.00   0.0  0
 MB9  CONST_16  C1S   C1G  C1F  C1P     0.00   0.0  0
 MB9  CONST_17  C1R   C1S  C1G  C1F   180.00   0.0  0
 MB9  CONST_18  C1Q   C1O  N1N  C1W     0.00   0.0  0
 MB9  CONST_19  C1A   N1V  C1Q  C1O     0.00   0.0  0
 MB9  CONST_20  C1R   C1Q  N1V  C1A   180.00   0.0  0
 MB9  CONST_21  C1H   C1T  N1V  C1A     0.00   0.0  0
 MB9  CONST_22  C1S   C1T  N1V  C1A   180.00   0.0  0
 MB9  CONST_23  CL1D  C1P  C1H  C1T   180.00   0.0  0
 MB9  CONST_24  C1G   C1F  C1P  CL1D  180.00   0.0  0
 MB9  CONST_25  O1C   C1O  N1N  C1W   180.00   0.0  0
 MB9  CONST_26  H1H   C1H  C1T  N1V     0.00   0.0  0
 MB9  CONST_27  H1G   C1G  C1S  C1T   180.00   0.0  0
 MB9  CONST_28  H1F   C1F  C1P  C1H   180.00   0.0  0
 MB9  CONST_29  HN1N  N1N  C1O  C1Q   180.00   0.0  0
 MB9  Var_01    C1J   N1M  C1I  C1K   -52.95  30.0  1
 MB9  Var_02    C1J   C1L  C1W  C1K    51.43  30.0  3
 MB9  Var_03    C1O   N1N  C1W  C1K   166.51  30.0  1
 MB9  Var_04    C1L   C1W  C1K  C1I   -50.36  30.0  3
 MB9  Var_05    C1L   C1J  N1M  C1I    54.41  30.0  1
 MB9  Var_06    C1W   C1K  C1I  N1M    52.72  30.0  1
 MB9  Var_07    C1W   C1L  C1J  N1M   -55.15  30.0  1
 MB9  Var_08    N1V   C1Q  C1O  N1N   171.46  30.0  1
 MB9  Var_09    H1A   C1A  N1V  C1Q    70.06  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
 MB9  chir_01  C1U  C1W  C1R  C1E  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
 MB9  plan-1  C1W   0.020
 MB9  plan-1  N1N   0.020
 MB9  plan-1  C1O   0.020
 MB9  plan-1  O1C   0.020
 MB9  plan-1  C1Q   0.020
 MB9  plan-1  HN1N  0.020
 MB9  plan-2  C1O   0.020
 MB9  plan-2  C1Q   0.020
 MB9  plan-2  N1V   0.020
 MB9  plan-2  C1A   0.020
 MB9  plan-2  C1T   0.020
 MB9  plan-2  C1H   0.020
 MB9  plan-2  C1P   0.020
 MB9  plan-2  CL1D  0.020
 MB9  plan-2  C1F   0.020
 MB9  plan-2  C1G   0.020
 MB9  plan-2  C1S   0.020
 MB9  plan-2  C1R   0.020
 MB9  plan-2  C1U   0.020
 MB9  plan-2  H1H   0.020
 MB9  plan-2  H1F   0.020
 MB9  plan-2  H1G   0.020

