# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 01:02:48 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (4R)-7,8-dichloro-1',9-dimethyl-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: CN1CCC2(CC1)NC(=O)c3n(C)c4c(Cl)c(Cl)ccc4c3[C@H]2C#N
#
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
 MB0  MB0  (4R)-7,8-dichloro-1',9-dimethyl-1-oxo-1,2,4,9-tetrahydrospiro[beta-carboline-3,4'-piperidine]-4-carbonitrile  ligand  43  25  .  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_MB0
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
 MB0  C1L   C   CH2   0  -0.396  -2.6569  -0.1884  -1.3738
 MB0  C1J   C   CH2   0  -0.281  -3.9082   0.5502  -1.8153
 MB0  N1W   N   N     0  -0.409  -5.1003  -0.1916  -1.4579
 MB0  C1A   C   CH3   0  -0.517  -6.2952   0.4230  -1.9895
 MB0  C1K   C   CH2   0  -0.289  -5.1873  -0.3783  -0.0264
 MB0  C1M   C   CH2   0  -0.457  -3.9741  -1.1247   0.5114
 MB0  C1Y   C   CT    0   0.072  -2.6540  -0.4488   0.1400
 MB0  N1N   N   NC1   0  -0.660  -2.5286   0.7957   0.8945
 MB0  C1O   C   C     0   0.522  -1.4032   1.5306   1.0351
 MB0  O1D   O   O     0  -0.468  -1.3973   2.6381   1.5514
 MB0  C1R   C   CR5   0   0.170  -0.1943   0.8176   0.5794
 MB0  N1X   N   NR5   0  -0.601   1.0690   1.3260   0.4076
 MB0  C1B   C   CH3   0  -0.550   1.4184   2.7386   0.4253
 MB0  C1U   C   CR56  0   0.479   1.8966   0.2826   0.0890
 MB0  C1Q   C   CR6   0  -0.079   3.2735   0.2280  -0.1800
 MB0  CL1F  CL  CL    0  -0.077   4.2818   1.6213  -0.1252
 MB0  C1P   C   CR6   0  -0.039   3.8270  -1.0051  -0.4758
 MB0  CL1E  CL  CL    0  -0.091   5.5147  -1.1310  -0.8072
 MB0  C1H   C   CR16  0  -0.240   3.0624  -2.1814  -0.5114
 MB0  C1I   C   CR16  0  -0.366   1.7179  -2.1389  -0.2435
 MB0  C1T   C   CR56  0   0.027   1.1289  -0.9077   0.0555
 MB0  C1S   C   CR5   0   0.121  -0.1959  -0.5298   0.3658
 MB0  C1V   C   CH1   0  -0.458  -1.4435  -1.3420   0.4939
 MB0  C1G   C   CSP   0   0.151  -1.5370  -1.8750   1.8549
 MB0  N1C   N   N     0  -0.251  -1.5871  -2.2882   2.9272
 MB0  H1L   H   HCH2  0   0.242  -2.6154  -1.1490  -1.8945
 MB0  H1LA  H   HCH2  0   0.256  -1.7735   0.3761  -1.6754
 MB0  H1J   H   HCH2  0   0.196  -3.9148   1.5716  -1.3957
 MB0  H1JA  H   HCH2  0   0.247  -3.8788   0.6650  -2.9010
 MB0  H1A   H   HCH3  0   0.234  -6.2248   0.4956  -3.0757
 MB0  H1AA  H   HCH3  0   0.234  -7.1670  -0.1878  -1.7510
 MB0  H1AB  H   HCH3  0   0.194  -6.4767   1.4351  -1.5961
 MB0  H1K   H   HCH2  0   0.195  -5.3189   0.5834   0.5039
 MB0  H1KA  H   HCH2  0   0.254  -6.0790  -0.9659   0.2033
 MB0  H1M   H   HCH2  0   0.266  -4.0643  -1.2226   1.5955
 MB0  H1MA  H   HCH2  0   0.258  -3.9653  -2.1345   0.0943
 MB0  HN1N  H   HNC1  0   0.408  -3.3743   1.2331   1.2323
 MB0  H1B   H   HCH3  0   0.260   2.1113   2.9562   1.2341
 MB0  H1BA  H   HCH3  0   0.260   1.8638   3.0298  -0.5218
 MB0  H1BB  H   HCH3  0   0.284   0.5189   3.3188   0.5795
 MB0  H1H   H   HCR6  0   0.287   3.5467  -3.1180  -0.7490
 MB0  H1I   H   HCR6  0   0.267   1.1276  -3.0455  -0.2663
 MB0  H1V   H   HCH1  0   0.350  -1.4301  -2.1962  -0.1898

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
 MB0  C1L  C1J   single    1.519  0.020  1.519
 MB0  C1L  C1Y   single    1.536  0.020  1.536
 MB0  C1J  N1W   single    1.449  0.020  1.449
 MB0  N1W  C1A   single    1.445  0.020  1.445
 MB0  N1W  C1K   single    1.446  0.020  1.446
 MB0  C1K  C1M   aromatic  1.523  0.020  1.523
 MB0  C1M  C1Y   single    1.529  0.020  1.529
 MB0  C1Y  N1N   single    1.461  0.020  1.461
 MB0  C1Y  C1V   single    1.545  0.020  1.545
 MB0  N1N  C1O   single    1.351  0.020  1.351
 MB0  C1O  O1D   double    1.222  0.020  1.222
 MB0  C1O  C1R   single    1.476  0.020  1.476
 MB0  C1R  N1X   aromatic  1.373  0.020  1.373
 MB0  C1R  C1S   aromatic  1.364  0.020  1.364
 MB0  N1X  C1B   aromatic  1.455  0.020  1.455
 MB0  N1X  C1U   aromatic  1.369  0.020  1.369
 MB0  C1U  C1Q   aromatic  1.404  0.020  1.404
 MB0  C1U  C1T   aromatic  1.417  0.020  1.417
 MB0  C1Q  CL1F  single    1.721  0.020  1.721
 MB0  C1Q  C1P   aromatic  1.384  0.020  1.384
 MB0  C1P  CL1E  single    1.725  0.020  1.725
 MB0  C1P  C1H   aromatic  1.403  0.020  1.403
 MB0  C1H  C1I   aromatic  1.372  0.020  1.372
 MB0  C1I  C1T   aromatic  1.397  0.020  1.397
 MB0  C1T  C1S   aromatic  1.412  0.020  1.412
 MB0  C1S  C1V   aromatic  1.494  0.020  1.494
 MB0  C1V  C1G   aromatic  1.465  0.020  1.465
 MB0  C1G  N1C   aromatic  1.150  0.020  1.150
 MB0  C1L  H1L   single    0.970  0.020  1.090
 MB0  C1L  H1LA  single    0.970  0.020  1.090
 MB0  C1J  H1J   single    0.970  0.020  1.090
 MB0  C1J  H1JA  aromatic  0.970  0.020  1.090
 MB0  C1A  H1A   aromatic  0.970  0.020  1.090
 MB0  C1A  H1AA  single    0.970  0.020  1.090
 MB0  C1A  H1AB  aromatic  0.970  0.020  1.090
 MB0  C1K  H1K   single    0.970  0.020  1.090
 MB0  C1K  H1KA  aromatic  0.970  0.020  1.090
 MB0  C1M  H1M   aromatic  0.970  0.020  1.090
 MB0  C1M  H1MA  single    0.970  0.020  1.090
 MB0  N1N  HN1N  aromatic  0.860  0.020  1.020
 MB0  C1B  H1B   single    0.970  0.020  1.090
 MB0  C1B  H1BA  aromatic  0.970  0.020  1.090
 MB0  C1B  H1BB  single    0.970  0.020  1.090
 MB0  C1H  H1H   single    0.930  0.020  1.080
 MB0  C1I  H1I   single    0.930  0.020  1.080
 MB0  C1V  H1V   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
 MB0  H1LA  C1L  H1L   106.99  3.000
 MB0  H1LA  C1L  C1Y   111.02  3.000
 MB0  H1L   C1L  C1Y   108.69  3.000
 MB0  H1LA  C1L  C1J   109.58  3.000
 MB0  H1L   C1L  C1J   108.67  3.000
 MB0  C1Y   C1L  C1J   111.74  3.000
 MB0  H1JA  C1J  H1J   106.30  3.000
 MB0  H1JA  C1J  N1W   108.74  3.000
 MB0  H1J   C1J  N1W   112.03  3.000
 MB0  H1JA  C1J  C1L   108.53  3.000
 MB0  H1J   C1J  C1L   110.15  3.000
 MB0  N1W   C1J  C1L   110.93  3.000
 MB0  C1K   N1W  C1A   111.67  3.000
 MB0  C1K   N1W  C1J   111.09  3.000
 MB0  C1A   N1W  C1J   111.83  3.000
 MB0  H1AB  C1A  H1AA  107.75  3.000
 MB0  H1AB  C1A  H1A   107.77  3.000
 MB0  H1AA  C1A  H1A   107.85  3.000
 MB0  H1AB  C1A  N1W   113.32  3.000
 MB0  H1AA  C1A  N1W   110.02  3.000
 MB0  H1A   C1A  N1W   109.95  3.000
 MB0  H1KA  C1K  H1K   105.65  3.000
 MB0  H1KA  C1K  C1M   108.21  3.000
 MB0  H1K   C1K  C1M   110.59  3.000
 MB0  H1KA  C1K  N1W   109.07  3.000
 MB0  H1K   C1K  N1W   111.68  3.000
 MB0  C1M   C1K  N1W   111.40  3.000
 MB0  H1MA  C1M  H1M   107.26  3.000
 MB0  H1MA  C1M  C1Y   108.00  3.000
 MB0  H1M   C1M  C1Y   110.62  3.000
 MB0  H1MA  C1M  C1K   108.94  3.000
 MB0  H1M   C1M  C1K   109.19  3.000
 MB0  C1Y   C1M  C1K   112.67  3.000
 MB0  C1V   C1Y  N1N   107.87  3.000
 MB0  C1V   C1Y  C1M   111.42  3.000
 MB0  N1N   C1Y  C1M   108.98  3.000
 MB0  C1V   C1Y  C1L   108.97  3.000
 MB0  N1N   C1Y  C1L   111.40  3.000
 MB0  C1M   C1Y  C1L   108.23  3.000
 MB0  HN1N  N1N  C1O   115.26  3.000
 MB0  HN1N  N1N  C1Y   118.02  3.000
 MB0  C1O   N1N  C1Y   126.05  3.000
 MB0  C1R   C1O  O1D   124.36  3.000
 MB0  C1R   C1O  N1N   112.79  3.000
 MB0  O1D   C1O  N1N   122.74  3.000
 MB0  C1S   C1R  N1X   110.32  3.000
 MB0  C1S   C1R  C1O   121.64  3.000
 MB0  N1X   C1R  C1O   127.86  3.000
 MB0  C1U   N1X  C1B   126.68  3.000
 MB0  C1U   N1X  C1R   107.65  3.000
 MB0  C1B   N1X  C1R   125.38  3.000
 MB0  H1BB  C1B  H1BA  108.75  3.000
 MB0  H1BB  C1B  H1B   108.46  3.000
 MB0  H1BA  C1B  H1B   109.49  3.000
 MB0  H1BB  C1B  N1X   108.83  3.000
 MB0  H1BA  C1B  N1X   110.37  3.000
 MB0  H1B   C1B  N1X   110.88  3.000
 MB0  C1T   C1U  C1Q   119.62  3.000
 MB0  C1T   C1U  N1X   108.55  3.000
 MB0  C1Q   C1U  N1X   131.83  3.000
 MB0  C1P   C1Q  CL1F  119.60  3.000
 MB0  C1P   C1Q  C1U   117.90  3.000
 MB0  CL1F  C1Q  C1U   122.49  3.000
 MB0  C1H   C1P  CL1E  117.85  3.000
 MB0  C1H   C1P  C1Q   122.31  3.000
 MB0  CL1E  C1P  C1Q   119.84  3.000
 MB0  H1H   C1H  C1I   120.59  3.000
 MB0  H1H   C1H  C1P   119.20  3.000
 MB0  C1I   C1H  C1P   120.21  3.000
 MB0  H1I   C1I  C1T   120.86  3.000
 MB0  H1I   C1I  C1H   120.31  3.000
 MB0  C1T   C1I  C1H   118.83  3.000
 MB0  C1S   C1T  C1I   132.71  3.000
 MB0  C1S   C1T  C1U   106.16  3.000
 MB0  C1I   C1T  C1U   121.13  3.000
 MB0  C1V   C1S  C1T   131.05  3.000
 MB0  C1V   C1S  C1R   121.63  3.000
 MB0  C1T   C1S  C1R   107.31  3.000
 MB0  H1V   C1V  C1G   107.30  3.000
 MB0  H1V   C1V  C1S   111.13  3.000
 MB0  C1G   C1V  C1S   109.31  3.000
 MB0  H1V   C1V  C1Y   108.52  3.000
 MB0  C1G   C1V  C1Y   111.91  3.000
 MB0  C1S   C1V  C1Y   108.68  3.000
 MB0  N1C   C1G  C1V   178.80  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
 MB0  CONST_01  C1Q   C1U  N1X  C1R   180.00   0.0  0
 MB0  CONST_02  C1T   C1U  N1X  C1R     0.00   0.0  0
 MB0  CONST_03  C1U   C1T  C1S  C1R     0.00   0.0  0
 MB0  CONST_04  C1I   C1T  C1S  C1R   180.00   0.0  0
 MB0  CONST_05  C1T   C1S  C1R  N1X     0.00   0.0  0
 MB0  CONST_06  C1V   C1S  C1R  N1X   180.00   0.0  0
 MB0  CONST_07  C1P   C1Q  C1U  N1X   180.00   0.0  0
 MB0  CONST_08  C1I   C1T  C1U  N1X   180.00   0.0  0
 MB0  CONST_09  C1S   C1T  C1U  N1X     0.00   0.0  0
 MB0  CONST_10  C1S   C1R  N1X  C1U     0.00   0.0  0
 MB0  CONST_11  C1H   C1P  C1Q  C1U     0.00   0.0  0
 MB0  CONST_12  C1H   C1I  C1T  C1U     0.00   0.0  0
 MB0  CONST_13  C1V   C1S  C1T  C1U   180.00   0.0  0
 MB0  CONST_14  C1I   C1T  C1U  C1Q     0.00   0.0  0
 MB0  CONST_15  C1S   C1T  C1U  C1Q   180.00   0.0  0
 MB0  CONST_16  C1I   C1H  C1P  C1Q     0.00   0.0  0
 MB0  CONST_17  C1T   C1U  C1Q  C1P     0.00   0.0  0
 MB0  CONST_18  C1T   C1I  C1H  C1P     0.00   0.0  0
 MB0  CONST_19  C1S   C1T  C1I  C1H   180.00   0.0  0
 MB0  CONST_20  C1V   C1S  C1T  C1I     0.00   0.0  0
 MB0  CONST_23  C1S   C1R  N1X  C1B   180.00   0.0  0
 MB0  CONST_24  C1Q   C1U  N1X  C1B     0.00   0.0  0
 MB0  CONST_25  C1T   C1U  N1X  C1B   180.00   0.0  0
 MB0  CONST_27  C1B   N1X  C1R  C1O     0.00   0.0  0
 MB0  CONST_28  CL1F  C1Q  C1U  N1X     0.00   0.0  0
 MB0  CONST_29  CL1E  C1P  C1Q  C1U   180.00   0.0  0
 MB0  CONST_30  C1T   C1U  C1Q  CL1F  180.00   0.0  0
 MB0  CONST_31  C1H   C1P  C1Q  CL1F  180.00   0.0  0
 MB0  CONST_32  C1I   C1H  C1P  CL1E  180.00   0.0  0
 MB0  CONST_33  H1I   C1I  C1T  C1U   180.00   0.0  0
 MB0  CONST_34  H1H   C1H  C1P  C1Q   180.00   0.0  0
 MB0  Var_01    C1K   N1W  C1J  C1L    60.48  30.0  1
 MB0  Var_02    C1K   C1M  C1Y  C1L   -50.86  30.0  2
 MB0  Var_03    C1O   N1N  C1Y  C1L   -74.38  30.0  1
 MB0  Var_04    C1S   C1V  C1Y  C1L    71.84  30.0  1
 MB0  Var_05    C1M   C1Y  C1L  C1J    52.13  30.0  3
 MB0  Var_06    C1M   C1K  N1W  C1J   -58.90  30.0  1
 MB0  Var_07    C1Y   C1L  C1J  N1W   -57.93  30.0  1
 MB0  Var_08    C1R   C1O  N1N  C1Y   -12.10  30.0  1
 MB0  Var_09    C1R   C1S  C1V  C1Y    29.51  30.0  1
 MB0  Var_10    N1X   C1R  C1O  N1N   170.14  30.0  1
 MB0  Var_11    H1A   C1A  N1W  C1J    58.21  30.0  2
 MB0  Var_12    H1B   C1B  N1X  C1R   118.32  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
 MB0  chir_01  C1V  C1Y  C1S  C1G  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
 MB0  plan-1  N1N   0.020
 MB0  plan-1  C1O   0.020
 MB0  plan-1  O1D   0.020
 MB0  plan-1  C1R   0.020
 MB0  plan-2  C1O   0.020
 MB0  plan-2  C1R   0.020
 MB0  plan-2  N1X   0.020
 MB0  plan-2  C1B   0.020
 MB0  plan-2  C1U   0.020
 MB0  plan-2  C1Q   0.020
 MB0  plan-2  CL1F  0.020
 MB0  plan-2  C1P   0.020
 MB0  plan-2  CL1E  0.020
 MB0  plan-2  C1H   0.020
 MB0  plan-2  C1I   0.020
 MB0  plan-2  C1T   0.020
 MB0  plan-2  C1S   0.020
 MB0  plan-2  C1V   0.020
 MB0  plan-2  H1H   0.020
 MB0  plan-2  H1I   0.020

