# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:32:55 2020
#   Inital geometry file: a 108 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
 7CP  7CP  (4R)-7,8-dichloro-1',9-dimethyl-1-oxo-1,2,4,9-tetrahydrospiro[beta-carboline-3,4'-piperidine]-4-carbonitrile  ligand  43  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7CP
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
 7CP  C1L   C   CH2   0  -0.412  -2.6641  -0.2680  -1.3540
 7CP  C1J   C   CH2   0  -0.325  -3.8959   0.4063  -1.9564
 7CP  N1W   N   NT    0  -0.390  -5.1544  -0.1536  -1.5012
 7CP  C1A   C   CH3   0  -0.530  -5.4414  -1.4605  -2.0567
 7CP  C1K   C   CH2   0  -0.334  -5.2296  -0.1085  -0.0548
 7CP  C1M   C   CH2   0  -0.474  -4.0479  -0.7757   0.6583
 7CP  C1Y   C   CT    0   0.090  -2.6965  -0.2338   0.1846
 7CP  N1N   N   NH1   0  -0.661  -2.5302   1.1264   0.6943
 7CP  C1O   C   C     0   0.522  -1.3775   1.8315   0.7247
 7CP  O1D   O   O     0  -0.468  -1.3350   3.0146   1.0277
 7CP  C1R   C   CR5   0   0.170  -0.1915   1.0019   0.4359
 7CP  N1X   N   NR5   0  -0.601   1.0917   1.4207   0.1858
 7CP  C1B   C   CH3   0  -0.550   1.4985   2.7982  -0.0458
 7CP  C1U   C   CR56  0   0.479   1.8764   0.3049   0.0644
 7CP  C1Q   C   CR6   0  -0.080   3.2479   0.1468  -0.1904
 7CP  CL1F  CL  CL    0  -0.077   4.3130   1.4848  -0.3823
 7CP  C1P   C   CR6   0  -0.038   3.7481  -1.1412  -0.2686
 7CP  CL1E  CL  CL    0  -0.091   5.4255  -1.3927  -0.5794
 7CP  C1H   C   CR16  0  -0.240   2.9367  -2.2730  -0.0957
 7CP  C1I   C   CR16  0  -0.367   1.5978  -2.1286   0.1636
 7CP  C1T   C   CR56  0   0.028   1.0617  -0.8406   0.2416
 7CP  C1S   C   CR5   0   0.122  -0.2464  -0.3607   0.4707
 7CP  C1V   C   CH1   0  -0.459  -1.5269  -1.0868   0.7264
 7CP  C1G   C   CSP   0   0.152  -1.6581  -1.3472   2.1617
 7CP  N1C   N   NS    0  -0.251  -1.7380  -1.5452   3.2919
 7CP  H1L   H   HCH2  0   0.244  -2.6203  -1.3130  -1.6744
 7CP  H1LA  H   HCH2  0   0.257  -1.7609   0.2119  -1.7353
 7CP  H1J   H   HCH2  0   0.235  -3.8831   1.4743  -1.7147
 7CP  H1JA  H   HCH2  0   0.249  -3.8470   0.3375  -3.0450
 7CP  H1A   H   HCH3  0   0.200  -4.7421  -2.2580  -1.7685
 7CP  H1AA  H   HCH3  0   0.236  -6.4397  -1.7774  -1.7509
 7CP  H1AB  H   HCH3  0   0.235  -5.4347  -1.4017  -3.1460
 7CP  H1K   H   HCH2  0   0.237  -5.3134   0.9404   0.2507
 7CP  H1KA  H   HCH2  0   0.256  -6.1538  -0.5879   0.2733
 7CP  H1M   H   HCH2  0   0.267  -4.1555  -0.6427   1.7375
 7CP  H1MA  H   HCH2  0   0.259  -4.0666  -1.8525   0.4693
 7CP  HN1N  H   HNH1  0   0.409  -3.3616   1.6523   0.9241
 7CP  H1B   H   HCH3  0   0.260   2.1902   3.1342   0.7227
 7CP  H1BA  H   HCH3  0   0.259   1.9646   2.8962  -1.0220
 7CP  H1BB  H   HCH3  0   0.284   0.6217   3.4302  -0.0162
 7CP  H1H   H   HCR6  0   0.286   3.3808  -3.2558  -0.1676
 7CP  H1I   H   HCR6  0   0.265   0.9712  -3.0000   0.3019
 7CP  H1V   H   HCH1  0   0.346  -1.5389  -2.0545   0.2178

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
 7CP  C1L  C1J   single    1.528  0.020  1.528
 7CP  C1L  C1Y   single    1.539  0.020  1.539
 7CP  C1J  N1W   single    1.451  0.020  1.451
 7CP  N1W  C1A   single    1.449  0.020  1.449
 7CP  N1W  C1K   single    1.449  0.020  1.449
 7CP  C1K  C1M   single    1.533  0.020  1.533
 7CP  C1M  C1Y   single    1.531  0.020  1.531
 7CP  C1Y  N1N   single    1.462  0.020  1.462
 7CP  C1Y  C1V   single    1.546  0.020  1.546
 7CP  N1N  C1O   single    1.352  0.020  1.352
 7CP  C1O  O1D   double    1.222  0.020  1.222
 7CP  C1O  C1R   single    1.476  0.020  1.476
 7CP  C1R  N1X   aromatic  1.373  0.020  1.373
 7CP  C1R  C1S   aromatic  1.364  0.020  1.364
 7CP  N1X  C1B   single    1.455  0.020  1.455
 7CP  N1X  C1U   aromatic  1.369  0.020  1.369
 7CP  C1U  C1Q   aromatic  1.404  0.020  1.404
 7CP  C1U  C1T   aromatic  1.417  0.020  1.417
 7CP  C1Q  CL1F  single    1.721  0.020  1.721
 7CP  C1Q  C1P   aromatic  1.384  0.020  1.384
 7CP  C1P  CL1E  single    1.724  0.020  1.724
 7CP  C1P  C1H   aromatic  1.403  0.020  1.403
 7CP  C1H  C1I   aromatic  1.371  0.020  1.371
 7CP  C1I  C1T   aromatic  1.397  0.020  1.397
 7CP  C1T  C1S   aromatic  1.412  0.020  1.412
 7CP  C1S  C1V   single    1.494  0.020  1.494
 7CP  C1V  C1G   single    1.465  0.020  1.465
 7CP  C1G  N1C   triple    1.150  0.020  1.150
 7CP  C1L  H1L   single    0.970  0.020  1.090
 7CP  C1L  H1LA  single    0.970  0.020  1.090
 7CP  C1J  H1J   single    0.970  0.020  1.090
 7CP  C1J  H1JA  single    0.970  0.020  1.090
 7CP  C1A  H1A   single    0.970  0.020  1.090
 7CP  C1A  H1AA  single    0.970  0.020  1.090
 7CP  C1A  H1AB  single    0.970  0.020  1.090
 7CP  C1K  H1K   single    0.970  0.020  1.090
 7CP  C1K  H1KA  single    0.970  0.020  1.090
 7CP  C1M  H1M   single    0.970  0.020  1.090
 7CP  C1M  H1MA  single    0.970  0.020  1.090
 7CP  N1N  HN1N  single    0.860  0.020  1.020
 7CP  C1B  H1B   single    0.970  0.020  1.090
 7CP  C1B  H1BA  single    0.970  0.020  1.090
 7CP  C1B  H1BB  single    0.970  0.020  1.090
 7CP  C1H  H1H   single    0.930  0.020  1.080
 7CP  C1I  H1I   single    0.930  0.020  1.080
 7CP  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
 7CP  H1LA  C1L  H1L   106.53  3.000
 7CP  H1LA  C1L  C1Y   110.91  3.000
 7CP  H1L   C1L  C1Y   108.35  3.000
 7CP  H1LA  C1L  C1J   109.59  3.000
 7CP  H1L   C1L  C1J   109.78  3.000
 7CP  C1Y   C1L  C1J   111.55  3.000
 7CP  H1JA  C1J  H1J   106.32  3.000
 7CP  H1JA  C1J  N1W   109.11  3.000
 7CP  H1J   C1J  N1W   108.50  3.000
 7CP  H1JA  C1J  C1L   109.22  3.000
 7CP  H1J   C1J  C1L   109.51  3.000
 7CP  N1W   C1J  C1L   113.91  3.000
 7CP  C1K   N1W  C1A   113.61  3.000
 7CP  C1K   N1W  C1J   110.26  3.000
 7CP  C1A   N1W  C1J   113.56  3.000
 7CP  H1AB  C1A  H1AA  107.53  3.000
 7CP  H1AB  C1A  H1A   107.28  3.000
 7CP  H1AA  C1A  H1A   107.33  3.000
 7CP  H1AB  C1A  N1W   109.45  3.000
 7CP  H1AA  C1A  N1W   109.62  3.000
 7CP  H1A   C1A  N1W   115.34  3.000
 7CP  H1KA  C1K  H1K   105.78  3.000
 7CP  H1KA  C1K  C1M   108.77  3.000
 7CP  H1K   C1K  C1M   110.24  3.000
 7CP  H1KA  C1K  N1W   109.29  3.000
 7CP  H1K   C1K  N1W   108.18  3.000
 7CP  C1M   C1K  N1W   114.25  3.000
 7CP  H1MA  C1M  H1M   106.79  3.000
 7CP  H1MA  C1M  C1Y   108.07  3.000
 7CP  H1M   C1M  C1Y   110.45  3.000
 7CP  H1MA  C1M  C1K   109.57  3.000
 7CP  H1M   C1M  C1K   109.30  3.000
 7CP  C1Y   C1M  C1K   112.49  3.000
 7CP  C1V   C1Y  N1N   107.77  3.000
 7CP  C1V   C1Y  C1M   111.36  3.000
 7CP  N1N   C1Y  C1M   108.77  3.000
 7CP  C1V   C1Y  C1L   108.79  3.000
 7CP  N1N   C1Y  C1L   111.51  3.000
 7CP  C1M   C1Y  C1L   108.66  3.000
 7CP  HN1N  N1N  C1O   115.17  3.000
 7CP  HN1N  N1N  C1Y   118.03  3.000
 7CP  C1O   N1N  C1Y   126.17  3.000
 7CP  C1R   C1O  O1D   124.39  3.000
 7CP  C1R   C1O  N1N   112.81  3.000
 7CP  O1D   C1O  N1N   122.70  3.000
 7CP  C1S   C1R  N1X   110.30  3.000
 7CP  C1S   C1R  C1O   121.61  3.000
 7CP  N1X   C1R  C1O   127.97  3.000
 7CP  C1U   N1X  C1B   126.66  3.000
 7CP  C1U   N1X  C1R   107.65  3.000
 7CP  C1B   N1X  C1R   125.40  3.000
 7CP  H1BB  C1B  H1BA  108.65  3.000
 7CP  H1BB  C1B  H1B   108.42  3.000
 7CP  H1BA  C1B  H1B   109.54  3.000
 7CP  H1BB  C1B  N1X   108.80  3.000
 7CP  H1BA  C1B  N1X   110.39  3.000
 7CP  H1B   C1B  N1X   110.98  3.000
 7CP  C1T   C1U  C1Q   119.56  3.000
 7CP  C1T   C1U  N1X   108.55  3.000
 7CP  C1Q   C1U  N1X   131.88  3.000
 7CP  C1P   C1Q  CL1F  119.58  3.000
 7CP  C1P   C1Q  C1U   117.91  3.000
 7CP  CL1F  C1Q  C1U   122.50  3.000
 7CP  C1H   C1P  CL1E  117.84  3.000
 7CP  C1H   C1P  C1Q   122.32  3.000
 7CP  CL1E  C1P  C1Q   119.83  3.000
 7CP  H1H   C1H  C1I   120.63  3.000
 7CP  H1H   C1H  C1P   119.18  3.000
 7CP  C1I   C1H  C1P   120.19  3.000
 7CP  H1I   C1I  C1T   120.86  3.000
 7CP  H1I   C1I  C1H   120.31  3.000
 7CP  C1T   C1I  C1H   118.83  3.000
 7CP  C1S   C1T  C1I   132.67  3.000
 7CP  C1S   C1T  C1U   106.15  3.000
 7CP  C1I   C1T  C1U   121.18  3.000
 7CP  C1V   C1S  C1T   131.03  3.000
 7CP  C1V   C1S  C1R   121.62  3.000
 7CP  C1T   C1S  C1R   107.34  3.000
 7CP  H1V   C1V  C1G   107.31  3.000
 7CP  H1V   C1V  C1S   111.10  3.000
 7CP  C1G   C1V  C1S   109.33  3.000
 7CP  H1V   C1V  C1Y   108.49  3.000
 7CP  C1G   C1V  C1Y   111.95  3.000
 7CP  C1S   C1V  C1Y   108.68  3.000
 7CP  N1C   C1G  C1V   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
 7CP  CONST_01  C1Q   C1U  N1X  C1R   180.00   0.0  0
 7CP  CONST_02  C1T   C1U  N1X  C1R     0.00   0.0  0
 7CP  CONST_03  C1U   C1T  C1S  C1R     0.00   0.0  0
 7CP  CONST_04  C1I   C1T  C1S  C1R   180.00   0.0  0
 7CP  CONST_05  C1T   C1S  C1R  N1X     0.00   0.0  0
 7CP  CONST_06  C1P   C1Q  C1U  N1X   180.00   0.0  0
 7CP  CONST_07  C1I   C1T  C1U  N1X   180.00   0.0  0
 7CP  CONST_08  C1S   C1T  C1U  N1X     0.00   0.0  0
 7CP  CONST_09  C1S   C1R  N1X  C1U     0.00   0.0  0
 7CP  CONST_10  C1H   C1P  C1Q  C1U     0.00   0.0  0
 7CP  CONST_11  C1H   C1I  C1T  C1U     0.00   0.0  0
 7CP  CONST_12  C1I   C1T  C1U  C1Q     0.00   0.0  0
 7CP  CONST_13  C1S   C1T  C1U  C1Q   180.00   0.0  0
 7CP  CONST_14  C1I   C1H  C1P  C1Q     0.00   0.0  0
 7CP  CONST_15  C1T   C1U  C1Q  C1P     0.00   0.0  0
 7CP  CONST_16  C1T   C1I  C1H  C1P     0.00   0.0  0
 7CP  CONST_17  C1S   C1T  C1I  C1H   180.00   0.0  0
 7CP  CONST_18  C1R   C1O  N1N  C1Y     0.00   0.0  0
 7CP  CONST_19  C1B   N1X  C1R  C1O     0.00   0.0  0
 7CP  CONST_20  CL1F  C1Q  C1U  N1X     0.00   0.0  0
 7CP  CONST_21  C1S   C1R  N1X  C1B   180.00   0.0  0
 7CP  CONST_22  C1Q   C1U  N1X  C1B     0.00   0.0  0
 7CP  CONST_23  C1T   C1U  N1X  C1B   180.00   0.0  0
 7CP  CONST_24  CL1E  C1P  C1Q  C1U   180.00   0.0  0
 7CP  CONST_25  C1T   C1U  C1Q  CL1F  180.00   0.0  0
 7CP  CONST_26  C1H   C1P  C1Q  CL1F  180.00   0.0  0
 7CP  CONST_27  C1I   C1H  C1P  CL1E  180.00   0.0  0
 7CP  CONST_28  O1D   C1O  N1N  C1Y   180.00   0.0  0
 7CP  CONST_29  H1I   C1I  C1T  C1U   180.00   0.0  0
 7CP  CONST_30  H1H   C1H  C1P  C1Q   180.00   0.0  0
 7CP  CONST_31  HN1N  N1N  C1O  C1R   180.00   0.0  0
 7CP  Var_01    C1K   N1W  C1J  C1L    56.10  30.0  1
 7CP  Var_02    C1K   C1M  C1Y  C1L   -50.11  30.0  3
 7CP  Var_03    C1O   N1N  C1Y  C1L   -74.53  30.0  1
 7CP  Var_04    C1M   C1Y  C1L  C1J    51.31  30.0  3
 7CP  Var_05    C1M   C1K  N1W  C1J   -54.47  30.0  1
 7CP  Var_06    C1Y   C1L  C1J  N1W   -56.26  30.0  1
 7CP  Var_07    C1Y   C1M  C1K  N1W    53.53  30.0  1
 7CP  Var_08    N1X   C1R  C1O  N1N   169.17  30.0  1
 7CP  Var_09    H1A   C1A  N1W  C1J    64.19  30.0  3
 7CP  Var_10    H1B   C1B  N1X  C1R   117.62  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
 7CP  chir_01  C1V  C1Y  C1S  C1G  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
 7CP  plan-1  C1Y   0.020
 7CP  plan-1  N1N   0.020
 7CP  plan-1  C1O   0.020
 7CP  plan-1  O1D   0.020
 7CP  plan-1  C1R   0.020
 7CP  plan-1  HN1N  0.020
 7CP  plan-2  C1O   0.020
 7CP  plan-2  C1R   0.020
 7CP  plan-2  N1X   0.020
 7CP  plan-2  C1B   0.020
 7CP  plan-2  C1U   0.020
 7CP  plan-2  C1Q   0.020
 7CP  plan-2  CL1F  0.020
 7CP  plan-2  C1P   0.020
 7CP  plan-2  CL1E  0.020
 7CP  plan-2  C1H   0.020
 7CP  plan-2  C1I   0.020
 7CP  plan-2  C1T   0.020
 7CP  plan-2  C1S   0.020
 7CP  plan-2  C1V   0.020
 7CP  plan-2  H1H   0.020
 7CP  plan-2  H1I   0.020

