# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 17:53:48 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-cyclohexyl-N-{[1-(4-methylphenyl)-1H-indol-3-yl]methyl}methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)n2cc(CNCC3CCCCC3)c4ccccc24
#
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
 047  047  1-cyclohexyl-N-{[1-(4-methylphenyl)-1H-indol-3-yl]methyl}methanamine  ligand  53  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_047
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
 047  N1    N  NR5   0  -0.638   7.9505  -5.5315  -0.5391
 047  C2    C  CR56  0   0.345   8.7751  -4.7662  -1.3328
 047  C3    C  CR56  0   0.032   7.9534  -4.0113  -2.1958
 047  C4    C  CR5   0  -0.009   6.5927  -4.3388  -1.8823
 047  C5    C  CR15  0  -0.095   6.6440  -5.2580  -0.8802
 047  C7    C  CH2   0  -0.355   5.3680  -3.7674  -2.5116
 047  N10   N  NH1   0  -0.580   5.3985  -3.9037  -3.9547
 047  C12   C  CH2   0  -0.234   4.2357  -3.3283  -4.5990
 047  C15   C  CH1   0  -0.259   4.2920  -3.4580  -6.1158
 047  C17   C  CH2   0  -0.405   5.5092  -2.7581  -6.7178
 047  C20   C  CH2   0  -0.432   5.5369  -2.8799  -8.2385
 047  C23   C  CH2   0  -0.429   4.2492  -2.3530  -8.8633
 047  C26   C  CH2   0  -0.430   3.0259  -3.0422  -8.2677
 047  C29   C  CH2   0  -0.416   3.0063  -2.9238  -6.7469
 047  C32   C  CR16  0  -0.369   8.5423  -3.1353  -3.1136
 047  C34   C  CR16  0  -0.269   9.9181  -3.0154  -3.1328
 047  C36   C  CR16  0  -0.278  10.7184  -3.7569  -2.2493
 047  C38   C  CR16  0  -0.301  10.1636  -4.6390  -1.3411
 047  C40   C  CR6   0   0.313   8.3436  -6.4166   0.4836
 047  C41   C  CR16  0  -0.284   7.7306  -6.3481   1.7310
 047  C43   C  CR16  0  -0.291   8.1008  -7.2286   2.7342
 047  C45   C  CR6   0   0.094   9.0993  -8.1797   2.5310
 047  C46   C  CR16  0  -0.300   9.7081  -8.2280   1.2800
 047  C48   C  CR16  0  -0.289   9.3305  -7.3686   0.2582
 047  C50   C  CH3   0  -0.722   9.4866  -9.1334   3.6228
 047  H5    H  HCR5  0   0.292   5.8350  -5.7671  -0.3784
 047  H71   H  HCH2  0   0.205   4.4767  -4.2241  -2.0518
 047  H72   H  HCH2  0   0.225   5.3057  -2.6972  -2.2829
 047  HN10  H  HNH1  0   0.334   5.4581  -4.8876  -4.1914
 047  H121  H  HCH2  0   0.190   3.2927  -3.7726  -4.2354
 047  H122  H  HCH2  0   0.206   4.1911  -2.2655  -4.3325
 047  H15   H  HCH1  0   0.204   4.3603  -4.5281  -6.3629
 047  H171  H  HCH2  0   0.230   6.4254  -3.1621  -6.2830
 047  H172  H  HCH2  0   0.196   5.4786  -1.6968  -6.4396
 047  H201  H  HCH2  0   0.206   5.6701  -3.9321  -8.5145
 047  H202  H  HCH2  0   0.223   6.4003  -2.3449  -8.6425
 047  H231  H  HCH2  0   0.206   4.1779  -1.2742  -8.6846
 047  H232  H  HCH2  0   0.223   4.2690  -2.4862  -9.9481
 047  H261  H  HCH2  0   0.224   2.1101  -2.6203  -8.6890
 047  H262  H  HCH2  0   0.207   3.0356  -4.1019  -8.5463
 047  H291  H  HCH2  0   0.204   2.8817  -1.8700  -6.4687
 047  H292  H  HCH2  0   0.222   2.1410  -3.4546  -6.3386
 047  H32   H  HCR6  0   0.247   7.9211  -2.5736  -3.7988
 047  H34   H  HCR6  0   0.246  10.3912  -2.3425  -3.8367
 047  H36   H  HCR6  0   0.250  11.7938  -3.6374  -2.2791
 047  H38   H  HCR6  0   0.265  10.7933  -5.2008  -0.6642
 047  H41   H  HCR6  0   0.271   6.9719  -5.5989   1.9201
 047  H43   H  HCR6  0   0.254   7.6131  -7.1618   3.6995
 047  H46   H  HCR6  0   0.255  10.4852  -8.9593   1.0921
 047  H48   H  HCR6  0   0.274   9.7991  -7.4500  -0.7141
 047  H501  H  HCH3  0   0.245  10.4529  -9.5955   3.4258
 047  H502  H  HCH3  0   0.246   9.5422  -8.6318   4.5890
 047  H503  H  HCH3  0   0.250   8.7525  -9.9359   3.7194

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
 047  N1   C2    single    1.377  0.020  1.377
 047  N1   C40   single    1.408  0.020  1.408
 047  N1   C5    single    1.378  0.020  1.378
 047  C2   C38   aromatic  1.394  0.020  1.394
 047  C2   C3    aromatic  1.411  0.020  1.411
 047  C3   C32   aromatic  1.399  0.020  1.399
 047  C3   C4    single    1.434  0.020  1.434
 047  C4   C7    single    1.491  0.020  1.491
 047  C4   C5    double    1.361  0.020  1.361
 047  C5   H5    single    0.930  0.020  1.080
 047  C7   N10   single    1.450  0.020  1.450
 047  C7   H71   single    0.970  0.020  1.090
 047  C7   H72   single    0.970  0.020  1.090
 047  N10  C12   single    1.449  0.020  1.449
 047  N10  HN10  single    0.890  0.020  1.040
 047  C12  C15   single    1.523  0.020  1.523
 047  C12  H121  single    0.970  0.020  1.090
 047  C12  H122  single    0.970  0.020  1.090
 047  C15  C29   single    1.529  0.020  1.529
 047  C15  C17   single    1.528  0.020  1.528
 047  C15  H15   single    0.970  0.020  1.090
 047  C17  C20   single    1.526  0.020  1.526
 047  C17  H171  single    0.970  0.020  1.090
 047  C17  H172  single    0.970  0.020  1.090
 047  C20  C23   single    1.525  0.020  1.525
 047  C20  H201  single    0.970  0.020  1.090
 047  C20  H202  single    0.970  0.020  1.090
 047  C23  C26   single    1.525  0.020  1.525
 047  C23  H231  single    0.970  0.020  1.090
 047  C23  H232  single    0.970  0.020  1.090
 047  C26  C29   single    1.526  0.020  1.526
 047  C26  H261  single    0.970  0.020  1.090
 047  C26  H262  single    0.970  0.020  1.090
 047  C29  H291  single    0.970  0.020  1.090
 047  C29  H292  single    0.970  0.020  1.090
 047  C32  C34   aromatic  1.381  0.020  1.381
 047  C32  H32   single    0.930  0.020  1.080
 047  C34  C36   aromatic  1.404  0.020  1.404
 047  C34  H34   single    0.930  0.020  1.080
 047  C36  C38   aromatic  1.382  0.020  1.382
 047  C36  H36   single    0.930  0.020  1.080
 047  C38  H38   single    0.930  0.020  1.080
 047  C40  C41   aromatic  1.392  0.020  1.392
 047  C40  C48   aromatic  1.390  0.020  1.390
 047  C41  C43   aromatic  1.385  0.020  1.385
 047  C41  H41   single    0.930  0.020  1.080
 047  C43  C45   aromatic  1.394  0.020  1.394
 047  C43  H43   single    0.930  0.020  1.080
 047  C45  C46   aromatic  1.392  0.020  1.392
 047  C45  C50   single    1.500  0.020  1.500
 047  C46  C48   aromatic  1.387  0.020  1.387
 047  C46  H46   single    0.930  0.020  1.080
 047  C48  H48   single    0.930  0.020  1.080
 047  C50  H501  single    0.970  0.020  1.090
 047  C50  H502  single    0.970  0.020  1.090
 047  C50  H503  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
 047  C40   N1   C5    124.70  3.000
 047  C5    N1   C2    108.35  3.000
 047  C40   N1   C2    126.92  3.000
 047  C38   C2   C3    121.85  3.000
 047  C3    C2   N1    107.53  3.000
 047  C38   C2   N1    130.58  3.000
 047  C32   C3   C4    133.30  3.000
 047  C4    C3   C2    107.26  3.000
 047  C32   C3   C2    119.43  3.000
 047  C7    C4   C5    126.92  3.000
 047  C5    C4   C3    106.23  3.000
 047  C7    C4   C3    126.84  3.000
 047  H5    C5   C4    129.24  3.000
 047  H5    C5   N1    120.13  3.000
 047  C4    C5   N1    110.62  3.000
 047  H72   C7   H71   105.76  3.000
 047  H72   C7   N10   107.49  3.000
 047  H71   C7   N10   113.17  3.000
 047  H72   C7   C4    109.44  3.000
 047  H71   C7   C4    109.24  3.000
 047  N10   C7   C4    111.52  3.000
 047  HN10  N10  C12   109.19  3.000
 047  HN10  N10  C7    108.96  3.000
 047  C12   N10  C7    112.86  3.000
 047  H122  C12  H121  105.97  3.000
 047  H122  C12  C15   109.03  3.000
 047  H121  C12  C15   108.98  3.000
 047  H122  C12  N10   108.03  3.000
 047  H121  C12  N10   112.30  3.000
 047  C15   C12  N10   112.30  3.000
 047  H15   C15  C29   107.42  3.000
 047  H15   C15  C17   107.91  3.000
 047  C29   C15  C17   110.32  3.000
 047  H15   C15  C12   107.98  3.000
 047  C17   C15  C12   112.51  3.000
 047  C29   C15  C12   110.50  3.000
 047  H172  C17  H171  106.28  3.000
 047  H172  C17  C20   109.29  3.000
 047  H171  C17  C20   110.62  3.000
 047  H172  C17  C15   108.72  3.000
 047  H171  C17  C15   110.01  3.000
 047  C20   C17  C15   111.75  3.000
 047  H202  C20  H201  106.31  3.000
 047  H202  C20  C23   110.26  3.000
 047  H201  C20  C23   109.34  3.000
 047  H202  C20  C17   110.10  3.000
 047  H201  C20  C17   109.26  3.000
 047  C23   C20  C17   111.43  3.000
 047  H232  C23  H231  106.44  3.000
 047  H232  C23  C26   110.30  3.000
 047  H231  C23  C26   109.21  3.000
 047  H232  C23  C20   110.43  3.000
 047  H231  C23  C20   109.16  3.000
 047  C26   C23  C20   111.16  3.000
 047  H262  C26  H261  106.42  3.000
 047  H262  C26  C29   109.18  3.000
 047  H261  C26  C29   110.10  3.000
 047  H262  C26  C23   109.31  3.000
 047  H261  C26  C23   110.31  3.000
 047  C29   C26  C23   111.38  3.000
 047  H292  C29  H291  106.35  3.000
 047  H292  C29  C26   110.15  3.000
 047  H291  C29  C26   109.19  3.000
 047  H292  C29  C15   109.97  3.000
 047  H291  C29  C15   109.06  3.000
 047  C26   C29  C15   111.94  3.000
 047  H32   C32  C34   121.19  3.000
 047  H32   C32  C3    119.93  3.000
 047  C34   C32  C3    118.88  3.000
 047  H34   C34  C36   119.23  3.000
 047  H34   C34  C32   119.89  3.000
 047  C36   C34  C32   120.88  3.000
 047  H36   C36  C38   119.16  3.000
 047  H36   C36  C34   119.39  3.000
 047  C38   C36  C34   121.45  3.000
 047  H38   C38  C36   120.59  3.000
 047  H38   C38  C2    121.91  3.000
 047  C36   C38  C2    117.50  3.000
 047  C48   C40  C41   119.47  3.000
 047  C48   C40  N1    120.73  3.000
 047  C41   C40  N1    119.80  3.000
 047  H41   C41  C43   120.03  3.000
 047  H41   C41  C40   119.95  3.000
 047  C43   C41  C40   120.01  3.000
 047  H43   C43  C45   119.62  3.000
 047  H43   C43  C41   119.06  3.000
 047  C45   C43  C41   121.31  3.000
 047  C50   C45  C46   121.27  3.000
 047  C50   C45  C43   120.83  3.000
 047  C46   C45  C43   117.89  3.000
 047  H46   C46  C48   119.05  3.000
 047  H46   C46  C45   119.53  3.000
 047  C48   C46  C45   121.42  3.000
 047  H48   C48  C46   119.81  3.000
 047  H48   C48  C40   120.31  3.000
 047  C46   C48  C40   119.88  3.000
 047  H503  C50  H502  107.10  3.000
 047  H503  C50  H501  107.50  3.000
 047  H502  C50  H501  108.08  3.000
 047  H503  C50  C45   110.97  3.000
 047  H502  C50  C45   111.45  3.000
 047  H501  C50  C45   111.54  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
 047  CONST_01  C34   C36  C38  C2      0.00   0.0  0
 047  CONST_02  C34   C32  C3   C2      0.00   0.0  0
 047  CONST_03  C36   C38  C2   C3      0.00   0.0  0
 047  CONST_04  C36   C34  C32  C3      0.00   0.0  0
 047  CONST_05  C38   C2   C3   C32     0.00   0.0  0
 047  CONST_06  C38   C36  C34  C32     0.00   0.0  0
 047  CONST_07  C45   C43  C41  C40     0.00   0.0  0
 047  CONST_08  C45   C46  C48  C40     0.00   0.0  0
 047  CONST_09  C46   C48  C40  C41     0.00   0.0  0
 047  CONST_10  C46   C45  C43  C41     0.00   0.0  0
 047  CONST_11  C48   C40  C41  C43     0.00   0.0  0
 047  CONST_12  C48   C46  C45  C43     0.00   0.0  0
 047  CONST_13  C43   C41  C40  N1    180.00   0.0  0
 047  CONST_14  C46   C48  C40  N1    180.00   0.0  0
 047  CONST_15  C50   C45  C43  C41   180.00   0.0  0
 047  CONST_16  C50   C45  C46  C48   180.00   0.0  0
 047  CONST_17  H38   C38  C2   N1      0.00   0.0  0
 047  CONST_18  H41   C41  C40  N1      0.00   0.0  0
 047  CONST_19  H48   C48  C40  N1      0.00   0.0  0
 047  CONST_20  H36   C36  C38  C2    180.00   0.0  0
 047  CONST_21  H32   C32  C3   C2    180.00   0.0  0
 047  CONST_22  H34   C34  C32  C3    180.00   0.0  0
 047  CONST_23  H43   C43  C41  C40   180.00   0.0  0
 047  CONST_24  H46   C46  C48  C40   180.00   0.0  0
 047  Var_01    C41   C40  N1   C2    130.95  30.0  2
 047  Var_02    C23   C26  C29  C15   -55.30  30.0  1
 047  Var_03    C23   C20  C17  C15    55.60  30.0  1
 047  Var_04    C26   C23  C20  C17   -54.86  30.0  1
 047  Var_05    C29   C26  C23  C20    54.65  30.0  1
 047  Var_06    N10   C7   C4   C3     54.15  30.0  3
 047  Var_07    H501  C50  C45  C43  -162.88  30.0  2
 047  Var_08    C12   N10  C7   C4   -178.60  30.0  3
 047  Var_09    C15   C12  N10  C7    179.06  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
 047  chir_01  C15  C12  C29  C17  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
 047  plan-1  N1   0.020
 047  plan-1  C40  0.020
 047  plan-1  C41  0.020
 047  plan-1  C43  0.020
 047  plan-1  C45  0.020
 047  plan-1  C46  0.020
 047  plan-1  C48  0.020
 047  plan-1  C50  0.020
 047  plan-1  H41  0.020
 047  plan-1  H43  0.020
 047  plan-1  H46  0.020
 047  plan-1  H48  0.020
 047  plan-2  N1   0.020
 047  plan-2  C2   0.020
 047  plan-2  C3   0.020
 047  plan-2  C4   0.020
 047  plan-2  C5   0.020
 047  plan-2  C7   0.020
 047  plan-2  C32  0.020
 047  plan-2  C34  0.020
 047  plan-2  C36  0.020
 047  plan-2  C38  0.020
 047  plan-2  C40  0.020
 047  plan-2  H5   0.020
 047  plan-2  H32  0.020
 047  plan-2  H34  0.020
 047  plan-2  H36  0.020
 047  plan-2  H38  0.020

