# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:51:09 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 9-[(4-chlorophenyl)methyl]-6-methoxy-1-methyl-4,9-dihydro-3H-beta-carboline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2n(Cc3ccc(Cl)cc3)c4C(=NCCc4c2c1)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
 Y8A  Y8A  9-[(4-chlorophenyl)methyl]-6-methoxy-1-methyl-4,9-dihydro-3H-beta-carboline  ligand  43  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y8A
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
 Y8A  C01   C   CR16  0  -0.484   3.3081   0.3835   0.7265
 Y8A  C02   C   CR6   0   0.388   3.4607   1.6979   0.3189
 Y8A  C03   C   CR16  0  -0.398   2.5645   2.2650  -0.6092
 Y8A  C04   C   CR16  0  -0.291   1.5201   1.5301  -1.1409
 Y8A  C05   C   CR56  0   0.331   1.3749   0.2054  -0.7440
 Y8A  C06   C   CR56  0   0.071   2.2542  -0.3667   0.1993
 Y8A  C08   C   CR5   0   0.234   0.7107  -1.8899  -0.4010
 Y8A  C09   C   CR5   0   0.008   1.7989  -1.6946   0.4104
 Y8A  C10   C   C     0   0.226   0.0892  -3.2169  -0.4778
 Y8A  C12   C   CH2   0  -0.328   1.1414  -3.7258   1.5674
 Y8A  C13   C   CH2   0  -0.538   2.3174  -2.8099   1.2467
 Y8A  C14   C   CH3   0  -0.760  -0.7882  -3.6146  -1.6269
 Y8A  C16   C   CR6   0   0.157  -1.7817   0.2895  -1.0710
 Y8A  C17   C   CR16  0  -0.325  -2.1988   1.5783  -1.3790
 Y8A  C18   C   CR16  0  -0.193  -3.1745   2.2174  -0.6254
 Y8A  C19   C   CR6   0  -0.054  -3.7342   1.5509   0.4511
 Y8A  C20   C   CR16  0  -0.194  -3.3373   0.2629   0.7808
 Y8A  C21   C   CR16  0  -0.296  -2.3642  -0.3585   0.0158
 Y8A  C24   C   CH3   0  -0.435   4.6960   3.7264   0.4918
 Y8A  N07   N   NR5   0  -0.598   0.4544  -0.7403  -1.1256
 Y8A  N11   N   N     0  -0.386   0.3243  -4.0889   0.4232
 Y8A  O23   O   O2    0  -0.482   4.4968   2.3793   0.8627
 Y8A  CL22  CL  CL    0  -0.128  -4.9512   2.3355   1.4037
 Y8A  H1    H   HCR6  0   0.249   3.9932  -0.0477   1.4472
 Y8A  H2    H   HCR6  0   0.278   2.6768   3.2923  -0.9271
 Y8A  H3    H   HCR6  0   0.261   0.8507   1.9976  -1.8508
 Y8A  H4    H   HCH2  0   0.239   1.4909  -4.6440   2.0407
 Y8A  H5    H   HCH2  0   0.236   0.4930  -3.2269   2.2994
 Y8A  H6    H   HCH2  0   0.244   3.1060  -3.3572   0.7170
 Y8A  H7    H   HCH2  0   0.253   2.7605  -2.4471   2.1762
 Y8A  H8    H   HCH3  0   0.256  -0.3475  -3.3466  -2.5880
 Y8A  H9    H   HCH3  0   0.269  -0.9468  -4.6905  -1.6030
 Y8A  H10   H   HCH3  0   0.250  -1.7684  -3.1369  -1.5657
 Y8A  H11   H   HCH2  0   0.305  -1.1164  -1.2841  -2.3738
 Y8A  H12   H   HCH2  0   0.292  -0.4054   0.2603  -2.7141
 Y8A  H13   H   HCR6  0   0.268  -1.7625   2.1022  -2.2209
 Y8A  H14   H   HCR6  0   0.282  -3.4867   3.2221  -0.8756
 Y8A  H15   H   HCR6  0   0.282  -3.7825  -0.2533   1.6204
 Y8A  H16   H   HCR6  0   0.259  -2.0657  -1.3658   0.2801
 Y8A  H17   H   HCH3  0   0.224   4.8845   3.8370  -0.5797
 Y8A  H18   H   HCH3  0   0.224   3.8480   4.3604   0.7658
 Y8A  H19   H   HCH3  0   0.257   5.5733   4.0692   1.0354
 Y8A  C15   C   CH2   0  -0.452  -0.7193  -0.3919  -1.8976

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
 Y8A  CL22  C19  single    1.733  0.020  1.733
 Y8A  C19   C18  aromatic  1.384  0.020  1.384
 Y8A  C19   C20  aromatic  1.388  0.020  1.388
 Y8A  C18   C17  aromatic  1.389  0.020  1.389
 Y8A  C20   C21  aromatic  1.385  0.020  1.385
 Y8A  C17   C16  aromatic  1.389  0.020  1.389
 Y8A  C03   C04  aromatic  1.383  0.020  1.383
 Y8A  C03   C02  aromatic  1.409  0.020  1.409
 Y8A  O23   C02  single    1.354  0.020  1.354
 Y8A  O23   C24  single    1.411  0.020  1.411
 Y8A  C04   C05  aromatic  1.391  0.020  1.391
 Y8A  C21   C16  aromatic  1.393  0.020  1.393
 Y8A  C16   C15  single    1.509  0.020  1.509
 Y8A  C02   C01  aromatic  1.385  0.020  1.385
 Y8A  C05   N07  aromatic  1.374  0.020  1.374
 Y8A  C05   C06  aromatic  1.411  0.020  1.411
 Y8A  C15   N07  single    1.447  0.020  1.447
 Y8A  C01   C06  aromatic  1.397  0.020  1.397
 Y8A  N07   C08  aromatic  1.383  0.020  1.383
 Y8A  C06   C09  aromatic  1.420  0.020  1.420
 Y8A  C08   C09  aromatic  1.371  0.020  1.371
 Y8A  C08   C10  single    1.467  0.020  1.467
 Y8A  C09   C13  single    1.487  0.020  1.487
 Y8A  C10   C14  single    1.499  0.020  1.499
 Y8A  C10   N11  double    1.276  0.020  1.276
 Y8A  C13   C12  single    1.525  0.020  1.525
 Y8A  N11   C12  single    1.452  0.020  1.452
 Y8A  C01   H1   single    0.930  0.020  1.080
 Y8A  C03   H2   single    0.930  0.020  1.080
 Y8A  C04   H3   single    0.930  0.020  1.080
 Y8A  C12   H4   single    0.970  0.020  1.090
 Y8A  C12   H5   single    0.970  0.020  1.090
 Y8A  C13   H6   single    0.970  0.020  1.090
 Y8A  C13   H7   single    0.970  0.020  1.090
 Y8A  C14   H8   single    0.970  0.020  1.090
 Y8A  C14   H9   single    0.970  0.020  1.090
 Y8A  C14   H10  single    0.970  0.020  1.090
 Y8A  C15   H11  single    0.970  0.020  1.090
 Y8A  C15   H12  single    0.970  0.020  1.090
 Y8A  C17   H13  single    0.930  0.020  1.080
 Y8A  C18   H14  single    0.930  0.020  1.080
 Y8A  C20   H15  single    0.930  0.020  1.080
 Y8A  C21   H16  single    0.930  0.020  1.080
 Y8A  C24   H17  single    0.970  0.020  1.090
 Y8A  C24   H18  single    0.970  0.020  1.090
 Y8A  C24   H19  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
 Y8A  H1    C01  C06  120.94  3.000
 Y8A  H1    C01  C02  120.25  3.000
 Y8A  C06   C01  C02  118.81  3.000
 Y8A  O23   C02  C03  123.27  3.000
 Y8A  O23   C02  C01  116.35  3.000
 Y8A  C03   C02  C01  120.38  3.000
 Y8A  H2    C03  C04  118.04  3.000
 Y8A  H2    C03  C02  120.66  3.000
 Y8A  C04   C03  C02  121.30  3.000
 Y8A  H3    C04  C05  122.30  3.000
 Y8A  H3    C04  C03  119.33  3.000
 Y8A  C05   C04  C03  118.38  3.000
 Y8A  N07   C05  C06  108.92  3.000
 Y8A  C06   C05  C04  120.80  3.000
 Y8A  N07   C05  C04  130.28  3.000
 Y8A  C09   C06  C05  106.19  3.000
 Y8A  C09   C06  C01  133.49  3.000
 Y8A  C05   C06  C01  120.32  3.000
 Y8A  N07   C08  C10  130.23  3.000
 Y8A  C10   C08  C09  119.73  3.000
 Y8A  N07   C08  C09  109.80  3.000
 Y8A  C13   C09  C08  120.17  3.000
 Y8A  C13   C09  C06  132.32  3.000
 Y8A  C08   C09  C06  107.44  3.000
 Y8A  N11   C10  C14  117.89  3.000
 Y8A  N11   C10  C08  120.20  3.000
 Y8A  C14   C10  C08  121.86  3.000
 Y8A  H5    C12  H4   106.41  3.000
 Y8A  H5    C12  N11  107.86  3.000
 Y8A  H4    C12  N11  108.17  3.000
 Y8A  H5    C12  C13  108.83  3.000
 Y8A  H4    C12  C13  110.48  3.000
 Y8A  N11   C12  C13  114.74  3.000
 Y8A  H7    C13  H6   106.58  3.000
 Y8A  H7    C13  C12  109.49  3.000
 Y8A  H6    C13  C12  110.89  3.000
 Y8A  H7    C13  C09  111.78  3.000
 Y8A  H6    C13  C09  110.70  3.000
 Y8A  C12   C13  C09  107.45  3.000
 Y8A  H10   C14  H9   107.49  3.000
 Y8A  H10   C14  H8   107.73  3.000
 Y8A  H9    C14  H8   108.74  3.000
 Y8A  H10   C14  C10  111.48  3.000
 Y8A  H9    C14  C10  109.32  3.000
 Y8A  H8    C14  C10  111.95  3.000
 Y8A  C21   C16  C17  118.62  3.000
 Y8A  C21   C16  C15  120.78  3.000
 Y8A  C17   C16  C15  120.60  3.000
 Y8A  H13   C17  C18  118.83  3.000
 Y8A  H13   C17  C16  120.00  3.000
 Y8A  C18   C17  C16  121.17  3.000
 Y8A  H14   C18  C19  120.69  3.000
 Y8A  H14   C18  C17  120.32  3.000
 Y8A  C19   C18  C17  118.98  3.000
 Y8A  CL22  C19  C20  119.37  3.000
 Y8A  C20   C19  C18  121.07  3.000
 Y8A  CL22  C19  C18  119.56  3.000
 Y8A  H15   C20  C21  120.26  3.000
 Y8A  H15   C20  C19  120.65  3.000
 Y8A  C21   C20  C19  119.09  3.000
 Y8A  H16   C21  C20  118.42  3.000
 Y8A  H16   C21  C16  120.52  3.000
 Y8A  C20   C21  C16  121.06  3.000
 Y8A  H19   C24  H18  108.51  3.000
 Y8A  H19   C24  H17  108.60  3.000
 Y8A  H18   C24  H17  108.69  3.000
 Y8A  H19   C24  O23  106.46  3.000
 Y8A  H18   C24  O23  112.21  3.000
 Y8A  H17   C24  O23  112.23  3.000
 Y8A  C15   N07  C08  129.04  3.000
 Y8A  C08   N07  C05  107.61  3.000
 Y8A  C15   N07  C05  121.72  3.000
 Y8A  C12   N11  C10  119.29  3.000
 Y8A  C24   O23  C02  118.87  3.000
 Y8A  H12   C15  H11  105.55  3.000
 Y8A  H12   C15  N07  108.04  3.000
 Y8A  H11   C15  N07  109.43  3.000
 Y8A  H12   C15  C16  110.03  3.000
 Y8A  H11   C15  C16  110.71  3.000
 Y8A  N07   C15  C16  112.80  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
 Y8A  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 Y8A  CONST_02  C04   C05  C06  C01    0.00   0.0  0
 Y8A  CONST_03  N07   C05  C06  C01  180.00   0.0  0
 Y8A  CONST_04  C08   C09  C06  C01  180.00   0.0  0
 Y8A  CONST_05  C05   C04  C03  C02    0.00   0.0  0
 Y8A  CONST_06  C05   C06  C01  C02    0.00   0.0  0
 Y8A  CONST_07  C09   C06  C01  C02  180.00   0.0  0
 Y8A  CONST_08  N07   C05  C04  C03  180.00   0.0  0
 Y8A  CONST_09  C06   C05  C04  C03    0.00   0.0  0
 Y8A  CONST_10  C06   C01  C02  C03    0.00   0.0  0
 Y8A  CONST_11  C08   N07  C05  C04  180.00   0.0  0
 Y8A  CONST_12  C09   C06  C05  C04  180.00   0.0  0
 Y8A  CONST_13  C09   C08  N07  C05    0.00   0.0  0
 Y8A  CONST_14  C08   C09  C06  C05    0.00   0.0  0
 Y8A  CONST_15  C08   N07  C05  C06    0.00   0.0  0
 Y8A  CONST_16  N07   C08  C09  C06    0.00   0.0  0
 Y8A  CONST_17  N07   C05  C06  C09    0.00   0.0  0
 Y8A  CONST_18  C19   C18  C17  C16    0.00   0.0  0
 Y8A  CONST_19  C19   C20  C21  C16    0.00   0.0  0
 Y8A  CONST_20  C20   C19  C18  C17    0.00   0.0  0
 Y8A  CONST_21  C20   C21  C16  C17    0.00   0.0  0
 Y8A  CONST_22  C21   C20  C19  C18    0.00   0.0  0
 Y8A  CONST_23  C21   C16  C17  C18    0.00   0.0  0
 Y8A  CONST_24  O23   C02  C03  C04  180.00   0.0  0
 Y8A  CONST_25  C15   N07  C05  C04    0.00   0.0  0
 Y8A  CONST_26  C15   N07  C05  C06  180.00   0.0  0
 Y8A  CONST_27  O23   C02  C01  C06  180.00   0.0  0
 Y8A  CONST_28  C15   N07  C08  C09  180.00   0.0  0
 Y8A  CONST_30  C18   C17  C16  C15  180.00   0.0  0
 Y8A  CONST_31  C20   C21  C16  C15  180.00   0.0  0
 Y8A  CONST_32  CL22  C19  C18  C17  180.00   0.0  0
 Y8A  CONST_33  CL22  C19  C20  C21  180.00   0.0  0
 Y8A  CONST_34  H2    C03  C02  C01  180.00   0.0  0
 Y8A  CONST_35  H3    C04  C03  C02  180.00   0.0  0
 Y8A  CONST_36  H1    C01  C02  C03  180.00   0.0  0
 Y8A  CONST_37  H14   C18  C17  C16  180.00   0.0  0
 Y8A  CONST_38  H15   C20  C21  C16  180.00   0.0  0
 Y8A  CONST_39  H16   C21  C16  C17  180.00   0.0  0
 Y8A  CONST_40  H13   C17  C18  C19  180.00   0.0  0
 Y8A  Var_01    C12   C13  C09  C06  154.89  30.0  1
 Y8A  Var_02    N11   C10  C08  C09   17.37  30.0  1
 Y8A  Var_03    N11   C12  C13  C09   48.23  30.0  1
 Y8A  Var_04    C13   C12  N11  C10  -38.28  30.0  1
 Y8A  Var_05    C16   C15  N07  C05  -75.60  30.0  2
 Y8A  Var_06    N07   C15  C16  C17  119.26  30.0  2
 Y8A  Var_07    H8    C14  C10  C08   46.29  30.0  3
 Y8A  Var_08    H17   C24  O23  C02  -60.97  30.0  3

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
 Y8A  plan-1  C16   0.020
 Y8A  plan-1  C17   0.020
 Y8A  plan-1  C18   0.020
 Y8A  plan-1  C19   0.020
 Y8A  plan-1  C20   0.020
 Y8A  plan-1  C21   0.020
 Y8A  plan-1  CL22  0.020
 Y8A  plan-1  H13   0.020
 Y8A  plan-1  H14   0.020
 Y8A  plan-1  H15   0.020
 Y8A  plan-1  H16   0.020
 Y8A  plan-1  C15   0.020
 Y8A  plan-2  C01   0.020
 Y8A  plan-2  C02   0.020
 Y8A  plan-2  C03   0.020
 Y8A  plan-2  C04   0.020
 Y8A  plan-2  C05   0.020
 Y8A  plan-2  C06   0.020
 Y8A  plan-2  C08   0.020
 Y8A  plan-2  C09   0.020
 Y8A  plan-2  C10   0.020
 Y8A  plan-2  C13   0.020
 Y8A  plan-2  N07   0.020
 Y8A  plan-2  O23   0.020
 Y8A  plan-2  H1    0.020
 Y8A  plan-2  H2    0.020
 Y8A  plan-2  H3    0.020
 Y8A  plan-2  C15   0.020

