# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 16:54:35 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (1~{S},2~{S},4~{R})-~{N}-(2,4,6-trimethylphenyl)bicyclo[2.2.1]heptane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(NC(=O)[C@H]2C[C@@H]3CC[C@H]2C3)c(C)c1
#
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
 7YV  7YV  "(1S,2S,4R)-N-(2,4,6-trimethylphenyl)bicyclo[2.2.1]heptane-2-carboxamid"  ligand  42  19  .  2022-09-16  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7YV
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
 7YV  C10   C  C     0   0.556  128.1517  110.4190  110.3417
 7YV  C13   C  CR6   0   0.131  126.2650  108.4623  108.6597
 7YV  C15   C  CR16  0  -0.397  125.0189  108.0024  108.2405
 7YV  O01   O  O     0  -0.470  127.4427  110.0335  111.2573
 7YV  N02   N  NH1   0  -0.734  127.7617  110.3442  109.0470
 7YV  C03   C  CH1   0  -0.254  130.5971  109.8206  110.4742
 7YV  C04   C  CH1   0  -0.255  130.9960  110.7874  112.4620
 7YV  C05   C  CH2   0  -0.433  130.6750  109.3840  111.9398
 7YV  C06   C  CH1   0  -0.398  129.5519  110.9664  110.5291
 7YV  C07   C  CH2   0  -0.424  129.8071  111.5905  111.9210
 7YV  C08   C  CH2   0  -0.438  131.9764  110.4639  110.2763
 7YV  C09   C  CH2   0  -0.436  132.2429  111.1506  111.6418
 7YV  C11   C  CR6   0   0.201  126.5057  109.8364  108.6360
 7YV  C12   C  CR6   0   0.114  125.5302  110.7345  108.1941
 7YV  C14   C  CR16  0  -0.389  124.3041  110.2336  107.7747
 7YV  C16   C  CR6   0   0.136  124.0289  108.8692  107.7934
 7YV  C19   C  CH3   0  -0.723  122.7029  108.3519  107.3157
 7YV  H151  H  HCR6  0   0.238  124.8221  106.9359  108.2571
 7YV  H172  H  HCH3  0   0.246  126.0805  112.5746  109.1722
 7YV  H173  H  HCH3  0   0.245  126.6218  112.4671  107.5081
 7YV  H171  H  HCH3  0   0.247  124.9231  112.7646  107.8577
 7YV  H021  H  HNH1  0   0.401  128.3541  110.7647  108.3466
 7YV  H031  H  HCH1  0   0.241  130.3646  109.0459  109.7420
 7YV  H041  H  HCH1  0   0.223  131.1322  110.8821  113.5398
 7YV  H051  H  HCH2  0   0.236  129.7411  108.9766  112.3306
 7YV  H052  H  HCH2  0   0.232  131.4730  108.6598  112.1211
 7YV  H061  H  HCH1  0   0.262  129.7523  111.6833  109.7275
 7YV  H071  H  HCH2  0   0.233  130.0218  112.6582  111.8544
 7YV  H072  H  HCH2  0   0.239  128.9360  111.4711  112.5670
 7YV  H082  H  HCH2  0   0.235  132.7234  109.6945  110.0717
 7YV  H081  H  HCH2  0   0.230  131.9931  111.1589  109.4350
 7YV  H091  H  HCH2  0   0.232  133.1470  110.7578  112.1109
 7YV  H092  H  HCH2  0   0.225  132.3714  112.2310  111.5530
 7YV  H141  H  HCR6  0   0.238  123.5419  110.9263  107.4336
 7YV  H181  H  HCH3  0   0.243  128.2853  107.7103  108.6652
 7YV  H182  H  HCH3  0   0.247  127.4532  107.5371  110.1983
 7YV  H183  H  HCH3  0   0.247  127.0429  106.4729  108.8579
 7YV  H191  H  HCH3  0   0.246  122.6535  108.3489  106.2248
 7YV  H192  H  HCH3  0   0.243  122.5259  107.3317  107.6537
 7YV  H193  H  HCH3  0   0.242  121.8805  108.9733  107.6708
 7YV  C18   C  CH3   0  -0.737  127.3163  107.4947  109.1168
 7YV  C17   C  CH3   0  -0.723  125.8024  112.2102  108.1820

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
 7YV  C19  C16   single    1.501  0.020  1.501
 7YV  C16  C14   aromatic  1.392  0.020  1.392
 7YV  C16  C15   aromatic  1.390  0.020  1.390
 7YV  C14  C12   aromatic  1.389  0.020  1.389
 7YV  C15  C13   aromatic  1.393  0.020  1.393
 7YV  C12  C17   single    1.501  0.020  1.501
 7YV  C12  C11   aromatic  1.398  0.020  1.398
 7YV  C13  C11   aromatic  1.395  0.020  1.395
 7YV  C13  C18   single    1.500  0.020  1.500
 7YV  C11  N02   single    1.416  0.020  1.416
 7YV  N02  C10   single    1.354  0.020  1.354
 7YV  C08  C03   single    1.535  0.020  1.535
 7YV  C08  C09   single    1.551  0.020  1.551
 7YV  C10  C06   single    1.515  0.020  1.515
 7YV  C10  O01   double    1.220  0.020  1.220
 7YV  C06  C03   single    1.552  0.020  1.552
 7YV  C06  C07   single    1.547  0.020  1.547
 7YV  C03  C05   single    1.531  0.020  1.531
 7YV  C09  C04   single    1.536  0.020  1.536
 7YV  C05  C04   single    1.531  0.020  1.531
 7YV  C07  C04   single    1.533  0.020  1.533
 7YV  C15  H151  single    0.930  0.020  1.080
 7YV  C17  H172  single    0.970  0.020  1.090
 7YV  C17  H173  single    0.970  0.020  1.090
 7YV  C17  H171  single    0.970  0.020  1.090
 7YV  N02  H021  single    0.860  0.020  1.020
 7YV  C03  H031  single    0.970  0.020  1.090
 7YV  C04  H041  single    0.970  0.020  1.090
 7YV  C05  H051  single    0.970  0.020  1.090
 7YV  C05  H052  single    0.970  0.020  1.090
 7YV  C06  H061  single    0.970  0.020  1.090
 7YV  C07  H071  single    0.970  0.020  1.090
 7YV  C07  H072  single    0.970  0.020  1.090
 7YV  C08  H082  single    0.970  0.020  1.090
 7YV  C08  H081  single    0.970  0.020  1.090
 7YV  C09  H091  single    0.970  0.020  1.090
 7YV  C09  H092  single    0.970  0.020  1.090
 7YV  C14  H141  single    0.930  0.020  1.080
 7YV  C18  H181  single    0.970  0.020  1.090
 7YV  C18  H182  single    0.970  0.020  1.090
 7YV  C18  H183  single    0.970  0.020  1.090
 7YV  C19  H191  single    0.970  0.020  1.090
 7YV  C19  H192  single    0.970  0.020  1.090
 7YV  C19  H193  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
 7YV  C06   C10  N02   113.85  3.000
 7YV  C06   C10  O01   123.93  3.000
 7YV  N02   C10  O01   122.18  3.000
 7YV  C18   C13  C11   121.30  3.000
 7YV  C18   C13  C15   120.38  3.000
 7YV  C11   C13  C15   118.32  3.000
 7YV  H151  C15  C16   119.27  3.000
 7YV  H151  C15  C13   118.84  3.000
 7YV  C16   C15  C13   121.89  3.000
 7YV  H021  N02  C11   117.96  3.000
 7YV  H021  N02  C10   118.13  3.000
 7YV  C11   N02  C10   123.56  3.000
 7YV  H031  C03  C08   113.74  3.000
 7YV  H031  C03  C06   113.86  3.000
 7YV  C08   C03  C06   107.48  3.000
 7YV  H031  C03  C05   116.79  3.000
 7YV  C06   C03  C05   102.18  3.000
 7YV  C08   C03  C05   101.38  3.000
 7YV  H041  C04  C09   113.94  3.000
 7YV  H041  C04  C07   113.59  3.000
 7YV  C09   C04  C07   108.49  3.000
 7YV  H041  C04  C05   116.28  3.000
 7YV  C07   C04  C05   101.37  3.000
 7YV  C09   C04  C05   101.81  3.000
 7YV  H052  C05  H051  108.55  3.000
 7YV  H052  C05  C04   113.43  3.000
 7YV  H051  C05  C04   113.54  3.000
 7YV  H052  C05  C03   112.64  3.000
 7YV  H051  C05  C03   113.93  3.000
 7YV  C04   C05  C03    94.34  3.000
 7YV  H061  C06  C07   111.40  3.000
 7YV  H061  C06  C03   109.55  3.000
 7YV  C07   C06  C03   102.63  3.000
 7YV  H061  C06  C10   108.39  3.000
 7YV  C07   C06  C10   114.18  3.000
 7YV  C03   C06  C10   110.57  3.000
 7YV  H072  C07  H071  107.48  3.000
 7YV  H072  C07  C06   110.92  3.000
 7YV  H071  C07  C06   111.86  3.000
 7YV  H072  C07  C04   110.66  3.000
 7YV  H071  C07  C04   112.42  3.000
 7YV  C06   C07  C04   103.54  3.000
 7YV  H081  C08  H082  107.08  3.000
 7YV  H081  C08  C09   113.20  3.000
 7YV  H082  C08  C09   111.06  3.000
 7YV  H081  C08  C03   112.34  3.000
 7YV  H082  C08  C03   110.10  3.000
 7YV  C09   C08  C03   103.09  3.000
 7YV  H092  C09  H091  107.07  3.000
 7YV  H092  C09  C08   112.75  3.000
 7YV  H091  C09  C08   111.17  3.000
 7YV  H092  C09  C04   111.90  3.000
 7YV  H091  C09  C04   110.97  3.000
 7YV  C08   C09  C04   103.05  3.000
 7YV  C12   C11  N02   118.72  3.000
 7YV  N02   C11  C13   120.09  3.000
 7YV  C12   C11  C13   121.18  3.000
 7YV  C14   C12  C11   118.67  3.000
 7YV  C11   C12  C17   120.52  3.000
 7YV  C14   C12  C17   120.81  3.000
 7YV  H141  C14  C16   119.42  3.000
 7YV  H141  C14  C12   118.99  3.000
 7YV  C16   C14  C12   121.59  3.000
 7YV  C19   C16  C14   120.54  3.000
 7YV  C14   C16  C15   118.35  3.000
 7YV  C19   C16  C15   121.11  3.000
 7YV  H193  C19  H192  108.07  3.000
 7YV  H193  C19  H191  107.03  3.000
 7YV  H192  C19  H191  107.46  3.000
 7YV  H193  C19  C16   111.48  3.000
 7YV  H192  C19  C16   111.56  3.000
 7YV  H191  C19  C16   111.02  3.000
 7YV  H183  C18  H182  107.68  3.000
 7YV  H183  C18  H181  108.07  3.000
 7YV  H182  C18  H181  106.94  3.000
 7YV  H183  C18  C13   110.91  3.000
 7YV  H182  C18  C13   111.40  3.000
 7YV  H181  C18  C13   111.65  3.000
 7YV  H171  C17  H173  107.61  3.000
 7YV  H171  C17  H172  107.82  3.000
 7YV  H173  C17  H172  106.87  3.000
 7YV  H171  C17  C12   110.90  3.000
 7YV  H173  C17  C12   111.88  3.000
 7YV  H172  C17  C12   111.55  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
 7YV  CONST_01  C14   C16  C15  C13     0.00   0.0  0
 7YV  CONST_02  C14   C12  C11  C13     0.00   0.0  0
 7YV  CONST_03  C12   C14  C16  C15     0.00   0.0  0
 7YV  CONST_04  C12   C11  C13  C15     0.00   0.0  0
 7YV  CONST_05  C16   C14  C12  C11     0.00   0.0  0
 7YV  CONST_06  C16   C15  C13  C11     0.00   0.0  0
 7YV  CONST_07  C19   C16  C15  C13   180.00   0.0  0
 7YV  CONST_08  C17   C12  C11  C13   180.00   0.0  0
 7YV  CONST_09  N02   C11  C13  C15   180.00   0.0  0
 7YV  CONST_10  C16   C14  C12  C17   180.00   0.0  0
 7YV  CONST_11  C14   C12  C11  N02   180.00   0.0  0
 7YV  CONST_12  C19   C16  C14  C12   180.00   0.0  0
 7YV  CONST_13  C18   C13  C11  C12   180.00   0.0  0
 7YV  CONST_14  C18   C13  C15  C16   180.00   0.0  0
 7YV  CONST_15  H141  C14  C16  C15   180.00   0.0  0
 7YV  CONST_16  H141  C14  C12  C11   180.00   0.0  0
 7YV  CONST_17  H151  C15  C13  C11   180.00   0.0  0
 7YV  CONST_18  H151  C15  C16  C14   180.00   0.0  0
 7YV  CONST_19  C11   N02  C10  C06   180.00   0.0  0
 7YV  CONST_24  C11   N02  C10  O01     0.00   0.0  0
 7YV  CONST_25  H021  N02  C10  C06     0.00   0.0  0
 7YV  CONST_26  H021  N02  C10  O01   180.00   0.0  0
 7YV  Var_01    C04   C09  C08  C03     1.23  30.0  1
 7YV  Var_02    H091  C09  C08  C03   120.16  30.0  1
 7YV  Var_03    H092  C09  C08  C03  -119.59  30.0  1
 7YV  Var_04    H082  C08  C09  C04  -116.65  30.0  1
 7YV  Var_05    H081  C08  C09  C04   122.85  30.0  1
 7YV  Var_06    H191  C19  C16  C15  -102.03  30.0  2
 7YV  Var_07    H192  C19  C16  C15    17.81  30.0  2
 7YV  Var_08    H193  C19  C16  C15   138.73  30.0  2
 7YV  Var_09    H181  C18  C13  C15   133.20  30.0  2
 7YV  Var_10    H182  C18  C13  C15  -107.31  30.0  2
 7YV  Var_11    H183  C18  C13  C15    12.61  30.0  2
 7YV  Var_12    H172  C17  C12  C11   -56.97  30.0  2
 7YV  Var_13    H173  C17  C12  C11    62.69  30.0  2
 7YV  Var_14    H171  C17  C12  C11  -177.16  30.0  2
 7YV  Var_15    H181  C18  C13  C11   -46.49  30.0  2
 7YV  Var_16    H182  C18  C13  C11    73.00  30.0  2
 7YV  Var_17    H183  C18  C13  C11  -167.08  30.0  2
 7YV  Var_18    H191  C19  C16  C14    76.77  30.0  2
 7YV  Var_19    H192  C19  C16  C14  -163.39  30.0  2
 7YV  Var_20    H193  C19  C16  C14   -42.47  30.0  2
 7YV  Var_21    H172  C17  C12  C14   122.67  30.0  2
 7YV  Var_22    H173  C17  C12  C14  -117.67  30.0  2
 7YV  Var_23    H171  C17  C12  C14     2.47  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
 7YV  chir_01  C03  C08  C06  C05  positiv
 7YV  chir_02  C04  C09  C05  C07  positiv
 7YV  chir_03  C06  C07  C03  C10  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
 7YV  plan-1  C13   0.020
 7YV  plan-1  C15   0.020
 7YV  plan-1  N02   0.020
 7YV  plan-1  C11   0.020
 7YV  plan-1  C12   0.020
 7YV  plan-1  C14   0.020
 7YV  plan-1  C16   0.020
 7YV  plan-1  C19   0.020
 7YV  plan-1  H151  0.020
 7YV  plan-1  H141  0.020
 7YV  plan-1  C18   0.020
 7YV  plan-1  C17   0.020
 7YV  plan-2  C10   0.020
 7YV  plan-2  O01   0.020
 7YV  plan-2  N02   0.020
 7YV  plan-2  C06   0.020
 7YV  plan-2  C11   0.020
 7YV  plan-2  H021  0.020

