# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:30:58 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: Nalpha-[(trans-4-methylcyclohexyl)carbonyl]-N-pyridin-4-yl-D-tryptophanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC[C@H](CC1)C(=O)N[C@H](Cc2c[nH]c3ccccc23)C(=O)Nc4ccncc4
#
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
 RT8  RT8  Nalpha-[(trans-4-methylcyclohexyl)carbonyl]-N-pyridin-4-yl-D-tryptophanamide  ligand  58  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RT8
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
 RT8  O2    O  O     0  -0.442   1.2932  -1.7026  -1.3202
 RT8  C6    C  C     0   0.548   1.5733  -0.8422  -0.5145
 RT8  N2    N  NH1   0  -0.741   2.7274  -0.8034   0.2053
 RT8  C5    C  CR6   0   0.468   3.8065  -1.6736   0.1722
 RT8  C4    C  CR16  0  -0.420   4.8938  -1.3827   1.0000
 RT8  C3    C  CR16  0  -0.062   5.9888  -2.2235   0.9952
 RT8  N1    N  N     0  -0.417   6.0822  -3.3156   0.2421
 RT8  C2    C  CR16  0  -0.069   5.0441  -3.5852  -0.5391
 RT8  C1    C  CR16  0  -0.378   3.8922  -2.8181  -0.6211
 RT8  C7    C  CH1   0  -0.178   0.6707   0.3702  -0.2831
 RT8  N3    N  NH1   0  -0.646  -0.7043  -0.0354  -0.2890
 RT8  C8    C  C     0   0.600  -1.1623  -0.9842   0.5473
 RT8  O1    O  O     0  -0.496  -0.4293  -1.5084   1.3757
 RT8  C9    C  CH1   0  -0.397  -2.6075  -1.3834   0.3442
 RT8  C15   C  CH2   0  -0.416  -3.2625  -1.8568   1.6389
 RT8  C14   C  CH2   0  -0.417  -4.6997  -2.3007   1.3892
 RT8  C12   C  CH1   0  -0.228  -4.7887  -3.3959   0.3281
 RT8  C13   C  CH3   0  -0.654  -6.2307  -3.8157   0.0794
 RT8  C11   C  CH2   0  -0.415  -4.1158  -2.9270  -0.9610
 RT8  C10   C  CH2   0  -0.417  -2.6771  -2.4830  -0.7267
 RT8  C16   C  CH2   0  -0.571   0.9289   1.3821  -1.4152
 RT8  C17   C  CR5   0   0.003   0.0267   2.5663  -1.3582
 RT8  C20   C  CR56  0   0.037   0.0504   3.6283  -0.3959
 RT8  C21   C  CR16  0  -0.378   0.8614   3.9230   0.7065
 RT8  C22   C  CR16  0  -0.266   0.6114   5.0708   1.4328
 RT8  C23   C  CR16  0  -0.283  -0.4380   5.9362   1.0813
 RT8  C24   C  CR16  0  -0.303  -1.2543   5.6724  -0.0014
 RT8  C19   C  CR56  0   0.356  -0.9981   4.5130  -0.7321
 RT8  N4    N  NR15  0  -0.686  -1.6207   4.0073  -1.8356
 RT8  C18   C  CR15  0  -0.084  -1.0073   2.8464  -2.2087
 RT8  H2    H  HNH1  0   0.419   2.8135  -0.0496   0.8710
 RT8  H7    H  HCH1  0   0.279   0.9174   0.8352   0.6784
 RT8  H4    H  HCR6  0   0.285   4.8870  -0.5086   1.6391
 RT8  H1    H  HCR6  0   0.290   3.1010  -3.1214  -1.2853
 RT8  H3    H  HCR6  0   0.267   6.8346  -1.9990   1.6356
 RT8  HA    H  HCR6  0   0.266   5.1190  -4.4771  -1.1517
 RT8  HB    H  HNH1  0   0.399  -1.3349   0.4074  -0.9393
 RT8  H161  H  HCH2  0   0.271   1.9740   1.6961  -1.3551
 RT8  H162  H  HCH2  0   0.274   0.8112   0.8736  -2.3752
 RT8  H9    H  HCH1  0   0.248  -3.1653  -0.5153  -0.0288
 RT8  H151  H  HCH2  0   0.219  -2.6889  -2.6910   2.0518
 RT8  H152  H  HCH2  0   0.235  -3.2409  -1.0592   2.3857
 RT8  H101  H  HCH2  0   0.238  -2.2348  -2.1295  -1.6610
 RT8  H102  H  HCH2  0   0.224  -2.0787  -3.3395  -0.3979
 RT8  H141  H  HCH2  0   0.227  -5.1449  -2.6498   2.3249
 RT8  H142  H  HCH2  0   0.206  -5.2971  -1.4398   1.0643
 RT8  H12   H  HCH1  0   0.210  -4.2323  -4.2678   0.6969
 RT8  H131  H  HCH3  0   0.212  -6.8201  -2.9776  -0.3012
 RT8  H132  H  HCH3  0   0.224  -6.2912  -4.6227  -0.6533
 RT8  H133  H  HCH3  0   0.224  -6.7087  -4.1660   0.9961
 RT8  H111  H  HCH2  0   0.229  -4.1369  -3.7266  -1.7065
 RT8  H112  H  HCH2  0   0.209  -4.6916  -2.0937  -1.3814
 RT8  H18   H  HCR5  0   0.290  -1.3502   2.2972  -3.0724
 RT8  H21   H  HCR6  0   0.238   1.6770   3.2682   0.9896
 RT8  H22   H  HCR6  0   0.248   1.2317   5.3115   2.2865
 RT8  H23   H  HCR6  0   0.251  -0.6080   6.8290   1.6690
 RT8  H24   H  HCR6  0   0.260  -2.0593   6.3435  -0.2729
 RT8  HC    H  HNR5  0   0.411  -2.3989   4.4281  -2.3148

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
 RT8  O2   C6    double    1.212  0.020  1.212
 RT8  C6   N2    single    1.361  0.020  1.361
 RT8  C6   C7    single    1.529  0.020  1.529
 RT8  N2   C5    single    1.387  0.020  1.387
 RT8  C5   C4    aromatic  1.397  0.020  1.397
 RT8  C5   C1    aromatic  1.395  0.020  1.395
 RT8  C4   C3    aromatic  1.381  0.020  1.381
 RT8  C3   N1    aromatic  1.330  0.020  1.330
 RT8  N1   C2    aromatic  1.327  0.020  1.327
 RT8  C2   C1    aromatic  1.386  0.020  1.386
 RT8  C7   N3    single    1.434  0.020  1.434
 RT8  C7   C16   single    1.540  0.020  1.540
 RT8  N3   C8    single    1.345  0.020  1.345
 RT8  C8   O1    double    1.224  0.020  1.224
 RT8  C8   C9    single    1.513  0.020  1.513
 RT8  C9   C15   single    1.526  0.020  1.526
 RT8  C9   C10   single    1.536  0.020  1.536
 RT8  C15  C14   single    1.525  0.020  1.525
 RT8  C14  C12   single    1.528  0.020  1.528
 RT8  C12  C13   single    1.522  0.020  1.522
 RT8  C12  C11   single    1.528  0.020  1.528
 RT8  C11  C10   single    1.524  0.020  1.524
 RT8  C16  C17   single    1.490  0.020  1.490
 RT8  C17  C20   aromatic  1.433  0.020  1.433
 RT8  C17  C18   aromatic  1.368  0.020  1.368
 RT8  C20  C21   aromatic  1.400  0.020  1.400
 RT8  C20  C19   aromatic  1.412  0.020  1.412
 RT8  C21  C22   aromatic  1.381  0.020  1.381
 RT8  C22  C23   aromatic  1.405  0.020  1.405
 RT8  C23  C24   aromatic  1.381  0.020  1.381
 RT8  C24  C19   aromatic  1.394  0.020  1.394
 RT8  C19  N4    aromatic  1.364  0.020  1.364
 RT8  N4   C18   aromatic  1.365  0.020  1.365
 RT8  N2   H2    single    0.860  0.020  1.020
 RT8  C7   H7    single    0.970  0.020  1.090
 RT8  C4   H4    single    0.930  0.020  1.080
 RT8  C1   H1    single    0.930  0.020  1.080
 RT8  C3   H3    single    0.930  0.020  1.080
 RT8  C2   HA    single    0.930  0.020  1.080
 RT8  N3   HB    single    0.860  0.020  1.020
 RT8  C16  H161  single    0.970  0.020  1.090
 RT8  C16  H162  single    0.970  0.020  1.090
 RT8  C9   H9    single    0.970  0.020  1.090
 RT8  C15  H151  single    0.970  0.020  1.090
 RT8  C15  H152  single    0.970  0.020  1.090
 RT8  C10  H101  single    0.970  0.020  1.090
 RT8  C10  H102  single    0.970  0.020  1.090
 RT8  C14  H141  single    0.970  0.020  1.090
 RT8  C14  H142  single    0.970  0.020  1.090
 RT8  C12  H12   single    0.970  0.020  1.090
 RT8  C13  H131  single    0.970  0.020  1.090
 RT8  C13  H132  single    0.970  0.020  1.090
 RT8  C13  H133  single    0.970  0.020  1.090
 RT8  C11  H111  single    0.970  0.020  1.090
 RT8  C11  H112  single    0.970  0.020  1.090
 RT8  C18  H18   single    0.930  0.020  1.080
 RT8  C21  H21   single    0.930  0.020  1.080
 RT8  C22  H22   single    0.930  0.020  1.080
 RT8  C23  H23   single    0.930  0.020  1.080
 RT8  C24  H24   single    0.930  0.020  1.080
 RT8  N4   HC    single    0.860  0.020  1.020

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
 RT8  C7    C6   N2    113.45  3.000
 RT8  C7    C6   O2    121.82  3.000
 RT8  N2    C6   O2    124.62  3.000
 RT8  H2    N2   C5    114.72  3.000
 RT8  H2    N2   C6    116.26  3.000
 RT8  C5    N2   C6    129.01  3.000
 RT8  C1    C5   C4    117.38  3.000
 RT8  C1    C5   N2    125.18  3.000
 RT8  C4    C5   N2    117.44  3.000
 RT8  H4    C4   C3    119.91  3.000
 RT8  H4    C4   C5    120.86  3.000
 RT8  C3    C4   C5    119.23  3.000
 RT8  H3    C3   N1    116.73  3.000
 RT8  H3    C3   C4    119.37  3.000
 RT8  N1    C3   C4    123.90  3.000
 RT8  C2    N1   C3    116.45  3.000
 RT8  HA    C2   C1    118.62  3.000
 RT8  HA    C2   N1    116.46  3.000
 RT8  C1    C2   N1    124.92  3.000
 RT8  H1    C1   C2    119.42  3.000
 RT8  H1    C1   C5    122.46  3.000
 RT8  C2    C1   C5    118.12  3.000
 RT8  H7    C7   C16   109.17  3.000
 RT8  H7    C7   N3    109.84  3.000
 RT8  C16   C7   N3    110.10  3.000
 RT8  H7    C7   C6    109.64  3.000
 RT8  C16   C7   C6    108.10  3.000
 RT8  N3    C7   C6    109.95  3.000
 RT8  HB    N3   C8    119.86  3.000
 RT8  HB    N3   C7    118.57  3.000
 RT8  C8    N3   C7    121.58  3.000
 RT8  C9    C8   O1    123.35  3.000
 RT8  C9    C8   N3    115.33  3.000
 RT8  O1    C8   N3    121.26  3.000
 RT8  H9    C9   C10   107.83  3.000
 RT8  H9    C9   C15   108.40  3.000
 RT8  C10   C9   C15   110.48  3.000
 RT8  H9    C9   C8    108.81  3.000
 RT8  C10   C9   C8    109.00  3.000
 RT8  C15   C9   C8    112.21  3.000
 RT8  H152  C15  H151  106.77  3.000
 RT8  H152  C15  C14   110.06  3.000
 RT8  H151  C15  C14   109.53  3.000
 RT8  H152  C15  C9    110.17  3.000
 RT8  H151  C15  C9    109.38  3.000
 RT8  C14   C15  C9    110.85  3.000
 RT8  H142  C14  H141  106.39  3.000
 RT8  H142  C14  C12   108.98  3.000
 RT8  H141  C14  C12   109.99  3.000
 RT8  H142  C14  C15   109.47  3.000
 RT8  H141  C14  C15   109.67  3.000
 RT8  C12   C14  C15   112.17  3.000
 RT8  H12   C12  C11   107.69  3.000
 RT8  H12   C12  C13   108.41  3.000
 RT8  C11   C12  C13   111.35  3.000
 RT8  H12   C12  C14   107.85  3.000
 RT8  C11   C12  C14   109.90  3.000
 RT8  C13   C12  C14   111.49  3.000
 RT8  H133  C13  H132  107.59  3.000
 RT8  H133  C13  H131  107.60  3.000
 RT8  H132  C13  H131  107.64  3.000
 RT8  H133  C13  C12   111.48  3.000
 RT8  H132  C13  C12   111.47  3.000
 RT8  H131  C13  C12   110.87  3.000
 RT8  H112  C11  H111  106.51  3.000
 RT8  H112  C11  C10   109.47  3.000
 RT8  H111  C11  C10   109.65  3.000
 RT8  H112  C11  C12   108.99  3.000
 RT8  H111  C11  C12   110.01  3.000
 RT8  C10   C11  C12   112.06  3.000
 RT8  H102  C10  H101  106.77  3.000
 RT8  H102  C10  C11   109.52  3.000
 RT8  H101  C10  C11   110.18  3.000
 RT8  H102  C10  C9    109.00  3.000
 RT8  H101  C10  C9    110.25  3.000
 RT8  C11   C10  C9    111.01  3.000
 RT8  H162  C16  H161  106.56  3.000
 RT8  H162  C16  C17   109.77  3.000
 RT8  H161  C16  C17   110.40  3.000
 RT8  H162  C16  C7    108.78  3.000
 RT8  H161  C16  C7    107.98  3.000
 RT8  C17   C16  C7    113.11  3.000
 RT8  C18   C17  C20   106.15  3.000
 RT8  C18   C17  C16   126.64  3.000
 RT8  C20   C17  C16   127.20  3.000
 RT8  C19   C20  C21   119.05  3.000
 RT8  C19   C20  C17   106.98  3.000
 RT8  C21   C20  C17   133.97  3.000
 RT8  H21   C21  C22   120.08  3.000
 RT8  H21   C21  C20   120.97  3.000
 RT8  C22   C21  C20   118.96  3.000
 RT8  H22   C22  C23   119.24  3.000
 RT8  H22   C22  C21   119.72  3.000
 RT8  C23   C22  C21   121.04  3.000
 RT8  H23   C23  C24   119.36  3.000
 RT8  H23   C23  C22   119.31  3.000
 RT8  C24   C23  C22   121.32  3.000
 RT8  H24   C24  C19   121.38  3.000
 RT8  H24   C24  C23   121.17  3.000
 RT8  C19   C24  C23   117.45  3.000
 RT8  N4    C19  C24   130.41  3.000
 RT8  N4    C19  C20   107.40  3.000
 RT8  C24   C19  C20   122.18  3.000
 RT8  HC    N4   C18   124.96  3.000
 RT8  HC    N4   C19   125.68  3.000
 RT8  C18   N4   C19   109.35  3.000
 RT8  H18   C18  N4    120.58  3.000
 RT8  H18   C18  C17   129.30  3.000
 RT8  N4    C18  C17   110.11  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
 RT8  CONST_01  N1   C3   C4   C5     0.00   0.0  0
 RT8  CONST_02  N1   C2   C1   C5     0.00   0.0  0
 RT8  CONST_03  C2   C1   C5   C4     0.00   0.0  0
 RT8  CONST_04  C2   N1   C3   C4     0.00   0.0  0
 RT8  CONST_05  C1   C5   C4   C3     0.00   0.0  0
 RT8  CONST_06  C1   C2   N1   C3     0.00   0.0  0
 RT8  CONST_07  C22  C21  C20  C17  180.00   0.0  0
 RT8  CONST_08  C24  C19  C20  C17  180.00   0.0  0
 RT8  CONST_09  N4   C19  C20  C17    0.00   0.0  0
 RT8  CONST_10  C19  N4   C18  C17    0.00   0.0  0
 RT8  CONST_11  N4   C18  C17  C20    0.00   0.0  0
 RT8  CONST_12  C23  C22  C21  C20    0.00   0.0  0
 RT8  CONST_13  C23  C24  C19  C20    0.00   0.0  0
 RT8  CONST_14  C18  N4   C19  C20    0.00   0.0  0
 RT8  CONST_15  C18  C17  C20  C21  180.00   0.0  0
 RT8  CONST_16  C24  C19  C20  C21    0.00   0.0  0
 RT8  CONST_17  N4   C19  C20  C21  180.00   0.0  0
 RT8  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 RT8  CONST_19  C19  C20  C21  C22    0.00   0.0  0
 RT8  CONST_20  C19  C24  C23  C22    0.00   0.0  0
 RT8  CONST_21  N4   C19  C24  C23  180.00   0.0  0
 RT8  CONST_22  C18  N4   C19  C24  180.00   0.0  0
 RT8  CONST_23  C18  C17  C20  C19    0.00   0.0  0
 RT8  CONST_24  C3   C4   C5   N2   180.00   0.0  0
 RT8  CONST_25  C2   C1   C5   N2   180.00   0.0  0
 RT8  CONST_26  C21  C20  C17  C16    0.00   0.0  0
 RT8  CONST_27  C19  C20  C17  C16  180.00   0.0  0
 RT8  CONST_28  N4   C18  C17  C16  180.00   0.0  0
 RT8  CONST_29  H3   C3   C4   C5   180.00   0.0  0
 RT8  CONST_30  HA   C2   C1   C5   180.00   0.0  0
 RT8  CONST_31  H1   C1   C5   C4   180.00   0.0  0
 RT8  CONST_32  H4   C4   C3   N1   180.00   0.0  0
 RT8  CONST_33  H21  C21  C20  C17    0.00   0.0  0
 RT8  CONST_34  HC   N4   C18  C17  180.00   0.0  0
 RT8  CONST_35  H18  C18  C17  C20  180.00   0.0  0
 RT8  CONST_36  H22  C22  C21  C20  180.00   0.0  0
 RT8  CONST_37  H24  C24  C19  C20  180.00   0.0  0
 RT8  CONST_38  H23  C23  C22  C21  180.00   0.0  0
 RT8  CONST_39  C4   C5   N2   C6   180.00   0.0  0
 RT8  CONST_40  C1   C5   N2   C6     0.00   0.0  0
 RT8  CONST_41  H2   N2   C5   C4     0.00   0.0  0
 RT8  CONST_42  C5   N2   C6   O2     0.00   0.0  0
 RT8  CONST_43  C7   C6   N2   C5   180.00   0.0  0
 RT8  CONST_44  C9   C8   N3   C7   180.00   0.0  0
 RT8  CONST_45  HB   N3   C8   C9     0.00   0.0  0
 RT8  CONST_46  O1   C8   N3   C7     0.00   0.0  0
 RT8  Var_01    C12  C14  C15  C9    56.61  30.0  1
 RT8  Var_02    C12  C11  C10  C9   -56.06  30.0  1
 RT8  Var_03    C20  C17  C16  C7    70.77  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
 RT8  chir_01  C7   C6   N3   C16  positiv
 RT8  chir_02  C9   C8   C15  C10  positiv
 RT8  chir_03  C12  C11  C13  C14  positiv

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
 RT8  plan-1  N2   0.020
 RT8  plan-1  C5   0.020
 RT8  plan-1  C4   0.020
 RT8  plan-1  C3   0.020
 RT8  plan-1  N1   0.020
 RT8  plan-1  C2   0.020
 RT8  plan-1  C1   0.020
 RT8  plan-1  H4   0.020
 RT8  plan-1  H1   0.020
 RT8  plan-1  H3   0.020
 RT8  plan-1  HA   0.020
 RT8  plan-2  C16  0.020
 RT8  plan-2  C17  0.020
 RT8  plan-2  C20  0.020
 RT8  plan-2  C21  0.020
 RT8  plan-2  C22  0.020
 RT8  plan-2  C23  0.020
 RT8  plan-2  C24  0.020
 RT8  plan-2  C19  0.020
 RT8  plan-2  N4   0.020
 RT8  plan-2  C18  0.020
 RT8  plan-2  H18  0.020
 RT8  plan-2  H21  0.020
 RT8  plan-2  H22  0.020
 RT8  plan-2  H23  0.020
 RT8  plan-2  H24  0.020
 RT8  plan-2  HC   0.020
 RT8  plan-3  C7   0.020
 RT8  plan-3  N3   0.020
 RT8  plan-3  C8   0.020
 RT8  plan-3  O1   0.020
 RT8  plan-3  C9   0.020
 RT8  plan-3  HB   0.020
 RT8  plan-4  O2   0.020
 RT8  plan-4  C6   0.020
 RT8  plan-4  N2   0.020
 RT8  plan-4  C5   0.020
 RT8  plan-4  C7   0.020
 RT8  plan-4  H2   0.020

