# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 12:08:40 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2ccccc12)C(=O)NC3CCN(CC3)Cc4c[nH]c5ccccc45
#
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
 RND  RND  N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide  ligand  60  31  .  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_RND
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
 RND  C01  C  CR16  0  -0.364  -5.7982   0.3800   0.0906
 RND  C02  C  CR16  0  -0.271  -6.9227   0.4850   0.8863
 RND  C03  C  CR16  0  -0.284  -7.4597  -0.6399   1.5351
 RND  C04  C  CR16  0  -0.308  -6.8836  -1.8892   1.4029
 RND  C05  C  CR56  0   0.349  -5.7516  -1.9920   0.5948
 RND  C06  C  CR56  0   0.031  -5.1994  -0.8751  -0.0719
 RND  N07  N  NR15  0  -0.688  -4.9813  -3.0739   0.2826
 RND  C08  C  CR5   0  -0.008  -4.0595  -1.3438  -0.8035
 RND  C09  C  CR15  0  -0.087  -3.9678  -2.6818  -0.5477
 RND  C10  C  CH2   0  -0.351  -3.1743  -0.5328  -1.6887
 RND  N11  N  NT    0  -0.401  -2.7112   0.6819  -1.0442
 RND  C12  C  CH2   0  -0.290  -2.0670   1.5734  -1.9860
 RND  C13  C  CH2   0  -0.462  -1.7114   2.9014  -1.3308
 RND  C14  C  CH1   0  -0.101  -0.8565   2.7150  -0.0806
 RND  C15  C  CH2   0  -0.436  -1.5425   1.7080   0.8423
 RND  C16  C  CH2   0  -0.277  -1.8737   0.4191   0.1099
 RND  N17  N  NH1   0  -0.638   0.4766   2.2762  -0.4618
 RND  C18  C  C     0   0.553   1.5441   2.3308   0.3473
 RND  C19  C  CH1   0  -0.219   2.7966   1.6608  -0.2022
 RND  O20  O  O     0  -0.499   1.5178   2.8263   1.4657
 RND  C21  C  CH2   0  -0.554   2.7175   0.1559   0.1551
 RND  N22  N  NH2   0  -0.785   3.9650   2.3567   0.2879
 RND  C23  C  CR5   0   0.015   3.8988  -0.6191  -0.3232
 RND  N24  N  NR15  0  -0.685   5.2661  -1.8266  -1.6282
 RND  C25  C  CR15  0  -0.079   4.0352  -1.2415  -1.5334
 RND  C26  C  CR56  0   0.018   5.1327  -0.8389   0.3732
 RND  C27  C  CR56  0   0.353   5.9629  -1.6025  -0.4781
 RND  C28  C  CR16  0  -0.305   7.2446  -2.0033  -0.1013
 RND  C29  C  CR16  0  -0.285   7.6887  -1.6264   1.1513
 RND  C30  C  CR16  0  -0.268   6.8789  -0.8696   2.0154
 RND  C31  C  CR16  0  -0.377   5.6111  -0.4740   1.6378
 RND  H1   H  HCR6  0   0.238  -5.3698   1.2502  -0.3889
 RND  H2   H  HCR6  0   0.242  -7.3972   1.4487   1.0213
 RND  H3   H  HCR6  0   0.247  -8.3402  -0.5257   2.1544
 RND  H4   H  HCR6  0   0.257  -7.2944  -2.7527   1.9109
 RND  H5   H  HNR5  0   0.406  -5.1200  -4.0112   0.6201
 RND  H6   H  HCR5  0   0.280  -3.2430  -3.3976  -0.9038
 RND  H7   H  HCH2  0   0.203  -2.3377  -1.1596  -2.0458
 RND  H8   H  HCH2  0   0.235  -3.7274  -0.2307  -2.5847
 RND  H10  H  HCH2  0   0.184  -1.1672   1.1142  -2.4388
 RND  H11  H  HCH2  0   0.243  -2.7518   1.7574  -2.8175
 RND  H12  H  HCH2  0   0.246  -1.2053   3.5484  -2.0513
 RND  H13  H  HCH2  0   0.243  -2.6336   3.4072  -1.0368
 RND  H14  H  HCH1  0   0.257  -0.7596   3.6738   0.4336
 RND  H15  H  HCH2  0   0.240  -0.9165   1.4949   1.7101
 RND  H16  H  HCH2  0   0.229  -2.4685   2.1541   1.2148
 RND  H17  H  HCH2  0   0.245  -2.4065  -0.2512   0.7863
 RND  H18  H  HCH2  0   0.184  -0.9415  -0.1033  -0.1765
 RND  H19  H  HNH1  0   0.397   0.5970   1.8590  -1.3708
 RND  H20  H  HCH1  0   0.256   2.7976   1.7408  -1.2942
 RND  H21  H  HCH2  0   0.246   2.6211   0.0588   1.2415
 RND  H22  H  HCH2  0   0.251   1.8018  -0.2632  -0.2723
 RND  H23  H  HNH2  0   0.340   4.0187   2.2781   1.2963
 RND  H24  H  HNH2  0   0.356   4.7969   1.9139  -0.0809
 RND  H26  H  HNR5  0   0.408   5.5912  -2.3577  -2.4184
 RND  H27  H  HCR5  0   0.281   3.3291  -1.3173  -2.3460
 RND  H28  H  HCR6  0   0.259   7.8682  -2.5903  -0.7638
 RND  H29  H  HCR6  0   0.248   8.6789  -1.9218   1.4732
 RND  H30  H  HCR6  0   0.246   7.2585  -0.5932   2.9907
 RND  H31  H  HCR6  0   0.238   4.9976   0.1091   2.3142

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
 RND  C15  C16  single    1.519  0.020  1.519
 RND  C15  C14  single    1.529  0.020  1.529
 RND  N22  C19  single    1.446  0.020  1.446
 RND  C16  N11  single    1.450  0.020  1.450
 RND  C30  C31  aromatic  1.381  0.020  1.381
 RND  C30  C29  aromatic  1.405  0.020  1.405
 RND  C14  N17  single    1.454  0.020  1.454
 RND  C14  C13  single    1.526  0.020  1.526
 RND  N17  C18  single    1.341  0.020  1.341
 RND  C31  C26  aromatic  1.401  0.020  1.401
 RND  C18  C19  single    1.523  0.020  1.523
 RND  C18  O20  double    1.224  0.020  1.224
 RND  C19  C21  single    1.549  0.020  1.549
 RND  C29  C28  aromatic  1.381  0.020  1.381
 RND  N11  C10  single    1.451  0.020  1.451
 RND  N11  C12  single    1.448  0.020  1.448
 RND  C10  C08  single    1.492  0.020  1.492
 RND  C13  C12  single    1.523  0.020  1.523
 RND  C26  C23  aromatic  1.434  0.020  1.434
 RND  C26  C27  aromatic  1.413  0.020  1.413
 RND  C21  C23  single    1.492  0.020  1.492
 RND  C09  C08  aromatic  1.365  0.020  1.365
 RND  C09  N07  aromatic  1.368  0.020  1.368
 RND  C08  C06  aromatic  1.433  0.020  1.433
 RND  C28  C27  aromatic  1.395  0.020  1.395
 RND  C23  C25  aromatic  1.368  0.020  1.368
 RND  C27  N24  aromatic  1.363  0.020  1.363
 RND  N07  C05  aromatic  1.364  0.020  1.364
 RND  C06  C05  aromatic  1.413  0.020  1.413
 RND  C06  C01  aromatic  1.400  0.020  1.400
 RND  C25  N24  aromatic  1.366  0.020  1.366
 RND  C05  C04  aromatic  1.395  0.020  1.395
 RND  C01  C02  aromatic  1.381  0.020  1.381
 RND  C04  C03  aromatic  1.382  0.020  1.382
 RND  C02  C03  aromatic  1.405  0.020  1.405
 RND  C01  H1   single    0.930  0.020  1.080
 RND  C02  H2   single    0.930  0.020  1.080
 RND  C03  H3   single    0.930  0.020  1.080
 RND  C04  H4   single    0.930  0.020  1.080
 RND  N07  H5   single    0.860  0.020  1.020
 RND  C09  H6   single    0.930  0.020  1.080
 RND  C10  H7   single    0.970  0.020  1.090
 RND  C10  H8   single    0.970  0.020  1.090
 RND  C12  H10  single    0.970  0.020  1.090
 RND  C12  H11  single    0.970  0.020  1.090
 RND  C13  H12  single    0.970  0.020  1.090
 RND  C13  H13  single    0.970  0.020  1.090
 RND  C14  H14  single    0.970  0.020  1.090
 RND  C15  H15  single    0.970  0.020  1.090
 RND  C15  H16  single    0.970  0.020  1.090
 RND  C16  H17  single    0.970  0.020  1.090
 RND  C16  H18  single    0.970  0.020  1.090
 RND  N17  H19  single    0.860  0.020  1.020
 RND  C19  H20  single    0.970  0.020  1.090
 RND  C21  H21  single    0.970  0.020  1.090
 RND  C21  H22  single    0.970  0.020  1.090
 RND  N22  H23  single    0.890  0.020  1.040
 RND  N22  H24  single    0.890  0.020  1.040
 RND  N24  H26  single    0.860  0.020  1.020
 RND  C25  H27  single    0.930  0.020  1.080
 RND  C28  H28  single    0.930  0.020  1.080
 RND  C29  H29  single    0.930  0.020  1.080
 RND  C30  H30  single    0.930  0.020  1.080
 RND  C31  H31  single    0.930  0.020  1.080

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
 RND  H1   C01  C06  120.01  3.000
 RND  H1   C01  C02  121.09  3.000
 RND  C06  C01  C02  118.89  3.000
 RND  H2   C02  C03  119.17  3.000
 RND  H2   C02  C01  119.75  3.000
 RND  C03  C02  C01  121.07  3.000
 RND  H3   C03  C04  119.28  3.000
 RND  H3   C03  C02  119.38  3.000
 RND  C04  C03  C02  121.34  3.000
 RND  H4   C04  C05  121.40  3.000
 RND  H4   C04  C03  121.19  3.000
 RND  C05  C04  C03  117.41  3.000
 RND  N07  C05  C06  107.35  3.000
 RND  C06  C05  C04  122.16  3.000
 RND  N07  C05  C04  130.49  3.000
 RND  C08  C06  C05  107.04  3.000
 RND  C05  C06  C01  119.12  3.000
 RND  C08  C06  C01  133.83  3.000
 RND  H5   N07  C09  124.97  3.000
 RND  H5   N07  C05  125.76  3.000
 RND  C09  N07  C05  109.26  3.000
 RND  C10  C08  C09  127.17  3.000
 RND  C09  C08  C06  106.16  3.000
 RND  C10  C08  C06  126.66  3.000
 RND  H6   C09  C08  129.30  3.000
 RND  H6   C09  N07  120.52  3.000
 RND  C08  C09  N07  110.18  3.000
 RND  H8   C10  H7   105.93  3.000
 RND  H8   C10  N11  107.07  3.000
 RND  H7   C10  N11  112.14  3.000
 RND  H8   C10  C08  109.61  3.000
 RND  H7   C10  C08  109.44  3.000
 RND  N11  C10  C08  112.39  3.000
 RND  C16  N11  C12  111.86  3.000
 RND  C12  N11  C10  111.62  3.000
 RND  C16  N11  C10  112.71  3.000
 RND  H11  C12  H10  105.55  3.000
 RND  H11  C12  C13  109.07  3.000
 RND  H10  C12  C13  110.36  3.000
 RND  H11  C12  N11  108.65  3.000
 RND  H10  C12  N11  111.86  3.000
 RND  C13  C12  N11  111.16  3.000
 RND  H13  C13  H12  107.12  3.000
 RND  H13  C13  C14  108.01  3.000
 RND  H12  C13  C14  110.68  3.000
 RND  H13  C13  C12  108.81  3.000
 RND  H12  C13  C12  109.93  3.000
 RND  C14  C13  C12  112.13  3.000
 RND  H14  C14  N17  107.88  3.000
 RND  H14  C14  C15  109.51  3.000
 RND  N17  C14  C15  111.77  3.000
 RND  H14  C14  C13  109.16  3.000
 RND  N17  C14  C13  109.61  3.000
 RND  C15  C14  C13  108.89  3.000
 RND  H16  C15  H15  107.14  3.000
 RND  H16  C15  C16  109.02  3.000
 RND  H15  C15  C16  110.05  3.000
 RND  H16  C15  C14  108.48  3.000
 RND  H15  C15  C14  110.57  3.000
 RND  C16  C15  C14  111.46  3.000
 RND  H18  C16  H17  106.37  3.000
 RND  H18  C16  C15  109.99  3.000
 RND  H17  C16  C15  109.20  3.000
 RND  H18  C16  N11  111.49  3.000
 RND  H17  C16  N11  108.82  3.000
 RND  C15  C16  N11  110.85  3.000
 RND  H19  N17  C18  117.79  3.000
 RND  H19  N17  C14  118.10  3.000
 RND  C18  N17  C14  124.02  3.000
 RND  O20  C18  C19  121.71  3.000
 RND  O20  C18  N17  123.44  3.000
 RND  C19  C18  N17  114.78  3.000
 RND  H20  C19  N22  107.59  3.000
 RND  H20  C19  C21  107.52  3.000
 RND  N22  C19  C21  115.52  3.000
 RND  H20  C19  C18  109.18  3.000
 RND  C21  C19  C18  107.59  3.000
 RND  N22  C19  C18  109.31  3.000
 RND  H22  C21  H21  106.26  3.000
 RND  H22  C21  C23  109.79  3.000
 RND  H21  C21  C23  109.99  3.000
 RND  H22  C21  C19  108.96  3.000
 RND  H21  C21  C19  108.64  3.000
 RND  C23  C21  C19  112.98  3.000
 RND  H24  N22  H23  106.58  3.000
 RND  H24  N22  C19  109.28  3.000
 RND  H23  N22  C19  110.06  3.000
 RND  C26  C23  C25  105.91  3.000
 RND  C25  C23  C21  126.81  3.000
 RND  C26  C23  C21  127.26  3.000
 RND  H26  N24  C27  125.75  3.000
 RND  H26  N24  C25  124.87  3.000
 RND  C27  N24  C25  109.37  3.000
 RND  H27  C25  N24  120.47  3.000
 RND  H27  C25  C23  129.27  3.000
 RND  N24  C25  C23  110.25  3.000
 RND  C31  C26  C27  118.95  3.000
 RND  C27  C26  C23  107.21  3.000
 RND  C31  C26  C23  133.84  3.000
 RND  C28  C27  C26  122.17  3.000
 RND  C28  C27  N24  130.57  3.000
 RND  C26  C27  N24  107.26  3.000
 RND  H28  C28  C29  121.17  3.000
 RND  H28  C28  C27  121.32  3.000
 RND  C29  C28  C27  117.51  3.000
 RND  H29  C29  C30  119.42  3.000
 RND  H29  C29  C28  119.30  3.000
 RND  C30  C29  C28  121.28  3.000
 RND  H30  C30  C31  119.68  3.000
 RND  H30  C30  C29  119.31  3.000
 RND  C31  C30  C29  121.01  3.000
 RND  H31  C31  C30  120.23  3.000
 RND  H31  C31  C26  120.70  3.000
 RND  C30  C31  C26  119.07  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
 RND  CONST_01  C09  C08  C06  C01  180.00   0.0  0
 RND  CONST_02  N07  C05  C06  C01  180.00   0.0  0
 RND  CONST_03  C04  C05  C06  C01    0.00   0.0  0
 RND  CONST_04  C04  C03  C02  C01    0.00   0.0  0
 RND  CONST_05  C08  C06  C01  C02  180.00   0.0  0
 RND  CONST_06  C05  C06  C01  C02    0.00   0.0  0
 RND  CONST_07  C05  C04  C03  C02    0.00   0.0  0
 RND  CONST_08  N07  C05  C04  C03  180.00   0.0  0
 RND  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 RND  CONST_10  C06  C01  C02  C03    0.00   0.0  0
 RND  CONST_11  C09  N07  C05  C04  180.00   0.0  0
 RND  CONST_12  C08  C06  C05  C04  180.00   0.0  0
 RND  CONST_13  C08  C09  N07  C05    0.00   0.0  0
 RND  CONST_14  C09  C08  C06  C05    0.00   0.0  0
 RND  CONST_15  N07  C09  C08  C06    0.00   0.0  0
 RND  CONST_16  C09  N07  C05  C06    0.00   0.0  0
 RND  CONST_17  C08  C06  C05  N07    0.00   0.0  0
 RND  CONST_18  C30  C31  C26  C23  180.00   0.0  0
 RND  CONST_19  C28  C27  C26  C23  180.00   0.0  0
 RND  CONST_20  N24  C27  C26  C23    0.00   0.0  0
 RND  CONST_21  C27  N24  C25  C23    0.00   0.0  0
 RND  CONST_22  C31  C26  C27  N24  180.00   0.0  0
 RND  CONST_23  C29  C28  C27  N24  180.00   0.0  0
 RND  CONST_24  C26  C23  C25  N24    0.00   0.0  0
 RND  CONST_25  C31  C26  C23  C25  180.00   0.0  0
 RND  CONST_26  C27  C26  C23  C25    0.00   0.0  0
 RND  CONST_27  C26  C27  N24  C25    0.00   0.0  0
 RND  CONST_28  C28  C27  N24  C25  180.00   0.0  0
 RND  CONST_29  C29  C30  C31  C26    0.00   0.0  0
 RND  CONST_30  C29  C28  C27  C26    0.00   0.0  0
 RND  CONST_31  C30  C31  C26  C27    0.00   0.0  0
 RND  CONST_32  C30  C29  C28  C27    0.00   0.0  0
 RND  CONST_33  C31  C30  C29  C28    0.00   0.0  0
 RND  CONST_34  C31  C26  C27  C28    0.00   0.0  0
 RND  CONST_35  C10  C08  C06  C01    0.00   0.0  0
 RND  CONST_36  C10  C08  C06  C05  180.00   0.0  0
 RND  CONST_37  C10  C08  C09  N07  180.00   0.0  0
 RND  CONST_38  C31  C26  C23  C21    0.00   0.0  0
 RND  CONST_39  C27  C26  C23  C21  180.00   0.0  0
 RND  CONST_40  N24  C25  C23  C21  180.00   0.0  0
 RND  CONST_41  H3   C03  C02  C01  180.00   0.0  0
 RND  CONST_42  H4   C04  C03  C02  180.00   0.0  0
 RND  CONST_43  H1   C01  C02  C03  180.00   0.0  0
 RND  CONST_44  H5   N07  C05  C04    0.00   0.0  0
 RND  CONST_45  H2   C02  C03  C04  180.00   0.0  0
 RND  CONST_46  H6   C09  N07  C05  180.00   0.0  0
 RND  CONST_47  H31  C31  C26  C23    0.00   0.0  0
 RND  CONST_48  H26  N24  C25  C23  180.00   0.0  0
 RND  CONST_49  H28  C28  C27  N24    0.00   0.0  0
 RND  CONST_50  H30  C30  C31  C26  180.00   0.0  0
 RND  CONST_51  H27  C25  C23  C26  180.00   0.0  0
 RND  CONST_52  H29  C29  C28  C27  180.00   0.0  0
 RND  CONST_53  C19  C18  N17  C14  180.00   0.0  0
 RND  CONST_54  O20  C18  N17  C14    0.00   0.0  0
 RND  CONST_55  H19  N17  C18  C19    0.00   0.0  0
 RND  Var_01    C14  C15  C16  N11  -57.22  30.0  1
 RND  Var_02    C14  C13  C12  N11   55.05  30.0  1
 RND  Var_03    C15  C16  N11  C12   59.65  30.0  1
 RND  Var_04    C16  N11  C12  C13  -58.40  30.0  1
 RND  Var_05    N11  C10  C08  C06   50.26  30.0  2
 RND  Var_06    C26  C23  C21  C19   88.49  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
 RND  chir_01  C14  C15  N17  C13  negativ
 RND  chir_02  C19  N22  C18  C21  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
 RND  plan-1  C01  0.020
 RND  plan-1  C02  0.020
 RND  plan-1  C03  0.020
 RND  plan-1  C04  0.020
 RND  plan-1  C05  0.020
 RND  plan-1  C06  0.020
 RND  plan-1  N07  0.020
 RND  plan-1  C08  0.020
 RND  plan-1  C09  0.020
 RND  plan-1  C10  0.020
 RND  plan-1  H1   0.020
 RND  plan-1  H2   0.020
 RND  plan-1  H3   0.020
 RND  plan-1  H4   0.020
 RND  plan-1  H5   0.020
 RND  plan-1  H6   0.020
 RND  plan-2  C21  0.020
 RND  plan-2  C23  0.020
 RND  plan-2  N24  0.020
 RND  plan-2  C25  0.020
 RND  plan-2  C26  0.020
 RND  plan-2  C27  0.020
 RND  plan-2  C28  0.020
 RND  plan-2  C29  0.020
 RND  plan-2  C30  0.020
 RND  plan-2  C31  0.020
 RND  plan-2  H26  0.020
 RND  plan-2  H27  0.020
 RND  plan-2  H28  0.020
 RND  plan-2  H29  0.020
 RND  plan-2  H30  0.020
 RND  plan-2  H31  0.020
 RND  plan-3  C14  0.020
 RND  plan-3  N17  0.020
 RND  plan-3  C18  0.020
 RND  plan-3  C19  0.020
 RND  plan-3  O20  0.020
 RND  plan-3  H19  0.020

