# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:10:42 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1ccccc1)c2ccc3[C@@H](CCCc3c2)CNc4cnccc4C(O)=O
#
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
 9DJ  9DJ  '3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid'  ligand  54  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9DJ
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
 9DJ  C5   C  CR16  0  -0.111  -6.1273   2.1618   1.7300
 9DJ  C6   C  CR16  0  -0.322  -6.5281   1.0478   1.0263
 9DJ  C7   C  C     0   0.567  -6.0081  -0.9333  -0.3951
 9DJ  C13  C  CH2   0  -0.433  -1.1845  -2.1106   0.0372
 9DJ  C15  C  CH2   0  -0.505   1.2430  -2.4607   0.4074
 9DJ  C17  C  CR6   0   0.082   0.4801  -0.3579  -0.7703
 9DJ  C20  C  CR16  0  -0.365   2.1330   1.2814  -1.4905
 9DJ  C21  C  CR16  0  -0.290   0.8269   0.8272  -1.4140
 9DJ  C24  C  CR6   0   0.285   5.4429   0.5454  -0.0536
 9DJ  C26  C  CR16  0  -0.252   6.1186   0.2450   2.2441
 9DJ  C28  C  CR16  0  -0.251   7.6550  -0.2656   0.4758
 9DJ  O9   O  O     0  -0.460  -5.2518  -1.6602  -1.0082
 9DJ  O8   O  OH1   0  -0.590  -7.3132  -1.1536  -0.3476
 9DJ  C1   C  CR6   0  -0.104  -5.5879   0.2611   0.3583
 9DJ  N4   N  N     0  -0.371  -4.8469   2.5299   1.7971
 9DJ  C3   C  CR16  0  -0.171  -3.9409   1.8099   1.1782
 9DJ  C2   C  CR6   0   0.337  -4.2236   0.6388   0.4282
 9DJ  N10  N  NH1   0  -0.706  -3.2300  -0.0466  -0.1636
 9DJ  C11  C  CH2   0  -0.255  -1.8324   0.3125  -0.1016
 9DJ  C12  C  CH1   0  -0.353  -0.9728  -0.7935  -0.7201
 9DJ  C19  C  CR6   0   0.359   3.1717   0.5347  -0.9223
 9DJ  C18  C  CR16  0  -0.381   2.8321  -0.6791  -0.3145
 9DJ  C16  C  CR6   0   0.079   1.5196  -1.1244  -0.2296
 9DJ  C14  C  CH2   0  -0.445  -0.0296  -3.0800  -0.1460
 9DJ  N22  N  NT    0  -0.596   4.4933   0.9413  -1.0179
 9DJ  C23  C  CH3   0  -0.552   4.8314   2.0565  -1.8778
 9DJ  C29  C  CR16  0  -0.303   6.6967   0.0931  -0.4617
 9DJ  C27  C  CR16  0  -0.268   7.3700  -0.1975   1.8329
 9DJ  C25  C  CR16  0  -0.281   5.1650   0.6242   1.3115
 9DJ  H1   H  HCR6  0   0.259  -6.8476   2.7787   2.2522
 9DJ  H2   H  HCR6  0   0.277  -7.5776   0.7924   1.0009
 9DJ  H3   H  HCH2  0   0.224  -1.2972  -1.9010   1.1069
 9DJ  H4   H  HCH2  0   0.236  -2.1191  -2.5756  -0.2829
 9DJ  H5   H  HCH2  0   0.246   2.0987  -3.1230   0.2581
 9DJ  H6   H  HCH2  0   0.241   1.1394  -2.3385   1.4911
 9DJ  H7   H  HCR6  0   0.262   2.3295   2.2181  -1.9935
 9DJ  H8   H  HCR6  0   0.245   0.0556   1.4293  -1.8809
 9DJ  H9   H  HCR6  0   0.257   5.8862   0.3118   3.2993
 9DJ  H10  H  HCR6  0   0.257   8.6231  -0.6145   0.1404
 9DJ  H11  H  HOH1  0   0.490  -7.5308  -1.9448  -0.8622
 9DJ  H12  H  HCR6  0   0.275  -2.9177   2.1565   1.2601
 9DJ  H13  H  HNH1  0   0.412  -3.5006  -0.8320  -0.7340
 9DJ  H14  H  HCH2  0   0.248  -1.6617   1.2660  -0.6117
 9DJ  H15  H  HCH2  0   0.237  -1.5206   0.4490   0.9401
 9DJ  H16  H  HCH1  0   0.254  -1.3085  -0.9361  -1.7559
 9DJ  H17  H  HCR6  0   0.254   3.6138  -1.3110   0.0909
 9DJ  H18  H  HCH2  0   0.237  -0.2468  -4.0203   0.3645
 9DJ  H19  H  HCH2  0   0.223   0.1015  -3.3188  -1.2060
 9DJ  H20  H  HCH3  0   0.242   4.4490   1.9010  -2.8874
 9DJ  H21  H  HCH3  0   0.233   4.4395   3.0087  -1.5049
 9DJ  H22  H  HCH3  0   0.264   5.9120   2.1480  -1.9439
 9DJ  H23  H  HCR6  0   0.262   6.9212   0.0162  -1.5186
 9DJ  H24  H  HCR6  0   0.254   8.1149  -0.4854   2.5632
 9DJ  H25  H  HCR6  0   0.264   4.1997   0.9844   1.6446

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
 9DJ  C28  C27  aromatic  1.388  0.020  1.388
 9DJ  C28  C29  aromatic  1.388  0.020  1.388
 9DJ  C27  C26  aromatic  1.390  0.020  1.390
 9DJ  C29  C24  aromatic  1.394  0.020  1.394
 9DJ  C26  C25  aromatic  1.387  0.020  1.387
 9DJ  C24  C25  aromatic  1.395  0.020  1.395
 9DJ  C24  N22  single    1.410  0.020  1.410
 9DJ  C20  C21  aromatic  1.385  0.020  1.385
 9DJ  C20  C19  aromatic  1.400  0.020  1.400
 9DJ  C21  C17  aromatic  1.393  0.020  1.393
 9DJ  N22  C19  single    1.386  0.020  1.386
 9DJ  N22  C23  single    1.448  0.020  1.448
 9DJ  C19  C18  aromatic  1.399  0.020  1.399
 9DJ  C17  C12  single    1.518  0.020  1.518
 9DJ  C17  C16  aromatic  1.400  0.020  1.400
 9DJ  C12  C11  single    1.531  0.020  1.531
 9DJ  C12  C13  single    1.534  0.020  1.534
 9DJ  C18  C16  aromatic  1.389  0.020  1.389
 9DJ  C16  C15  single    1.506  0.020  1.506
 9DJ  C11  N10  single    1.444  0.020  1.444
 9DJ  N10  C2   single    1.344  0.020  1.344
 9DJ  C13  C14  single    1.519  0.020  1.519
 9DJ  C14  C15  single    1.520  0.020  1.520
 9DJ  C3   C2   aromatic  1.419  0.020  1.419
 9DJ  C3   N4   aromatic  1.312  0.020  1.312
 9DJ  C2   C1   aromatic  1.417  0.020  1.417
 9DJ  O9   C7   double    1.215  0.020  1.215
 9DJ  N4   C5   aromatic  1.334  0.020  1.334
 9DJ  C1   C7   single    1.473  0.020  1.473
 9DJ  C1   C6   aromatic  1.396  0.020  1.396
 9DJ  C7   O8   single    1.324  0.020  1.324
 9DJ  C5   C6   aromatic  1.377  0.020  1.377
 9DJ  C5   H1   single    0.930  0.020  1.080
 9DJ  C6   H2   single    0.930  0.020  1.080
 9DJ  C13  H3   single    0.970  0.020  1.090
 9DJ  C13  H4   single    0.970  0.020  1.090
 9DJ  C15  H5   single    0.970  0.020  1.090
 9DJ  C15  H6   single    0.970  0.020  1.090
 9DJ  C20  H7   single    0.930  0.020  1.080
 9DJ  C21  H8   single    0.930  0.020  1.080
 9DJ  C26  H9   single    0.930  0.020  1.080
 9DJ  C28  H10  single    0.930  0.020  1.080
 9DJ  O8   H11  single    0.850  0.020  0.980
 9DJ  C3   H12  single    0.930  0.020  1.080
 9DJ  N10  H13  single    0.860  0.020  1.020
 9DJ  C11  H14  single    0.970  0.020  1.090
 9DJ  C11  H15  single    0.970  0.020  1.090
 9DJ  C12  H16  single    0.970  0.020  1.090
 9DJ  C18  H17  single    0.930  0.020  1.080
 9DJ  C14  H18  single    0.970  0.020  1.090
 9DJ  C14  H19  single    0.970  0.020  1.090
 9DJ  C23  H20  single    0.970  0.020  1.090
 9DJ  C23  H21  single    0.970  0.020  1.090
 9DJ  C23  H22  single    0.970  0.020  1.090
 9DJ  C29  H23  single    0.930  0.020  1.080
 9DJ  C27  H24  single    0.930  0.020  1.080
 9DJ  C25  H25  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
 9DJ  H1   C5   N4   117.20  3.000
 9DJ  H1   C5   C6   120.91  3.000
 9DJ  N4   C5   C6   121.89  3.000
 9DJ  H2   C6   C1   120.65  3.000
 9DJ  H2   C6   C5   119.07  3.000
 9DJ  C1   C6   C5   120.28  3.000
 9DJ  C1   C7   O8   113.43  3.000
 9DJ  O8   C7   O9   122.14  3.000
 9DJ  C1   C7   O9   124.43  3.000
 9DJ  H4   C13  H3   106.23  3.000
 9DJ  H4   C13  C14  110.11  3.000
 9DJ  H3   C13  C14  108.54  3.000
 9DJ  H4   C13  C12  109.82  3.000
 9DJ  H3   C13  C12  109.38  3.000
 9DJ  C14  C13  C12  112.55  3.000
 9DJ  H6   C15  H5   106.08  3.000
 9DJ  H6   C15  C14  109.06  3.000
 9DJ  H5   C15  C14  111.05  3.000
 9DJ  H6   C15  C16  109.69  3.000
 9DJ  H5   C15  C16  109.66  3.000
 9DJ  C14  C15  C16  111.19  3.000
 9DJ  C16  C17  C12  122.74  3.000
 9DJ  C16  C17  C21  117.35  3.000
 9DJ  C12  C17  C21  119.87  3.000
 9DJ  H7   C20  C19  121.08  3.000
 9DJ  H7   C20  C21  118.76  3.000
 9DJ  C19  C20  C21  120.16  3.000
 9DJ  H8   C21  C20  117.71  3.000
 9DJ  H8   C21  C17  119.64  3.000
 9DJ  C20  C21  C17  122.65  3.000
 9DJ  C25  C24  C29  118.94  3.000
 9DJ  C25  C24  N22  121.27  3.000
 9DJ  C29  C24  N22  119.77  3.000
 9DJ  H9   C26  C25  119.41  3.000
 9DJ  H9   C26  C27  120.10  3.000
 9DJ  C25  C26  C27  120.49  3.000
 9DJ  H10  C28  C27  120.15  3.000
 9DJ  H10  C28  C29  119.45  3.000
 9DJ  C27  C28  C29  120.39  3.000
 9DJ  H11  O8   C7   109.77  3.000
 9DJ  C2   C1   C7   121.05  3.000
 9DJ  C7   C1   C6   120.62  3.000
 9DJ  C2   C1   C6   118.32  3.000
 9DJ  C3   N4   C5   119.18  3.000
 9DJ  H12  C3   C2   119.47  3.000
 9DJ  H12  C3   N4   116.16  3.000
 9DJ  C2   C3   N4   124.36  3.000
 9DJ  N10  C2   C3   120.41  3.000
 9DJ  C3   C2   C1   115.96  3.000
 9DJ  N10  C2   C1   123.63  3.000
 9DJ  H13  N10  C11  118.55  3.000
 9DJ  H13  N10  C2   116.62  3.000
 9DJ  C11  N10  C2   124.72  3.000
 9DJ  H15  C11  H14  106.86  3.000
 9DJ  H15  C11  C12  108.31  3.000
 9DJ  H14  C11  C12  110.69  3.000
 9DJ  H15  C11  N10  110.31  3.000
 9DJ  H14  C11  N10  110.34  3.000
 9DJ  C12  C11  N10  110.26  3.000
 9DJ  H16  C12  C11  107.64  3.000
 9DJ  H16  C12  C17  107.38  3.000
 9DJ  C11  C12  C17  110.09  3.000
 9DJ  H16  C12  C13  108.18  3.000
 9DJ  C11  C12  C13  110.08  3.000
 9DJ  C17  C12  C13  113.26  3.000
 9DJ  N22  C19  C18  121.05  3.000
 9DJ  C18  C19  C20  117.32  3.000
 9DJ  N22  C19  C20  121.53  3.000
 9DJ  H17  C18  C16  118.16  3.000
 9DJ  H17  C18  C19  119.55  3.000
 9DJ  C16  C18  C19  122.28  3.000
 9DJ  C18  C16  C17  120.17  3.000
 9DJ  C18  C16  C15  118.95  3.000
 9DJ  C17  C16  C15  120.85  3.000
 9DJ  H19  C14  H18  106.79  3.000
 9DJ  H19  C14  C15  109.96  3.000
 9DJ  H18  C14  C15  110.32  3.000
 9DJ  H19  C14  C13  110.31  3.000
 9DJ  H18  C14  C13  110.00  3.000
 9DJ  C15  C14  C13  109.43  3.000
 9DJ  C23  N22  C19  119.30  3.000
 9DJ  C23  N22  C24  117.72  3.000
 9DJ  C19  N22  C24  120.83  3.000
 9DJ  H22  C23  H21  107.66  3.000
 9DJ  H22  C23  H20  107.72  3.000
 9DJ  H21  C23  H20  108.29  3.000
 9DJ  H22  C23  N22  109.46  3.000
 9DJ  H21  C23  N22  112.57  3.000
 9DJ  H20  C23  N22  110.97  3.000
 9DJ  H23  C29  C28  119.84  3.000
 9DJ  H23  C29  C24  119.68  3.000
 9DJ  C28  C29  C24  120.47  3.000
 9DJ  H24  C27  C28  120.35  3.000
 9DJ  H24  C27  C26  120.32  3.000
 9DJ  C28  C27  C26  119.32  3.000
 9DJ  H25  C25  C26  119.81  3.000
 9DJ  H25  C25  C24  119.82  3.000
 9DJ  C26  C25  C24  120.37  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
 9DJ  CONST_01  C2   C3   N4   C5     0.00   0.0  0
 9DJ  CONST_02  C2   C1   C6   C5     0.00   0.0  0
 9DJ  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 9DJ  CONST_04  C3   N4   C5   C6     0.00   0.0  0
 9DJ  CONST_05  C19  C20  C21  C17    0.00   0.0  0
 9DJ  CONST_06  C19  C18  C16  C17    0.00   0.0  0
 9DJ  CONST_07  C16  C17  C21  C20    0.00   0.0  0
 9DJ  CONST_08  C16  C18  C19  C20    0.00   0.0  0
 9DJ  CONST_09  C18  C19  C20  C21    0.00   0.0  0
 9DJ  CONST_10  C18  C16  C17  C21    0.00   0.0  0
 9DJ  CONST_11  C27  C28  C29  C24    0.00   0.0  0
 9DJ  CONST_12  C27  C26  C25  C24    0.00   0.0  0
 9DJ  CONST_13  C29  C28  C27  C26    0.00   0.0  0
 9DJ  CONST_14  C29  C24  C25  C26    0.00   0.0  0
 9DJ  CONST_15  C25  C26  C27  C28    0.00   0.0  0
 9DJ  CONST_16  C25  C24  C29  C28    0.00   0.0  0
 9DJ  CONST_17  N4   C3   C2   C1     0.00   0.0  0
 9DJ  CONST_18  N4   C5   C6   C1     0.00   0.0  0
 9DJ  CONST_19  C7   C1   C6   C5   180.00   0.0  0
 9DJ  CONST_20  N10  C2   C1   C6   180.00   0.0  0
 9DJ  CONST_21  C3   C2   C1   C7   180.00   0.0  0
 9DJ  CONST_22  N22  C19  C20  C21  180.00   0.0  0
 9DJ  CONST_23  N22  C24  C25  C26  180.00   0.0  0
 9DJ  CONST_24  N22  C24  C29  C28  180.00   0.0  0
 9DJ  CONST_25  N10  C2   C3   N4   180.00   0.0  0
 9DJ  CONST_26  N22  C19  C18  C16  180.00   0.0  0
 9DJ  CONST_27  H12  C3   N4   C5   180.00   0.0  0
 9DJ  CONST_28  H17  C18  C16  C15    0.00   0.0  0
 9DJ  CONST_29  H7   C20  C21  C17  180.00   0.0  0
 9DJ  CONST_30  H10  C28  C29  C24  180.00   0.0  0
 9DJ  CONST_31  H9   C26  C25  C24  180.00   0.0  0
 9DJ  CONST_32  H1   C5   C6   C1   180.00   0.0  0
 9DJ  CONST_33  H2   C6   C5   N4   180.00   0.0  0
 9DJ  CONST_34  H8   C21  C17  C12    0.00   0.0  0
 9DJ  CONST_35  H24  C27  C28  C29  180.00   0.0  0
 9DJ  CONST_36  H25  C25  C24  C29  180.00   0.0  0
 9DJ  CONST_37  H23  C29  C28  C27  180.00   0.0  0
 9DJ  CONST_38  C11  N10  C2   C1   180.00   0.0  0
 9DJ  CONST_39  C11  N10  C2   C3     0.00   0.0  0
 9DJ  CONST_40  H13  N10  C2   C1     0.00   0.0  0
 9DJ  CONST_41  H11  O8   C7   C1   180.00   0.0  0
 9DJ  Var_01    C16  C15  C14  C13  -55.67  30.0  1
 9DJ  Var_02    C12  C13  C14  C15   61.67  30.0  1
 9DJ  Var_03    C14  C15  C16  C17   25.16  30.0  1
 9DJ  Var_04    C24  N22  C19  C20  154.22  30.0  2
 9DJ  Var_05    C29  C24  N22  C19  135.12  30.0  2
 9DJ  Var_06    O9   C7   C1   C6   179.45  30.0  2
 9DJ  Var_07    C12  C11  N10  C2   172.08  30.0  1
 9DJ  Var_08    H20  C23  N22  C24  143.28  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
 9DJ  chir_01  C12  C17  C11  C13  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
 9DJ  plan-1  C24  0.020
 9DJ  plan-1  C26  0.020
 9DJ  plan-1  C28  0.020
 9DJ  plan-1  N22  0.020
 9DJ  plan-1  C29  0.020
 9DJ  plan-1  C27  0.020
 9DJ  plan-1  C25  0.020
 9DJ  plan-1  H9   0.020
 9DJ  plan-1  H10  0.020
 9DJ  plan-1  H23  0.020
 9DJ  plan-1  H24  0.020
 9DJ  plan-1  H25  0.020
 9DJ  plan-2  C5   0.020
 9DJ  plan-2  C6   0.020
 9DJ  plan-2  C7   0.020
 9DJ  plan-2  C1   0.020
 9DJ  plan-2  N4   0.020
 9DJ  plan-2  C3   0.020
 9DJ  plan-2  C2   0.020
 9DJ  plan-2  N10  0.020
 9DJ  plan-2  H1   0.020
 9DJ  plan-2  H2   0.020
 9DJ  plan-2  H12  0.020
 9DJ  plan-3  C15  0.020
 9DJ  plan-3  C17  0.020
 9DJ  plan-3  C20  0.020
 9DJ  plan-3  C21  0.020
 9DJ  plan-3  C12  0.020
 9DJ  plan-3  C19  0.020
 9DJ  plan-3  C18  0.020
 9DJ  plan-3  C16  0.020
 9DJ  plan-3  N22  0.020
 9DJ  plan-3  H7   0.020
 9DJ  plan-3  H8   0.020
 9DJ  plan-3  H17  0.020
 9DJ  plan-4  C2   0.020
 9DJ  plan-4  N10  0.020
 9DJ  plan-4  C11  0.020
 9DJ  plan-4  H13  0.020
 9DJ  plan-5  C7   0.020
 9DJ  plan-5  O9   0.020
 9DJ  plan-5  O8   0.020
 9DJ  plan-5  C1   0.020
 9DJ  plan-5  H11  0.020

