# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 16:48:04 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N1CC[C@@H](CC1)C(=O)NCc2ccc3OCOc3c2)c4cccc5ccccc45
#
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
 GRM  GRM  N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]piperidine-4-carboxamide  ligand  59  31  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GRM
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
 GRM  C1    C  CH1   0  -0.090  -2.8269  -0.8115   0.5335
 GRM  C2    C  CH3   0  -0.691  -4.0481  -1.4401   1.2084
 GRM  C3    C  CR6   0   0.056  -3.3278   0.2654  -0.4146
 GRM  N4    N  NT    0  -0.423  -2.0013  -1.7788  -0.1823
 GRM  C5    C  CH2   0  -0.284  -1.7449  -2.9984   0.5707
 GRM  C6    C  CH2   0  -0.427  -0.9195  -3.9933  -0.2367
 GRM  C7    C  CH1   0  -0.410   0.3717  -3.4182  -0.8091
 GRM  C8    C  CH2   0  -0.442   0.0495  -2.0843  -1.4973
 GRM  C9    C  CH2   0  -0.286  -0.7488  -1.1641  -0.5935
 GRM  C10   C  C     0   0.576   1.4697  -3.2363   0.2287
 GRM  O11   O  O     0  -0.492   1.2735  -3.2792   1.4352
 GRM  N12   N  NH1   0  -0.621   2.6894  -3.0124  -0.3013
 GRM  C13   C  CH2   0  -0.388   3.8451  -2.5956   0.4619
 GRM  C14   C  CR6   0   0.107   4.0776  -1.1073   0.3725
 GRM  C15   C  CR16  0  -0.383   3.1149  -0.2264   0.8987
 GRM  C16   C  CR56  0   0.318   3.3521   1.1161   0.7664
 GRM  C17   C  CR56  0   0.289   4.4908   1.6075   0.1432
 GRM  C18   C  CR16  0  -0.333   5.4447   0.7703  -0.3739
 GRM  C19   C  CR16  0  -0.326   5.2116  -0.6073  -0.2477
 GRM  O20   O  O     0  -0.486   2.5768   2.1535   1.1655
 GRM  C21   C  CH2   0   0.070   3.3460   3.3297   0.9535
 GRM  O22   O  O     0  -0.486   4.4495   2.9626   0.1364
 GRM  C23   C  CR66  0   0.093  -3.5677   1.5978   0.0355
 GRM  C24   C  CR66  0   0.107  -4.1033   2.5512  -0.8763
 GRM  C25   C  CR16  0  -0.335  -4.3941   2.1644  -2.2045
 GRM  C26   C  CR16  0  -0.240  -4.1649   0.8804  -2.6104
 GRM  C27   C  CR16  0  -0.309  -3.6339  -0.0637  -1.7114
 GRM  C28   C  CR16  0  -0.349  -3.3044   2.0268   1.3619
 GRM  C29   C  CR16  0  -0.249  -3.5482   3.3153   1.7548
 GRM  C30   C  CR16  0  -0.263  -4.0728   4.2547   0.8449
 GRM  C31   C  CR16  0  -0.310  -4.3421   3.8765  -0.4409
 GRM  H1    H  HCH1  0   0.208  -2.2209  -0.3425   1.3259
 GRM  H2    H  HCH3  0   0.248  -4.6917  -0.6558   1.6071
 GRM  H2A   H  HCH3  0   0.232  -4.6323  -2.0198   0.4921
 GRM  H2B   H  HCH3  0   0.241  -3.7782  -2.0858   2.0432
 GRM  H5    H  HCH2  0   0.198  -1.2505  -2.7844   1.5289
 GRM  H5A   H  HCH2  0   0.241  -2.6931  -3.4812   0.8059
 GRM  H6    H  HCH2  0   0.238  -0.7206  -4.8721   0.3789
 GRM  H6A   H  HCH2  0   0.232  -1.5255  -4.3334  -1.0810
 GRM  H7    H  HCH1  0   0.274   0.7564  -4.1067  -1.5688
 GRM  H8    H  HCH2  0   0.239   0.9566  -1.5744  -1.8290
 GRM  H8A   H  HCH2  0   0.240  -0.5389  -2.2934  -2.3942
 GRM  H9    H  HCH2  0   0.248  -0.9650  -0.2436  -1.1371
 GRM  H9A   H  HCH2  0   0.196  -0.1460  -0.8663   0.2838
 GRM  HN12  H  HNH1  0   0.399   2.7696  -2.9581  -1.3044
 GRM  H13   H  HCH2  0   0.264   3.6953  -2.9023   1.4965
 GRM  H13A  H  HCH2  0   0.268   4.7224  -3.1293   0.0937
 GRM  H15   H  HCR6  0   0.266   2.2220  -0.5933   1.3895
 GRM  H18   H  HCR6  0   0.272   6.3324   1.1477  -0.8629
 GRM  H19   H  HCR6  0   0.255   5.9438  -1.2962  -0.6501
 GRM  H21   H  HCH2  0   0.245   2.7413   4.0791   0.4429
 GRM  H21A  H  HCH2  0   0.233   3.7064   3.7162   1.9128
 GRM  H25   H  HCR6  0   0.251  -4.8006   2.8986  -2.8900
 GRM  H26   H  HCR6  0   0.253  -4.3896   0.5809  -3.6261
 GRM  H27   H  HCR6  0   0.249  -3.4439  -1.0745  -2.0496
 GRM  H28   H  HCR6  0   0.249  -2.9032   1.3309   2.0861
 GRM  H29   H  HCR6  0   0.257  -3.3356   3.6147   2.7728
 GRM  H30   H  HCR6  0   0.257  -4.2609   5.2710   1.1658
 GRM  H31   H  HCR6  0   0.253  -4.7463   4.5908  -1.1485

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
 GRM  C1   C2    single    1.530  0.020  1.530
 GRM  C1   C3    single    1.520  0.020  1.520
 GRM  C1   N4    single    1.459  0.020  1.459
 GRM  C3   C23   aromatic  1.427  0.020  1.427
 GRM  C3   C27   aromatic  1.372  0.020  1.372
 GRM  N4   C5    single    1.456  0.020  1.456
 GRM  N4   C9    single    1.454  0.020  1.454
 GRM  C5   C6    single    1.524  0.020  1.524
 GRM  C6   C7    single    1.525  0.020  1.525
 GRM  C7   C8    single    1.535  0.020  1.535
 GRM  C7   C10   single    1.522  0.020  1.522
 GRM  C8   C9    single    1.517  0.020  1.517
 GRM  C10  O11   double    1.223  0.020  1.223
 GRM  C10  N12   single    1.349  0.020  1.349
 GRM  N12  C13   single    1.446  0.020  1.446
 GRM  C13  C14   single    1.509  0.020  1.509
 GRM  C14  C15   aromatic  1.407  0.020  1.407
 GRM  C14  C19   aromatic  1.386  0.020  1.386
 GRM  C15  C16   aromatic  1.370  0.020  1.370
 GRM  C16  C17   aromatic  1.388  0.020  1.388
 GRM  C16  O20   single    1.355  0.020  1.355
 GRM  C17  C18   aromatic  1.370  0.020  1.370
 GRM  C17  O22   single    1.356  0.020  1.356
 GRM  C18  C19   aromatic  1.403  0.020  1.403
 GRM  O20  C21   single    1.421  0.020  1.421
 GRM  C21  O22   single    1.421  0.020  1.421
 GRM  C23  C24   aromatic  1.424  0.020  1.424
 GRM  C23  C28   aromatic  1.419  0.020  1.419
 GRM  C24  C25   aromatic  1.414  0.020  1.414
 GRM  C24  C31   aromatic  1.415  0.020  1.415
 GRM  C25  C26   aromatic  1.366  0.020  1.366
 GRM  C26  C27   aromatic  1.408  0.020  1.408
 GRM  C28  C29   aromatic  1.369  0.020  1.369
 GRM  C29  C30   aromatic  1.409  0.020  1.409
 GRM  C30  C31   aromatic  1.367  0.020  1.367
 GRM  C1   H1    single    0.970  0.020  1.090
 GRM  C2   H2    single    0.970  0.020  1.090
 GRM  C2   H2A   single    0.970  0.020  1.090
 GRM  C2   H2B   single    0.970  0.020  1.090
 GRM  C5   H5    single    0.970  0.020  1.090
 GRM  C5   H5A   single    0.970  0.020  1.090
 GRM  C6   H6    single    0.970  0.020  1.090
 GRM  C6   H6A   single    0.970  0.020  1.090
 GRM  C7   H7    single    0.970  0.020  1.090
 GRM  C8   H8    single    0.970  0.020  1.090
 GRM  C8   H8A   single    0.970  0.020  1.090
 GRM  C9   H9    single    0.970  0.020  1.090
 GRM  C9   H9A   single    0.970  0.020  1.090
 GRM  N12  HN12  single    0.860  0.020  1.020
 GRM  C13  H13   single    0.970  0.020  1.090
 GRM  C13  H13A  single    0.970  0.020  1.090
 GRM  C15  H15   single    0.930  0.020  1.080
 GRM  C18  H18   single    0.930  0.020  1.080
 GRM  C19  H19   single    0.930  0.020  1.080
 GRM  C21  H21   single    0.970  0.020  1.090
 GRM  C21  H21A  single    0.970  0.020  1.090
 GRM  C25  H25   single    0.930  0.020  1.080
 GRM  C26  H26   single    0.930  0.020  1.080
 GRM  C27  H27   single    0.930  0.020  1.080
 GRM  C28  H28   single    0.930  0.020  1.080
 GRM  C29  H29   single    0.930  0.020  1.080
 GRM  C30  H30   single    0.930  0.020  1.080
 GRM  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
 GRM  H1    C1   N4   108.88  3.000
 GRM  H1    C1   C3   109.16  3.000
 GRM  N4    C1   C3   110.49  3.000
 GRM  H1    C1   C2   107.25  3.000
 GRM  N4    C1   C2   113.30  3.000
 GRM  C3    C1   C2   107.65  3.000
 GRM  H2B   C2   H2A  108.71  3.000
 GRM  H2B   C2   H2   107.00  3.000
 GRM  H2A   C2   H2   107.83  3.000
 GRM  H2B   C2   C1   112.56  3.000
 GRM  H2A   C2   C1   110.86  3.000
 GRM  H2    C2   C1   109.69  3.000
 GRM  C27   C3   C23  118.98  3.000
 GRM  C27   C3   C1   119.54  3.000
 GRM  C23   C3   C1   121.36  3.000
 GRM  C9    N4   C5   110.40  3.000
 GRM  C9    N4   C1   110.22  3.000
 GRM  C5    N4   C1   113.65  3.000
 GRM  H5A   C5   H5   106.83  3.000
 GRM  H5A   C5   C6   107.24  3.000
 GRM  H5    C5   C6   110.20  3.000
 GRM  H5A   C5   N4   109.23  3.000
 GRM  H5    C5   N4   111.53  3.000
 GRM  C6    C5   N4   111.60  3.000
 GRM  H6A   C6   H6   106.62  3.000
 GRM  H6A   C6   C7   107.26  3.000
 GRM  H6    C6   C7   111.17  3.000
 GRM  H6A   C6   C5   108.18  3.000
 GRM  H6    C6   C5   109.00  3.000
 GRM  C7    C6   C5   114.28  3.000
 GRM  H7    C7   C10  107.14  3.000
 GRM  H7    C7   C8   108.00  3.000
 GRM  C10   C7   C8   110.69  3.000
 GRM  H7    C7   C6   108.70  3.000
 GRM  C10   C7   C6   113.58  3.000
 GRM  C8    C7   C6   108.56  3.000
 GRM  H8A   C8   H8   106.69  3.000
 GRM  H8A   C8   C9   108.77  3.000
 GRM  H8    C8   C9   109.56  3.000
 GRM  H8A   C8   C7   108.34  3.000
 GRM  H8    C8   C7   111.56  3.000
 GRM  C9    C8   C7   111.74  3.000
 GRM  H9A   C9   H9   106.04  3.000
 GRM  H9A   C9   C8   110.44  3.000
 GRM  H9    C9   C8   108.62  3.000
 GRM  H9A   C9   N4   111.05  3.000
 GRM  H9    C9   N4   109.08  3.000
 GRM  C8    C9   N4   111.42  3.000
 GRM  N12   C10  O11  122.58  3.000
 GRM  N12   C10  C7   113.86  3.000
 GRM  O11   C10  C7   123.56  3.000
 GRM  HN12  N12  C13  116.50  3.000
 GRM  HN12  N12  C10  118.17  3.000
 GRM  C13   N12  C10  124.28  3.000
 GRM  H13A  C13  H13  107.06  3.000
 GRM  H13A  C13  C14  109.79  3.000
 GRM  H13   C13  C14  110.80  3.000
 GRM  H13A  C13  N12  108.87  3.000
 GRM  H13   C13  N12  108.07  3.000
 GRM  C14   C13  N12  112.09  3.000
 GRM  C19   C14  C15  120.09  3.000
 GRM  C19   C14  C13  120.56  3.000
 GRM  C15   C14  C13  119.34  3.000
 GRM  H15   C15  C16  121.24  3.000
 GRM  H15   C15  C14  121.43  3.000
 GRM  C16   C15  C14  117.33  3.000
 GRM  O20   C16  C17  109.31  3.000
 GRM  O20   C16  C15  128.52  3.000
 GRM  C17   C16  C15  122.17  3.000
 GRM  O22   C17  C18  129.04  3.000
 GRM  O22   C17  C16  109.33  3.000
 GRM  C18   C17  C16  121.62  3.000
 GRM  H18   C18  C19  121.31  3.000
 GRM  H18   C18  C17  121.92  3.000
 GRM  C19   C18  C17  116.76  3.000
 GRM  H19   C19  C18  118.62  3.000
 GRM  H19   C19  C14  119.34  3.000
 GRM  C18   C19  C14  122.04  3.000
 GRM  C21   O20  C16  106.26  3.000
 GRM  H21A  C21  H21  110.51  3.000
 GRM  H21A  C21  O22  109.83  3.000
 GRM  H21   C21  O22  109.82  3.000
 GRM  H21A  C21  O20  109.84  3.000
 GRM  H21   C21  O20  109.79  3.000
 GRM  O22   C21  O20  106.99  3.000
 GRM  C21   O22  C17  106.20  3.000
 GRM  C28   C23  C24  117.78  3.000
 GRM  C28   C23  C3   123.11  3.000
 GRM  C24   C23  C3   119.12  3.000
 GRM  C31   C24  C25  120.71  3.000
 GRM  C31   C24  C23  119.57  3.000
 GRM  C25   C24  C23  119.73  3.000
 GRM  H25   C25  C26  120.79  3.000
 GRM  H25   C25  C24  119.09  3.000
 GRM  C26   C25  C24  120.12  3.000
 GRM  H26   C26  C27  119.47  3.000
 GRM  H26   C26  C25  120.27  3.000
 GRM  C27   C26  C25  120.26  3.000
 GRM  H27   C27  C26  119.52  3.000
 GRM  H27   C27  C3   118.68  3.000
 GRM  C26   C27  C3   121.79  3.000
 GRM  H28   C28  C29  118.65  3.000
 GRM  H28   C28  C23  120.02  3.000
 GRM  C29   C28  C23  121.33  3.000
 GRM  H29   C29  C30  119.74  3.000
 GRM  H29   C29  C28  119.70  3.000
 GRM  C30   C29  C28  120.56  3.000
 GRM  H30   C30  C31  120.30  3.000
 GRM  H30   C30  C29  119.96  3.000
 GRM  C31   C30  C29  119.75  3.000
 GRM  H31   C31  C30  120.35  3.000
 GRM  H31   C31  C24  118.63  3.000
 GRM  C30   C31  C24  121.02  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
 GRM  CONST_01  C25   C24  C23  C3     0.00   0.0  0
 GRM  CONST_02  C31   C24  C23  C3   180.00   0.0  0
 GRM  CONST_03  C29   C28  C23  C3   180.00   0.0  0
 GRM  CONST_04  C25   C26  C27  C3     0.00   0.0  0
 GRM  CONST_05  C17   C16  C15  C14    0.00   0.0  0
 GRM  CONST_06  C17   C18  C19  C14    0.00   0.0  0
 GRM  CONST_07  C18   C19  C14  C15    0.00   0.0  0
 GRM  CONST_08  C18   C17  C16  C15    0.00   0.0  0
 GRM  CONST_09  C19   C14  C15  C16    0.00   0.0  0
 GRM  CONST_10  C19   C18  C17  C16    0.00   0.0  0
 GRM  CONST_11  C26   C27  C3   C23    0.00   0.0  0
 GRM  CONST_12  C26   C25  C24  C23    0.00   0.0  0
 GRM  CONST_13  C30   C31  C24  C23    0.00   0.0  0
 GRM  CONST_14  C30   C29  C28  C23    0.00   0.0  0
 GRM  CONST_15  C27   C3   C23  C24    0.00   0.0  0
 GRM  CONST_16  C29   C28  C23  C24    0.00   0.0  0
 GRM  CONST_17  C27   C26  C25  C24    0.00   0.0  0
 GRM  CONST_18  C29   C30  C31  C24    0.00   0.0  0
 GRM  CONST_19  C28   C23  C24  C25  180.00   0.0  0
 GRM  CONST_20  C30   C31  C24  C25  180.00   0.0  0
 GRM  CONST_21  C31   C24  C25  C26  180.00   0.0  0
 GRM  CONST_22  C28   C23  C3   C27  180.00   0.0  0
 GRM  CONST_23  C31   C24  C23  C28    0.00   0.0  0
 GRM  CONST_24  C31   C30  C29  C28    0.00   0.0  0
 GRM  CONST_25  C24   C23  C3   C1   180.00   0.0  0
 GRM  CONST_26  C28   C23  C3   C1     0.00   0.0  0
 GRM  CONST_27  C26   C27  C3   C1   180.00   0.0  0
 GRM  CONST_28  C16   C15  C14  C13  180.00   0.0  0
 GRM  CONST_29  C18   C19  C14  C13  180.00   0.0  0
 GRM  CONST_30  H28   C28  C23  C3     0.00   0.0  0
 GRM  CONST_31  H26   C26  C27  C3   180.00   0.0  0
 GRM  CONST_32  H18   C18  C19  C14  180.00   0.0  0
 GRM  CONST_33  H19   C19  C14  C15  180.00   0.0  0
 GRM  CONST_34  H15   C15  C16  C17  180.00   0.0  0
 GRM  CONST_35  H27   C27  C3   C23  180.00   0.0  0
 GRM  CONST_36  H25   C25  C24  C23  180.00   0.0  0
 GRM  CONST_37  H31   C31  C24  C23  180.00   0.0  0
 GRM  CONST_38  H29   C29  C28  C23  180.00   0.0  0
 GRM  CONST_39  H30   C30  C31  C24  180.00   0.0  0
 GRM  CONST_40  C13   N12  C10  C7   180.00   0.0  0
 GRM  CONST_41  HN12  N12  C10  C7     0.00   0.0  0
 GRM  CONST_42  C13   N12  C10  O11    0.00   0.0  0
 GRM  Var_01    C7    C6   C5   N4    52.81  30.0  1
 GRM  Var_02    C7    C8   C9   N4   -58.75  30.0  1
 GRM  Var_03    C8    C9   N4   C5    61.23  30.0  1
 GRM  Var_04    C9    N4   C5   C6   -57.48  30.0  1
 GRM  Var_05    O22   C21  O20  C16   13.43  30.0  1
 GRM  Var_06    O20   C21  O22  C17  -13.52  30.0  1
 GRM  Var_07    C15   C14  C13  N12   64.07  30.0  2
 GRM  Var_08    C14   C13  N12  C10  -98.61  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
 GRM  chir_01  C1  C2  C3  N4   positiv
 GRM  chir_02  C7  C6  C8  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
 GRM  plan-1  C13   0.020
 GRM  plan-1  C14   0.020
 GRM  plan-1  C15   0.020
 GRM  plan-1  C16   0.020
 GRM  plan-1  C17   0.020
 GRM  plan-1  C18   0.020
 GRM  plan-1  C19   0.020
 GRM  plan-1  O20   0.020
 GRM  plan-1  O22   0.020
 GRM  plan-1  H15   0.020
 GRM  plan-1  H18   0.020
 GRM  plan-1  H19   0.020
 GRM  plan-2  C1    0.020
 GRM  plan-2  C3    0.020
 GRM  plan-2  C23   0.020
 GRM  plan-2  C24   0.020
 GRM  plan-2  C25   0.020
 GRM  plan-2  C26   0.020
 GRM  plan-2  C27   0.020
 GRM  plan-2  C28   0.020
 GRM  plan-2  C29   0.020
 GRM  plan-2  C30   0.020
 GRM  plan-2  C31   0.020
 GRM  plan-2  H25   0.020
 GRM  plan-2  H26   0.020
 GRM  plan-2  H27   0.020
 GRM  plan-2  H28   0.020
 GRM  plan-2  H29   0.020
 GRM  plan-2  H30   0.020
 GRM  plan-2  H31   0.020
 GRM  plan-3  C7    0.020
 GRM  plan-3  C10   0.020
 GRM  plan-3  O11   0.020
 GRM  plan-3  N12   0.020
 GRM  plan-3  C13   0.020
 GRM  plan-3  HN12  0.020

