# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:28:04 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)-3-[2-propyl-4-(1H-pyrazol-4-yl)thiophen-3-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1scc(c1C[C@H](NC2=NC(C)(C)Cc3cc(Cl)ccc23)C(O)=O)c4c[nH]nc4
#
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
 1BE  1BE  N-(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)-3-[2-propyl-4-(1H-pyrazol-4-yl)thiophen-3-yl]-L-alanine  ligand  59  32  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1BE
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
 1BE  CL1  CL  CL    0  -0.124  -6.4840  -0.3058   0.3519
 1BE  C1   C   CR6   0  -0.035  -4.8166   0.0272   0.0234
 1BE  C6   C   CR16  0  -0.215  -4.0340  -0.9446  -0.5780
 1BE  C5   C   CR16  0  -0.311  -2.7002  -0.6639  -0.8313
 1BE  C4   C   CR66  0   0.007  -2.1545   0.5719  -0.5006
 1BE  C12  C   CR6   0   0.480  -0.7311   0.9267  -0.7256
 1BE  N11  N   N     0  -0.420  -0.1330   1.8664  -0.1039
 1BE  C10  C   CR6   0   0.036  -0.8574   2.6129   0.9134
 1BE  C28  C   CH3   0  -0.628  -0.7792   1.8602   2.2448
 1BE  C27  C   CH3   0  -0.648  -0.1779   3.9704   1.0625
 1BE  C9   C   C     0  -0.493  -2.3151   2.8326   0.4924
 1BE  C3   C   CR66  0   0.114  -2.9542   1.5317   0.1236
 1BE  C2   C   CR16  0  -0.285  -4.2888   1.2580   0.3821
 1BE  N13  N   NH1   0  -0.685  -0.0706   0.1686  -1.6450
 1BE  C14  C   CH1   0  -0.201   1.3419   0.2449  -1.8503
 1BE  C15  C   CH2   0  -0.562   2.0573  -1.0167  -1.3137
 1BE  C7   C   C     0   0.543   1.6561   0.4629  -3.3167
 1BE  O8   O   O     0  -0.433   0.8398   0.4624  -4.2029
 1BE  O9   O   OH1   0  -0.588   2.9539   0.6466  -3.5126
 1BE  C11  C   CR5   0   0.184   1.8122  -1.1758   0.1538
 1BE  C13  C   CR5   0   0.189   2.4419  -0.3577   1.1527
 1BE  C16  C   CR15  0  -0.570   2.0024  -0.6473   2.4095
 1BE  S17  S   S2    0   0.201   0.8240  -1.8878   2.4003
 1BE  C18  C   CR5   0  -0.225   0.9080  -2.0498   0.6863
 1BE  C19  C   CH2   0  -0.515   0.1081  -3.1051  -0.0059
 1BE  C20  C   CH2   0  -0.408   0.8573  -4.4340  -0.1268
 1BE  C21  C   CH3   0  -0.668   0.0424  -5.4877  -0.8613
 1BE  C23  C   CR5   0  -0.158   3.4236   0.6889   0.8759
 1BE  C24  C   CR15  0   0.005   3.3990   1.9879   1.3391
 1BE  N25  N   NR15  0  -0.427   4.5001   2.5871   0.8636
 1BE  N26  N   N     0  -0.270   5.2506   1.7846   0.1188
 1BE  C29  C   CR15  0  -0.114   4.6111   0.6304   0.1151
 1BE  H1   H   HCR6  0   0.283  -4.4491  -1.9078  -0.8399
 1BE  H2   H   HCR6  0   0.255  -2.0968  -1.4422  -1.2796
 1BE  H3   H   HCH3  0   0.237   0.2630   1.7096   2.5271
 1BE  H4   H   HCH3  0   0.215  -1.2767   2.4172   3.0412
 1BE  H5   H   HCH3  0   0.226  -1.2376   0.8722   2.1800
 1BE  H6   H   HCH3  0   0.223  -0.2103   4.5302   0.1260
 1BE  H7   H   HCH3  0   0.217  -0.6656   4.5722   1.8317
 1BE  H8   H   HCH3  0   0.229   0.8690   3.8481   1.3433
 1BE  H9   H   H     0   0.252  -2.8802   3.3311   1.2827
 1BE  H10  H   H     0   0.256  -2.3348   3.4984  -0.3791
 1BE  H11  H   HCR6  0   0.274  -4.9094   2.0005   0.8674
 1BE  H12  H   HNH1  0   0.389  -0.6042  -0.4035  -2.2763
 1BE  H13  H   HCH1  0   0.314   1.7079   1.1140  -1.2964
 1BE  H14  H   HCH2  0   0.262   1.6932  -1.8907  -1.8591
 1BE  H15  H   HCH2  0   0.268   3.1248  -0.9493  -1.5227
 1BE  H16  H   HOH1  0   0.485   3.1363   0.7638  -4.4573
 1BE  H17  H   HCR5  0   0.279   2.3190  -0.1933   3.3361
 1BE  H18  H   HCH2  0   0.248  -0.8398  -3.2665   0.5149
 1BE  H19  H   HCH2  0   0.239  -0.1586  -2.7541  -1.0055
 1BE  H20  H   HCH2  0   0.224   1.8023  -4.2616  -0.6498
 1BE  H21  H   HCH2  0   0.223   1.1217  -4.7931   0.8713
 1BE  H22  H   HCH3  0   0.221  -0.8874  -5.7084  -0.3340
 1BE  H23  H   HCH3  0   0.220  -0.2209  -5.1511  -1.8657
 1BE  H24  H   HCH3  0   0.232   0.5968  -6.4212  -0.9594
 1BE  H25  H   HCR5  0   0.277   2.6787   2.5081   1.9479
 1BE  H26  H   HNR5  0   0.421   4.7800   3.5435   1.0103
 1BE  H27  H   HCR5  0   0.253   5.0227  -0.2162  -0.4137

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
 1BE  CL1  C1   single    1.732  0.020  1.732
 1BE  C6   C1   aromatic  1.385  0.020  1.385
 1BE  C6   C5   aromatic  1.386  0.020  1.386
 1BE  C1   C2   aromatic  1.386  0.020  1.386
 1BE  C5   C4   aromatic  1.391  0.020  1.391
 1BE  N25  N26  aromatic  1.327  0.020  1.327
 1BE  N25  C24  aromatic  1.341  0.020  1.341
 1BE  O8   C7   double    1.205  0.020  1.205
 1BE  C2   C3   aromatic  1.387  0.020  1.387
 1BE  N26  C29  aromatic  1.320  0.020  1.320
 1BE  C4   C3   aromatic  1.397  0.020  1.397
 1BE  C4   C12  single    1.484  0.020  1.484
 1BE  C24  C23  aromatic  1.379  0.020  1.379
 1BE  C3   C9   single    1.496  0.020  1.496
 1BE  N13  C12  single    1.362  0.020  1.362
 1BE  N13  C14  single    1.429  0.020  1.429
 1BE  C7   C14  single    1.515  0.020  1.515
 1BE  C7   O9   single    1.325  0.020  1.325
 1BE  C12  N11  double    1.276  0.020  1.276
 1BE  C29  C23  aromatic  1.411  0.020  1.411
 1BE  C23  C13  single    1.461  0.020  1.461
 1BE  C14  C15  single    1.546  0.020  1.546
 1BE  C9   C10  single    1.533  0.020  1.533
 1BE  C15  C11  single    1.496  0.020  1.496
 1BE  N11  C10  single    1.455  0.020  1.455
 1BE  C13  C11  aromatic  1.437  0.020  1.437
 1BE  C13  C16  aromatic  1.362  0.020  1.362
 1BE  C10  C28  single    1.531  0.020  1.531
 1BE  C10  C27  single    1.525  0.020  1.525
 1BE  C11  C18  aromatic  1.366  0.020  1.366
 1BE  C16  S17  aromatic  1.711  0.020  1.711
 1BE  C18  C19  single    1.494  0.020  1.494
 1BE  C18  S17  aromatic  1.724  0.020  1.724
 1BE  C19  C20  single    1.530  0.020  1.530
 1BE  C20  C21  single    1.521  0.020  1.521
 1BE  C6   H1   single    0.930  0.020  1.080
 1BE  C5   H2   single    0.930  0.020  1.080
 1BE  C28  H3   single    0.970  0.020  1.090
 1BE  C28  H4   single    0.970  0.020  1.090
 1BE  C28  H5   single    0.970  0.020  1.090
 1BE  C27  H6   single    0.970  0.020  1.090
 1BE  C27  H7   single    0.970  0.020  1.090
 1BE  C27  H8   single    0.970  0.020  1.090
 1BE  C9   H9   single    0.970  0.020  1.090
 1BE  C9   H10  single    0.970  0.020  1.090
 1BE  C2   H11  single    0.930  0.020  1.080
 1BE  N13  H12  single    0.860  0.020  1.020
 1BE  C14  H13  single    0.970  0.020  1.090
 1BE  C15  H14  single    0.970  0.020  1.090
 1BE  C15  H15  single    0.970  0.020  1.090
 1BE  O9   H16  single    0.850  0.020  0.980
 1BE  C16  H17  single    0.930  0.020  1.080
 1BE  C19  H18  single    0.970  0.020  1.090
 1BE  C19  H19  single    0.970  0.020  1.090
 1BE  C20  H20  single    0.970  0.020  1.090
 1BE  C20  H21  single    0.970  0.020  1.090
 1BE  C21  H22  single    0.970  0.020  1.090
 1BE  C21  H23  single    0.970  0.020  1.090
 1BE  C21  H24  single    0.970  0.020  1.090
 1BE  C24  H25  single    0.930  0.020  1.080
 1BE  N25  H26  single    0.860  0.020  1.020
 1BE  C29  H27  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
 1BE  C2   C1   C6   121.34  3.000
 1BE  C2   C1   CL1  119.22  3.000
 1BE  C6   C1   CL1  119.44  3.000
 1BE  H1   C6   C5   120.37  3.000
 1BE  H1   C6   C1   120.89  3.000
 1BE  C5   C6   C1   118.74  3.000
 1BE  H2   C5   C4   121.26  3.000
 1BE  H2   C5   C6   117.80  3.000
 1BE  C4   C5   C6   120.93  3.000
 1BE  C3   C4   C12  116.92  3.000
 1BE  C12  C4   C5   123.55  3.000
 1BE  C3   C4   C5   119.49  3.000
 1BE  N13  C12  N11  120.76  3.000
 1BE  N11  C12  C4   123.50  3.000
 1BE  N13  C12  C4   115.74  3.000
 1BE  C10  N11  C12  119.03  3.000
 1BE  C9   C10  C27  108.84  3.000
 1BE  C27  C10  C28  109.25  3.000
 1BE  C9   C10  C28  110.96  3.000
 1BE  C27  C10  N11  107.65  3.000
 1BE  C28  C10  N11  109.29  3.000
 1BE  C9   C10  N11  110.79  3.000
 1BE  H5   C28  H4   108.29  3.000
 1BE  H5   C28  H3   106.97  3.000
 1BE  H4   C28  H3   108.49  3.000
 1BE  H5   C28  C10  111.83  3.000
 1BE  H4   C28  C10  111.11  3.000
 1BE  H3   C28  C10  109.99  3.000
 1BE  H8   C27  H7   108.01  3.000
 1BE  H8   C27  H6   107.87  3.000
 1BE  H7   C27  H6   107.97  3.000
 1BE  H8   C27  C10  110.67  3.000
 1BE  H7   C27  C10  111.13  3.000
 1BE  H6   C27  C10  111.06  3.000
 1BE  H10  C9   H9   106.77  3.000
 1BE  H10  C9   C3   108.93  3.000
 1BE  H9   C9   C3   110.76  3.000
 1BE  H10  C9   C10  108.80  3.000
 1BE  H9   C9   C10  111.03  3.000
 1BE  C3   C9   C10  110.45  3.000
 1BE  C2   C3   C9   122.48  3.000
 1BE  C9   C3   C4   117.60  3.000
 1BE  C2   C3   C4   119.92  3.000
 1BE  H11  C2   C3   119.99  3.000
 1BE  H11  C2   C1   120.45  3.000
 1BE  C3   C2   C1   119.56  3.000
 1BE  H12  N13  C14  117.69  3.000
 1BE  H12  N13  C12  118.89  3.000
 1BE  C14  N13  C12  123.11  3.000
 1BE  H13  C14  C7   107.84  3.000
 1BE  H13  C14  C15  108.53  3.000
 1BE  C7   C14  C15  110.93  3.000
 1BE  H13  C14  N13  107.48  3.000
 1BE  C15  C14  N13  111.33  3.000
 1BE  C7   C14  N13  110.58  3.000
 1BE  H15  C15  H14  106.27  3.000
 1BE  H15  C15  C11  110.79  3.000
 1BE  H14  C15  C11  110.48  3.000
 1BE  H15  C15  C14  109.64  3.000
 1BE  H14  C15  C14  108.98  3.000
 1BE  C11  C15  C14  110.57  3.000
 1BE  O9   C7   O8   123.69  3.000
 1BE  O9   C7   C14  111.47  3.000
 1BE  O8   C7   C14  124.83  3.000
 1BE  H16  O9   C7   110.19  3.000
 1BE  C18  C11  C13  112.55  3.000
 1BE  C18  C11  C15  123.98  3.000
 1BE  C13  C11  C15  123.34  3.000
 1BE  C23  C13  C16  122.94  3.000
 1BE  C16  C13  C11  112.27  3.000
 1BE  C23  C13  C11  124.79  3.000
 1BE  H17  C16  S17  120.76  3.000
 1BE  H17  C16  C13  127.44  3.000
 1BE  S17  C16  C13  111.80  3.000
 1BE  C18  S17  C16   92.29  3.000
 1BE  C19  C18  S17  120.06  3.000
 1BE  S17  C18  C11  111.09  3.000
 1BE  C19  C18  C11  128.74  3.000
 1BE  H19  C19  H18  105.76  3.000
 1BE  H19  C19  C20  109.04  3.000
 1BE  H18  C19  C20  109.50  3.000
 1BE  H19  C19  C18  109.12  3.000
 1BE  H18  C19  C18  110.34  3.000
 1BE  C20  C19  C18  112.82  3.000
 1BE  H21  C20  H20  106.22  3.000
 1BE  H21  C20  C21  110.06  3.000
 1BE  H20  C20  C21  109.95  3.000
 1BE  H21  C20  C19  109.36  3.000
 1BE  H20  C20  C19  108.90  3.000
 1BE  C21  C20  C19  112.17  3.000
 1BE  H24  C21  H23  107.69  3.000
 1BE  H24  C21  H22  107.67  3.000
 1BE  H23  C21  H22  107.54  3.000
 1BE  H24  C21  C20  111.36  3.000
 1BE  H23  C21  C20  111.09  3.000
 1BE  H22  C21  C20  111.30  3.000
 1BE  C29  C23  C24  103.60  3.000
 1BE  C29  C23  C13  129.61  3.000
 1BE  C24  C23  C13  126.78  3.000
 1BE  H25  C24  N25  122.27  3.000
 1BE  H25  C24  C23  131.04  3.000
 1BE  N25  C24  C23  106.68  3.000
 1BE  H26  N25  N26  119.91  3.000
 1BE  H26  N25  C24  126.93  3.000
 1BE  N26  N25  C24  113.15  3.000
 1BE  C29  N26  N25  104.86  3.000
 1BE  H27  C29  N26  120.17  3.000
 1BE  H27  C29  C23  128.11  3.000
 1BE  N26  C29  C23  111.71  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
 1BE  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 1BE  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 1BE  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 1BE  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 1BE  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 1BE  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 1BE  CONST_09  S17  C16  C13  C11     0.00   0.0  0
 1BE  CONST_10  C16  S17  C18  C11     0.00   0.0  0
 1BE  CONST_11  N25  C24  C23  C13   180.00   0.0  0
 1BE  CONST_12  N26  C29  C23  C13   180.00   0.0  0
 1BE  CONST_13  S17  C18  C11  C13     0.00   0.0  0
 1BE  CONST_14  C18  S17  C16  C13     0.00   0.0  0
 1BE  CONST_17  C18  C11  C13  C16     0.00   0.0  0
 1BE  CONST_18  C23  C13  C16  S17   180.00   0.0  0
 1BE  CONST_19  C23  C13  C11  C18   180.00   0.0  0
 1BE  CONST_20  N26  N25  C24  C23     0.00   0.0  0
 1BE  CONST_21  N25  N26  C29  C23     0.00   0.0  0
 1BE  CONST_22  C29  N26  N25  C24     0.00   0.0  0
 1BE  CONST_23  N26  C29  C23  C24     0.00   0.0  0
 1BE  CONST_24  C29  C23  C24  N25     0.00   0.0  0
 1BE  CONST_25  C10  N11  C12  C4      0.00   0.0  0
 1BE  CONST_26  C5   C6   C1   CL1   180.00   0.0  0
 1BE  CONST_27  C3   C2   C1   CL1   180.00   0.0  0
 1BE  CONST_28  C23  C13  C11  C15     0.00   0.0  0
 1BE  CONST_29  C16  C13  C11  C15   180.00   0.0  0
 1BE  CONST_30  S17  C18  C11  C15   180.00   0.0  0
 1BE  CONST_31  C19  C18  C11  C13   180.00   0.0  0
 1BE  CONST_32  C19  C18  S17  C16   180.00   0.0  0
 1BE  CONST_33  N13  C12  N11  C10   180.00   0.0  0
 1BE  CONST_34  H2   C5   C6   C1    180.00   0.0  0
 1BE  CONST_35  H11  C2   C1   C6    180.00   0.0  0
 1BE  CONST_36  H1   C6   C5   C4    180.00   0.0  0
 1BE  CONST_37  H17  C16  C13  C11   180.00   0.0  0
 1BE  CONST_38  H25  C24  C23  C13     0.00   0.0  0
 1BE  CONST_39  H27  C29  C23  C13     0.00   0.0  0
 1BE  CONST_40  H26  N25  C24  C23   180.00   0.0  0
 1BE  CONST_41  C14  N13  C12  C4    180.00   0.0  0
 1BE  CONST_42  C14  N13  C12  N11     0.00   0.0  0
 1BE  CONST_44  H16  O9   C7   C14   180.00   0.0  0
 1BE  Var_01    N11  C12  C4   C5   -159.13  30.0  1
 1BE  Var_02    C10  C9   C3   C4    -34.77  30.0  1
 1BE  Var_03    C9   C10  N11  C12   -37.76  30.0  1
 1BE  Var_04    C3   C9   C10  N11    52.77  30.0  1
 1BE  Var_05    C13  C11  C15  C14   -74.14  30.0  2
 1BE  Var_06    C20  C19  C18  C11    86.66  30.0  2
 1BE  Var_07    H3   C28  C10  N11    57.34  30.0  3
 1BE  Var_08    H6   C27  C10  N11    61.02  30.0  3
 1BE  Var_09    C21  C20  C19  C18  -178.70  30.0  3
 1BE  Var_10    H22  C21  C20  C19   -61.12  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
 1BE  chir_01  C14  N13  C7  C15  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
 1BE  plan-1  C15  0.020
 1BE  plan-1  C11  0.020
 1BE  plan-1  C13  0.020
 1BE  plan-1  C16  0.020
 1BE  plan-1  S17  0.020
 1BE  plan-1  C18  0.020
 1BE  plan-1  C19  0.020
 1BE  plan-1  C23  0.020
 1BE  plan-1  H17  0.020
 1BE  plan-2  C13  0.020
 1BE  plan-2  C23  0.020
 1BE  plan-2  C24  0.020
 1BE  plan-2  N25  0.020
 1BE  plan-2  N26  0.020
 1BE  plan-2  C29  0.020
 1BE  plan-2  H25  0.020
 1BE  plan-2  H26  0.020
 1BE  plan-2  H27  0.020
 1BE  plan-3  CL1  0.020
 1BE  plan-3  C1   0.020
 1BE  plan-3  C6   0.020
 1BE  plan-3  C5   0.020
 1BE  plan-3  C4   0.020
 1BE  plan-3  C12  0.020
 1BE  plan-3  C9   0.020
 1BE  plan-3  C3   0.020
 1BE  plan-3  C2   0.020
 1BE  plan-3  H1   0.020
 1BE  plan-3  H2   0.020
 1BE  plan-3  H11  0.020
 1BE  plan-4  C4   0.020
 1BE  plan-4  C12  0.020
 1BE  plan-4  N11  0.020
 1BE  plan-4  C10  0.020
 1BE  plan-4  N13  0.020
 1BE  plan-4  C14  0.020
 1BE  plan-4  H12  0.020
 1BE  plan-5  C14  0.020
 1BE  plan-5  C7   0.020
 1BE  plan-5  O8   0.020
 1BE  plan-5  O9   0.020
 1BE  plan-5  H16  0.020

