# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:39:31 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](CN1CCOCC1)Cn2ccc(n2)c3ccc(OC(F)F)c(OC4CCCC4)c3
#
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
 DD5  DD5  (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol  ligand  60  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DD5
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
 DD5  C10  C  CR6   0   0.084   1.8533  -1.6398  -0.4079
 DD5  C13  C  CR5   0   0.300   0.5644  -2.3186  -0.5671
 DD5  C15  C  CH1   0   0.000  -3.5124  -1.4243  -0.2557
 DD5  C17  C  CH2   0  -0.303  -7.0205  -0.0675  -0.1185
 DD5  C20  C  CH2   0  -0.313  -5.0835   0.9130   0.8396
 DD5  C21  C  CR15  0   0.053  -1.0978  -3.7597  -0.6086
 DD5  C22  C  CR15  0  -0.566   0.2335  -3.6601  -0.2855
 DD5  C01  C  CH1   0   0.668   5.8726   0.7757   1.2250
 DD5  C02  C  CR6   0   0.228   4.2817  -0.3248  -0.0952
 DD5  C03  C  CR6   0   0.392   3.1569   0.4032  -0.5070
 DD5  O02  O  O2    0  -0.473   3.3520   1.7056  -0.7498
 DD5  C04  C  CR15  0   0.016   2.2509   2.5491  -1.0491
 DD5  C05  C  CH2   0  -0.460   2.7617   3.9048  -1.5112
 DD5  C06  C  CH2   0  -0.458   1.5285   4.8076  -1.3946
 DD5  C07  C  CH2   0  -0.453   0.6282   4.1560  -0.3139
 DD5  C08  C  CH2   0  -0.474   1.3706   2.8961   0.1488
 DD5  C09  C  CR16  0  -0.446   1.9508  -0.2688  -0.6572
 DD5  C11  C  CR16  0  -0.367   2.9856  -2.3434  -0.0126
 DD5  C12  C  CR16  0  -0.285   4.1950  -1.6813   0.1431
 DD5  N01  N  N     0  -0.319  -0.4938  -1.6677  -1.0293
 DD5  N02  N  NR5   0  -0.255  -1.4807  -2.5514  -1.0575
 DD5  C14  C  CH2   0  -0.305  -2.8130  -2.1306  -1.4171
 DD5  C16  C  CH2   0  -0.300  -4.8692  -0.9134  -0.7291
 DD5  N03  N  NT    0  -0.419  -5.6598  -0.3149   0.3233
 DD5  C18  C  CH2   0  -0.189  -7.8446   0.5084   1.0172
 DD5  O03  O  O2    0  -0.484  -7.2752   1.6952   1.5227
 DD5  C19  C  CH2   0  -0.185  -5.9513   1.4700   1.9521
 DD5  F01  F  F     0  -0.330   4.9068   1.5172   1.8118
 DD5  F02  F  F     0  -0.336   6.0938  -0.2608   2.0729
 DD5  O04  O  OH1   0  -0.652  -3.5995  -2.2546   0.8731
 DD5  H01  H  HCH1  0   0.243  -2.8803  -0.5808   0.0394
 DD5  H20  H  HCH2  0   0.243  -7.4746  -1.0081  -0.4405
 DD5  H26  H  HCH2  0   0.247  -4.0911   0.7232   1.2522
 DD5  H25  H  HCH2  0   0.197  -4.9677   1.6722   0.0458
 DD5  H27  H  HCR5  0   0.292  -1.7829  -4.5901  -0.5595
 DD5  H28  H  HCR5  0   0.263   0.8646  -4.4455   0.0952
 DD5  H02  H  HCH1  0   0.213   6.7833   1.3605   1.1190
 DD5  H03  H  HCR5  0   0.229   1.6443   2.1031  -1.8481
 DD5  H05  H  HCH2  0   0.233   3.5499   4.2385  -0.8305
 DD5  H04  H  HCH2  0   0.245   3.1809   3.8795  -2.5177
 DD5  H06  H  HCH2  0   0.238   1.8073   5.8290  -1.1379
 DD5  H07  H  HCH2  0   0.234   1.0007   4.8557  -2.3481
 DD5  H09  H  HCH2  0   0.238   0.4307   4.8290   0.5201
 DD5  H08  H  HCH2  0   0.234  -0.3400   3.8896  -0.7391
 DD5  H10  H  HCH2  0   0.246   0.6939   2.0942   0.4458
 DD5  H11  H  HCH2  0   0.235   2.0185   3.1143   1.0024
 DD5  H12  H  HCR6  0   0.277   1.0613   0.2599  -0.9690
 DD5  H13  H  HCR6  0   0.250   2.9396  -3.4075   0.1752
 DD5  H14  H  HCR6  0   0.274   5.0799  -2.2324   0.4326
 DD5  H16  H  HCH2  0   0.266  -3.3746  -3.0143  -1.7251
 DD5  H15  H  HCH2  0   0.271  -2.7417  -1.4674  -2.2797
 DD5  H18  H  HCH2  0   0.209  -4.7058  -0.2183  -1.5709
 DD5  H17  H  HCH2  0   0.241  -5.4395  -1.7580  -1.1334
 DD5  H22  H  HCH2  0   0.237  -8.8483   0.7505   0.6645
 DD5  H21  H  HCH2  0   0.199  -7.9387  -0.2429   1.8145
 DD5  H24  H  HCH2  0   0.200  -5.9361   0.7753   2.8041
 DD5  H23  H  HCH2  0   0.237  -5.5502   2.4261   2.2915
 DD5  H29  H  HOH1  0   0.445  -4.3415  -2.8582   0.7597
 DD5  O01  O  O2    0  -0.502   5.4919   0.3345   0.0028
 DD5  H19  H  HCH2  0   0.196  -7.0520   0.6207  -0.9815

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
 DD5  F02  C01  single    1.357  0.020  1.357
 DD5  F01  C01  single    1.352  0.020  1.352
 DD5  C01  O01  single    1.354  0.020  1.354
 DD5  C12  C11  aromatic  1.388  0.020  1.388
 DD5  C12  C02  aromatic  1.380  0.020  1.380
 DD5  C11  C10  aromatic  1.391  0.020  1.391
 DD5  O01  C02  single    1.382  0.020  1.382
 DD5  C02  C03  aromatic  1.402  0.020  1.402
 DD5  C22  C13  aromatic  1.410  0.020  1.410
 DD5  C22  C21  aromatic  1.374  0.020  1.374
 DD5  C10  C13  single    1.465  0.020  1.465
 DD5  C10  C09  aromatic  1.397  0.020  1.397
 DD5  C13  N01  aromatic  1.326  0.020  1.326
 DD5  C21  N02  aromatic  1.345  0.020  1.345
 DD5  C03  C09  aromatic  1.389  0.020  1.389
 DD5  C03  O02  single    1.339  0.020  1.339
 DD5  N01  N02  aromatic  1.325  0.020  1.325
 DD5  N02  C14  single    1.443  0.020  1.443
 DD5  O02  C04  single    1.419  0.020  1.419
 DD5  O04  C15  single    1.404  0.020  1.404
 DD5  C14  C15  single    1.529  0.020  1.529
 DD5  C04  C05  single    1.521  0.020  1.521
 DD5  C04  C08  single    1.527  0.020  1.527
 DD5  C15  C16  single    1.525  0.020  1.525
 DD5  C05  C06  single    1.533  0.020  1.533
 DD5  C08  C07  single    1.534  0.020  1.534
 DD5  C06  C07  single    1.550  0.020  1.550
 DD5  C16  N03  single    1.446  0.020  1.446
 DD5  N03  C20  single    1.451  0.020  1.451
 DD5  N03  C17  single    1.452  0.020  1.452
 DD5  C20  C19  single    1.517  0.020  1.517
 DD5  C17  C18  single    1.517  0.020  1.517
 DD5  C19  O03  single    1.410  0.020  1.410
 DD5  C18  O03  single    1.410  0.020  1.410
 DD5  C15  H01  single    0.970  0.020  1.090
 DD5  C17  H19  single    0.970  0.020  1.090
 DD5  C17  H20  single    0.970  0.020  1.090
 DD5  C20  H26  single    0.970  0.020  1.090
 DD5  C20  H25  single    0.970  0.020  1.090
 DD5  C21  H27  single    0.930  0.020  1.080
 DD5  C22  H28  single    0.930  0.020  1.080
 DD5  C01  H02  single    0.970  0.020  1.090
 DD5  C04  H03  single    0.970  0.020  1.090
 DD5  C05  H05  single    0.970  0.020  1.090
 DD5  C05  H04  single    0.970  0.020  1.090
 DD5  C06  H06  single    0.970  0.020  1.090
 DD5  C06  H07  single    0.970  0.020  1.090
 DD5  C07  H09  single    0.970  0.020  1.090
 DD5  C07  H08  single    0.970  0.020  1.090
 DD5  C08  H10  single    0.970  0.020  1.090
 DD5  C08  H11  single    0.970  0.020  1.090
 DD5  C09  H12  single    0.930  0.020  1.080
 DD5  C11  H13  single    0.930  0.020  1.080
 DD5  C12  H14  single    0.930  0.020  1.080
 DD5  C14  H16  single    0.970  0.020  1.090
 DD5  C14  H15  single    0.970  0.020  1.090
 DD5  C16  H18  single    0.970  0.020  1.090
 DD5  C16  H17  single    0.970  0.020  1.090
 DD5  C18  H22  single    0.970  0.020  1.090
 DD5  C18  H21  single    0.970  0.020  1.090
 DD5  C19  H24  single    0.970  0.020  1.090
 DD5  C19  H23  single    0.970  0.020  1.090
 DD5  O04  H29  single    0.850  0.020  0.980

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
 DD5  C11  C10  C09  119.38  3.000
 DD5  C09  C10  C13  119.78  3.000
 DD5  C11  C10  C13  120.85  3.000
 DD5  N01  C13  C22  110.45  3.000
 DD5  N01  C13  C10  120.84  3.000
 DD5  C22  C13  C10  128.71  3.000
 DD5  H01  C15  O04  105.95  3.000
 DD5  H01  C15  C16  109.83  3.000
 DD5  O04  C15  C16  113.11  3.000
 DD5  H01  C15  C14  107.25  3.000
 DD5  C16  C15  C14  109.02  3.000
 DD5  O04  C15  C14  111.47  3.000
 DD5  H20  C17  H19  107.11  3.000
 DD5  H20  C17  C18  108.76  3.000
 DD5  H19  C17  C18  109.45  3.000
 DD5  H20  C17  N03  109.42  3.000
 DD5  H19  C17  N03  111.76  3.000
 DD5  C18  C17  N03  110.25  3.000
 DD5  H25  C20  H26  107.21  3.000
 DD5  H25  C20  C19  109.55  3.000
 DD5  H26  C20  C19  107.87  3.000
 DD5  H25  C20  N03  111.56  3.000
 DD5  H26  C20  N03  110.39  3.000
 DD5  C19  C20  N03  110.15  3.000
 DD5  H27  C21  N02  121.78  3.000
 DD5  H27  C21  C22  131.40  3.000
 DD5  N02  C21  C22  106.82  3.000
 DD5  H28  C22  C21  126.74  3.000
 DD5  H28  C22  C13  128.81  3.000
 DD5  C21  C22  C13  104.45  3.000
 DD5  H02  C01  F02  109.58  3.000
 DD5  H02  C01  F01  110.23  3.000
 DD5  F02  C01  F01  105.32  3.000
 DD5  H02  C01  O01  108.82  3.000
 DD5  F01  C01  O01  111.70  3.000
 DD5  F02  C01  O01  111.15  3.000
 DD5  C12  C02  C03  120.72  3.000
 DD5  C03  C02  O01  118.42  3.000
 DD5  C12  C02  O01  120.79  3.000
 DD5  C09  C03  O02  125.28  3.000
 DD5  O02  C03  C02  116.20  3.000
 DD5  C09  C03  C02  118.51  3.000
 DD5  C04  O02  C03  120.22  3.000
 DD5  H03  C04  C08  110.17  3.000
 DD5  H03  C04  C05  109.07  3.000
 DD5  C08  C04  C05  103.27  3.000
 DD5  H03  C04  O02  109.93  3.000
 DD5  C08  C04  O02  114.65  3.000
 DD5  C05  C04  O02  109.47  3.000
 DD5  H04  C05  H05  107.73  3.000
 DD5  H04  C05  C06  113.14  3.000
 DD5  H05  C05  C06  110.66  3.000
 DD5  H04  C05  C04  112.89  3.000
 DD5  H05  C05  C04  108.97  3.000
 DD5  C06  C05  C04  103.39  3.000
 DD5  H07  C06  H06  106.77  3.000
 DD5  H07  C06  C07  110.30  3.000
 DD5  H06  C06  C07  112.23  3.000
 DD5  H07  C06  C05  110.41  3.000
 DD5  H06  C06  C05  111.35  3.000
 DD5  C07  C06  C05  105.83  3.000
 DD5  H08  C07  H09  106.75  3.000
 DD5  H08  C07  C08  110.29  3.000
 DD5  H09  C07  C08  111.36  3.000
 DD5  H08  C07  C06  110.27  3.000
 DD5  H09  C07  C06  112.29  3.000
 DD5  C08  C07  C06  105.93  3.000
 DD5  H11  C08  H10  107.56  3.000
 DD5  H11  C08  C07  111.00  3.000
 DD5  H10  C08  C07  112.70  3.000
 DD5  H11  C08  C04  108.43  3.000
 DD5  H10  C08  C04  113.85  3.000
 DD5  C07  C08  C04  103.24  3.000
 DD5  H12  C09  C03  120.61  3.000
 DD5  H12  C09  C10  118.31  3.000
 DD5  C03  C09  C10  121.08  3.000
 DD5  H13  C11  C12  119.15  3.000
 DD5  H13  C11  C10  120.84  3.000
 DD5  C12  C11  C10  120.01  3.000
 DD5  H14  C12  C11  119.99  3.000
 DD5  H14  C12  C02  119.70  3.000
 DD5  C11  C12  C02  120.29  3.000
 DD5  N02  N01  C13  105.93  3.000
 DD5  C14  N02  N01  119.90  3.000
 DD5  C14  N02  C21  127.47  3.000
 DD5  N01  N02  C21  112.34  3.000
 DD5  H15  C14  H16  107.63  3.000
 DD5  H15  C14  N02  108.31  3.000
 DD5  H16  C14  N02  108.02  3.000
 DD5  H15  C14  C15  110.49  3.000
 DD5  H16  C14  C15  110.68  3.000
 DD5  N02  C14  C15  111.59  3.000
 DD5  H17  C16  H18  106.32  3.000
 DD5  H17  C16  N03  107.63  3.000
 DD5  H18  C16  N03  112.05  3.000
 DD5  H17  C16  C15  108.61  3.000
 DD5  H18  C16  C15  108.42  3.000
 DD5  N03  C16  C15  113.52  3.000
 DD5  C16  N03  C20  113.08  3.000
 DD5  C20  N03  C17  109.65  3.000
 DD5  C16  N03  C17  111.19  3.000
 DD5  H21  C18  H22  107.89  3.000
 DD5  H21  C18  O03  110.47  3.000
 DD5  H22  C18  O03  107.49  3.000
 DD5  H21  C18  C17  109.27  3.000
 DD5  H22  C18  C17  110.00  3.000
 DD5  O03  C18  C17  111.63  3.000
 DD5  C19  O03  C18  110.73  3.000
 DD5  H23  C19  H24  107.92  3.000
 DD5  H23  C19  O03  107.46  3.000
 DD5  H24  C19  O03  110.49  3.000
 DD5  H23  C19  C20  109.85  3.000
 DD5  H24  C19  C20  109.17  3.000
 DD5  O03  C19  C20  111.87  3.000
 DD5  H29  O04  C15  108.89  3.000
 DD5  C02  O01  C01  117.76  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
 DD5  CONST_01  C02  C12  C11  C10    0.00   0.0  0
 DD5  CONST_02  C21  C22  C13  C10  180.00   0.0  0
 DD5  CONST_03  N02  N01  C13  C10  180.00   0.0  0
 DD5  CONST_04  C02  C03  C09  C10    0.00   0.0  0
 DD5  CONST_05  N02  C21  C22  C13    0.00   0.0  0
 DD5  CONST_06  C12  C11  C10  C13  180.00   0.0  0
 DD5  CONST_07  C03  C09  C10  C13  180.00   0.0  0
 DD5  CONST_08  C21  N02  N01  C13    0.00   0.0  0
 DD5  CONST_09  N01  C13  C22  C21    0.00   0.0  0
 DD5  CONST_10  C11  C10  C13  C22    0.00   0.0  0
 DD5  CONST_11  C09  C10  C13  C22  180.00   0.0  0
 DD5  CONST_12  N02  N01  C13  C22    0.00   0.0  0
 DD5  CONST_13  N01  N02  C21  C22    0.00   0.0  0
 DD5  CONST_14  C11  C12  C02  C03    0.00   0.0  0
 DD5  CONST_15  C11  C10  C09  C03    0.00   0.0  0
 DD5  CONST_16  C12  C11  C10  C09    0.00   0.0  0
 DD5  CONST_17  N01  C13  C10  C09    0.00   0.0  0
 DD5  CONST_18  C12  C02  C03  C09    0.00   0.0  0
 DD5  CONST_19  N01  C13  C10  C11  180.00   0.0  0
 DD5  CONST_20  O02  C03  C09  C10  180.00   0.0  0
 DD5  CONST_21  C14  N02  N01  C13  180.00   0.0  0
 DD5  CONST_22  C14  N02  C21  C22  180.00   0.0  0
 DD5  CONST_23  C11  C12  C02  O01  180.00   0.0  0
 DD5  CONST_24  C09  C03  C02  O01  180.00   0.0  0
 DD5  CONST_25  C12  C02  C03  O02  180.00   0.0  0
 DD5  CONST_26  H14  C12  C11  C10  180.00   0.0  0
 DD5  CONST_27  H28  C22  C13  C10    0.00   0.0  0
 DD5  CONST_28  H27  C21  C22  C13  180.00   0.0  0
 DD5  CONST_29  H13  C11  C10  C13    0.00   0.0  0
 DD5  CONST_30  H12  C09  C10  C13    0.00   0.0  0
 DD5  Var_01    C19  C20  N03  C17   56.23  30.0  1
 DD5  Var_02    C18  C17  N03  C20  -56.46  30.0  1
 DD5  Var_03    C07  C06  C05  C04   25.49  30.0  1
 DD5  Var_04    C06  C07  C08  C04  -24.85  30.0  1
 DD5  Var_05    C08  C07  C06  C05   -0.32  30.0  1
 DD5  Var_06    O03  C19  C20  N03  -57.01  30.0  1
 DD5  Var_07    O03  C18  C17  N03   57.26  30.0  1
 DD5  Var_08    C09  C03  O02  C04    7.27  30.0  2
 DD5  Var_09    C21  N02  C14  C15   95.28  30.0  2
 DD5  Var_10    C20  N03  C16  C15   66.48  30.0  3
 DD5  Var_11    C12  C02  O01  C01  -85.75  30.0  2
 DD5  Var_12    F02  C01  O01  C02   65.26  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
 DD5  chir_01  C15  O04  C14  C16  negativ
 DD5  chir_02  C04  O02  C05  C08  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
 DD5  plan-1  C10  0.020
 DD5  plan-1  C13  0.020
 DD5  plan-1  C21  0.020
 DD5  plan-1  C22  0.020
 DD5  plan-1  N01  0.020
 DD5  plan-1  N02  0.020
 DD5  plan-1  C14  0.020
 DD5  plan-1  H27  0.020
 DD5  plan-1  H28  0.020
 DD5  plan-2  C10  0.020
 DD5  plan-2  C13  0.020
 DD5  plan-2  C02  0.020
 DD5  plan-2  C03  0.020
 DD5  plan-2  O02  0.020
 DD5  plan-2  C09  0.020
 DD5  plan-2  C11  0.020
 DD5  plan-2  C12  0.020
 DD5  plan-2  H12  0.020
 DD5  plan-2  H13  0.020
 DD5  plan-2  H14  0.020
 DD5  plan-2  O01  0.020

