# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:36:46 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2~{R})-2-[6-ethyl-5-(1~{H}-indol-5-yl)thieno[2,3-d]pyrimidin-4-yl]oxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2ncnc(O[C@H](C)C(O)=O)c2c1c3ccc4[nH]ccc4c3
#
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
 JLB  JLB  '(2~{R})-2-[6-ethyl-5-(1~{H}-indol-5-yl)thieno[2,3-d]pyrimidin-4-yl]oxypropanoic acid'  ligand  42  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JLB
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
 JLB  C10  C  C      0   0.205   0.9782   1.0341  -0.0066
 JLB  C13  C  CH3    0  -0.663   1.7222   4.1080   1.7946
 JLB  C15  C  CR6    0  -0.017   3.1435   0.0854   0.0948
 JLB  C17  C  CR16   0   0.037   3.6661  -2.0608  -0.1128
 JLB  C20  C  CR16   0  -0.294  -2.6507   0.3428   0.7649
 JLB  C21  C  CR56   0   0.335  -3.2620   1.1370  -0.2056
 JLB  C22  C  CR56   0   0.073  -2.5109   1.8926  -1.1311
 JLB  C24  C  CR15   0  -0.430  -3.4501   2.5663  -1.9729
 JLB  C26  C  CR15   0  -0.029  -4.6928   2.2070  -1.5382
 JLB  N01  N  N      0  -0.461   2.4069  -2.4385  -0.3152
 JLB  C02  C  CR6    0   0.534   1.4654  -1.5135  -0.3150
 JLB  O03  O  O2     0  -0.445   0.2225  -1.8239  -0.5894
 JLB  C04  C  CH1    0  -0.096  -0.1941  -3.1877  -0.4833
 JLB  C05  C  CH3    0  -0.678  -1.6258  -3.2341  -0.9836
 JLB  C06  C  C      0   0.404  -0.0861  -3.6939   0.9732
 JLB  O07  O  OC    -1  -0.613  -0.3080  -4.9126   1.1049
 JLB  O08  O  O      0  -0.580   0.1833  -2.8683   1.8603
 JLB  C09  C  CR6    0  -0.040   1.7836  -0.1587  -0.0828
 JLB  C11  C  C      0  -0.243   1.7451   2.1390   0.2166
 JLB  C12  C  CH2    0  -0.509   1.3247   3.5579   0.4258
 JLB  S14  S  S2     0   0.209   3.4469   1.7660   0.3348
 JLB  N16  N  N      0  -0.427   4.1051  -0.8357   0.0846
 JLB  C18  C  CR6    0   0.016  -0.4953   1.0673  -0.1079
 JLB  C19  C  CR16   0  -0.291  -1.2741   0.3167   0.7986
 JLB  C23  C  CR16   0  -0.397  -1.1135   1.8462  -1.0709
 JLB  N25  N  NR15   0  -0.680  -4.5809   1.3511  -0.4787
 JLB  H1   H  HCH3   0   0.241   1.3729   5.1344   1.9048
 JLB  H2   H  HCH3   0   0.233   1.2833   3.5145   2.5968
 JLB  H3   H  HCH3   0   0.227   2.8038   4.1136   1.9348
 JLB  H4   H  HCR6   0   0.259   4.4096  -2.8499  -0.1185
 JLB  H7   H  HCR5   0   0.280  -5.6639   2.4965  -1.9059
 JLB  H8   H  HCH1   0   0.234   0.4373  -3.8125  -1.1215
 JLB  H9   H  HCH3   0   0.235  -2.2787  -2.6046  -0.3774
 JLB  H10  H  HCH3   0   0.231  -1.6954  -2.9011  -2.0198
 JLB  H11  H  HCH3   0   0.231  -1.9927  -4.2577  -0.9370
 JLB  H13  H  HCH2   0   0.259   0.2429   3.6181   0.3100
 JLB  H14  H  HCH2   0   0.256   1.7514   4.1872  -0.3601
 JLB  H15  H  HCR6   0   0.244  -0.7775  -0.3133   1.5248
 JLB  H16  H  HCR6   0   0.245  -0.5174   2.4066  -1.7819
 JLB  H17  H  HNR5   0   0.408  -5.3559   0.9466   0.0193
 JLB  H5   H  HCR6   0   0.254  -3.2343  -0.2408   1.4653
 JLB  H6   H  HCR5   0   0.245  -3.2330   3.2292  -2.7953

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
 JLB  C26  C24  aromatic  1.365  0.020  1.365
 JLB  C26  N25  aromatic  1.367  0.020  1.367
 JLB  C24  C22  aromatic  1.430  0.020  1.430
 JLB  O08  C06  deloc     1.241  0.020  1.241
 JLB  O07  C06  deloc     1.246  0.020  1.246
 JLB  N25  C21  aromatic  1.364  0.020  1.364
 JLB  C06  C04  single    1.546  0.020  1.546
 JLB  C22  C21  aromatic  1.411  0.020  1.411
 JLB  C22  C23  aromatic  1.399  0.020  1.399
 JLB  C21  C20  aromatic  1.395  0.020  1.395
 JLB  C05  C04  single    1.517  0.020  1.517
 JLB  C23  C18  aromatic  1.384  0.020  1.384
 JLB  C04  O03  single    1.430  0.020  1.430
 JLB  O03  C02  single    1.310  0.020  1.310
 JLB  C20  C19  aromatic  1.377  0.020  1.377
 JLB  C18  C19  aromatic  1.411  0.020  1.411
 JLB  C18  C10  single    1.477  0.020  1.477
 JLB  C02  N01  aromatic  1.320  0.020  1.320
 JLB  C02  C09  aromatic  1.411  0.020  1.411
 JLB  N01  C17  aromatic  1.330  0.020  1.330
 JLB  C10  C09  aromatic  1.441  0.020  1.441
 JLB  C10  C11  aromatic  1.363  0.020  1.363
 JLB  C09  C15  aromatic  1.393  0.020  1.393
 JLB  C17  N16  aromatic  1.316  0.020  1.316
 JLB  C11  C12  single    1.495  0.020  1.495
 JLB  C11  S14  aromatic  1.746  0.020  1.746
 JLB  C15  N16  aromatic  1.332  0.020  1.332
 JLB  C15  S14  aromatic  1.725  0.020  1.725
 JLB  C13  C12  single    1.528  0.020  1.528
 JLB  C13  H1   single    0.970  0.020  1.090
 JLB  C13  H2   single    0.970  0.020  1.090
 JLB  C13  H3   single    0.970  0.020  1.090
 JLB  C17  H4   single    0.930  0.020  1.080
 JLB  C20  H5   single    0.930  0.020  1.080
 JLB  C24  H6   single    0.930  0.020  1.080
 JLB  C26  H7   single    0.930  0.020  1.080
 JLB  C04  H8   single    0.970  0.020  1.090
 JLB  C05  H9   single    0.970  0.020  1.090
 JLB  C05  H10  single    0.970  0.020  1.090
 JLB  C05  H11  single    0.970  0.020  1.090
 JLB  C12  H13  single    0.970  0.020  1.090
 JLB  C12  H14  single    0.970  0.020  1.090
 JLB  C19  H15  single    0.930  0.020  1.080
 JLB  C23  H16  single    0.930  0.020  1.080
 JLB  N25  H17  single    0.860  0.020  1.020

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
 JLB  C18  C10  C11  123.65  3.000
 JLB  C11  C10  C09  111.41  3.000
 JLB  C18  C10  C09  124.91  3.000
 JLB  H3   C13  H2   107.91  3.000
 JLB  H3   C13  H1   107.45  3.000
 JLB  H2   C13  H1   108.02  3.000
 JLB  H3   C13  C12  112.03  3.000
 JLB  H2   C13  C12  111.01  3.000
 JLB  H1   C13  C12  110.26  3.000
 JLB  N16  C15  S14  123.24  3.000
 JLB  S14  C15  C09  111.12  3.000
 JLB  N16  C15  C09  125.64  3.000
 JLB  H4   C17  N16  116.71  3.000
 JLB  H4   C17  N01  116.21  3.000
 JLB  N16  C17  N01  127.07  3.000
 JLB  H5   C20  C19  120.85  3.000
 JLB  H5   C20  C21  121.38  3.000
 JLB  C19  C20  C21  117.76  3.000
 JLB  N25  C21  C22  107.42  3.000
 JLB  C22  C21  C20  121.85  3.000
 JLB  N25  C21  C20  130.73  3.000
 JLB  C23  C22  C24  134.17  3.000
 JLB  C23  C22  C21  119.05  3.000
 JLB  C24  C22  C21  106.78  3.000
 JLB  H6   C24  C26  126.03  3.000
 JLB  H6   C24  C22  127.32  3.000
 JLB  C26  C24  C22  106.65  3.000
 JLB  H7   C26  N25  120.42  3.000
 JLB  H7   C26  C24  129.86  3.000
 JLB  N25  C26  C24  109.71  3.000
 JLB  C02  N01  C17  118.44  3.000
 JLB  C09  C02  O03  118.42  3.000
 JLB  C09  C02  N01  120.80  3.000
 JLB  O03  C02  N01  120.71  3.000
 JLB  C04  O03  C02  119.13  3.000
 JLB  H8   C04  C06  108.80  3.000
 JLB  H8   C04  C05  109.57  3.000
 JLB  C06  C04  C05  111.50  3.000
 JLB  H8   C04  O03  109.47  3.000
 JLB  C05  C04  O03  106.24  3.000
 JLB  C06  C04  O03  111.22  3.000
 JLB  H11  C05  H10  107.83  3.000
 JLB  H11  C05  H9   108.49  3.000
 JLB  H10  C05  H9   108.28  3.000
 JLB  H11  C05  C04  109.44  3.000
 JLB  H10  C05  C04  111.35  3.000
 JLB  H9   C05  C04  111.34  3.000
 JLB  O08  C06  O07  127.86  3.000
 JLB  O07  C06  C04  114.05  3.000
 JLB  O08  C06  C04  118.08  3.000
 JLB  C02  C09  C15  114.17  3.000
 JLB  C15  C09  C10  113.19  3.000
 JLB  C02  C09  C10  132.64  3.000
 JLB  S14  C11  C12  117.87  3.000
 JLB  S14  C11  C10  112.72  3.000
 JLB  C12  C11  C10  129.35  3.000
 JLB  H14  C12  H13  106.21  3.000
 JLB  H14  C12  C11  109.63  3.000
 JLB  H13  C12  C11  108.47  3.000
 JLB  H14  C12  C13  109.58  3.000
 JLB  H13  C12  C13  109.49  3.000
 JLB  C11  C12  C13  113.21  3.000
 JLB  C11  S14  C15   91.56  3.000
 JLB  C17  N16  C15  113.84  3.000
 JLB  C23  C18  C19  119.98  3.000
 JLB  C19  C18  C10  119.63  3.000
 JLB  C23  C18  C10  120.39  3.000
 JLB  H15  C19  C18  119.18  3.000
 JLB  H15  C19  C20  119.09  3.000
 JLB  C18  C19  C20  121.72  3.000
 JLB  H16  C23  C18  120.11  3.000
 JLB  H16  C23  C22  120.25  3.000
 JLB  C18  C23  C22  119.64  3.000
 JLB  H17  N25  C26  124.92  3.000
 JLB  H17  N25  C21  125.64  3.000
 JLB  C26  N25  C21  109.43  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
 JLB  CONST_01  C22  C23  C18  C10   180.00   0.0  0
 JLB  CONST_02  C20  C19  C18  C10   180.00   0.0  0
 JLB  CONST_03  N01  C02  C09  C10   180.00   0.0  0
 JLB  CONST_04  N16  C15  C09  C10   180.00   0.0  0
 JLB  CONST_05  S14  C15  C09  C10     0.00   0.0  0
 JLB  CONST_06  C15  S14  C11  C10     0.00   0.0  0
 JLB  CONST_07  N01  C02  C09  C15     0.00   0.0  0
 JLB  CONST_08  C18  C10  C09  C15   180.00   0.0  0
 JLB  CONST_09  C11  C10  C09  C15     0.00   0.0  0
 JLB  CONST_10  N01  C17  N16  C15     0.00   0.0  0
 JLB  CONST_11  C09  C02  N01  C17     0.00   0.0  0
 JLB  CONST_12  C09  C15  N16  C17     0.00   0.0  0
 JLB  CONST_13  S14  C15  N16  C17   180.00   0.0  0
 JLB  CONST_14  C26  N25  C21  C20   180.00   0.0  0
 JLB  CONST_15  C24  C22  C21  C20   180.00   0.0  0
 JLB  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 JLB  CONST_17  C23  C18  C19  C20     0.00   0.0  0
 JLB  CONST_18  C24  C26  N25  C21     0.00   0.0  0
 JLB  CONST_19  C26  C24  C22  C21     0.00   0.0  0
 JLB  CONST_20  C18  C23  C22  C21     0.00   0.0  0
 JLB  CONST_21  C18  C19  C20  C21     0.00   0.0  0
 JLB  CONST_22  N25  C26  C24  C22     0.00   0.0  0
 JLB  CONST_23  C26  N25  C21  C22     0.00   0.0  0
 JLB  CONST_24  C19  C20  C21  C22     0.00   0.0  0
 JLB  CONST_25  C19  C18  C23  C22     0.00   0.0  0
 JLB  CONST_26  N25  C21  C22  C24     0.00   0.0  0
 JLB  CONST_27  C18  C23  C22  C24   180.00   0.0  0
 JLB  CONST_28  C23  C22  C24  C26   180.00   0.0  0
 JLB  CONST_29  N16  C17  N01  C02     0.00   0.0  0
 JLB  CONST_30  C18  C10  C09  C02     0.00   0.0  0
 JLB  CONST_31  C11  C10  C09  C02   180.00   0.0  0
 JLB  CONST_32  N16  C15  C09  C02     0.00   0.0  0
 JLB  CONST_33  S14  C15  C09  C02   180.00   0.0  0
 JLB  CONST_36  S14  C11  C10  C09     0.00   0.0  0
 JLB  CONST_37  C11  S14  C15  C09     0.00   0.0  0
 JLB  CONST_40  N16  C15  S14  C11   180.00   0.0  0
 JLB  CONST_41  C18  C10  C11  S14   180.00   0.0  0
 JLB  CONST_42  N25  C21  C20  C19   180.00   0.0  0
 JLB  CONST_43  N25  C21  C22  C23   180.00   0.0  0
 JLB  CONST_44  O03  C02  C09  C10     0.00   0.0  0
 JLB  CONST_45  O03  C02  C09  C15   180.00   0.0  0
 JLB  CONST_46  C12  C11  S14  C15   180.00   0.0  0
 JLB  CONST_47  O03  C02  N01  C17   180.00   0.0  0
 JLB  CONST_48  C12  C11  C10  C09   180.00   0.0  0
 JLB  CONST_49  C18  C10  C11  C12     0.00   0.0  0
 JLB  CONST_50  H16  C23  C18  C10     0.00   0.0  0
 JLB  CONST_51  H15  C19  C18  C10     0.00   0.0  0
 JLB  CONST_52  H4   C17  N16  C15   180.00   0.0  0
 JLB  CONST_53  H17  N25  C21  C20     0.00   0.0  0
 JLB  CONST_54  H7   C26  N25  C21   180.00   0.0  0
 JLB  CONST_55  H6   C24  C22  C21   180.00   0.0  0
 JLB  CONST_56  H5   C20  C21  C22   180.00   0.0  0
 JLB  Var_01    C13  C12  C11  C10   118.12  30.0  2
 JLB  Var_02    C09  C02  O03  C04  -163.77  30.0  2
 JLB  Var_03    H1   C13  C12  C11  -178.67  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
 JLB  chir_01  C04  C06  C05  O03  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
 JLB  plan-1  C10  0.020
 JLB  plan-1  C15  0.020
 JLB  plan-1  C17  0.020
 JLB  plan-1  N01  0.020
 JLB  plan-1  C02  0.020
 JLB  plan-1  O03  0.020
 JLB  plan-1  C09  0.020
 JLB  plan-1  C11  0.020
 JLB  plan-1  C12  0.020
 JLB  plan-1  S14  0.020
 JLB  plan-1  N16  0.020
 JLB  plan-1  C18  0.020
 JLB  plan-1  H4   0.020
 JLB  plan-2  C10  0.020
 JLB  plan-2  C20  0.020
 JLB  plan-2  C21  0.020
 JLB  plan-2  C22  0.020
 JLB  plan-2  C24  0.020
 JLB  plan-2  C26  0.020
 JLB  plan-2  C18  0.020
 JLB  plan-2  C19  0.020
 JLB  plan-2  C23  0.020
 JLB  plan-2  N25  0.020
 JLB  plan-2  H7   0.020
 JLB  plan-2  H15  0.020
 JLB  plan-2  H16  0.020
 JLB  plan-2  H17  0.020
 JLB  plan-2  H5   0.020
 JLB  plan-2  H6   0.020
 JLB  plan-3  C04  0.020
 JLB  plan-3  C06  0.020
 JLB  plan-3  O07  0.020
 JLB  plan-3  O08  0.020

