# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:16:25 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (1R,2S,3R,5R)-3-({5-(1,3-benzothiazol-2-yl)-6-chloro-2-[(3-methoxypropyl)amino]pyrimidin-4-yl}amino)-5-(hydroxymethyl)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCNc1nc(Cl)c(c(N[C@@H]2C[C@H](CO)[C@@H](O)[C@H]2O)n1)c3sc4ccccc4n3
#
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
 42P  42P  (1R,2S,3R,5R)-3-({5-(1,3-benzothiazol-2-yl)-6-chloro-2-[(3-methoxypropyl)amino]pyrimidin-4-yl}amino)-5-(hydroxymethyl)cyclopentane-1,2-diol  ligand  58  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_42P
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
 42P  C01  C   CR6   0   0.564   -0.1276  -0.1288   0.0539
 42P  N02  N   N     0  -0.518   -1.3838  -0.5552   0.1052
 42P  C03  C   CR6   0   0.623   -2.3601   0.3394   0.1307
 42P  N04  N   N     0  -0.477   -2.1906   1.6703   0.1011
 42P  C05  C   CR6   0   0.129   -0.9559   2.0867   0.0489
 42P  C06  C   CR6   0  -0.087    0.1892   1.2916   0.0228
 42P  N07  N   NH1   0  -0.687    0.8356  -1.0452   0.0480
 42P  N08  N   NH1   0  -0.656   -3.6142  -0.1149   0.1904
 42P  CL9  CL  CL    0  -0.091   -0.8416   3.8168   0.0122
 42P  C10  C   CR5   0   0.122    1.5638   1.7575  -0.0302
 42P  C11  C   CH1   0  -0.094    0.6420  -2.4712   0.0331
 42P  C12  C   CH1   0   0.022    1.0645  -3.1195  -1.2817
 42P  C13  C   CH1   0   0.010    1.1123  -4.6060  -0.9191
 42P  C14  C   CH1   0  -0.294    1.7508  -4.6165   0.4777
 42P  C15  C   CH2   0  -0.451    1.5152  -3.2013   1.0586
 42P  O16  O   OH1   0  -0.660    0.1723  -2.8015  -2.3154
 42P  O17  O   OH1   0  -0.677   -0.1912  -5.1364  -0.8356
 42P  C18  C   CH2   0  -0.147    3.2242  -4.9770   0.3988
 42P  O19  O   OH1   0  -0.670    3.7701  -4.9384   1.6972
 42P  C20  C   CH2   0  -0.242   -4.7894   0.7271   0.2274
 42P  C21  C   CH2   0  -0.518   -6.0435  -0.1317   0.2690
 42P  C22  C   CH2   0  -0.121   -7.2866   0.7346   0.3239
 42P  O23  O   O2    0  -0.486   -8.4220  -0.0923   0.3550
 42P  C24  C   CH3   0  -0.397   -9.6179   0.6396   0.4350
 42P  S25  S   S2    0   0.219    2.0573   3.4528  -0.0640
 42P  C26  C   CR56  0  -0.269    3.7133   2.9593  -0.1102
 42P  C27  C   CR56  0   0.434    3.7845   1.5622  -0.0987
 42P  N28  N   N     0  -0.539    2.5713   0.9354  -0.0537
 42P  C29  C   CR16  0  -0.282    4.8574   3.7478  -0.1532
 42P  C30  C   CR16  0  -0.268    6.0835   3.1065  -0.1845
 42P  C31  C   CR16  0  -0.257    6.1666   1.7089  -0.1735
 42P  C32  C   CR16  0  -0.315    5.0278   0.9283  -0.1311
 42P  H1   H   HNH1  0   0.417    1.7848  -0.6773   0.0019
 42P  H2   H   HNH1  0   0.401   -3.7279  -1.1159   0.2081
 42P  H3   H   HCH1  0   0.271   -0.4129  -2.6750   0.2120
 42P  H4   H   HCH1  0   0.213    2.0867  -2.7890  -1.5195
 42P  H5   H   HCH1  0   0.221    1.7140  -5.1739  -1.6447
 42P  H6   H   HCH1  0   0.255    1.2492  -5.3743   1.0853
 42P  H7   H   HCH2  0   0.234    2.4662  -2.6729   1.1726
 42P  H8   H   HCH2  0   0.256    1.0524  -3.2206   2.0443
 42P  H9   H   HOH1  0   0.459    0.5879  -3.0095  -3.1582
 42P  H10  H   HOH1  0   0.441   -0.6843  -4.8087  -1.5970
 42P  H11  H   HCH2  0   0.207    3.3260  -5.9747  -0.0490
 42P  H12  H   HCH2  0   0.191    3.7406  -4.2752  -0.2729
 42P  H13  H   HOH1  0   0.454    4.7184  -5.0799   1.6289
 42P  H14  H   HCH2  0   0.236   -4.7561   1.3804   1.1041
 42P  H15  H   HCH2  0   0.237   -4.8126   1.3779  -0.6509
 42P  H16  H   HCH2  0   0.244   -6.0808  -0.7721  -0.6168
 42P  H17  H   HCH2  0   0.243   -6.0148  -0.7844   1.1463
 42P  H18  H   HCH2  0   0.198   -7.2521   1.3808   1.2136
 42P  H19  H   HCH2  0   0.199   -7.3174   1.4031  -0.5495
 42P  H20  H   HCH3  0   0.204   -9.6673   1.2489   1.3458
 42P  H21  H   HCH3  0   0.203   -9.7485   1.3104  -0.4231
 42P  H22  H   HCH3  0   0.233  -10.4474  -0.0663   0.4484
 42P  H23  H   HCR6  0   0.274    4.7953   4.8277  -0.1617
 42P  H24  H   HCR6  0   0.264    6.9897   3.6964  -0.2180
 42P  H25  H   HCR6  0   0.263    7.1387   1.2345  -0.1987
 42P  H26  H   HCR6  0   0.263    5.0874  -0.1523  -0.1224

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
 42P  C30  C31  aromatic  1.400  0.020  1.400
 42P  C30  C29  aromatic  1.384  0.020  1.384
 42P  C31  C32  aromatic  1.381  0.020  1.381
 42P  C29  C26  aromatic  1.390  0.020  1.390
 42P  C32  C27  aromatic  1.396  0.020  1.396
 42P  C26  C27  aromatic  1.399  0.020  1.399
 42P  C26  S25  aromatic  1.729  0.020  1.729
 42P  C27  N28  aromatic  1.366  0.020  1.366
 42P  S25  C10  aromatic  1.766  0.020  1.766
 42P  N28  C10  aromatic  1.301  0.020  1.301
 42P  C10  C06  single    1.452  0.020  1.452
 42P  CL9  C05  single    1.734  0.020  1.734
 42P  C06  C05  aromatic  1.394  0.020  1.394
 42P  C06  C01  aromatic  1.456  0.020  1.456
 42P  C05  N04  aromatic  1.304  0.020  1.304
 42P  N07  C01  single    1.329  0.020  1.329
 42P  N07  C11  single    1.439  0.020  1.439
 42P  C18  O19  single    1.409  0.020  1.409
 42P  C18  C14  single    1.519  0.020  1.519
 42P  C01  N02  aromatic  1.328  0.020  1.328
 42P  C15  C11  single    1.532  0.020  1.532
 42P  C15  C14  single    1.548  0.020  1.548
 42P  N04  C03  aromatic  1.342  0.020  1.342
 42P  C11  C12  single    1.526  0.020  1.526
 42P  C14  C13  single    1.536  0.020  1.536
 42P  N02  C03  aromatic  1.324  0.020  1.324
 42P  C03  N08  single    1.335  0.020  1.335
 42P  C13  C12  single    1.531  0.020  1.531
 42P  C13  O17  single    1.410  0.020  1.410
 42P  C12  O16  single    1.402  0.020  1.402
 42P  N08  C20  single    1.446  0.020  1.446
 42P  C20  C21  single    1.520  0.020  1.520
 42P  C21  C22  single    1.516  0.020  1.516
 42P  C22  O23  single    1.405  0.020  1.405
 42P  O23  C24  single    1.404  0.020  1.404
 42P  N07  H1   single    0.860  0.020  1.020
 42P  N08  H2   single    0.860  0.020  1.020
 42P  C11  H3   single    0.970  0.020  1.090
 42P  C12  H4   single    0.970  0.020  1.090
 42P  C13  H5   single    0.970  0.020  1.090
 42P  C14  H6   single    0.970  0.020  1.090
 42P  C15  H7   single    0.970  0.020  1.090
 42P  C15  H8   single    0.970  0.020  1.090
 42P  O16  H9   single    0.850  0.020  0.980
 42P  O17  H10  single    0.850  0.020  0.980
 42P  C18  H11  single    0.970  0.020  1.090
 42P  C18  H12  single    0.970  0.020  1.090
 42P  O19  H13  single    0.850  0.020  0.980
 42P  C20  H14  single    0.970  0.020  1.090
 42P  C20  H15  single    0.970  0.020  1.090
 42P  C21  H16  single    0.970  0.020  1.090
 42P  C21  H17  single    0.970  0.020  1.090
 42P  C22  H18  single    0.970  0.020  1.090
 42P  C22  H19  single    0.970  0.020  1.090
 42P  C24  H20  single    0.970  0.020  1.090
 42P  C24  H21  single    0.970  0.020  1.090
 42P  C24  H22  single    0.970  0.020  1.090
 42P  C29  H23  single    0.930  0.020  1.080
 42P  C30  H24  single    0.930  0.020  1.080
 42P  C31  H25  single    0.930  0.020  1.080
 42P  C32  H26  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
 42P  N07  C01  C06  120.99  3.000
 42P  N07  C01  N02  117.67  3.000
 42P  C06  C01  N02  121.34  3.000
 42P  C03  N02  C01  118.77  3.000
 42P  N08  C03  N04  117.20  3.000
 42P  N08  C03  N02  117.60  3.000
 42P  N04  C03  N02  125.19  3.000
 42P  C05  N04  C03  115.93  3.000
 42P  CL9  C05  C06  120.95  3.000
 42P  C06  C05  N04  126.60  3.000
 42P  CL9  C05  N04  112.45  3.000
 42P  C10  C06  C05  126.51  3.000
 42P  C05  C06  C01  112.17  3.000
 42P  C10  C06  C01  121.32  3.000
 42P  H1   N07  C11  118.85  3.000
 42P  H1   N07  C01  115.23  3.000
 42P  C11  N07  C01  125.84  3.000
 42P  H2   N08  C20  119.10  3.000
 42P  H2   N08  C03  116.41  3.000
 42P  C20  N08  C03  124.49  3.000
 42P  N28  C10  S25  112.95  3.000
 42P  N28  C10  C06  122.08  3.000
 42P  S25  C10  C06  124.97  3.000
 42P  H3   C11  C15  110.67  3.000
 42P  H3   C11  C12  109.28  3.000
 42P  C15  C11  C12  102.51  3.000
 42P  H3   C11  N07  108.30  3.000
 42P  C12  C11  N07  113.12  3.000
 42P  C15  C11  N07  112.86  3.000
 42P  H4   C12  O16  111.33  3.000
 42P  H4   C12  C13  108.29  3.000
 42P  O16  C12  C13  114.51  3.000
 42P  H4   C12  C11  108.41  3.000
 42P  O16  C12  C11  111.27  3.000
 42P  C13  C12  C11  102.54  3.000
 42P  H5   C13  O17  110.51  3.000
 42P  H5   C13  C14  111.64  3.000
 42P  O17  C13  C14  109.15  3.000
 42P  H5   C13  C12  111.22  3.000
 42P  O17  C13  C12  110.52  3.000
 42P  C14  C13  C12  103.60  3.000
 42P  H6   C14  C18  108.02  3.000
 42P  H6   C14  C15  110.81  3.000
 42P  C18  C14  C15  112.59  3.000
 42P  H6   C14  C13  108.63  3.000
 42P  C15  C14  C13  105.77  3.000
 42P  C18  C14  C13  110.96  3.000
 42P  H8   C15  H7   106.48  3.000
 42P  H8   C15  C14  112.84  3.000
 42P  H7   C15  C14  110.39  3.000
 42P  H8   C15  C11  111.84  3.000
 42P  H7   C15  C11  109.58  3.000
 42P  C14  C15  C11  105.73  3.000
 42P  H9   O16  C12  108.77  3.000
 42P  H10  O17  C13  107.34  3.000
 42P  H12  C18  H11  106.67  3.000
 42P  H12  C18  O19  111.30  3.000
 42P  H11  C18  O19  111.39  3.000
 42P  H12  C18  C14  109.61  3.000
 42P  H11  C18  C14  109.07  3.000
 42P  O19  C18  C14  108.75  3.000
 42P  H13  O19  C18  108.22  3.000
 42P  H15  C20  H14  106.79  3.000
 42P  H15  C20  C21  109.92  3.000
 42P  H14  C20  C21  109.91  3.000
 42P  H15  C20  N08  110.07  3.000
 42P  H14  C20  N08  110.09  3.000
 42P  C21  C20  N08  110.01  3.000
 42P  H17  C21  H16  107.52  3.000
 42P  H17  C21  C22  109.48  3.000
 42P  H16  C21  C22  109.63  3.000
 42P  H17  C21  C20  109.72  3.000
 42P  H16  C21  C20  109.68  3.000
 42P  C22  C21  C20  110.76  3.000
 42P  H19  C22  H18  106.62  3.000
 42P  H19  C22  O23  110.64  3.000
 42P  H18  C22  O23  110.67  3.000
 42P  H19  C22  C21  109.96  3.000
 42P  H18  C22  C21  109.83  3.000
 42P  O23  C22  C21  109.09  3.000
 42P  C24  O23  C22  112.50  3.000
 42P  H22  C24  H21  108.38  3.000
 42P  H22  C24  H20  108.39  3.000
 42P  H21  C24  H20  107.73  3.000
 42P  H22  C24  O23  108.14  3.000
 42P  H21  C24  O23  112.05  3.000
 42P  H20  C24  O23  112.03  3.000
 42P  C26  S25  C10   89.66  3.000
 42P  C29  C26  C27  121.66  3.000
 42P  C27  C26  S25  109.49  3.000
 42P  C29  C26  S25  128.85  3.000
 42P  C32  C27  N28  125.69  3.000
 42P  N28  C27  C26  114.41  3.000
 42P  C32  C27  C26  119.91  3.000
 42P  C27  N28  C10  113.49  3.000
 42P  H23  C29  C30  120.88  3.000
 42P  H23  C29  C26  121.28  3.000
 42P  C30  C29  C26  117.84  3.000
 42P  H24  C30  C31  119.66  3.000
 42P  H24  C30  C29  119.35  3.000
 42P  C31  C30  C29  121.00  3.000
 42P  H25  C31  C32  119.58  3.000
 42P  H25  C31  C30  119.40  3.000
 42P  C32  C31  C30  121.02  3.000
 42P  H26  C32  C31  121.27  3.000
 42P  H26  C32  C27  120.15  3.000
 42P  C31  C32  C27  118.58  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
 42P  CONST_01  S25  C10  C06  C01  180.00   0.0  0
 42P  CONST_02  N28  C10  C06  C01    0.00   0.0  0
 42P  CONST_03  N04  C05  C06  C01    0.00   0.0  0
 42P  CONST_04  N04  C03  N02  C01    0.00   0.0  0
 42P  CONST_05  C10  C06  C01  N02  180.00   0.0  0
 42P  CONST_06  C05  C06  C01  N02    0.00   0.0  0
 42P  CONST_07  C05  N04  C03  N02    0.00   0.0  0
 42P  CONST_08  C06  C05  N04  C03    0.00   0.0  0
 42P  CONST_09  C06  C01  N02  C03    0.00   0.0  0
 42P  CONST_10  C10  C06  C05  N04  180.00   0.0  0
 42P  CONST_11  S25  C10  C06  C05    0.00   0.0  0
 42P  CONST_12  N28  C10  C06  C05  180.00   0.0  0
 42P  CONST_13  C26  S25  C10  C06  180.00   0.0  0
 42P  CONST_14  C27  N28  C10  C06  180.00   0.0  0
 42P  CONST_15  C29  C26  S25  C10  180.00   0.0  0
 42P  CONST_16  C27  C26  S25  C10    0.00   0.0  0
 42P  CONST_17  C32  C27  N28  C10  180.00   0.0  0
 42P  CONST_18  C26  C27  N28  C10    0.00   0.0  0
 42P  CONST_19  C30  C29  C26  S25  180.00   0.0  0
 42P  CONST_20  C32  C27  C26  S25  180.00   0.0  0
 42P  CONST_21  N28  C27  C26  S25    0.00   0.0  0
 42P  CONST_22  C27  N28  C10  S25    0.00   0.0  0
 42P  CONST_23  C31  C30  C29  C26    0.00   0.0  0
 42P  CONST_24  C31  C32  C27  C26    0.00   0.0  0
 42P  CONST_25  N28  C10  S25  C26    0.00   0.0  0
 42P  CONST_26  C30  C31  C32  C27    0.00   0.0  0
 42P  CONST_27  C30  C29  C26  C27    0.00   0.0  0
 42P  CONST_28  C31  C32  C27  N28  180.00   0.0  0
 42P  CONST_29  C29  C26  C27  N28  180.00   0.0  0
 42P  CONST_30  C32  C31  C30  C29    0.00   0.0  0
 42P  CONST_31  C32  C27  C26  C29    0.00   0.0  0
 42P  CONST_32  CL9  C05  C06  C01  180.00   0.0  0
 42P  CONST_33  N08  C03  N02  C01  180.00   0.0  0
 42P  CONST_34  CL9  C05  N04  C03  180.00   0.0  0
 42P  CONST_35  N07  C01  N02  C03  180.00   0.0  0
 42P  CONST_36  N07  C01  C06  C05  180.00   0.0  0
 42P  CONST_37  N08  C03  N04  C05  180.00   0.0  0
 42P  CONST_38  C10  C06  C01  N07    0.00   0.0  0
 42P  CONST_39  C10  C06  C05  CL9    0.00   0.0  0
 42P  CONST_40  C11  N07  C01  N02    0.00   0.0  0
 42P  CONST_41  C11  N07  C01  C06  180.00   0.0  0
 42P  CONST_42  H23  C29  C26  S25    0.00   0.0  0
 42P  CONST_43  H24  C30  C29  C26  180.00   0.0  0
 42P  CONST_44  H26  C32  C27  C26  180.00   0.0  0
 42P  CONST_45  H25  C31  C32  C27  180.00   0.0  0
 42P  CONST_46  C20  N08  C03  N02  180.00   0.0  0
 42P  CONST_47  C20  N08  C03  N04    0.00   0.0  0
 42P  CONST_48  H1   N07  C01  N02  180.00   0.0  0
 42P  CONST_49  H2   N08  C03  N02    0.00   0.0  0
 42P  Var_01    C21  C20  N08  C03  179.03  30.0  3
 42P  Var_02    C22  C21  C20  N08  179.37  30.0  3
 42P  Var_03    O23  C22  C21  C20  179.74  30.0  3
 42P  Var_04    H20  C24  O23  C22  -60.96  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
 42P  chir_01  C11  N07  C15  C12  positiv
 42P  chir_02  C12  O16  C11  C13  negativ
 42P  chir_03  C13  O17  C12  C14  negativ
 42P  chir_04  C14  C13  C15  C18  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
 42P  plan-1  C01  0.020
 42P  plan-1  N02  0.020
 42P  plan-1  C03  0.020
 42P  plan-1  N04  0.020
 42P  plan-1  C05  0.020
 42P  plan-1  C06  0.020
 42P  plan-1  N07  0.020
 42P  plan-1  N08  0.020
 42P  plan-1  CL9  0.020
 42P  plan-1  C10  0.020
 42P  plan-2  C06  0.020
 42P  plan-2  C10  0.020
 42P  plan-2  S25  0.020
 42P  plan-2  C26  0.020
 42P  plan-2  C27  0.020
 42P  plan-2  N28  0.020
 42P  plan-2  C29  0.020
 42P  plan-2  C30  0.020
 42P  plan-2  C31  0.020
 42P  plan-2  C32  0.020
 42P  plan-2  H23  0.020
 42P  plan-2  H24  0.020
 42P  plan-2  H25  0.020
 42P  plan-2  H26  0.020
 42P  plan-3  C01  0.020
 42P  plan-3  N07  0.020
 42P  plan-3  C11  0.020
 42P  plan-3  H1   0.020
 42P  plan-4  C03  0.020
 42P  plan-4  N08  0.020
 42P  plan-4  C20  0.020
 42P  plan-4  H2   0.020

