# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 13:49:59 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: 4'-chloro-3'-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl][1,1'-biphenyl]-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@H](C)c2cc(ccc2Cl)c3ccc(cc3)C(N)=O
#
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
 4SI  4SI  "4'-chloro-3'-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl][1,1'-biphenyl]-4-carboxamide"
  ligand  52  30  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4SI
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
 4SI  C14   C   CR6   0   0.256  87.0679  -12.2326  -2.3967
 4SI  C10   C   CR6   0  -0.353  91.9177  -12.0003  -1.8723
 4SI  C12   C   CSP   0   0.159  89.3372  -11.5754  -1.6696
 4SI  C13   C   CH1   0  -0.507  87.9101  -11.2963  -1.5522
 4SI  C01   C   CH3   0  -0.676  91.2468  -13.1091  -4.8790
 4SI  C03   C   CR6   0   0.255  92.5932  -11.9967  -3.0921
 4SI  C05   C   CR6   0   0.537  94.5530  -12.4233  -2.0316
 4SI  C08   C   CR6   0   0.469  92.7114  -12.2386  -0.7185
 4SI  C15   C   CR16  0  -0.388  87.4404  -13.5612  -2.5721
 4SI  C16   C   CR6   0   0.128  86.6594  -14.4675  -3.2854
 4SI  C17   C   CR6   0   0.087  87.0730  -15.8759  -3.4353
 4SI  C18   C   CR16  0  -0.293  86.1261  -16.8997  -3.4051
 4SI  C19   C   CR16  0  -0.263  86.5045  -18.2246  -3.5423
 4SI  C20   C   CR6   0  -0.049  87.8432  -18.5648  -3.7197
 4SI  C21   C   C     0   0.481  88.3041  -19.9759  -3.9074
 4SI  C24   C   CR16  0  -0.253  88.7904  -17.5450  -3.7684
 4SI  C25   C   CR16  0  -0.305  88.4130  -16.2225  -3.6169
 4SI  C26   C   CR16  0  -0.336  85.4692  -14.0126  -3.8524
 4SI  C27   C   CR16  0  -0.176  85.0727  -12.6978  -3.6953
 4SI  C28   C   CR6   0  -0.146  85.8644  -11.8239  -2.9654
 4SI  C30   C   CH3   0  -0.637  87.4629  -11.3570  -0.0834
 4SI  N04   N   N     0  -0.496  93.9000  -12.2061  -3.1796
 4SI  N06   N   NH2   0  -0.818  95.8738  -12.6631  -2.1247
 4SI  N07   N   N     0  -0.503  94.0200  -12.4459  -0.8117
 4SI  N09   N   NH2   0  -0.827  92.1631  -12.2656   0.5008
 4SI  N22   N   NH2   0  -0.811  87.5218  -20.9337  -3.3830
 4SI  O23   O   O     0  -0.471  89.3361  -20.2230  -4.5146
 4SI  CL29  CL  CL    0  -0.123  85.3033  -10.1922  -2.7742
 4SI  H1    H   HCH1  0   0.283  87.7517  -10.2742  -1.9077
 4SI  H2    H   HCH3  0   0.238  90.7310  -12.9559  -5.8266
 4SI  H3    H   HCH3  0   0.229  92.0212  -13.8604  -5.0360
 4SI  H4    H   HCH3  0   0.240  90.5245  -13.5126  -4.1683
 4SI  H5    H   HCH2  0   0.249  92.5400  -11.4013  -5.1227
 4SI  H6    H   HCH2  0   0.245  91.0562  -11.0591  -4.2395
 4SI  H7    H   HCR6  0   0.260  88.3640  -13.8952  -2.1134
 4SI  H8    H   HCR6  0   0.262  85.0792  -16.6678  -3.2570
 4SI  H9    H   HCR6  0   0.261  85.7331  -18.9840  -3.5263
 4SI  H10   H   HCR6  0   0.262  89.8339  -17.7844  -3.9241
 4SI  H11   H   HCR6  0   0.272  89.1702  -15.4501  -3.6664
 4SI  H12   H   HCR6  0   0.266  84.8509  -14.6789  -4.4397
 4SI  H13   H   HCR6  0   0.281  84.1518  -12.3513  -4.1443
 4SI  H14   H   HCH3  0   0.246  88.0283  -10.6467   0.5186
 4SI  H15   H   HCH3  0   0.244  86.4049  -11.1106   0.0010
 4SI  H16   H   HCH3  0   0.236  87.6176  -12.3563   0.3223
 4SI  H17   H   HNH2  0   0.394  96.3397  -12.4965  -2.9992
 4SI  H18   H   HNH2  0   0.393  96.4347  -12.6684  -1.2909
 4SI  H19   H   HNH2  0   0.397  92.7471  -12.3877   1.3099
 4SI  H20   H   HNH2  0   0.407  91.1886  -12.0643   0.6427
 4SI  H21   H   HNH2  0   0.403  87.8044  -21.8974  -3.4599
 4SI  H22   H   HNH2  0   0.411  86.7648  -20.7339  -2.7525
 4SI  C11   C   CSP   0   0.105  90.5242  -11.7736  -1.7680
 4SI  C02   C   CH2   0  -0.523  91.8487  -11.7966  -4.3774

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
 4SI  O23  C21   double    1.223  0.020  1.223
 4SI  C21  C20   single    1.496  0.020  1.496
 4SI  C21  N22   single    1.343  0.020  1.343
 4SI  C01  C02   single    1.529  0.020  1.529
 4SI  C02  C03   single    1.499  0.020  1.499
 4SI  C20  C19   aromatic  1.393  0.020  1.393
 4SI  C20  C24   aromatic  1.393  0.020  1.393
 4SI  C19  C18   aromatic  1.385  0.020  1.385
 4SI  C24  C25   aromatic  1.384  0.020  1.384
 4SI  C26  C27   aromatic  1.382  0.020  1.382
 4SI  C26  C16   aromatic  1.395  0.020  1.395
 4SI  C18  C17   aromatic  1.395  0.020  1.395
 4SI  C25  C17   aromatic  1.396  0.020  1.396
 4SI  C27  C28   aromatic  1.387  0.020  1.387
 4SI  C17  C16   single    1.476  0.020  1.476
 4SI  C16  C15   aromatic  1.393  0.020  1.393
 4SI  N04  C03   aromatic  1.326  0.020  1.326
 4SI  N04  C05   aromatic  1.338  0.020  1.338
 4SI  C03  C10   aromatic  1.394  0.020  1.394
 4SI  C28  CL29  single    1.736  0.020  1.736
 4SI  C28  C14   aromatic  1.392  0.020  1.392
 4SI  C15  C14   aromatic  1.391  0.020  1.391
 4SI  C14  C13   single    1.516  0.020  1.516
 4SI  N06  C05   single    1.346  0.020  1.346
 4SI  C05  N07   aromatic  1.332  0.020  1.332
 4SI  C10  C11   single    1.416  0.020  1.416
 4SI  C10  C08   aromatic  1.421  0.020  1.421
 4SI  C11  C12   triple    1.208  0.020  1.208
 4SI  C12  C13   single    1.459  0.020  1.459
 4SI  C13  C30   single    1.537  0.020  1.537
 4SI  N07  C08   aromatic  1.328  0.020  1.328
 4SI  C08  N09   single    1.337  0.020  1.337
 4SI  C13  H1    single    0.970  0.020  1.090
 4SI  C01  H2    single    0.970  0.020  1.090
 4SI  C01  H3    single    0.970  0.020  1.090
 4SI  C01  H4    single    0.970  0.020  1.090
 4SI  C02  H5    single    0.970  0.020  1.090
 4SI  C02  H6    single    0.970  0.020  1.090
 4SI  C15  H7    single    0.930  0.020  1.080
 4SI  C18  H8    single    0.930  0.020  1.080
 4SI  C19  H9    single    0.930  0.020  1.080
 4SI  C24  H10   single    0.930  0.020  1.080
 4SI  C25  H11   single    0.930  0.020  1.080
 4SI  C26  H12   single    0.930  0.020  1.080
 4SI  C27  H13   single    0.930  0.020  1.080
 4SI  C30  H14   single    0.970  0.020  1.090
 4SI  C30  H15   single    0.970  0.020  1.090
 4SI  C30  H16   single    0.970  0.020  1.090
 4SI  N06  H17   single    0.890  0.020  1.040
 4SI  N06  H18   single    0.890  0.020  1.040
 4SI  N09  H19   single    0.860  0.020  1.020
 4SI  N09  H20   single    0.860  0.020  1.020
 4SI  N22  H21   single    0.860  0.020  1.020
 4SI  N22  H22   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
 4SI  C28   C14  C15  117.41  3.000
 4SI  C15   C14  C13  120.75  3.000
 4SI  C28   C14  C13  121.76  3.000
 4SI  C08   C10  C03  116.13  3.000
 4SI  C08   C10  C11  121.13  3.000
 4SI  C03   C10  C11  122.74  3.000
 4SI  C13   C12  C11  180.00  3.000
 4SI  H1    C13  C30  107.79  3.000
 4SI  H1    C13  C12  107.12  3.000
 4SI  C30   C13  C12  110.74  3.000
 4SI  H1    C13  C14  108.40  3.000
 4SI  C30   C13  C14  110.26  3.000
 4SI  C12   C13  C14  112.35  3.000
 4SI  H4    C01  H3   108.02  3.000
 4SI  H4    C01  H2   107.77  3.000
 4SI  H3    C01  H2   107.93  3.000
 4SI  H4    C01  C02  111.38  3.000
 4SI  H3    C01  C02  111.06  3.000
 4SI  H2    C01  C02  110.55  3.000
 4SI  N04   C03  C02  116.99  3.000
 4SI  N04   C03  C10  122.31  3.000
 4SI  C02   C03  C10  120.66  3.000
 4SI  N07   C05  N06  116.95  3.000
 4SI  N07   C05  N04  126.39  3.000
 4SI  N06   C05  N04  116.65  3.000
 4SI  N09   C08  N07  117.70  3.000
 4SI  N09   C08  C10  120.99  3.000
 4SI  N07   C08  C10  121.31  3.000
 4SI  H7    C15  C16  119.61  3.000
 4SI  H7    C15  C14  117.98  3.000
 4SI  C16   C15  C14  122.40  3.000
 4SI  C26   C16  C17  120.62  3.000
 4SI  C17   C16  C15  121.05  3.000
 4SI  C26   C16  C15  118.33  3.000
 4SI  C25   C17  C18  118.18  3.000
 4SI  C25   C17  C16  121.28  3.000
 4SI  C18   C17  C16  120.53  3.000
 4SI  H8    C18  C19  118.88  3.000
 4SI  H8    C18  C17  120.15  3.000
 4SI  C19   C18  C17  120.97  3.000
 4SI  H9    C19  C20  121.03  3.000
 4SI  H9    C19  C18  118.36  3.000
 4SI  C20   C19  C18  120.60  3.000
 4SI  C24   C20  C21  118.47  3.000
 4SI  C24   C20  C19  118.64  3.000
 4SI  C21   C20  C19  122.86  3.000
 4SI  O23   C21  N22  122.78  3.000
 4SI  N22   C21  C20  116.36  3.000
 4SI  O23   C21  C20  120.86  3.000
 4SI  H10   C24  C25  119.37  3.000
 4SI  H10   C24  C20  119.93  3.000
 4SI  C25   C24  C20  120.70  3.000
 4SI  H11   C25  C24  119.08  3.000
 4SI  H11   C25  C17  120.01  3.000
 4SI  C24   C25  C17  120.89  3.000
 4SI  H12   C26  C27  118.91  3.000
 4SI  H12   C26  C16  120.49  3.000
 4SI  C27   C26  C16  120.59  3.000
 4SI  H13   C27  C28  120.18  3.000
 4SI  H13   C27  C26  120.12  3.000
 4SI  C28   C27  C26  119.70  3.000
 4SI  CL29  C28  C27  117.76  3.000
 4SI  CL29  C28  C14  120.68  3.000
 4SI  C27   C28  C14  121.56  3.000
 4SI  H16   C30  H15  108.45  3.000
 4SI  H16   C30  H14  108.58  3.000
 4SI  H15   C30  H14  108.29  3.000
 4SI  H16   C30  C13  110.54  3.000
 4SI  H15   C30  C13  110.34  3.000
 4SI  H14   C30  C13  110.57  3.000
 4SI  C05   N04  C03  116.73  3.000
 4SI  H18   N06  H17  117.65  3.000
 4SI  H18   N06  C05  119.44  3.000
 4SI  H17   N06  C05  119.07  3.000
 4SI  C08   N07  C05  117.13  3.000
 4SI  H20   N09  H19  118.29  3.000
 4SI  H20   N09  C08  121.48  3.000
 4SI  H19   N09  C08  119.88  3.000
 4SI  H22   N22  H21  116.70  3.000
 4SI  H22   N22  C21  122.80  3.000
 4SI  H21   N22  C21  119.28  3.000
 4SI  C12   C11  C10  180.00  3.000
 4SI  H6    C02  H5   107.56  3.000
 4SI  H6    C02  C03  110.03  3.000
 4SI  H5    C02  C03  108.64  3.000
 4SI  H6    C02  C01  109.62  3.000
 4SI  H5    C02  C01  109.67  3.000
 4SI  C03   C02  C01  111.24  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
 4SI  CONST_01  C26   C27  C28  C14     0.00   0.0  0
 4SI  CONST_02  C26   C16  C15  C14     0.00   0.0  0
 4SI  CONST_03  C17   C16  C15  C14   180.00   0.0  0
 4SI  CONST_04  C05   N04  C03  C10     0.00   0.0  0
 4SI  CONST_05  C05   N07  C08  C10     0.00   0.0  0
 4SI  CONST_06  N07   C05  N04  C03     0.00   0.0  0
 4SI  CONST_07  N07   C08  C10  C03     0.00   0.0  0
 4SI  CONST_08  N04   C03  C10  C08     0.00   0.0  0
 4SI  CONST_09  N04   C05  N07  C08     0.00   0.0  0
 4SI  CONST_10  C27   C26  C16  C15     0.00   0.0  0
 4SI  CONST_13  C27   C28  C14  C15     0.00   0.0  0
 4SI  CONST_14  C28   C27  C26  C16     0.00   0.0  0
 4SI  CONST_15  C19   C18  C17  C16   180.00   0.0  0
 4SI  CONST_16  C24   C25  C17  C16   180.00   0.0  0
 4SI  CONST_17  C28   C14  C15  C16     0.00   0.0  0
 4SI  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 4SI  CONST_19  C20   C24  C25  C17     0.00   0.0  0
 4SI  CONST_20  C27   C26  C16  C17   180.00   0.0  0
 4SI  CONST_21  C24   C20  C19  C18     0.00   0.0  0
 4SI  CONST_22  C24   C25  C17  C18     0.00   0.0  0
 4SI  CONST_24  C25   C24  C20  C19     0.00   0.0  0
 4SI  CONST_25  C25   C17  C18  C19     0.00   0.0  0
 4SI  CONST_27  N04   C03  C10  C11   180.00   0.0  0
 4SI  CONST_28  N07   C08  C10  C11   180.00   0.0  0
 4SI  CONST_29  C27   C28  C14  C13   180.00   0.0  0
 4SI  CONST_30  C16   C15  C14  C13   180.00   0.0  0
 4SI  CONST_31  C05   N04  C03  C02   180.00   0.0  0
 4SI  CONST_32  C08   C10  C03  C02   180.00   0.0  0
 4SI  CONST_33  N06   C05  N04  C03   180.00   0.0  0
 4SI  CONST_34  N09   C08  C10  C03   180.00   0.0  0
 4SI  CONST_35  N09   C08  N07  C05   180.00   0.0  0
 4SI  CONST_36  N06   C05  N07  C08   180.00   0.0  0
 4SI  CONST_37  CL29  C28  C14  C15   180.00   0.0  0
 4SI  CONST_38  C21   C20  C19  C18   180.00   0.0  0
 4SI  CONST_39  C25   C24  C20  C21   180.00   0.0  0
 4SI  CONST_40  CL29  C28  C27  C26   180.00   0.0  0
 4SI  CONST_41  H13   C27  C28  C14   180.00   0.0  0
 4SI  CONST_42  H12   C26  C16  C15   180.00   0.0  0
 4SI  CONST_43  H13   C27  C26  C16   180.00   0.0  0
 4SI  CONST_44  H8    C18  C17  C16     0.00   0.0  0
 4SI  CONST_45  H11   C25  C17  C16     0.00   0.0  0
 4SI  CONST_46  H9    C19  C18  C17   180.00   0.0  0
 4SI  CONST_47  H10   C24  C25  C17   180.00   0.0  0
 4SI  CONST_48  H12   C26  C16  C17     0.00   0.0  0
 4SI  CONST_49  H7    C15  C16  C17     0.00   0.0  0
 4SI  CONST_50  H11   C25  C17  C18   180.00   0.0  0
 4SI  CONST_51  H10   C24  C20  C19   180.00   0.0  0
 4SI  CONST_52  H8    C18  C19  C20   180.00   0.0  0
 4SI  CONST_53  H11   C25  C24  C20   180.00   0.0  0
 4SI  CONST_54  H9    C19  C20  C24   180.00   0.0  0
 4SI  CONST_55  H8    C18  C17  C25   180.00   0.0  0
 4SI  CONST_56  H7    C15  C16  C26   180.00   0.0  0
 4SI  CONST_57  H12   C26  C27  C28   180.00   0.0  0
 4SI  CONST_58  H7    C15  C14  C28   180.00   0.0  0
 4SI  CONST_59  H19   N09  C08  C10   180.00   0.0  0
 4SI  CONST_60  H20   N09  C08  C10     0.00   0.0  0
 4SI  CONST_61  H17   N06  C05  N04     0.00   0.0  0
 4SI  CONST_62  H18   N06  C05  N04   180.00   0.0  0
 4SI  CONST_63  H17   N06  C05  N07   180.00   0.0  0
 4SI  CONST_64  H18   N06  C05  N07     0.00   0.0  0
 4SI  CONST_65  H19   N09  C08  N07     0.00   0.0  0
 4SI  CONST_66  H20   N09  C08  N07   180.00   0.0  0
 4SI  CONST_67  H21   N22  C21  C20   180.00   0.0  0
 4SI  CONST_68  H22   N22  C21  C20     0.00   0.0  0
 4SI  CONST_69  H21   N22  C21  O23     0.00   0.0  0
 4SI  CONST_70  H22   N22  C21  O23   180.00   0.0  0
 4SI  Var_01    C01   C02  C03  C10   -83.51  30.0  1
 4SI  Var_02    N04   C03  C02  C01    94.58  30.0  2
 4SI  Var_03    O23   C21  C20  C19   153.58  30.0  2
 4SI  Var_04    N22   C21  C20  C19   -26.04  30.0  2
 4SI  Var_05    O23   C21  C20  C24   -24.27  30.0  2
 4SI  Var_06    N22   C21  C20  C24   156.11  30.0  2
 4SI  Var_07    H5    C02  C03  C10   155.68  30.0  1
 4SI  Var_08    H6    C02  C03  C10    38.18  30.0  1
 4SI  Var_09    H5    C02  C03  N04   -26.23  30.0  1
 4SI  Var_10    H6    C02  C03  N04  -143.73  30.0  1
 4SI  Var_11    C13   C12  C11  C10    64.22  30.0  1
 4SI  Var_12    H2    C01  C02  C03  -178.51  30.0  3
 4SI  Var_13    H3    C01  C02  C03   -58.73  30.0  3
 4SI  Var_14    H4    C01  C02  C03    61.71  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
 4SI  chir_01  C13  C14  C12  C30  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
 4SI  plan-1  C16   0.020
 4SI  plan-1  C17   0.020
 4SI  plan-1  C18   0.020
 4SI  plan-1  C19   0.020
 4SI  plan-1  C20   0.020
 4SI  plan-1  C21   0.020
 4SI  plan-1  C24   0.020
 4SI  plan-1  C25   0.020
 4SI  plan-1  H8    0.020
 4SI  plan-1  H9    0.020
 4SI  plan-1  H10   0.020
 4SI  plan-1  H11   0.020
 4SI  plan-2  C14   0.020
 4SI  plan-2  C13   0.020
 4SI  plan-2  C15   0.020
 4SI  plan-2  C16   0.020
 4SI  plan-2  C17   0.020
 4SI  plan-2  C26   0.020
 4SI  plan-2  C27   0.020
 4SI  plan-2  C28   0.020
 4SI  plan-2  CL29  0.020
 4SI  plan-2  H7    0.020
 4SI  plan-2  H12   0.020
 4SI  plan-2  H13   0.020
 4SI  plan-3  C10   0.020
 4SI  plan-3  C12   0.020
 4SI  plan-3  C03   0.020
 4SI  plan-3  C05   0.020
 4SI  plan-3  C08   0.020
 4SI  plan-3  N04   0.020
 4SI  plan-3  N06   0.020
 4SI  plan-3  N07   0.020
 4SI  plan-3  N09   0.020
 4SI  plan-3  C11   0.020
 4SI  plan-3  C02   0.020
 4SI  plan-4  C20   0.020
 4SI  plan-4  C21   0.020
 4SI  plan-4  N22   0.020
 4SI  plan-4  O23   0.020
 4SI  plan-4  H21   0.020
 4SI  plan-4  H22   0.020
 4SI  plan-5  C05   0.020
 4SI  plan-5  N06   0.020
 4SI  plan-5  H17   0.020
 4SI  plan-5  H18   0.020
 4SI  plan-6  C08   0.020
 4SI  plan-6  N09   0.020
 4SI  plan-6  H19   0.020
 4SI  plan-6  H20   0.020

