# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:32:58 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (1R)-3-(2,4-diamino-6-methylpyrimidin-5-yl)-1-(3,4,5-trimethoxyphenyl)prop-2-yn-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)[C@@H](O)C#Cc2c(C)nc(N)nc2N
#
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
 5WA  5WA  (1R)-3-(2,4-diamino-6-methylpyrimidin-5-yl)-1-(3,4,5-trimethoxyphenyl)prop-2-yn-1-ol  ligand  45  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5WA
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
 5WA  N1    N  N     0  -0.501  -4.4325  -1.3278  -1.5021
 5WA  C2    C  CR6   0   0.544  -5.5508  -0.8318  -0.9553
 5WA  N3    N  N     0  -0.503  -5.6218   0.1258  -0.0332
 5WA  C4    C  CR6   0   0.470  -4.4751   0.6392   0.3957
 5WA  C5    C  CR6   0  -0.331  -3.2283   0.1860  -0.1117
 5WA  C6    C  CR6   0   0.263  -3.2854  -0.8156  -1.0823
 5WA  C1A   C  CH3   0  -0.439   4.7549   0.4944   3.3905
 5WA  C1B   C  CH3   0  -0.446   1.7680  -0.8424  -2.9699
 5WA  C1C   C  CH3   0  -0.408   4.8585  -2.4938  -0.0754
 5WA  C1D   C  CH3   0  -0.764  -2.0356  -1.3362  -1.7156
 5WA  N1E   N  NH2   0  -0.817  -6.7111  -1.3729  -1.3646
 5WA  N1F   N  NH2   0  -0.822  -4.5319   1.5883   1.3382
 5WA  O1G   O  OH1   0  -0.639   0.4359   3.1332   0.8085
 5WA  C1H   C  CSP   0   0.166  -2.0104   0.7367   0.3470
 5WA  C1I   C  CSP   0   0.022  -0.9770   1.2116   0.7547
 5WA  C1J   C  CR16  0  -0.485   2.5374   0.8236   1.7004
 5WA  C1K   C  CR16  0  -0.452   1.5312   0.3812  -0.4492
 5WA  C1U   C  CR6   0   0.127   1.4728   0.9447   0.8188
 5WA  C1V   C  CR6   0   0.346   3.6781   0.1217   1.3137
 5WA  C1W   C  CR6   0   0.349   2.6709  -0.3161  -0.8421
 5WA  C1X   C  CR6   0   0.171   3.7506  -0.4407   0.0368
 5WA  C1Y   C  CH1   0  -0.228   0.2823   1.7920   1.2256
 5WA  H1A   H  HCH3  0   0.230   4.6607   1.5831   3.3674
 5WA  H1AA  H  HCH3  0   0.230   3.9540   0.0828   4.0099
 5WA  H1AB  H  HCH3  0   0.262   5.7113   0.2353   3.8376
 5WA  H1B   H  HCH3  0   0.265   2.1153  -1.3467  -3.8679
 5WA  H1BA  H  HCH3  0   0.230   0.8802  -1.3630  -2.6006
 5WA  H1BB  H  HCH3  0   0.231   1.4963   0.1847  -3.2257
 5WA  H1C   H  HCH3  0   0.222   4.0444  -3.0024  -0.5973
 5WA  H1CA  H  HCH3  0   0.237   5.8051  -2.9006  -0.4263
 5WA  H1CB  H  HCH3  0   0.222   4.7685  -2.6923   0.9952
 5WA  H1D   H  HCH3  0   0.260  -1.7193  -0.6639  -2.5171
 5WA  H1DA  H  HCH3  0   0.249  -1.2133  -1.3978  -1.0042
 5WA  H1DB  H  HCH3  0   0.260  -2.2064  -2.3171  -2.1537
 5WA  HN1E  H  HNH2  0   0.396  -6.7114  -1.9703  -2.1727
 5WA  HN1A  H  HNH2  0   0.396  -7.5770  -0.9271  -1.1168
 5WA  HN1F  H  HNH2  0   0.398  -5.4243   1.9844   1.5796
 5WA  HN1B  H  HNH2  0   0.405  -3.7111   2.1126   1.5881
 5WA  HO1G  H  HOH1  0   0.450   0.4933   3.1489  -0.1538
 5WA  H1J   H  HCR6  0   0.282   2.4652   1.2711   2.6832
 5WA  H1K   H  HCR6  0   0.278   0.6823   0.4770  -1.1135
 5WA  H1Y   H  HCH1  0   0.278   0.2507   1.8353   2.3184
 5WA  O1N   O  O2    0  -0.462   4.7576  -0.0628   2.0906
 5WA  O1O   O  O2    0  -0.461   2.8325  -0.8979  -2.0419
 5WA  O1P   O  O2    0  -0.480   4.8728  -1.0991  -0.3528

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
 5WA  C6   N1    aromatic  1.325  0.020  1.325
 5WA  N1   C2    aromatic  1.340  0.020  1.340
 5WA  C2   N1E   single    1.344  0.020  1.344
 5WA  C2   N3    aromatic  1.331  0.020  1.331
 5WA  C4   N3    aromatic  1.328  0.020  1.328
 5WA  C5   C4    aromatic  1.420  0.020  1.420
 5WA  C4   N1F   single    1.339  0.020  1.339
 5WA  C6   C5    aromatic  1.396  0.020  1.396
 5WA  C1H  C5    single    1.413  0.020  1.413
 5WA  C1D  C6    single    1.495  0.020  1.495
 5WA  O1N  C1A   single    1.414  0.020  1.414
 5WA  C1A  H1A   single    0.970  0.020  1.090
 5WA  C1A  H1AA  single    0.970  0.020  1.090
 5WA  C1A  H1AB  single    0.970  0.020  1.090
 5WA  O1O  C1B   single    1.413  0.020  1.413
 5WA  C1B  H1B   single    0.970  0.020  1.090
 5WA  C1B  H1BA  single    0.970  0.020  1.090
 5WA  C1B  H1BB  single    0.970  0.020  1.090
 5WA  C1C  O1P   single    1.422  0.020  1.422
 5WA  C1C  H1C   single    0.970  0.020  1.090
 5WA  C1C  H1CA  single    0.970  0.020  1.090
 5WA  C1C  H1CB  single    0.970  0.020  1.090
 5WA  C1D  H1D   single    0.970  0.020  1.090
 5WA  C1D  H1DA  single    0.970  0.020  1.090
 5WA  C1D  H1DB  single    0.970  0.020  1.090
 5WA  N1E  HN1E  single    0.890  0.020  1.040
 5WA  N1E  HN1A  single    0.890  0.020  1.040
 5WA  N1F  HN1F  single    0.860  0.020  1.020
 5WA  N1F  HN1B  single    0.860  0.020  1.020
 5WA  C1Y  O1G   single    1.413  0.020  1.413
 5WA  O1G  HO1G  single    0.850  0.020  0.980
 5WA  C1I  C1H   triple    1.208  0.020  1.208
 5WA  C1Y  C1I   single    1.464  0.020  1.464
 5WA  C1V  C1J   aromatic  1.394  0.020  1.394
 5WA  C1J  C1U   aromatic  1.388  0.020  1.388
 5WA  C1J  H1J   single    0.930  0.020  1.080
 5WA  C1W  C1K   aromatic  1.393  0.020  1.393
 5WA  C1K  C1U   aromatic  1.389  0.020  1.389
 5WA  C1K  H1K   single    0.930  0.020  1.080
 5WA  O1N  C1V   single    1.343  0.020  1.343
 5WA  O1O  C1W   single    1.343  0.020  1.343
 5WA  O1P  C1X   single    1.358  0.020  1.358
 5WA  C1U  C1Y   single    1.517  0.020  1.517
 5WA  C1X  C1V   aromatic  1.397  0.020  1.397
 5WA  C1X  C1W   aromatic  1.398  0.020  1.398
 5WA  C1Y  H1Y   single    0.970  0.020  1.090

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
 5WA  C6    N1   C2    116.76  3.000
 5WA  N1E   C2   N3    117.03  3.000
 5WA  N3    C2   N1    126.40  3.000
 5WA  N1E   C2   N1    116.56  3.000
 5WA  C4    N3   C2    117.12  3.000
 5WA  N1F   C4   C5    120.99  3.000
 5WA  N1F   C4   N3    117.71  3.000
 5WA  C5    C4   N3    121.29  3.000
 5WA  C1H   C5   C6    122.73  3.000
 5WA  C1H   C5   C4    121.08  3.000
 5WA  C6    C5   C4    116.19  3.000
 5WA  C1D   C6   C5    120.69  3.000
 5WA  C1D   C6   N1    117.07  3.000
 5WA  C5    C6   N1    122.23  3.000
 5WA  H1AB  C1A  H1AA  108.78  3.000
 5WA  H1AB  C1A  H1A   108.78  3.000
 5WA  H1AA  C1A  H1A   108.90  3.000
 5WA  H1AB  C1A  O1N   106.41  3.000
 5WA  H1AA  C1A  O1N   111.96  3.000
 5WA  H1A   C1A  O1N   111.91  3.000
 5WA  H1BB  C1B  H1BA  108.95  3.000
 5WA  H1BB  C1B  H1B   108.79  3.000
 5WA  H1BA  C1B  H1B   108.52  3.000
 5WA  H1BB  C1B  O1O   112.20  3.000
 5WA  H1BA  C1B  O1O   111.79  3.000
 5WA  H1B   C1B  O1O   106.48  3.000
 5WA  H1CB  C1C  H1CA  108.64  3.000
 5WA  H1CB  C1C  H1C   108.79  3.000
 5WA  H1CA  C1C  H1C   108.67  3.000
 5WA  H1CB  C1C  O1P   111.73  3.000
 5WA  H1CA  C1C  O1P   107.15  3.000
 5WA  H1C   C1C  O1P   111.77  3.000
 5WA  H1DB  C1D  H1DA  109.31  3.000
 5WA  H1DB  C1D  H1D   107.75  3.000
 5WA  H1DA  C1D  H1D   107.18  3.000
 5WA  H1DB  C1D  C6    110.70  3.000
 5WA  H1DA  C1D  C6    111.97  3.000
 5WA  H1D   C1D  C6    109.78  3.000
 5WA  HN1A  N1E  HN1E  117.50  3.000
 5WA  HN1A  N1E  C2    119.35  3.000
 5WA  HN1E  N1E  C2    118.98  3.000
 5WA  HN1B  N1F  HN1F  117.34  3.000
 5WA  HN1B  N1F  C4    120.66  3.000
 5WA  HN1F  N1F  C4    119.07  3.000
 5WA  HO1G  O1G  C1Y   108.46  3.000
 5WA  C1I   C1H  C5    180.00  3.000
 5WA  C1Y   C1I  C1H   180.00  3.000
 5WA  H1J   C1J  C1V   120.98  3.000
 5WA  H1J   C1J  C1U   119.32  3.000
 5WA  C1V   C1J  C1U   119.70  3.000
 5WA  H1K   C1K  C1W   120.87  3.000
 5WA  H1K   C1K  C1U   119.44  3.000
 5WA  C1W   C1K  C1U   119.68  3.000
 5WA  C1Y   C1U  C1K   120.30  3.000
 5WA  C1Y   C1U  C1J   118.72  3.000
 5WA  C1K   C1U  C1J   120.82  3.000
 5WA  C1X   C1V  O1N   115.58  3.000
 5WA  C1X   C1V  C1J   119.91  3.000
 5WA  O1N   C1V  C1J   124.51  3.000
 5WA  C1X   C1W  O1O   115.48  3.000
 5WA  C1X   C1W  C1K   119.96  3.000
 5WA  O1O   C1W  C1K   124.56  3.000
 5WA  C1W   C1X  C1V   119.92  3.000
 5WA  C1W   C1X  O1P   120.07  3.000
 5WA  C1V   C1X  O1P   120.01  3.000
 5WA  H1Y   C1Y  C1U   108.22  3.000
 5WA  H1Y   C1Y  C1I   108.18  3.000
 5WA  C1U   C1Y  C1I   111.55  3.000
 5WA  H1Y   C1Y  O1G   105.09  3.000
 5WA  C1U   C1Y  O1G   111.46  3.000
 5WA  C1I   C1Y  O1G   112.01  3.000
 5WA  C1V   O1N  C1A   118.43  3.000
 5WA  C1W   O1O  C1B   118.62  3.000
 5WA  C1X   O1P  C1C   114.28  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
 5WA  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 5WA  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 5WA  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 5WA  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 5WA  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 5WA  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 5WA  CONST_07  C1W   C1X  C1V  C1J    0.00   0.0  0
 5WA  CONST_08  C1W   C1K  C1U  C1J    0.00   0.0  0
 5WA  CONST_09  C1V   C1X  C1W  C1K    0.00   0.0  0
 5WA  CONST_10  C1V   C1J  C1U  C1K    0.00   0.0  0
 5WA  CONST_11  C1X   C1V  C1J  C1U    0.00   0.0  0
 5WA  CONST_12  C1X   C1W  C1K  C1U    0.00   0.0  0
 5WA  CONST_13  C1H   C5   C6   N1   180.00   0.0  0
 5WA  CONST_14  C1D   C6   N1   C2   180.00   0.0  0
 5WA  CONST_15  N1F   C4   N3   C2   180.00   0.0  0
 5WA  CONST_16  C1H   C5   C4   N3   180.00   0.0  0
 5WA  CONST_17  N1E   C2   N3   C4   180.00   0.0  0
 5WA  CONST_18  C1D   C6   C5   C4   180.00   0.0  0
 5WA  CONST_19  N1E   C2   N1   C6   180.00   0.0  0
 5WA  CONST_20  N1F   C4   C5   C6   180.00   0.0  0
 5WA  CONST_21  O1P   C1X  C1V  C1J  180.00   0.0  0
 5WA  CONST_22  O1P   C1X  C1W  C1K  180.00   0.0  0
 5WA  CONST_23  C1U   C1J  C1V  O1N  180.00   0.0  0
 5WA  CONST_24  C1W   C1X  C1V  O1N  180.00   0.0  0
 5WA  CONST_25  C1U   C1K  C1W  O1O  180.00   0.0  0
 5WA  CONST_26  C1V   C1X  C1W  O1O  180.00   0.0  0
 5WA  CONST_27  C1Y   C1U  C1J  C1V  180.00   0.0  0
 5WA  CONST_28  C1Y   C1U  C1K  C1W  180.00   0.0  0
 5WA  CONST_29  H1K   C1K  C1U  C1J  180.00   0.0  0
 5WA  CONST_30  H1J   C1J  C1U  C1K  180.00   0.0  0
 5WA  CONST_31  HN1E  N1E  C2   N1     0.00   0.0  0
 5WA  CONST_32  HN1A  N1E  C2   N1   180.00   0.0  0
 5WA  CONST_33  HN1F  N1F  C4   N3     0.00   0.0  0
 5WA  CONST_34  HN1B  N1F  C4   N3   180.00   0.0  0
 5WA  Var_01    C1J   C1V  O1N  C1A   -0.40  30.0  2
 5WA  Var_02    C1K   C1W  O1O  C1B   -1.93  30.0  2
 5WA  Var_03    C1V   C1X  O1P  C1C   90.75  30.0  2
 5WA  Var_04    H1D   C1D  C6   N1    97.00  30.0  2
 5WA  Var_05    H1A   C1A  O1N  C1V  -60.96  30.0  3
 5WA  Var_06    H1B   C1B  O1O  C1W  178.71  30.0  3
 5WA  Var_07    H1C   C1C  O1P  C1X   61.39  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
 5WA  chir_01  C1Y  O1G  C1I  C1U  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
 5WA  plan-1  N1    0.020
 5WA  plan-1  C2    0.020
 5WA  plan-1  N3    0.020
 5WA  plan-1  C4    0.020
 5WA  plan-1  C5    0.020
 5WA  plan-1  C6    0.020
 5WA  plan-1  C1D   0.020
 5WA  plan-1  N1E   0.020
 5WA  plan-1  N1F   0.020
 5WA  plan-1  C1H   0.020
 5WA  plan-1  C1I   0.020
 5WA  plan-2  C1J   0.020
 5WA  plan-2  C1K   0.020
 5WA  plan-2  C1U   0.020
 5WA  plan-2  C1V   0.020
 5WA  plan-2  C1W   0.020
 5WA  plan-2  C1X   0.020
 5WA  plan-2  C1Y   0.020
 5WA  plan-2  H1J   0.020
 5WA  plan-2  H1K   0.020
 5WA  plan-2  O1N   0.020
 5WA  plan-2  O1O   0.020
 5WA  plan-2  O1P   0.020
 5WA  plan-3  C2    0.020
 5WA  plan-3  N1E   0.020
 5WA  plan-3  HN1E  0.020
 5WA  plan-3  HN1A  0.020
 5WA  plan-4  C4    0.020
 5WA  plan-4  N1F   0.020
 5WA  plan-4  HN1F  0.020
 5WA  plan-4  HN1B  0.020

