# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:52:45 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)C(C)(C)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
 55V  55V  6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine  ligand  50  26  .  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_55V
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
 55V  C1P   C  CH3   0  -0.442  -1.4520  -2.8558  -1.7934
 55V  O1O   O  O2    0  -0.464  -2.5990  -2.3575  -1.1370
 55V  C1N   C  CR6   0   0.351  -2.5751  -1.0982  -0.6658
 55V  C1M   C  CR16  0  -0.464  -1.5018  -0.2247  -0.8098
 55V  C1Q   C  CR6   0   0.159  -3.7315  -0.6849   0.0015
 55V  O1V   O  O2    0  -0.482  -4.7917  -1.5275   0.1229
 55V  C1W   C  CH3   0  -0.410  -4.7456  -2.3599   1.2741
 55V  C1R   C  CR6   0   0.365  -3.7929   0.6033   0.5322
 55V  O1T   O  O2    0  -0.466  -4.9355   0.9150   1.1698
 55V  C1U   C  CH3   0  -0.440  -5.0646   2.2062   1.7304
 55V  C1S   C  CR16  0  -0.507  -2.7148   1.4763   0.3818
 55V  C1L   C  CR6   0   0.212  -1.5702   1.0627  -0.2866
 55V  C1J   C  CT    0  -0.351  -0.4094   2.0296  -0.5298
 55V  C1K   C  CH3   0  -0.620  -0.5166   2.5657  -1.9708
 55V  C1X   C  CH3   0  -0.665  -0.4073   3.2154   0.4447
 55V  C1I   C  CSP   0   0.229   0.8635   1.3179  -0.3710
 55V  C1H   C  CSP   0   0.069   1.9255   0.7602  -0.2306
 55V  C5    C  CR6   0  -0.369   3.1857   0.1349  -0.0651
 55V  C4    C  CR6   0   0.243   3.3297  -1.2256   0.2030
 55V  C1Y   C  CH3   0  -0.765   2.1287  -2.1098   0.3027
 55V  N3    N  N     0  -0.503   4.5168  -1.7964   0.3586
 55V  C2    C  CR6   0   0.545   5.5877  -1.0003   0.2398
 55V  N1Z   N  NH2   0  -0.822   6.7880  -1.5799   0.3884
 55V  N1    N  N     0  -0.505   5.5755   0.3074  -0.0151
 55V  C6    C  CR6   0   0.456   4.3883   0.8821  -0.1670
 55V  N1G   N  NH2   0  -0.825   4.3602   2.2005  -0.4027
 55V  H1P   H  HCH3  0   0.230  -1.2047  -2.2798  -2.6887
 55V  H1PA  H  HCH3  0   0.225  -0.5800  -2.8719  -1.1340
 55V  H1PB  H  HCH3  0   0.263  -1.6837  -3.8761  -2.0887
 55V  H1M   H  HCR6  0   0.271  -0.6038  -0.5399  -1.3241
 55V  H1W   H  HCH3  0   0.237  -5.6360  -2.9859   1.2540
 55V  H1WA  H  HCH3  0   0.221  -3.8643  -3.0053   1.2726
 55V  H1WB  H  HCH3  0   0.220  -4.7505  -1.7755   2.1975
 55V  H1U   H  HCH3  0   0.262  -6.0516   2.2471   2.1841
 55V  H1UA  H  HCH3  0   0.229  -4.3144   2.3935   2.5027
 55V  H1UB  H  HCH3  0   0.228  -4.9926   2.9909   0.9732
 55V  H1S   H  HCR6  0   0.276  -2.7714   2.4756   0.7871
 55V  H1K   H  HCH3  0   0.239  -1.4649   3.0891  -2.1014
 55V  H1KA  H  HCH3  0   0.236   0.2919   3.2677  -2.1795
 55V  H1KB  H  HCH3  0   0.239  -0.4668   1.7566  -2.6990
 55V  H1X   H  HCH3  0   0.244  -0.3923   2.8803   1.4815
 55V  H1XA  H  HCH3  0   0.251   0.4757   3.8309   0.2752
 55V  H1XB  H  HCH3  0   0.241  -1.2798   3.8528   0.2980
 55V  H1Y   H  HCH3  0   0.255   1.7361  -2.3195  -0.6950
 55V  H1YA  H  HCH3  0   0.256   2.3877  -3.0579   0.7687
 55V  H1YB  H  HCH3  0   0.252   1.3260  -1.6382   0.8690
 55V  HN1Z  H  HNH2  0   0.397   6.8559  -2.5594   0.5979
 55V  HN1A  H  HNH2  0   0.397   7.6304  -1.0372   0.3279
 55V  HN1G  H  HNH2  0   0.402   3.5004   2.6599  -0.6487
 55V  HN1B  H  HNH2  0   0.397   5.2201   2.6862  -0.5915

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
 55V  C1P  O1O   single    1.412  0.020  1.412
 55V  C1P  H1P   single    0.970  0.020  1.090
 55V  C1P  H1PA  single    0.970  0.020  1.090
 55V  C1P  H1PB  single    0.970  0.020  1.090
 55V  O1O  C1N   single    1.345  0.020  1.345
 55V  C1M  C1N   aromatic  1.391  0.020  1.391
 55V  C1N  C1Q   aromatic  1.398  0.020  1.398
 55V  C1M  C1L   aromatic  1.391  0.020  1.391
 55V  C1M  H1M   single    0.930  0.020  1.080
 55V  C1Q  O1V   single    1.360  0.020  1.360
 55V  C1Q  C1R   aromatic  1.395  0.020  1.395
 55V  O1V  C1W   single    1.421  0.020  1.421
 55V  C1W  H1W   single    0.970  0.020  1.090
 55V  C1W  H1WA  single    0.970  0.020  1.090
 55V  C1W  H1WB  single    0.970  0.020  1.090
 55V  C1S  C1R   aromatic  1.395  0.020  1.395
 55V  C1R  O1T   single    1.345  0.020  1.345
 55V  O1T  C1U   single    1.414  0.020  1.414
 55V  C1U  H1U   single    0.970  0.020  1.090
 55V  C1U  H1UA  single    0.970  0.020  1.090
 55V  C1U  H1UB  single    0.970  0.020  1.090
 55V  C1L  C1S   aromatic  1.388  0.020  1.388
 55V  C1S  H1S   single    0.930  0.020  1.080
 55V  C1J  C1L   single    1.530  0.020  1.530
 55V  C1K  C1J   single    1.541  0.020  1.541
 55V  C1J  C1I   single    1.467  0.020  1.467
 55V  C1J  C1X   single    1.535  0.020  1.535
 55V  C1K  H1K   single    0.970  0.020  1.090
 55V  C1K  H1KA  single    0.970  0.020  1.090
 55V  C1K  H1KB  single    0.970  0.020  1.090
 55V  C1X  H1X   single    0.970  0.020  1.090
 55V  C1X  H1XA  single    0.970  0.020  1.090
 55V  C1X  H1XB  single    0.970  0.020  1.090
 55V  C1I  C1H   triple    1.208  0.020  1.208
 55V  C1H  C5    single    1.416  0.020  1.416
 55V  C4   C5    aromatic  1.394  0.020  1.394
 55V  C5   C6    aromatic  1.420  0.020  1.420
 55V  C1Y  C4    single    1.495  0.020  1.495
 55V  C4   N3    aromatic  1.326  0.020  1.326
 55V  C1Y  H1Y   single    0.970  0.020  1.090
 55V  C1Y  H1YA  single    0.970  0.020  1.090
 55V  C1Y  H1YB  single    0.970  0.020  1.090
 55V  N3   C2    aromatic  1.340  0.020  1.340
 55V  C2   N1Z   single    1.341  0.020  1.341
 55V  C2   N1    aromatic  1.332  0.020  1.332
 55V  N1Z  HN1Z  single    0.860  0.020  1.020
 55V  N1Z  HN1A  single    0.860  0.020  1.020
 55V  C6   N1    aromatic  1.328  0.020  1.328
 55V  C6   N1G   single    1.340  0.020  1.340
 55V  N1G  HN1G  single    0.860  0.020  1.020
 55V  N1G  HN1B  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
 55V  H1PB  C1P  H1PA  108.66  3.000
 55V  H1PB  C1P  H1P   108.68  3.000
 55V  H1PA  C1P  H1P   108.75  3.000
 55V  H1PB  C1P  O1O   106.51  3.000
 55V  H1PA  C1P  O1O   111.88  3.000
 55V  H1P   C1P  O1O   112.24  3.000
 55V  C1N   O1O  C1P   118.61  3.000
 55V  C1Q   C1N  C1M   120.13  3.000
 55V  C1Q   C1N  O1O   115.44  3.000
 55V  C1M   C1N  O1O   124.43  3.000
 55V  H1M   C1M  C1L   119.28  3.000
 55V  H1M   C1M  C1N   120.44  3.000
 55V  C1L   C1M  C1N   120.27  3.000
 55V  C1R   C1Q  O1V   120.27  3.000
 55V  C1R   C1Q  C1N   119.43  3.000
 55V  O1V   C1Q  C1N   120.30  3.000
 55V  C1W   O1V  C1Q   114.20  3.000
 55V  H1WB  C1W  H1WA  108.71  3.000
 55V  H1WB  C1W  H1W   108.63  3.000
 55V  H1WA  C1W  H1W   108.67  3.000
 55V  H1WB  C1W  O1V   111.78  3.000
 55V  H1WA  C1W  O1V   111.78  3.000
 55V  H1W   C1W  O1V   107.17  3.000
 55V  C1S   C1R  O1T   124.23  3.000
 55V  O1T   C1R  C1Q   115.58  3.000
 55V  C1S   C1R  C1Q   120.19  3.000
 55V  C1U   O1T  C1R   118.50  3.000
 55V  H1UB  C1U  H1UA  108.75  3.000
 55V  H1UB  C1U  H1U   108.78  3.000
 55V  H1UA  C1U  H1U   108.78  3.000
 55V  H1UB  C1U  O1T   112.03  3.000
 55V  H1UA  C1U  O1T   111.97  3.000
 55V  H1U   C1U  O1T   106.43  3.000
 55V  H1S   C1S  C1L   119.98  3.000
 55V  H1S   C1S  C1R   119.86  3.000
 55V  C1L   C1S  C1R   120.16  3.000
 55V  C1J   C1L  C1S   120.90  3.000
 55V  C1J   C1L  C1M   119.19  3.000
 55V  C1S   C1L  C1M   119.81  3.000
 55V  C1I   C1J  C1X   107.75  3.000
 55V  C1X   C1J  C1K   108.96  3.000
 55V  C1I   C1J  C1K   109.28  3.000
 55V  C1X   C1J  C1L   112.85  3.000
 55V  C1I   C1J  C1L   109.54  3.000
 55V  C1K   C1J  C1L   108.40  3.000
 55V  H1KB  C1K  H1KA  108.43  3.000
 55V  H1KB  C1K  H1K   108.41  3.000
 55V  H1KA  C1K  H1K   108.21  3.000
 55V  H1KB  C1K  C1J   111.31  3.000
 55V  H1KA  C1K  C1J   110.56  3.000
 55V  H1K   C1K  C1J   109.83  3.000
 55V  H1XB  C1X  H1XA  107.30  3.000
 55V  H1XB  C1X  H1X   108.58  3.000
 55V  H1XA  C1X  H1X   108.09  3.000
 55V  H1XB  C1X  C1J   111.41  3.000
 55V  H1XA  C1X  C1J   109.81  3.000
 55V  H1X   C1X  C1J   111.50  3.000
 55V  C1H   C1I  C1J   180.00  3.000
 55V  C5    C1H  C1I   180.00  3.000
 55V  C6    C5   C4    116.10  3.000
 55V  C6    C5   C1H   120.86  3.000
 55V  C4    C5   C1H   123.04  3.000
 55V  N3    C4   C1Y   117.17  3.000
 55V  N3    C4   C5    122.35  3.000
 55V  C1Y   C4   C5    120.47  3.000
 55V  H1YB  C1Y  H1YA  109.27  3.000
 55V  H1YB  C1Y  H1Y   107.04  3.000
 55V  H1YA  C1Y  H1Y   108.03  3.000
 55V  H1YB  C1Y  C4    111.74  3.000
 55V  H1YA  C1Y  C4    110.66  3.000
 55V  H1Y   C1Y  C4    109.96  3.000
 55V  C2    N3   C4    116.70  3.000
 55V  N1    C2   N1Z   116.97  3.000
 55V  N1    C2   N3    126.36  3.000
 55V  N1Z   C2   N3    116.67  3.000
 55V  HN1A  N1Z  HN1Z  118.90  3.000
 55V  HN1A  N1Z  C2    120.71  3.000
 55V  HN1Z  N1Z  C2    120.35  3.000
 55V  C6    N1   C2    117.06  3.000
 55V  N1G   C6   N1    117.70  3.000
 55V  N1G   C6   C5    120.86  3.000
 55V  N1    C6   C5    121.43  3.000
 55V  HN1B  N1G  HN1G  117.69  3.000
 55V  HN1B  N1G  C6    119.38  3.000
 55V  HN1G  N1G  C6    120.72  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
 55V  CONST_01  C1S   C1L  C1M  C1N     0.00   0.0  0
 55V  CONST_02  C1S   C1R  C1Q  C1N     0.00   0.0  0
 55V  CONST_03  C1R   C1Q  C1N  C1M     0.00   0.0  0
 55V  CONST_04  C1R   C1S  C1L  C1M     0.00   0.0  0
 55V  CONST_05  C1L   C1M  C1N  C1Q     0.00   0.0  0
 55V  CONST_06  C1L   C1S  C1R  C1Q     0.00   0.0  0
 55V  CONST_07  C2    N3   C4   C5      0.00   0.0  0
 55V  CONST_08  C2    N1   C6   C5      0.00   0.0  0
 55V  CONST_09  N1    C6   C5   C4      0.00   0.0  0
 55V  CONST_10  N1    C2   N3   C4      0.00   0.0  0
 55V  CONST_11  C6    C5   C4   N3      0.00   0.0  0
 55V  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 55V  CONST_13  C1L   C1M  C1N  O1O   180.00   0.0  0
 55V  CONST_14  C1R   C1Q  C1N  O1O   180.00   0.0  0
 55V  CONST_15  C1J   C1L  C1M  C1N   180.00   0.0  0
 55V  CONST_16  O1T   C1R  C1Q  C1N   180.00   0.0  0
 55V  CONST_17  O1V   C1Q  C1N  C1M   180.00   0.0  0
 55V  CONST_18  C1S   C1R  C1Q  O1V   180.00   0.0  0
 55V  CONST_19  C1J   C1L  C1S  C1R   180.00   0.0  0
 55V  CONST_20  C1L   C1S  C1R  O1T   180.00   0.0  0
 55V  CONST_21  N3    C4   C5   C1H   180.00   0.0  0
 55V  CONST_22  N1    C6   C5   C1H   180.00   0.0  0
 55V  CONST_23  N1G   C6   C5   C4    180.00   0.0  0
 55V  CONST_24  N1Z   C2   N3   C4    180.00   0.0  0
 55V  CONST_25  C6    C5   C4   C1Y   180.00   0.0  0
 55V  CONST_26  C2    N3   C4   C1Y   180.00   0.0  0
 55V  CONST_27  N1G   C6   N1   C2    180.00   0.0  0
 55V  CONST_28  C6    N1   C2   N1Z   180.00   0.0  0
 55V  CONST_29  H1S   C1S  C1L  C1M   180.00   0.0  0
 55V  CONST_30  H1M   C1M  C1N  C1Q   180.00   0.0  0
 55V  CONST_31  HN1G  N1G  C6   C5      0.00   0.0  0
 55V  CONST_32  HN1B  N1G  C6   C5    180.00   0.0  0
 55V  CONST_33  HN1Z  N1Z  C2   N3      0.00   0.0  0
 55V  CONST_34  HN1A  N1Z  C2   N3    180.00   0.0  0
 55V  Var_01    C1M   C1N  O1O  C1P     1.81  30.0  2
 55V  Var_02    C1K   C1J  C1L  C1M    77.43  30.0  3
 55V  Var_03    C1R   C1Q  O1V  C1W   -92.00  30.0  3
 55V  Var_04    C1S   C1R  O1T  C1U    -0.12  30.0  3
 55V  Var_05    H1Y   C1Y  C4   C5     75.82  30.0  2
 55V  Var_06    H1P   C1P  O1O  C1N   -61.19  30.0  3
 55V  Var_07    H1W   C1W  O1V  C1Q  -179.62  30.0  3
 55V  Var_08    H1U   C1U  O1T  C1R   179.61  30.0  3
 55V  Var_09    H1K   C1K  C1J  C1L    60.15  30.0  3
 55V  Var_10    H1X   C1X  C1J  C1L    56.16  30.0  3

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
 55V  plan-1  O1O   0.020
 55V  plan-1  C1N   0.020
 55V  plan-1  C1M   0.020
 55V  plan-1  C1Q   0.020
 55V  plan-1  O1V   0.020
 55V  plan-1  C1R   0.020
 55V  plan-1  O1T   0.020
 55V  plan-1  C1S   0.020
 55V  plan-1  C1L   0.020
 55V  plan-1  C1J   0.020
 55V  plan-1  H1M   0.020
 55V  plan-1  H1S   0.020
 55V  plan-2  C1I   0.020
 55V  plan-2  C1H   0.020
 55V  plan-2  C5    0.020
 55V  plan-2  C4    0.020
 55V  plan-2  C1Y   0.020
 55V  plan-2  N3    0.020
 55V  plan-2  C2    0.020
 55V  plan-2  N1Z   0.020
 55V  plan-2  N1    0.020
 55V  plan-2  C6    0.020
 55V  plan-2  N1G   0.020
 55V  plan-3  C2    0.020
 55V  plan-3  N1Z   0.020
 55V  plan-3  HN1Z  0.020
 55V  plan-3  HN1A  0.020
 55V  plan-4  C6    0.020
 55V  plan-4  N1G   0.020
 55V  plan-4  HN1G  0.020
 55V  plan-4  HN1B  0.020

