# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:58:53 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-[(3S)-3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](C#Cc1c(C)nc(N)nc1N)c2cc(OC)c(OC)c(OC)c2
#
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
 5WB  5WB  5-[(3S)-3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  48  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 PERFECT
;

data_comp_5WB
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
 5WB  N1    N  N     0  -0.501  -4.3175  -1.8583   1.0212
 5WB  C2    C  CR6   0   0.546  -5.4442  -1.2654   0.5994
 5WB  N3    N  N     0  -0.504  -5.5336  -0.1058  -0.0483
 5WB  C4    C  CR6   0   0.474  -4.3967   0.5271  -0.3146
 5WB  C5    C  CR6   0  -0.334  -3.1434  -0.0125   0.0787
 5WB  C6    C  CR6   0   0.260  -3.1816  -1.2280   0.7643
 5WB  C1A   C  CH3   0  -0.439   4.3954   0.6040  -3.5770
 5WB  C1B   C  CH3   0  -0.444   1.9945  -1.4235   2.8453
 5WB  C1C   C  CH3   0  -0.409   5.8736  -1.0567   0.4443
 5WB  C1E   C  CH3   0  -0.764  -1.9192  -1.8556   1.2620
 5WB  N1F   N  NH2   0  -0.817  -6.5918  -1.9189   0.8406
 5WB  N1G   N  NH2   0  -0.824  -4.4689   1.6894  -0.9710
 5WB  C1H   C  CSP   0   0.166  -1.9365   0.6686  -0.1941
 5WB  C1I   C  CSP   0   0.016  -0.9062   1.2483  -0.4440
 5WB  C1J   C  CR16  0  -0.488   2.4570   0.9046  -1.5699
 5WB  C1K   C  CR16  0  -0.439   1.6547   0.2285   0.6060
 5WB  O1Q   O  O2    0  -0.470   0.5689   3.0018   0.2269
 5WB  C1U   C  CR6   0   0.131   1.5237   0.9884  -0.5494
 5WB  C1W   C  CR6   0   0.347   3.5441   0.0394  -1.4393
 5WB  C1X   C  CR6   0   0.347   2.7349  -0.6377   0.7385
 5WB  C1Y   C  CR6   0   0.168   3.6807  -0.7382  -0.2882
 5WB  C1Z   C  CH1   0  -0.177   0.3610   1.9456  -0.6828
 5WB  H1A   H  HCH3  0   0.230   4.4460   1.6835  -3.4135
 5WB  H1AA  H  HCH3  0   0.262   5.2412   0.3038  -4.1906
 5WB  H1AB  H  HCH3  0   0.230   3.4715   0.3703  -4.1119
 5WB  H1B   H  HCH3  0   0.264   2.3382  -2.1444   3.5828
 5WB  H1BA  H  HCH3  0   0.231   1.9099  -0.4448   3.3244
 5WB  H1BB  H  HCH3  0   0.229   1.0064  -1.7280   2.4894
 5WB  H1C   H  HCH3  0   0.238   6.6404  -1.8290   0.4384
 5WB  H1CA  H  HCH3  0   0.222   6.2491  -0.1871  -0.1001
 5WB  H1CB  H  HCH3  0   0.222   5.6782  -0.7662   1.4792
 5WB  H1D   H  HCH3  0   0.211  -1.3796   3.7366   0.3685
 5WB  H1DA  H  HCH3  0   0.243  -0.0587   4.8472   0.7700
 5WB  H1DB  H  HCH3  0   0.210  -0.3924   4.4457  -0.9250
 5WB  H1E   H  HCH3  0   0.253  -1.1377  -1.8467   0.5026
 5WB  H1EA  H  HCH3  0   0.259  -1.5358  -1.2937   2.1168
 5WB  H1EB  H  HCH3  0   0.257  -2.0978  -2.8798   1.5809
 5WB  HN1F  H  HNH2  0   0.397  -6.5854  -2.7278   1.4362
 5WB  HN1A  H  HNH2  0   0.397  -7.4705  -1.4616   0.6739
 5WB  HN1G  H  HNH2  0   0.400  -5.3654   2.0970  -1.1718
 5WB  HN1B  H  HNH2  0   0.404  -3.6475   2.2428  -1.1420
 5WB  H1J   H  HCR6  0   0.281   2.3320   1.5141  -2.4551
 5WB  H1K   H  HCR6  0   0.275   0.9039   0.3106   1.3803
 5WB  H1Z   H  HCH1  0   0.255   0.3451   2.3390  -1.7109
 5WB  O1N   O  O2    0  -0.464   4.5026  -0.1202  -2.3671
 5WB  C1D   C  CH3   0  -0.409  -0.3661   4.0491   0.0964
 5WB  O1O   O  O2    0  -0.462   2.9519  -1.4248   1.8055
 5WB  O1P   O  O2    0  -0.480   4.7186  -1.6069  -0.1763

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
 5WB  C6   N1    aromatic  1.324  0.020  1.324
 5WB  N1   C2    aromatic  1.341  0.020  1.341
 5WB  C2   N1F   single    1.343  0.020  1.343
 5WB  C2   N3    aromatic  1.331  0.020  1.331
 5WB  C4   N3    aromatic  1.328  0.020  1.328
 5WB  C5   C4    aromatic  1.420  0.020  1.420
 5WB  C4   N1G   single    1.337  0.020  1.337
 5WB  C6   C5    aromatic  1.396  0.020  1.396
 5WB  C1H  C5    single    1.412  0.020  1.412
 5WB  C1E  C6    single    1.495  0.020  1.495
 5WB  O1N  C1A   single    1.414  0.020  1.414
 5WB  C1A  H1A   single    0.970  0.020  1.090
 5WB  C1A  H1AA  single    0.970  0.020  1.090
 5WB  C1A  H1AB  single    0.970  0.020  1.090
 5WB  O1O  C1B   single    1.413  0.020  1.413
 5WB  C1B  H1B   single    0.970  0.020  1.090
 5WB  C1B  H1BA  single    0.970  0.020  1.090
 5WB  C1B  H1BB  single    0.970  0.020  1.090
 5WB  O1P  C1C   single    1.422  0.020  1.422
 5WB  C1C  H1C   single    0.970  0.020  1.090
 5WB  C1C  H1CA  single    0.970  0.020  1.090
 5WB  C1C  H1CB  single    0.970  0.020  1.090
 5WB  C1D  O1Q   single    1.410  0.020  1.410
 5WB  C1D  H1D   single    0.970  0.020  1.090
 5WB  C1D  H1DA  single    0.970  0.020  1.090
 5WB  C1D  H1DB  single    0.970  0.020  1.090
 5WB  C1E  H1E   single    0.970  0.020  1.090
 5WB  C1E  H1EA  single    0.970  0.020  1.090
 5WB  C1E  H1EB  single    0.970  0.020  1.090
 5WB  N1F  HN1F  single    0.860  0.020  1.020
 5WB  N1F  HN1A  single    0.860  0.020  1.020
 5WB  N1G  HN1G  single    0.860  0.020  1.020
 5WB  N1G  HN1B  single    0.860  0.020  1.020
 5WB  C1I  C1H   triple    1.208  0.020  1.208
 5WB  C1Z  C1I   single    1.466  0.020  1.466
 5WB  C1W  C1J   aromatic  1.396  0.020  1.396
 5WB  C1J  C1U   aromatic  1.385  0.020  1.385
 5WB  C1J  H1J   single    0.930  0.020  1.080
 5WB  C1X  C1K   aromatic  1.391  0.020  1.391
 5WB  C1K  C1U   aromatic  1.389  0.020  1.389
 5WB  C1K  H1K   single    0.930  0.020  1.080
 5WB  O1N  C1W   single    1.343  0.020  1.343
 5WB  O1O  C1X   single    1.343  0.020  1.343
 5WB  O1P  C1Y   single    1.358  0.020  1.358
 5WB  O1Q  C1Z   single    1.409  0.020  1.409
 5WB  C1U  C1Z   single    1.512  0.020  1.512
 5WB  C1Y  C1W   aromatic  1.396  0.020  1.396
 5WB  C1Y  C1X   aromatic  1.400  0.020  1.400
 5WB  C1Z  H1Z   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
 5WB  C6    N1   C2    116.69  3.000
 5WB  N1F   C2   N3    117.00  3.000
 5WB  N3    C2   N1    126.48  3.000
 5WB  N1F   C2   N1    116.52  3.000
 5WB  C4    N3   C2    117.07  3.000
 5WB  N1G   C4   C5    120.93  3.000
 5WB  N1G   C4   N3    117.81  3.000
 5WB  C5    C4   N3    121.26  3.000
 5WB  C1H   C5   C6    122.55  3.000
 5WB  C1H   C5   C4    121.16  3.000
 5WB  C6    C5   C4    116.28  3.000
 5WB  C1E   C6   C5    120.39  3.000
 5WB  C1E   C6   N1    117.38  3.000
 5WB  C5    C6   N1    122.22  3.000
 5WB  H1AB  C1A  H1AA  108.80  3.000
 5WB  H1AB  C1A  H1A   108.87  3.000
 5WB  H1AA  C1A  H1A   108.73  3.000
 5WB  H1AB  C1A  O1N   111.92  3.000
 5WB  H1AA  C1A  O1N   106.41  3.000
 5WB  H1A   C1A  O1N   111.98  3.000
 5WB  H1BB  C1B  H1BA  108.79  3.000
 5WB  H1BB  C1B  H1B   108.77  3.000
 5WB  H1BA  C1B  H1B   108.72  3.000
 5WB  H1BB  C1B  O1O   111.86  3.000
 5WB  H1BA  C1B  O1O   112.07  3.000
 5WB  H1B   C1B  O1O   106.52  3.000
 5WB  H1CB  C1C  H1CA  108.78  3.000
 5WB  H1CB  C1C  H1C   108.65  3.000
 5WB  H1CA  C1C  H1C   108.66  3.000
 5WB  H1CB  C1C  O1P   111.78  3.000
 5WB  H1CA  C1C  O1P   111.70  3.000
 5WB  H1C   C1C  O1P   107.18  3.000
 5WB  H1EB  C1E  H1EA  108.22  3.000
 5WB  H1EB  C1E  H1E   109.26  3.000
 5WB  H1EA  C1E  H1E   106.82  3.000
 5WB  H1EB  C1E  C6    110.75  3.000
 5WB  H1EA  C1E  C6    109.93  3.000
 5WB  H1E   C1E  C6    111.72  3.000
 5WB  HN1A  N1F  HN1F  118.08  3.000
 5WB  HN1A  N1F  C2    119.76  3.000
 5WB  HN1F  N1F  C2    119.54  3.000
 5WB  HN1B  N1G  HN1G  118.14  3.000
 5WB  HN1B  N1G  C4    121.22  3.000
 5WB  HN1G  N1G  C4    119.92  3.000
 5WB  C1I   C1H  C5    180.00  3.000
 5WB  C1Z   C1I  C1H   180.00  3.000
 5WB  H1J   C1J  C1W   121.05  3.000
 5WB  H1J   C1J  C1U   119.39  3.000
 5WB  C1W   C1J  C1U   119.56  3.000
 5WB  H1K   C1K  C1X   121.21  3.000
 5WB  H1K   C1K  C1U   119.24  3.000
 5WB  C1X   C1K  C1U   119.55  3.000
 5WB  C1Z   O1Q  C1D   113.52  3.000
 5WB  C1Z   C1U  C1K   119.49  3.000
 5WB  C1Z   C1U  C1J   119.43  3.000
 5WB  C1K   C1U  C1J   121.07  3.000
 5WB  C1Y   C1W  O1N   115.69  3.000
 5WB  C1Y   C1W  C1J   119.92  3.000
 5WB  O1N   C1W  C1J   124.39  3.000
 5WB  C1Y   C1X  O1O   115.56  3.000
 5WB  C1Y   C1X  C1K   119.97  3.000
 5WB  O1O   C1X  C1K   124.47  3.000
 5WB  C1X   C1Y  C1W   119.93  3.000
 5WB  C1X   C1Y  O1P   120.13  3.000
 5WB  C1W   C1Y  O1P   119.94  3.000
 5WB  H1Z   C1Z  C1U   108.65  3.000
 5WB  H1Z   C1Z  O1Q   109.70  3.000
 5WB  C1U   C1Z  O1Q   107.70  3.000
 5WB  H1Z   C1Z  C1I   108.04  3.000
 5WB  C1U   C1Z  C1I   110.44  3.000
 5WB  O1Q   C1Z  C1I   112.26  3.000
 5WB  C1W   O1N  C1A   118.42  3.000
 5WB  H1DB  C1D  H1DA  108.55  3.000
 5WB  H1DB  C1D  H1D   108.22  3.000
 5WB  H1DA  C1D  H1D   108.47  3.000
 5WB  H1DB  C1D  O1Q   111.78  3.000
 5WB  H1DA  C1D  O1Q   107.46  3.000
 5WB  H1D   C1D  O1Q   112.26  3.000
 5WB  C1X   O1O  C1B   118.32  3.000
 5WB  C1Y   O1P  C1C   114.16  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
 5WB  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 5WB  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 5WB  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 5WB  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 5WB  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 5WB  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 5WB  CONST_07  C1X   C1Y  C1W  C1J     0.00   0.0  0
 5WB  CONST_08  C1X   C1K  C1U  C1J     0.00   0.0  0
 5WB  CONST_09  C1W   C1Y  C1X  C1K     0.00   0.0  0
 5WB  CONST_10  C1W   C1J  C1U  C1K     0.00   0.0  0
 5WB  CONST_11  C1Y   C1W  C1J  C1U     0.00   0.0  0
 5WB  CONST_12  C1Y   C1X  C1K  C1U     0.00   0.0  0
 5WB  CONST_13  C1H   C5   C6   N1    180.00   0.0  0
 5WB  CONST_14  C1E   C6   N1   C2    180.00   0.0  0
 5WB  CONST_15  N1G   C4   N3   C2    180.00   0.0  0
 5WB  CONST_16  C1H   C5   C4   N3    180.00   0.0  0
 5WB  CONST_17  N1F   C2   N3   C4    180.00   0.0  0
 5WB  CONST_18  C1E   C6   C5   C4    180.00   0.0  0
 5WB  CONST_19  N1F   C2   N1   C6    180.00   0.0  0
 5WB  CONST_20  N1G   C4   C5   C6    180.00   0.0  0
 5WB  CONST_21  O1P   C1Y  C1W  C1J   180.00   0.0  0
 5WB  CONST_22  O1P   C1Y  C1X  C1K   180.00   0.0  0
 5WB  CONST_23  C1U   C1J  C1W  O1N   180.00   0.0  0
 5WB  CONST_24  C1X   C1Y  C1W  O1N   180.00   0.0  0
 5WB  CONST_25  C1U   C1K  C1X  O1O   180.00   0.0  0
 5WB  CONST_26  C1W   C1Y  C1X  O1O   180.00   0.0  0
 5WB  CONST_27  C1Z   C1U  C1J  C1W   180.00   0.0  0
 5WB  CONST_28  C1Z   C1U  C1K  C1X   180.00   0.0  0
 5WB  CONST_29  H1K   C1K  C1U  C1J   180.00   0.0  0
 5WB  CONST_30  H1J   C1J  C1U  C1K   180.00   0.0  0
 5WB  CONST_31  HN1F  N1F  C2   N1      0.00   0.0  0
 5WB  CONST_32  HN1A  N1F  C2   N1    180.00   0.0  0
 5WB  CONST_33  HN1G  N1G  C4   N3      0.00   0.0  0
 5WB  CONST_34  HN1B  N1G  C4   N3    180.00   0.0  0
 5WB  Var_01    C1J   C1W  O1N  C1A    -1.81  30.0  2
 5WB  Var_02    C1K   C1X  O1O  C1B     2.84  30.0  2
 5WB  Var_03    C1W   C1Y  O1P  C1C    91.42  30.0  2
 5WB  Var_04    H1E   C1E  C6   N1    135.07  30.0  2
 5WB  Var_05    H1A   C1A  O1N  C1W    63.36  30.0  3
 5WB  Var_06    H1B   C1B  O1O  C1X   177.96  30.0  3
 5WB  Var_07    H1C   C1C  O1P  C1Y  -177.74  30.0  3
 5WB  Var_08    H1D   C1D  O1Q  C1Z    66.30  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
 5WB  chir_01  C1Z  C1I  O1Q  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
 5WB  plan-1  N1    0.020
 5WB  plan-1  C2    0.020
 5WB  plan-1  N3    0.020
 5WB  plan-1  C4    0.020
 5WB  plan-1  C5    0.020
 5WB  plan-1  C6    0.020
 5WB  plan-1  C1E   0.020
 5WB  plan-1  N1F   0.020
 5WB  plan-1  N1G   0.020
 5WB  plan-1  C1H   0.020
 5WB  plan-1  C1I   0.020
 5WB  plan-2  C1J   0.020
 5WB  plan-2  C1K   0.020
 5WB  plan-2  C1U   0.020
 5WB  plan-2  C1W   0.020
 5WB  plan-2  C1X   0.020
 5WB  plan-2  C1Y   0.020
 5WB  plan-2  C1Z   0.020
 5WB  plan-2  H1J   0.020
 5WB  plan-2  H1K   0.020
 5WB  plan-2  O1N   0.020
 5WB  plan-2  O1O   0.020
 5WB  plan-2  O1P   0.020
 5WB  plan-3  C2    0.020
 5WB  plan-3  N1F   0.020
 5WB  plan-3  HN1F  0.020
 5WB  plan-3  HN1A  0.020
 5WB  plan-4  C4    0.020
 5WB  plan-4  N1G   0.020
 5WB  plan-4  HN1G  0.020
 5WB  plan-4  HN1B  0.020

