# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:32:00 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 6-ethyl-5-[3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(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
 EKB  EKB  6-ethyl-5-[3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]pyrimidine-2,4-diamine  ligand  47  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EKB
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
 EKB  N1    N  N     0  -0.507  -3.9495   1.2492  -1.5622
 EKB  C2    C  CR6   0   0.542  -5.1272   0.8154  -1.1135
 EKB  N3    N  N     0  -0.501  -5.3324   0.0478  -0.0358
 EKB  C4    C  CR6   0   0.271  -4.2568  -0.3174   0.6502
 EKB  C5    C  CR6   0  -0.320  -2.9708   0.0723   0.2831
 EKB  C6    C  CR6   0   0.468  -2.8717   0.8863  -0.8776
 EKB  C1A   C  CH3   0  -0.666  -4.3162  -2.6880   1.4375
 EKB  C1B   C  CH3   0  -0.438   3.5604   3.1529   1.6379
 EKB  C1C   C  CH3   0  -0.438   3.0103  -3.1025  -1.7846
 EKB  C1D   C  CH3   0  -0.408   6.0311   0.1887  -0.8508
 EKB  N1E   N  NH2   0  -0.822  -6.2142   1.1871  -1.8062
 EKB  N1F   N  NH2   0  -0.824  -1.6807   1.3037  -1.3215
 EKB  C1G   C  CSP   0   0.028  -0.7675  -0.6011   1.5369
 EKB  C1H   C  CSP   0   0.147  -1.8032  -0.3099   0.9880
 EKB  C1I   C  CR16  0  -0.459   2.2638   0.6743   1.4256
 EKB  C1J   C  CR16  0  -0.456   2.0817  -1.4380   0.2744
 EKB  C1K   C  CH2   0  -0.521  -4.4780  -1.2184   1.8274
 EKB  C1L   C  CH2   0  -0.684   0.5030  -0.9525   2.1609
 EKB  O1O   O  O2    0  -0.464   3.9593   2.2208   0.6524
 EKB  O1P   O  O2    0  -0.463   3.6075  -1.8403  -1.5625
 EKB  O1Q   O  O2    0  -0.482   4.7267   0.5586  -1.2770
 EKB  C1S   C  CR6   0   0.133   1.6606  -0.5650   1.2676
 EKB  C1V   C  CR6   0   0.342   3.3069   1.0480   0.5795
 EKB  C1W   C  CR6   0   0.342   3.1225  -1.0683  -0.5749
 EKB  C1Y   C  CR6   0   0.163   3.7323   0.1811  -0.4298
 EKB  H1A   H  HCH3  0   0.238  -4.5157  -3.3335   2.2927
 EKB  H1AA  H  HCH3  0   0.229  -5.0097  -2.9618   0.6422
 EKB  H1AB  H  HCH3  0   0.231  -3.3041  -2.8958   1.0900
 EKB  H1B   H  HCH3  0   0.229   2.5206   3.4652   1.5099
 EKB  H1BA  H  HCH3  0   0.229   3.6883   2.7594   2.6497
 EKB  H1BB  H  HCH3  0   0.261   4.2031   4.0213   1.5169
 EKB  H1C   H  HCH3  0   0.229   1.9565  -3.0122  -2.0600
 EKB  H1CA  H  HCH3  0   0.261   3.5508  -3.5569  -2.6110
 EKB  H1CB  H  HCH3  0   0.229   3.0908  -3.7543  -0.9111
 EKB  H1D   H  HCH3  0   0.220   6.2945   0.6564   0.1011
 EKB  H1DA  H  HCH3  0   0.221   6.1341  -0.8944  -0.7505
 EKB  H1DB  H  HCH3  0   0.236   6.7284   0.5356  -1.6118
 EKB  HN1E  H  HNH2  0   0.397  -6.1256   1.7517  -2.6314
 EKB  HN1A  H  HNH2  0   0.397  -7.1273   0.8825  -1.5213
 EKB  HN1F  H  HNH2  0   0.400  -0.8378   1.1133  -0.8085
 EKB  HN1B  H  HNH2  0   0.398  -1.6271   1.9183  -2.1147
 EKB  H1I   H  HCR6  0   0.276   1.9131   1.3348   2.2075
 EKB  H1J   H  HCR6  0   0.276   1.5959  -2.3996   0.1755
 EKB  H1K   H  HCH2  0   0.244  -3.7729  -0.9738   2.6238
 EKB  H1KA  H  HCH2  0   0.249  -5.4843  -1.0485   2.2116
 EKB  H1L   H  HCH2  0   0.283   0.5941  -0.4546   3.1297
 EKB  H1LA  H  HCH2  0   0.286   0.5268  -2.0269   2.3615

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
 EKB  C2   N1    aromatic  1.333  0.020  1.333
 EKB  C6   N1    aromatic  1.327  0.020  1.327
 EKB  N3   C2    aromatic  1.339  0.020  1.339
 EKB  C2   N1E   single    1.341  0.020  1.341
 EKB  C4   N3    aromatic  1.327  0.020  1.327
 EKB  C1K  C4    single    1.499  0.020  1.499
 EKB  C4   C5    aromatic  1.393  0.020  1.393
 EKB  C1H  C5    single    1.416  0.020  1.416
 EKB  C5   C6    aromatic  1.421  0.020  1.421
 EKB  C6   N1F   single    1.338  0.020  1.338
 EKB  C1A  C1K   single    1.529  0.020  1.529
 EKB  C1A  H1A   single    0.970  0.020  1.090
 EKB  C1A  H1AA  single    0.970  0.020  1.090
 EKB  C1A  H1AB  single    0.970  0.020  1.090
 EKB  O1O  C1B   single    1.414  0.020  1.414
 EKB  C1B  H1B   single    0.970  0.020  1.090
 EKB  C1B  H1BA  single    0.970  0.020  1.090
 EKB  C1B  H1BB  single    0.970  0.020  1.090
 EKB  O1P  C1C   single    1.414  0.020  1.414
 EKB  C1C  H1C   single    0.970  0.020  1.090
 EKB  C1C  H1CA  single    0.970  0.020  1.090
 EKB  C1C  H1CB  single    0.970  0.020  1.090
 EKB  C1D  O1Q   single    1.421  0.020  1.421
 EKB  C1D  H1D   single    0.970  0.020  1.090
 EKB  C1D  H1DA  single    0.970  0.020  1.090
 EKB  C1D  H1DB  single    0.970  0.020  1.090
 EKB  N1E  HN1E  single    0.860  0.020  1.020
 EKB  N1E  HN1A  single    0.860  0.020  1.020
 EKB  N1F  HN1F  single    0.860  0.020  1.020
 EKB  N1F  HN1B  single    0.860  0.020  1.020
 EKB  C1L  C1G   single    1.458  0.020  1.458
 EKB  C1G  C1H   triple    1.208  0.020  1.208
 EKB  C1V  C1I   aromatic  1.394  0.020  1.394
 EKB  C1I  C1S   aromatic  1.387  0.020  1.387
 EKB  C1I  H1I   single    0.930  0.020  1.080
 EKB  C1W  C1J   aromatic  1.393  0.020  1.393
 EKB  C1J  C1S   aromatic  1.388  0.020  1.388
 EKB  C1J  H1J   single    0.930  0.020  1.080
 EKB  C1K  H1K   single    0.970  0.020  1.090
 EKB  C1K  H1KA  single    0.970  0.020  1.090
 EKB  C1S  C1L   single    1.513  0.020  1.513
 EKB  C1L  H1L   single    0.970  0.020  1.090
 EKB  C1L  H1LA  single    0.970  0.020  1.090
 EKB  O1O  C1V   single    1.344  0.020  1.344
 EKB  O1P  C1W   single    1.344  0.020  1.344
 EKB  O1Q  C1Y   single    1.360  0.020  1.360
 EKB  C1Y  C1V   aromatic  1.397  0.020  1.397
 EKB  C1Y  C1W   aromatic  1.398  0.020  1.398

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
 EKB  C6    N1   C2    117.05  3.000
 EKB  N1E   C2   N3    116.76  3.000
 EKB  N1E   C2   N1    116.87  3.000
 EKB  N3    C2   N1    126.37  3.000
 EKB  C4    N3   C2    116.72  3.000
 EKB  C1K   C4   C5    120.76  3.000
 EKB  C5    C4   N3    122.35  3.000
 EKB  C1K   C4   N3    116.86  3.000
 EKB  C1H   C5   C6    120.24  3.000
 EKB  C6    C5   C4    116.09  3.000
 EKB  C1H   C5   C4    123.66  3.000
 EKB  N1F   C6   C5    120.78  3.000
 EKB  N1F   C6   N1    117.80  3.000
 EKB  C5    C6   N1    121.41  3.000
 EKB  H1AB  C1A  H1AA  108.07  3.000
 EKB  H1AB  C1A  H1A   107.89  3.000
 EKB  H1AA  C1A  H1A   107.90  3.000
 EKB  H1AB  C1A  C1K   111.27  3.000
 EKB  H1AA  C1A  C1K   111.10  3.000
 EKB  H1A   C1A  C1K   110.48  3.000
 EKB  H1BB  C1B  H1BA  108.74  3.000
 EKB  H1BB  C1B  H1B   108.73  3.000
 EKB  H1BA  C1B  H1B   108.81  3.000
 EKB  H1BB  C1B  O1O   106.40  3.000
 EKB  H1BA  C1B  O1O   112.01  3.000
 EKB  H1B   C1B  O1O   112.03  3.000
 EKB  H1CB  C1C  H1CA  108.77  3.000
 EKB  H1CB  C1C  H1C   108.77  3.000
 EKB  H1CA  C1C  H1C   108.80  3.000
 EKB  H1CB  C1C  O1P   112.07  3.000
 EKB  H1CA  C1C  O1P   106.41  3.000
 EKB  H1C   C1C  O1P   111.90  3.000
 EKB  H1DB  C1D  H1DA  108.63  3.000
 EKB  H1DB  C1D  H1D   108.55  3.000
 EKB  H1DA  C1D  H1D   108.76  3.000
 EKB  H1DB  C1D  O1Q   107.18  3.000
 EKB  H1DA  C1D  O1Q   111.84  3.000
 EKB  H1D   C1D  O1Q   111.78  3.000
 EKB  HN1A  N1E  HN1E  118.97  3.000
 EKB  HN1A  N1E  C2    120.42  3.000
 EKB  HN1E  N1E  C2    120.58  3.000
 EKB  HN1B  N1F  HN1F  118.30  3.000
 EKB  HN1B  N1F  C6    120.01  3.000
 EKB  HN1F  N1F  C6    121.21  3.000
 EKB  C1L   C1G  C1H   180.00  3.000
 EKB  C1G   C1H  C5    180.00  3.000
 EKB  H1I   C1I  C1V   121.16  3.000
 EKB  H1I   C1I  C1S   119.12  3.000
 EKB  C1V   C1I  C1S   119.71  3.000
 EKB  H1J   C1J  C1W   121.03  3.000
 EKB  H1J   C1J  C1S   119.23  3.000
 EKB  C1W   C1J  C1S   119.74  3.000
 EKB  H1KA  C1K  H1K   107.70  3.000
 EKB  H1KA  C1K  C1A   109.71  3.000
 EKB  H1K   C1K  C1A   109.45  3.000
 EKB  H1KA  C1K  C4    108.62  3.000
 EKB  H1K   C1K  C4    110.07  3.000
 EKB  C1A   C1K  C4    111.22  3.000
 EKB  H1LA  C1L  H1L   106.45  3.000
 EKB  H1LA  C1L  C1S   110.09  3.000
 EKB  H1L   C1L  C1S   110.05  3.000
 EKB  H1LA  C1L  C1G   109.53  3.000
 EKB  H1L   C1L  C1G   110.00  3.000
 EKB  C1S   C1L  C1G   110.63  3.000
 EKB  C1V   O1O  C1B   118.43  3.000
 EKB  C1W   O1P  C1C   118.41  3.000
 EKB  C1Y   O1Q  C1D   114.34  3.000
 EKB  C1L   C1S  C1J   119.58  3.000
 EKB  C1L   C1S  C1I   119.63  3.000
 EKB  C1J   C1S  C1I   120.76  3.000
 EKB  C1Y   C1V  O1O   115.65  3.000
 EKB  C1Y   C1V  C1I   120.00  3.000
 EKB  O1O   C1V  C1I   124.35  3.000
 EKB  C1Y   C1W  O1P   115.61  3.000
 EKB  C1Y   C1W  C1J   119.98  3.000
 EKB  O1P   C1W  C1J   124.41  3.000
 EKB  C1W   C1Y  C1V   119.79  3.000
 EKB  C1W   C1Y  O1Q   120.16  3.000
 EKB  C1V   C1Y  O1Q   120.04  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
 EKB  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 EKB  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 EKB  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 EKB  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 EKB  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 EKB  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 EKB  CONST_07  C1W   C1Y  C1V  C1I     0.00   0.0  0
 EKB  CONST_08  C1W   C1J  C1S  C1I     0.00   0.0  0
 EKB  CONST_09  C1V   C1Y  C1W  C1J     0.00   0.0  0
 EKB  CONST_10  C1V   C1I  C1S  C1J     0.00   0.0  0
 EKB  CONST_11  C1Y   C1V  C1I  C1S     0.00   0.0  0
 EKB  CONST_12  C1Y   C1W  C1J  C1S     0.00   0.0  0
 EKB  CONST_13  C1H   C5   C6   N1    180.00   0.0  0
 EKB  CONST_14  N1F   C6   N1   C2    180.00   0.0  0
 EKB  CONST_15  C1K   C4   N3   C2    180.00   0.0  0
 EKB  CONST_16  C1H   C5   C4   N3    180.00   0.0  0
 EKB  CONST_17  N1E   C2   N3   C4    180.00   0.0  0
 EKB  CONST_18  N1F   C6   C5   C4    180.00   0.0  0
 EKB  CONST_19  N1E   C2   N1   C6    180.00   0.0  0
 EKB  CONST_20  C1K   C4   C5   C6    180.00   0.0  0
 EKB  CONST_21  O1Q   C1Y  C1V  C1I   180.00   0.0  0
 EKB  CONST_22  O1Q   C1Y  C1W  C1J   180.00   0.0  0
 EKB  CONST_23  C1V   C1I  C1S  C1L   180.00   0.0  0
 EKB  CONST_24  C1W   C1J  C1S  C1L   180.00   0.0  0
 EKB  CONST_25  C1S   C1I  C1V  O1O   180.00   0.0  0
 EKB  CONST_26  C1W   C1Y  C1V  O1O   180.00   0.0  0
 EKB  CONST_27  C1S   C1J  C1W  O1P   180.00   0.0  0
 EKB  CONST_28  C1V   C1Y  C1W  O1P   180.00   0.0  0
 EKB  CONST_29  H1J   C1J  C1S  C1I   180.00   0.0  0
 EKB  CONST_30  H1I   C1I  C1S  C1J   180.00   0.0  0
 EKB  CONST_31  HN1E  N1E  C2   N1      0.00   0.0  0
 EKB  CONST_32  HN1A  N1E  C2   N1    180.00   0.0  0
 EKB  CONST_33  HN1F  N1F  C6   N1    180.00   0.0  0
 EKB  CONST_34  HN1B  N1F  C6   N1      0.00   0.0  0
 EKB  Var_01    C1A   C1K  C4   N3     93.79  30.0  1
 EKB  Var_02    C1I   C1V  O1O  C1B    -0.80  30.0  2
 EKB  Var_03    C1J   C1W  O1P  C1C     1.50  30.0  2
 EKB  Var_04    C1V   C1Y  O1Q  C1D    91.31  30.0  2
 EKB  Var_05    C1I   C1S  C1L  C1G    92.69  30.0  2
 EKB  Var_06    C1S   C1L  C1G  C1H    21.63  30.0  2
 EKB  Var_07    H1A   C1A  C1K  C4   -177.90  30.0  3
 EKB  Var_08    H1B   C1B  O1O  C1V   -60.83  30.0  3
 EKB  Var_09    H1C   C1C  O1P  C1W    61.63  30.0  3
 EKB  Var_10    H1D   C1D  O1Q  C1Y   -61.75  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
 EKB  plan-1  N1    0.020
 EKB  plan-1  C2    0.020
 EKB  plan-1  N3    0.020
 EKB  plan-1  C4    0.020
 EKB  plan-1  C5    0.020
 EKB  plan-1  C6    0.020
 EKB  plan-1  N1E   0.020
 EKB  plan-1  N1F   0.020
 EKB  plan-1  C1G   0.020
 EKB  plan-1  C1H   0.020
 EKB  plan-1  C1K   0.020
 EKB  plan-2  C1I   0.020
 EKB  plan-2  C1J   0.020
 EKB  plan-2  C1L   0.020
 EKB  plan-2  O1O   0.020
 EKB  plan-2  O1P   0.020
 EKB  plan-2  O1Q   0.020
 EKB  plan-2  C1S   0.020
 EKB  plan-2  C1V   0.020
 EKB  plan-2  C1W   0.020
 EKB  plan-2  C1Y   0.020
 EKB  plan-2  H1I   0.020
 EKB  plan-2  H1J   0.020
 EKB  plan-3  C2    0.020
 EKB  plan-3  N1E   0.020
 EKB  plan-3  HN1E  0.020
 EKB  plan-3  HN1A  0.020
 EKB  plan-4  C6    0.020
 EKB  plan-4  N1F   0.020
 EKB  plan-4  HN1F  0.020
 EKB  plan-4  HN1B  0.020

