# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:58:29 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: trans-4-{[2-(butylamino)-5-(pyridin-2-yl)pyrimidin-4-yl]amino}cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNc1ncc(c(N[C@@H]2CC[C@@H](O)CC2)n1)c3ccccn3
#
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
 24K  24K  trans-4-{[2-(butylamino)-5-(pyridin-2-yl)pyrimidin-4-yl]amino}cyclohexanol  ligand  52  25  .  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_24K
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
 24K  C01   C  CH3   0  -0.662   7.9257  -1.2194  -0.0377
 24K  C02   C  CH2   0  -0.422   6.8479  -0.1454  -0.0508
 24K  C03   C  CH2   0  -0.465   5.4425  -0.7226   0.0636
 24K  C04   C  CH2   0  -0.227   4.3816   0.3651   0.0433
 24K  N05   N  NH1   0  -0.659   3.0595  -0.2083   0.1499
 24K  C06   C  CR6   0   0.592   1.9232   0.5042   0.1055
 24K  N07   N  N     0  -0.496   2.0339   1.8294  -0.0497
 24K  C08   C  CR16  0  -0.070   0.8874   2.4903  -0.0700
 24K  C09   C  CR6   0  -0.168  -0.3719   1.9276   0.0514
 24K  C10   C  CR6   0   0.537  -0.3641   0.4960   0.1707
 24K  N11   N  NH1   0  -0.686  -1.4982  -0.2037   0.2725
 24K  C12   C  CH1   0  -0.042  -1.5674  -1.6468   0.3474
 24K  C13   C  CH2   0  -0.443  -1.4155  -2.2999  -1.0276
 24K  C14   C  CH2   0  -0.466  -1.5505  -3.8161  -0.9443
 24K  C15   C  CH1   0   0.086  -2.8777  -4.2104  -0.3173
 24K  O16   O  OH1   0  -0.679  -2.9342  -5.6212  -0.2561
 24K  C17   C  CH2   0  -0.478  -3.0254  -3.5703   1.0593
 24K  C18   C  CH2   0  -0.459  -2.8900  -2.0531   0.9908
 24K  N19   N  N     0  -0.525   0.7829  -0.1766   0.2053
 24K  C20   C  CR6   0   0.311  -1.5794   2.7616   0.0458
 24K  C21   C  CR16  0  -0.355  -1.5220   4.1459   0.2693
 24K  C22   C  CR16  0  -0.146  -2.6824   4.8916   0.2201
 24K  C23   C  CR16  0  -0.345  -3.8937   4.2582  -0.0307
 24K  C24   C  CR16  0  -0.051  -3.8696   2.8882  -0.2104
 24K  N25   N  N     0  -0.504  -2.7560   2.1663  -0.1768
 24K  H013  H  HCH3  0   0.229   8.9225  -0.7837  -0.1104
 24K  H012  H  HCH3  0   0.218   7.8879  -1.8053   0.8823
 24K  H011  H  HCH3  0   0.219   7.8047  -1.9099  -0.8739
 24K  H021  H  HCH2  0   0.218   7.0177   0.5573   0.7703
 24K  H022  H  HCH2  0   0.218   6.9237   0.4406  -0.9717
 24K  H032  H  HCH2  0   0.226   5.2666  -1.4224  -0.7601
 24K  H031  H  HCH2  0   0.226   5.3596  -1.3020   0.9893
 24K  H042  H  HCH2  0   0.222   4.5568   1.0672   0.8643
 24K  H041  H  HCH2  0   0.223   4.4660   0.9442  -0.8810
 24K  H051  H  HNH1  0   0.390   2.9661  -1.2053   0.2521
 24K  H081  H  HCR6  0   0.253   0.9847   3.5617  -0.2111
 24K  H111  H  HNH1  0   0.406  -2.3473   0.3288   0.1054
 24K  H121  H  HCH1  0   0.231  -0.7495  -1.9937   0.9851
 24K  H131  H  HCH2  0   0.215  -2.1798  -1.8926  -1.6983
 24K  H132  H  HCH2  0   0.244  -0.4464  -2.0327  -1.4528
 24K  H142  H  HCH2  0   0.238  -1.4608  -4.2517  -1.9426
 24K  H141  H  HCH2  0   0.218  -0.7312  -4.2265  -0.3430
 24K  H151  H  HCH1  0   0.185  -3.6841  -3.8224  -0.9602
 24K  H161  H  HOH1  0   0.446  -3.7853  -5.8729   0.1158
 24K  H172  H  HCH2  0   0.237  -3.9965  -3.8315   1.4906
 24K  H171  H  HCH2  0   0.220  -2.2607  -3.9816   1.7273
 24K  H181  H  HCH2  0   0.245  -2.9644  -1.6274   1.9938
 24K  H182  H  HCH2  0   0.221  -3.7208  -1.6367   0.4088
 24K  H211  H  HCR6  0   0.267  -0.5874   4.6385   0.4966
 24K  H221  H  HCR6  0   0.274  -2.6440   5.9600   0.3874
 24K  H231  H  HCR6  0   0.270  -4.8247   4.8055  -0.0719
 24K  H241  H  HCR6  0   0.264  -4.7866   2.3399  -0.3935

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
 24K  C01  C02   single    1.522  0.020  1.522
 24K  C02  C03   single    1.524  0.020  1.524
 24K  C03  C04   single    1.520  0.020  1.520
 24K  C04  N05   single    1.445  0.020  1.445
 24K  C14  C13   single    1.524  0.020  1.524
 24K  C14  C15   single    1.520  0.020  1.520
 24K  N05  C06   single    1.342  0.020  1.342
 24K  O16  C15   single    1.413  0.020  1.413
 24K  C13  C12   single    1.530  0.020  1.530
 24K  C15  C17   single    1.525  0.020  1.525
 24K  C06  N19   aromatic  1.332  0.020  1.332
 24K  C06  N07   aromatic  1.339  0.020  1.339
 24K  N19  C10   aromatic  1.330  0.020  1.330
 24K  C12  N11   single    1.447  0.020  1.447
 24K  C12  C18   single    1.526  0.020  1.526
 24K  N07  C08   aromatic  1.324  0.020  1.324
 24K  C17  C18   single    1.525  0.020  1.525
 24K  C10  N11   single    1.337  0.020  1.337
 24K  C10  C09   aromatic  1.437  0.020  1.437
 24K  C08  C09   aromatic  1.385  0.020  1.385
 24K  C09  C20   single    1.468  0.020  1.468
 24K  C20  C21   aromatic  1.403  0.020  1.403
 24K  C20  N25   aromatic  1.337  0.020  1.337
 24K  C21  C22   aromatic  1.380  0.020  1.380
 24K  N25  C24   aromatic  1.328  0.020  1.328
 24K  C22  C23   aromatic  1.390  0.020  1.390
 24K  C24  C23   aromatic  1.382  0.020  1.382
 24K  C01  H013  single    0.970  0.020  1.090
 24K  C01  H012  single    0.970  0.020  1.090
 24K  C01  H011  single    0.970  0.020  1.090
 24K  C02  H021  single    0.970  0.020  1.090
 24K  C02  H022  single    0.970  0.020  1.090
 24K  C03  H032  single    0.970  0.020  1.090
 24K  C03  H031  single    0.970  0.020  1.090
 24K  C04  H042  single    0.970  0.020  1.090
 24K  C04  H041  single    0.970  0.020  1.090
 24K  N05  H051  single    0.860  0.020  1.020
 24K  C08  H081  single    0.930  0.020  1.080
 24K  N11  H111  single    0.860  0.020  1.020
 24K  C12  H121  single    0.970  0.020  1.090
 24K  C13  H131  single    0.970  0.020  1.090
 24K  C13  H132  single    0.970  0.020  1.090
 24K  C14  H142  single    0.970  0.020  1.090
 24K  C14  H141  single    0.970  0.020  1.090
 24K  C15  H151  single    0.970  0.020  1.090
 24K  O16  H161  single    0.850  0.020  0.980
 24K  C17  H172  single    0.970  0.020  1.090
 24K  C17  H171  single    0.970  0.020  1.090
 24K  C18  H181  single    0.970  0.020  1.090
 24K  C18  H182  single    0.970  0.020  1.090
 24K  C21  H211  single    0.930  0.020  1.080
 24K  C22  H221  single    0.930  0.020  1.080
 24K  C23  H231  single    0.930  0.020  1.080
 24K  C24  H241  single    0.930  0.020  1.080

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
 24K  H011  C01  H012  107.61  3.000
 24K  H011  C01  H013  107.65  3.000
 24K  H012  C01  H013  107.60  3.000
 24K  H011  C01  C02   111.19  3.000
 24K  H012  C01  C02   111.20  3.000
 24K  H013  C01  C02   111.40  3.000
 24K  H022  C02  H021  106.08  3.000
 24K  H022  C02  C03   109.27  3.000
 24K  H021  C02  C03   109.28  3.000
 24K  H022  C02  C01   109.64  3.000
 24K  H021  C02  C01   109.69  3.000
 24K  C03   C02  C01   112.67  3.000
 24K  H031  C03  H032  106.59  3.000
 24K  H031  C03  C04   109.70  3.000
 24K  H032  C03  C04   109.59  3.000
 24K  H031  C03  C02   109.49  3.000
 24K  H032  C03  C02   109.50  3.000
 24K  C04   C03  C02   111.83  3.000
 24K  H041  C04  H042  106.38  3.000
 24K  H041  C04  N05   110.06  3.000
 24K  H042  C04  N05   110.22  3.000
 24K  H041  C04  C03   109.65  3.000
 24K  H042  C04  C03   109.72  3.000
 24K  N05   C04  C03   110.72  3.000
 24K  H051  N05  C06   116.79  3.000
 24K  H051  N05  C04   119.04  3.000
 24K  C06   N05  C04   124.16  3.000
 24K  N19   C06  N07   125.83  3.000
 24K  N07   C06  N05   117.35  3.000
 24K  N19   C06  N05   116.82  3.000
 24K  C08   N07  C06   115.11  3.000
 24K  H081  C08  C09   119.62  3.000
 24K  H081  C08  N07   114.67  3.000
 24K  C09   C08  N07   125.70  3.000
 24K  C20   C09  C10   124.83  3.000
 24K  C20   C09  C08   121.13  3.000
 24K  C10   C09  C08   114.04  3.000
 24K  N19   C10  N11   117.72  3.000
 24K  N11   C10  C09   121.56  3.000
 24K  N19   C10  C09   120.71  3.000
 24K  H111  N11  C12   119.43  3.000
 24K  H111  N11  C10   114.98  3.000
 24K  C12   N11  C10   124.52  3.000
 24K  H121  C12  C18   108.54  3.000
 24K  H121  C12  C13   108.33  3.000
 24K  C18   C12  C13   110.57  3.000
 24K  H121  C12  N11   108.11  3.000
 24K  C18   C12  N11   109.20  3.000
 24K  C13   C12  N11   112.00  3.000
 24K  H132  C13  H131  106.85  3.000
 24K  H132  C13  C14   110.08  3.000
 24K  H131  C13  C14   109.97  3.000
 24K  H132  C13  C12   109.50  3.000
 24K  H131  C13  C12   108.80  3.000
 24K  C14   C13  C12   111.51  3.000
 24K  H141  C14  H142  106.89  3.000
 24K  H141  C14  C15   109.23  3.000
 24K  H142  C14  C15   110.19  3.000
 24K  H141  C14  C13   109.64  3.000
 24K  H142  C14  C13   109.83  3.000
 24K  C15   C14  C13   110.97  3.000
 24K  H151  C15  C17   107.93  3.000
 24K  H151  C15  O16   110.33  3.000
 24K  C17   C15  O16   112.09  3.000
 24K  H151  C15  C14   107.88  3.000
 24K  C17   C15  C14   110.37  3.000
 24K  O16   C15  C14   108.17  3.000
 24K  H161  O16  C15   108.25  3.000
 24K  H171  C17  H172  106.83  3.000
 24K  H171  C17  C18   109.81  3.000
 24K  H172  C17  C18   109.51  3.000
 24K  H171  C17  C15   108.98  3.000
 24K  H172  C17  C15   109.97  3.000
 24K  C18   C17  C15   111.62  3.000
 24K  H182  C18  H181  106.72  3.000
 24K  H182  C18  C17   109.54  3.000
 24K  H181  C18  C17   109.91  3.000
 24K  H182  C18  C12   109.38  3.000
 24K  H181  C18  C12   110.03  3.000
 24K  C17   C18  C12   111.15  3.000
 24K  C10   N19  C06   118.55  3.000
 24K  N25   C20  C21   120.11  3.000
 24K  N25   C20  C09   118.14  3.000
 24K  C21   C20  C09   121.76  3.000
 24K  H211  C21  C22   119.23  3.000
 24K  H211  C21  C20   121.23  3.000
 24K  C22   C21  C20   119.53  3.000
 24K  H221  C22  C23   120.59  3.000
 24K  H221  C22  C21   119.87  3.000
 24K  C23   C22  C21   119.54  3.000
 24K  H231  C23  C24   120.80  3.000
 24K  H231  C23  C22   121.80  3.000
 24K  C24   C23  C22   117.39  3.000
 24K  H241  C24  N25   116.03  3.000
 24K  H241  C24  C23   120.58  3.000
 24K  N25   C24  C23   123.40  3.000
 24K  C24   N25  C20   120.01  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
 24K  CONST_01  C09   C10  N19  C06     0.00   0.0  0
 24K  CONST_02  C09   C08  N07  C06     0.00   0.0  0
 24K  CONST_03  C10   N19  C06  N07     0.00   0.0  0
 24K  CONST_04  C10   C09  C08  N07     0.00   0.0  0
 24K  CONST_05  C20   C09  C08  N07   180.00   0.0  0
 24K  CONST_06  N19   C06  N07  C08     0.00   0.0  0
 24K  CONST_07  N19   C10  C09  C08     0.00   0.0  0
 24K  CONST_10  C22   C21  C20  C09   180.00   0.0  0
 24K  CONST_11  C24   N25  C20  C09   180.00   0.0  0
 24K  CONST_14  C20   C09  C10  N19   180.00   0.0  0
 24K  CONST_15  C23   C22  C21  C20     0.00   0.0  0
 24K  CONST_16  C23   C24  N25  C20     0.00   0.0  0
 24K  CONST_17  C24   N25  C20  C21     0.00   0.0  0
 24K  CONST_18  C24   C23  C22  C21     0.00   0.0  0
 24K  CONST_19  N25   C20  C21  C22     0.00   0.0  0
 24K  CONST_20  N25   C24  C23  C22     0.00   0.0  0
 24K  CONST_21  C10   N19  C06  N05   180.00   0.0  0
 24K  CONST_22  C08   N07  C06  N05   180.00   0.0  0
 24K  CONST_23  N11   C10  N19  C06   180.00   0.0  0
 24K  CONST_24  N11   C10  C09  C08   180.00   0.0  0
 24K  CONST_25  C20   C09  C10  N11     0.00   0.0  0
 24K  CONST_26  C12   N11  C10  C09   180.00   0.0  0
 24K  CONST_27  N19   C10  N11  C12     0.00   0.0  0
 24K  CONST_28  H081  C08  N07  C06   180.00   0.0  0
 24K  CONST_29  H211  C21  C20  C09     0.00   0.0  0
 24K  CONST_30  H221  C22  C21  C20   180.00   0.0  0
 24K  CONST_31  H241  C24  N25  C20   180.00   0.0  0
 24K  CONST_32  H231  C23  C22  C21   180.00   0.0  0
 24K  CONST_33  N19   C06  N05  C04   180.00   0.0  0
 24K  CONST_34  N07   C06  N05  C04     0.00   0.0  0
 24K  CONST_35  H051  N05  C06  N07   180.00   0.0  0
 24K  CONST_36  H111  N11  C10  C09     0.00   0.0  0
 24K  Var_01    C15   C14  C13  C12    56.62  30.0  1
 24K  Var_02    C15   C17  C18  C12   -55.93  30.0  1
 24K  Var_03    C06   N05  C04  C03  -177.24  30.0  3
 24K  Var_04    C04   C03  C02  C01  -179.78  30.0  3
 24K  Var_05    N05   C04  C03  C02   179.87  30.0  3
 24K  Var_06    H013  C01  C02  C03  -179.43  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
 24K  chir_01  C12  C13  N11  C18  negativ
 24K  chir_02  C15  O16  C17  C14  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
 24K  plan-1  N05   0.020
 24K  plan-1  C06   0.020
 24K  plan-1  N07   0.020
 24K  plan-1  C08   0.020
 24K  plan-1  C09   0.020
 24K  plan-1  C10   0.020
 24K  plan-1  N11   0.020
 24K  plan-1  N19   0.020
 24K  plan-1  C20   0.020
 24K  plan-1  H081  0.020
 24K  plan-2  C09   0.020
 24K  plan-2  C20   0.020
 24K  plan-2  C21   0.020
 24K  plan-2  C22   0.020
 24K  plan-2  C23   0.020
 24K  plan-2  C24   0.020
 24K  plan-2  N25   0.020
 24K  plan-2  H211  0.020
 24K  plan-2  H221  0.020
 24K  plan-2  H231  0.020
 24K  plan-2  H241  0.020
 24K  plan-3  C04   0.020
 24K  plan-3  N05   0.020
 24K  plan-3  C06   0.020
 24K  plan-3  H051  0.020
 24K  plan-4  C10   0.020
 24K  plan-4  N11   0.020
 24K  plan-4  C12   0.020
 24K  plan-4  H111  0.020

