# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:50:55 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (1R)-1-[4-(pyrimidin-5-yl)phenyl]ethan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)c1ccc(cc1)c2cncnc2
#
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
 K2V  K2V  (1R)-1-[4-(pyrimidin-5-yl)phenyl]ethan-1-amine  ligand  28  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K2V
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
 K2V  N1   N  N     0  -0.387   4.0249  -1.0202   0.4874
 K2V  C4   C  CR16  0  -0.291  -0.3123   1.0682   0.2320
 K2V  C5   C  CR6   0   0.070   0.4544  -0.0642  -0.0474
 K2V  C6   C  CR16  0  -0.290  -0.2079  -1.2480  -0.3692
 K2V  C7   C  CR16  0  -0.301  -1.5928  -1.2920  -0.4105
 K2V  C8   C  CR6   0  -0.040   1.9226  -0.0085  -0.0123
 K2V  C10  C  CR16  0   0.048   4.5939   0.0905   0.0442
 K2V  N    N  NH2   0  -0.780  -4.5394   0.8750  -0.8185
 K2V  C    C  CH3   0  -0.650  -4.4250  -0.3972   1.2500
 K2V  C1   C  CH1   0  -0.177  -3.8752  -0.2405  -0.1642
 K2V  C11  C  CR16  0  -0.050   2.6399   1.1002  -0.4534
 K2V  C2   C  CR6   0   0.136  -2.3599  -0.1645  -0.1340
 K2V  C3   C  CR16  0  -0.302  -1.6957   1.0171   0.1863
 K2V  C9   C  CR16  0  -0.049   2.7008  -1.0619   0.4606
 K2V  N2   N  N     0  -0.386   3.9635   1.1565  -0.4243
 K2V  H2   H  HCR6  0   0.256   0.3576  -2.1378  -0.6180
 K2V  H3   H  HCR6  0   0.253  -2.0842  -2.2199  -0.6797
 K2V  H4   H  HCR6  0   0.267   5.6772   0.1300   0.0656
 K2V  H5   H  HNH2  0   0.344  -4.4626   1.7158  -0.2589
 K2V  H6   H  HNH2  0   0.348  -4.0947   1.0797  -1.7046
 K2V  H8   H  HCH3  0   0.236  -5.5074  -0.5283   1.2274
 K2V  H9   H  HCH3  0   0.235  -3.9868  -1.2619   1.7477
 K2V  H10  H  HCH3  0   0.222  -4.2026   0.4842   1.8560
 K2V  H11  H  HCH1  0   0.239  -4.1387  -1.1455  -0.7217
 K2V  H12  H  HCR6  0   0.275   2.1246   1.9653  -0.8574
 K2V  H13  H  HCR6  0   0.246  -2.2568   1.9165   0.4096
 K2V  H14  H  HCR6  0   0.275   2.2337  -1.9637   0.8425
 K2V  H1   H  HCR6  0   0.256   0.1726   1.9973   0.5060

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
 K2V  N1   C9   aromatic  1.325  0.020  1.325
 K2V  N1   C10  aromatic  1.324  0.020  1.324
 K2V  C9   C8   aromatic  1.392  0.020  1.392
 K2V  C10  N2   aromatic  1.324  0.020  1.324
 K2V  N2   C11  aromatic  1.325  0.020  1.325
 K2V  C8   C11  aromatic  1.392  0.020  1.392
 K2V  C8   C5   single    1.470  0.020  1.470
 K2V  C5   C6   aromatic  1.394  0.020  1.394
 K2V  C5   C4   aromatic  1.396  0.020  1.396
 K2V  C6   C7   aromatic  1.386  0.020  1.386
 K2V  C4   C3   aromatic  1.385  0.020  1.385
 K2V  C7   C2   aromatic  1.391  0.020  1.391
 K2V  C3   C2   aromatic  1.393  0.020  1.393
 K2V  C2   C1   single    1.517  0.020  1.517
 K2V  C    C1   single    1.525  0.020  1.525
 K2V  C1   N    single    1.454  0.020  1.454
 K2V  C4   H1   single    0.930  0.020  1.080
 K2V  C6   H2   single    0.930  0.020  1.080
 K2V  C7   H3   single    0.930  0.020  1.080
 K2V  C10  H4   single    0.930  0.020  1.080
 K2V  N    H5   single    0.890  0.020  1.040
 K2V  N    H6   single    0.890  0.020  1.040
 K2V  C    H8   single    0.970  0.020  1.090
 K2V  C    H9   single    0.970  0.020  1.090
 K2V  C    H10  single    0.970  0.020  1.090
 K2V  C1   H11  single    0.970  0.020  1.090
 K2V  C11  H12  single    0.930  0.020  1.080
 K2V  C3   H13  single    0.930  0.020  1.080
 K2V  C9   H14  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
 K2V  C9   N1   C10  116.68  3.000
 K2V  H1   C4   C3   119.15  3.000
 K2V  H1   C4   C5   120.04  3.000
 K2V  C3   C4   C5   120.80  3.000
 K2V  C8   C5   C6   120.81  3.000
 K2V  C6   C5   C4   118.31  3.000
 K2V  C8   C5   C4   120.88  3.000
 K2V  H2   C6   C7   119.25  3.000
 K2V  H2   C6   C5   120.17  3.000
 K2V  C7   C6   C5   120.56  3.000
 K2V  H3   C7   C2   119.54  3.000
 K2V  H3   C7   C6   119.18  3.000
 K2V  C2   C7   C6   121.27  3.000
 K2V  C9   C8   C11  114.96  3.000
 K2V  C11  C8   C5   122.50  3.000
 K2V  C9   C8   C5   122.53  3.000
 K2V  H4   C10  N2   116.96  3.000
 K2V  H4   C10  N1   116.95  3.000
 K2V  N2   C10  N1   126.09  3.000
 K2V  H6   N    H5   106.41  3.000
 K2V  H6   N    C1   110.39  3.000
 K2V  H5   N    C1   110.71  3.000
 K2V  H10  C    H9   107.76  3.000
 K2V  H10  C    H8   108.09  3.000
 K2V  H9   C    H8   108.26  3.000
 K2V  H10  C    C1   110.98  3.000
 K2V  H9   C    C1   111.10  3.000
 K2V  H8   C    C1   110.54  3.000
 K2V  H11  C1   C2   106.96  3.000
 K2V  H11  C1   C    107.48  3.000
 K2V  C2   C1   C    110.28  3.000
 K2V  H11  C1   N    107.16  3.000
 K2V  C    C1   N    109.35  3.000
 K2V  C2   C1   N    115.26  3.000
 K2V  H12  C11  N2   116.67  3.000
 K2V  H12  C11  C8   120.54  3.000
 K2V  N2   C11  C8   122.78  3.000
 K2V  C3   C2   C1   121.55  3.000
 K2V  C1   C2   C7   120.40  3.000
 K2V  C3   C2   C7   118.05  3.000
 K2V  H13  C3   C2   120.31  3.000
 K2V  H13  C3   C4   118.68  3.000
 K2V  C2   C3   C4   121.02  3.000
 K2V  H14  C9   C8   120.51  3.000
 K2V  H14  C9   N1   116.70  3.000
 K2V  C8   C9   N1   122.79  3.000
 K2V  C11  N2   C10  116.69  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
 K2V  CONST_01  C11  C8   C9   N1     0.00  0.0  0
 K2V  CONST_02  C5   C8   C9   N1   180.00  0.0  0
 K2V  CONST_03  C11  N2   C10  N1     0.00  0.0  0
 K2V  CONST_06  C7   C6   C5   C4     0.00  0.0  0
 K2V  CONST_07  C7   C2   C3   C4     0.00  0.0  0
 K2V  CONST_08  N2   C11  C8   C5   180.00  0.0  0
 K2V  CONST_09  C2   C7   C6   C5     0.00  0.0  0
 K2V  CONST_10  C2   C3   C4   C5     0.00  0.0  0
 K2V  CONST_13  C3   C4   C5   C6     0.00  0.0  0
 K2V  CONST_14  C3   C2   C7   C6     0.00  0.0  0
 K2V  CONST_15  C8   C5   C6   C7   180.00  0.0  0
 K2V  CONST_16  C10  N1   C9   C8     0.00  0.0  0
 K2V  CONST_17  C10  N2   C11  C8     0.00  0.0  0
 K2V  CONST_18  C3   C4   C5   C8   180.00  0.0  0
 K2V  CONST_19  N2   C10  N1   C9     0.00  0.0  0
 K2V  CONST_20  N2   C11  C8   C9     0.00  0.0  0
 K2V  CONST_21  C1   C2   C3   C4   180.00  0.0  0
 K2V  CONST_22  C1   C2   C7   C6   180.00  0.0  0
 K2V  CONST_23  H2   C6   C5   C4   180.00  0.0  0
 K2V  CONST_24  H14  C9   C8   C5     0.00  0.0  0
 K2V  CONST_25  H12  C11  C8   C5     0.00  0.0  0
 K2V  CONST_26  H3   C7   C6   C5   180.00  0.0  0
 K2V  CONST_27  H13  C3   C4   C5   180.00  0.0  0
 K2V  CONST_28  H1   C4   C5   C6   180.00  0.0  0
 K2V  CONST_29  H4   C10  N2   C11  180.00  0.0  0

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
 K2V  chir_01  C1  C2  C  N  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
 K2V  plan-1  N1   0.020
 K2V  plan-1  C5   0.020
 K2V  plan-1  C8   0.020
 K2V  plan-1  C10  0.020
 K2V  plan-1  C11  0.020
 K2V  plan-1  C9   0.020
 K2V  plan-1  N2   0.020
 K2V  plan-1  H4   0.020
 K2V  plan-1  H12  0.020
 K2V  plan-1  H14  0.020
 K2V  plan-2  C4   0.020
 K2V  plan-2  C5   0.020
 K2V  plan-2  C6   0.020
 K2V  plan-2  C7   0.020
 K2V  plan-2  C8   0.020
 K2V  plan-2  C1   0.020
 K2V  plan-2  C2   0.020
 K2V  plan-2  C3   0.020
 K2V  plan-2  H2   0.020
 K2V  plan-2  H3   0.020
 K2V  plan-2  H13  0.020
 K2V  plan-2  H1   0.020

