# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:16:48 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 6-(2-{2,3-difluoro-5-[3-(methylamino)prop-1-yn-1-yl]phenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC#Cc1cc(F)c(F)c(CCc2cc(C)cc(N)n2)c1
#
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
 KMV  KMV  6-(2-{2,3-difluoro-5-[3-(methylamino)prop-1-yn-1-yl]phenyl}ethyl)-4-methylpyridin-2-amine  ligand  42  23  .  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_KMV
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
 KMV  C02  C  CR6   0   0.439  -5.2011  -0.1794  -0.6127
 KMV  C03  C  CR16  0  -0.441  -5.6220  -1.4565  -0.2076
 KMV  C04  C  CR6   0   0.203  -4.7530  -2.2528   0.5120
 KMV  C05  C  CR16  0  -0.438  -3.4858  -1.7421   0.8101
 KMV  C06  C  CR6   0   0.275  -3.1557  -0.4693   0.3767
 KMV  C07  C  CH3   0  -0.725  -5.1461  -3.6340   0.9399
 KMV  C08  C  CH2   0  -0.489  -1.8038   0.1221   0.6583
 KMV  C09  C  CH2   0  -0.507  -0.9877   0.2980  -0.6302
 KMV  C11  C  CR6   0  -0.058   0.3586   0.9061  -0.3625
 KMV  C12  C  CR6   0   0.379   0.5081   2.2745  -0.2061
 KMV  C13  C  CR6   0   0.422   1.7425   2.8367   0.0722
 KMV  C14  C  CR16  0  -0.462   2.8658   2.0536   0.2040
 KMV  C15  C  CR6   0  -0.090   2.7436   0.6699   0.0548
 KMV  C16  C  CR16  0  -0.347   1.4940   0.1154  -0.2247
 KMV  C17  C  CSP   0   0.173   3.8922  -0.1645   0.1851
 KMV  C18  C  CSP   0   0.035   4.8648  -0.8671   0.2936
 KMV  C19  C  CH2   0  -0.459   6.0492  -1.7104   0.4158
 KMV  C21  C  CH3   0  -0.526   7.2823  -3.5426  -0.5226
 KMV  F12  F  F     0  -0.298  -0.5506   3.0827  -0.3235
 KMV  F13  F  F     0  -0.303   1.8302   4.1628   0.2099
 KMV  N01  N  N     0  -0.481  -3.9947   0.2969  -0.3204
 KMV  N02  N  NH2   0  -0.839  -6.0152   0.6167  -1.3677
 KMV  N20  N  NH1   0  -0.592   6.1154  -2.6913  -0.6525
 KMV  H1   H  HCR6  0   0.255  -6.6169  -1.8056  -0.4584
 KMV  H2   H  HCR6  0   0.245  -2.7755  -2.3264   1.3814
 KMV  H3   H  HCH3  0   0.256  -4.9488  -4.3496   0.1394
 KMV  H4   H  HCH3  0   0.247  -4.5810  -3.9584   1.8124
 KMV  H5   H  HCH3  0   0.248  -6.2083  -3.6955   1.1740
 KMV  H6   H  HCH2  0   0.253  -1.9320   1.0926   1.1440
 KMV  H7   H  HCH2  0   0.253  -1.2551  -0.5151   1.3541
 KMV  H8   H  HCH2  0   0.262  -0.8461  -0.6762  -1.1021
 KMV  H9   H  HCH2  0   0.263  -1.5554   0.9087  -1.3337
 KMV  H10  H  HCR6  0   0.291   3.8217   2.5109   0.4208
 KMV  H11  H  HCR6  0   0.267   1.4012  -0.9568  -0.3399
 KMV  H12  H  HCH2  0   0.240   6.9385  -1.0637   0.4693
 KMV  H13  H  HCH2  0   0.263   6.0072  -2.2408   1.3726
 KMV  H14  H  HCH3  0   0.200   8.2331  -2.9958  -0.4576
 KMV  H15  H  HCH3  0   0.228   7.1959  -4.1568   0.3755
 KMV  H16  H  HCH3  0   0.240   7.3387  -4.2140  -1.3785
 KMV  H17  H  HNH2  0   0.387  -7.0034   0.4304  -1.3352
 KMV  H18  H  HNH2  0   0.379  -5.7841   1.5965  -1.3810
 KMV  H19  H  HNH1  0   0.352   6.1610  -2.2033  -1.5381

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
 KMV  C21  N20  single    1.450  0.020  1.450
 KMV  N20  C19  single    1.452  0.020  1.452
 KMV  C19  C18  single    1.459  0.020  1.459
 KMV  C18  C17  triple    1.205  0.020  1.205
 KMV  C17  C15  single    1.426  0.020  1.426
 KMV  C15  C16  aromatic  1.395  0.020  1.395
 KMV  C15  C14  aromatic  1.397  0.020  1.397
 KMV  C16  C11  aromatic  1.390  0.020  1.390
 KMV  N02  C02  single    1.366  0.020  1.366
 KMV  C08  C06  single    1.502  0.020  1.502
 KMV  C08  C09  single    1.535  0.020  1.535
 KMV  N01  C02  aromatic  1.330  0.020  1.330
 KMV  N01  C06  aromatic  1.333  0.020  1.333
 KMV  C14  C13  aromatic  1.376  0.020  1.376
 KMV  C02  C03  aromatic  1.404  0.020  1.404
 KMV  C06  C05  aromatic  1.384  0.020  1.384
 KMV  C11  C09  single    1.501  0.020  1.501
 KMV  C11  C12  aromatic  1.385  0.020  1.385
 KMV  C13  C12  aromatic  1.385  0.020  1.385
 KMV  C13  F13  single    1.336  0.020  1.336
 KMV  C12  F12  single    1.337  0.020  1.337
 KMV  C03  C04  aromatic  1.381  0.020  1.381
 KMV  C05  C04  aromatic  1.398  0.020  1.398
 KMV  C04  C07  single    1.498  0.020  1.498
 KMV  C03  H1   single    0.930  0.020  1.080
 KMV  C05  H2   single    0.930  0.020  1.080
 KMV  C07  H3   single    0.970  0.020  1.090
 KMV  C07  H4   single    0.970  0.020  1.090
 KMV  C07  H5   single    0.970  0.020  1.090
 KMV  C08  H6   single    0.970  0.020  1.090
 KMV  C08  H7   single    0.970  0.020  1.090
 KMV  C09  H8   single    0.970  0.020  1.090
 KMV  C09  H9   single    0.970  0.020  1.090
 KMV  C14  H10  single    0.930  0.020  1.080
 KMV  C16  H11  single    0.930  0.020  1.080
 KMV  C19  H12  single    0.970  0.020  1.090
 KMV  C19  H13  single    0.970  0.020  1.090
 KMV  C21  H14  single    0.970  0.020  1.090
 KMV  C21  H15  single    0.970  0.020  1.090
 KMV  C21  H16  single    0.970  0.020  1.090
 KMV  N02  H17  single    0.890  0.020  1.040
 KMV  N02  H18  single    0.890  0.020  1.040
 KMV  N20  H19  single    0.890  0.020  1.040

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
 KMV  N02  C02  N01  116.96  3.000
 KMV  N01  C02  C03  122.29  3.000
 KMV  N02  C02  C03  120.72  3.000
 KMV  H1   C03  C04  120.83  3.000
 KMV  H1   C03  C02  120.08  3.000
 KMV  C04  C03  C02  119.09  3.000
 KMV  C07  C04  C05  120.90  3.000
 KMV  C07  C04  C03  121.01  3.000
 KMV  C05  C04  C03  118.08  3.000
 KMV  H2   C05  C06  120.32  3.000
 KMV  H2   C05  C04  120.66  3.000
 KMV  C06  C05  C04  119.02  3.000
 KMV  N01  C06  C08  115.99  3.000
 KMV  N01  C06  C05  122.82  3.000
 KMV  C08  C06  C05  121.18  3.000
 KMV  H5   C07  H4   108.48  3.000
 KMV  H5   C07  H3   107.27  3.000
 KMV  H4   C07  H3   107.37  3.000
 KMV  H5   C07  C04  111.66  3.000
 KMV  H4   C07  C04  111.54  3.000
 KMV  H3   C07  C04  110.33  3.000
 KMV  H7   C08  H6   107.10  3.000
 KMV  H7   C08  C09  109.56  3.000
 KMV  H6   C08  C09  109.49  3.000
 KMV  H7   C08  C06  110.01  3.000
 KMV  H6   C08  C06  109.11  3.000
 KMV  C09  C08  C06  111.48  3.000
 KMV  H9   C09  H8   106.76  3.000
 KMV  H9   C09  C11  110.79  3.000
 KMV  H8   C09  C11  108.79  3.000
 KMV  H9   C09  C08  109.19  3.000
 KMV  H8   C09  C08  109.23  3.000
 KMV  C11  C09  C08  111.93  3.000
 KMV  C16  C11  C12  117.54  3.000
 KMV  C12  C11  C09  121.13  3.000
 KMV  C16  C11  C09  121.31  3.000
 KMV  F12  C12  C13  118.56  3.000
 KMV  F12  C12  C11  120.11  3.000
 KMV  C13  C12  C11  121.33  3.000
 KMV  F13  C13  C14  120.10  3.000
 KMV  F13  C13  C12  118.83  3.000
 KMV  C14  C13  C12  121.07  3.000
 KMV  H10  C14  C15  121.16  3.000
 KMV  H10  C14  C13  120.02  3.000
 KMV  C15  C14  C13  118.82  3.000
 KMV  C17  C15  C16  120.48  3.000
 KMV  C16  C15  C14  119.56  3.000
 KMV  C17  C15  C14  119.96  3.000
 KMV  H11  C16  C15  119.46  3.000
 KMV  H11  C16  C11  118.87  3.000
 KMV  C15  C16  C11  121.68  3.000
 KMV  C18  C17  C15  180.00  3.000
 KMV  C19  C18  C17  180.00  3.000
 KMV  H13  C19  H12  105.85  3.000
 KMV  H13  C19  N20  108.51  3.000
 KMV  H12  C19  N20  113.32  3.000
 KMV  H13  C19  C18  108.79  3.000
 KMV  H12  C19  C18  108.68  3.000
 KMV  N20  C19  C18  111.46  3.000
 KMV  H16  C21  H15  107.69  3.000
 KMV  H16  C21  H14  107.97  3.000
 KMV  H15  C21  H14  107.45  3.000
 KMV  H16  C21  N20  109.46  3.000
 KMV  H15  C21  N20  109.89  3.000
 KMV  H14  C21  N20  114.17  3.000
 KMV  C06  N01  C02  118.70  3.000
 KMV  H18  N02  H17  113.96  3.000
 KMV  H18  N02  C02  115.95  3.000
 KMV  H17  N02  C02  117.36  3.000
 KMV  H19  N20  C21  108.97  3.000
 KMV  H19  N20  C19  108.67  3.000
 KMV  C21  N20  C19  111.56  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
 KMV  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 KMV  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 KMV  CONST_03  C06  N01  C02  C03     0.00   0.0  0
 KMV  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KMV  CONST_05  N01  C02  C03  C04     0.00   0.0  0
 KMV  CONST_06  N01  C06  C05  C04     0.00   0.0  0
 KMV  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 KMV  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KMV  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 KMV  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 KMV  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 KMV  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 KMV  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 KMV  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 KMV  CONST_15  N02  C02  C03  C04   180.00   0.0  0
 KMV  CONST_16  C08  C06  C05  C04   180.00   0.0  0
 KMV  CONST_17  N02  C02  N01  C06   180.00   0.0  0
 KMV  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 KMV  CONST_19  C15  C16  C11  C09   180.00   0.0  0
 KMV  CONST_20  C13  C12  C11  C09   180.00   0.0  0
 KMV  CONST_21  C17  C15  C16  C11   180.00   0.0  0
 KMV  CONST_22  F13  C13  C12  C11   180.00   0.0  0
 KMV  CONST_23  C17  C15  C14  C13   180.00   0.0  0
 KMV  CONST_24  F12  C12  C13  C14   180.00   0.0  0
 KMV  CONST_25  F13  C13  C14  C15   180.00   0.0  0
 KMV  CONST_26  F12  C12  C11  C16   180.00   0.0  0
 KMV  CONST_27  H2   C05  C04  C03   180.00   0.0  0
 KMV  CONST_28  H1   C03  C04  C05   180.00   0.0  0
 KMV  CONST_29  H11  C16  C11  C12   180.00   0.0  0
 KMV  CONST_30  H10  C14  C13  C12   180.00   0.0  0
 KMV  Var_01    C09  C08  C06  C05   112.54  30.0  1
 KMV  Var_02    C11  C09  C08  C06   179.22  30.0  3
 KMV  Var_03    C16  C11  C09  C08    96.64  30.0  2
 KMV  Var_04    H3   C07  C04  C03    85.05  30.0  2
 KMV  Var_05    N20  C19  C18  C17   -81.69  30.0  2
 KMV  Var_06    C21  N20  C19  C18  -179.21  30.0  2
 KMV  Var_07    H14  C21  N20  C19   -54.66  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
 KMV  plan-1  C09  0.020
 KMV  plan-1  C11  0.020
 KMV  plan-1  C12  0.020
 KMV  plan-1  C13  0.020
 KMV  plan-1  C14  0.020
 KMV  plan-1  C15  0.020
 KMV  plan-1  C16  0.020
 KMV  plan-1  C17  0.020
 KMV  plan-1  C18  0.020
 KMV  plan-1  F12  0.020
 KMV  plan-1  F13  0.020
 KMV  plan-1  H10  0.020
 KMV  plan-1  H11  0.020
 KMV  plan-2  C02  0.020
 KMV  plan-2  C03  0.020
 KMV  plan-2  C04  0.020
 KMV  plan-2  C05  0.020
 KMV  plan-2  C06  0.020
 KMV  plan-2  C07  0.020
 KMV  plan-2  C08  0.020
 KMV  plan-2  N01  0.020
 KMV  plan-2  N02  0.020
 KMV  plan-2  H1   0.020
 KMV  plan-2  H2   0.020
 KMV  plan-3  C02  0.020
 KMV  plan-3  N02  0.020
 KMV  plan-3  H17  0.020
 KMV  plan-3  H18  0.020

