# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 10:46:28 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cccc(c1)c2cccnc2
#
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
 3C5  3C5  N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine  ligand  29  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3C5
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
 3C5  C10  C  CR6   0  -0.008   1.8771  -0.0748   0.0589
 3C5  C01  C  CH3   0  -0.519  -5.2051   1.5478  -0.0421
 3C5  N02  N  NH1   0  -0.586  -4.0982   0.7079   0.3672
 3C5  C04  C  CR6   0   0.112  -1.8922  -0.1972  -0.1728
 3C5  C09  C  CR16  0  -0.379  -0.5781   0.2473  -0.2384
 3C5  C08  C  CR6   0   0.107   0.4911  -0.5726   0.1287
 3C5  C07  C  CR16  0  -0.326   0.2205  -1.8660   0.5711
 3C5  C06  C  CR16  0  -0.225  -1.0896  -2.3184   0.6455
 3C5  C05  C  CR16  0  -0.299  -2.1408  -1.4917   0.2802
 3C5  C15  C  CR16  0  -0.102   2.1908   1.2380   0.4158
 3C5  N14  N  N     0  -0.398   3.4137   1.7470   0.3771
 3C5  C13  C  CR16  0  -0.072   4.4055   0.9597  -0.0228
 3C5  C12  C  CR16  0  -0.315   4.2147  -0.3621  -0.3959
 3C5  C11  C  CR16  0  -0.196   2.9330  -0.8842  -0.3552
 3C5  H1   H  HCH3  0   0.234  -5.9602   1.5698   0.7432
 3C5  H2   H  HCH3  0   0.195  -4.9233   2.5855  -0.2685
 3C5  H3   H  HCH3  0   0.223  -5.6734   1.1344  -0.9379
 3C5  H4   H  HNH1  0   0.345  -3.7375   1.0415   1.2525
 3C5  H6   H  HCH2  0   0.238  -3.4327   0.3247  -1.5509
 3C5  H7   H  HCH2  0   0.212  -2.6298   1.7015  -0.8237
 3C5  H8   H  HCR6  0   0.250  -0.3804   1.2498  -0.6008
 3C5  H9   H  HCR6  0   0.254   1.0298  -2.5165   0.8798
 3C5  H10  H  HCR6  0   0.257  -1.2908  -3.3217   0.9983
 3C5  H11  H  HCR6  0   0.249  -3.1607  -1.8482   0.3488
 3C5  H12  H  HCR6  0   0.260   1.4077   1.9031   0.7663
 3C5  H13  H  HCR6  0   0.266   5.3967   1.3985  -0.0461
 3C5  H14  H  HCR6  0   0.273   5.0529  -0.9646  -0.7180
 3C5  H15  H  HCR6  0   0.270   2.7530  -1.9080  -0.6592
 3C5  C03  C  CH2   0  -0.320  -3.0242   0.6969  -0.6048

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
 3C5  C01  N02  single    1.449  0.020  1.449
 3C5  C12  C11  aromatic  1.385  0.020  1.385
 3C5  C12  C13  aromatic  1.387  0.020  1.387
 3C5  C03  N02  single    1.449  0.020  1.449
 3C5  C03  C04  single    1.506  0.020  1.506
 3C5  C11  C10  aromatic  1.393  0.020  1.393
 3C5  C13  N14  aromatic  1.328  0.020  1.328
 3C5  C09  C04  aromatic  1.389  0.020  1.389
 3C5  C09  C08  aromatic  1.397  0.020  1.397
 3C5  C04  C05  aromatic  1.394  0.020  1.394
 3C5  C10  C08  single    1.474  0.020  1.474
 3C5  C10  C15  aromatic  1.396  0.020  1.396
 3C5  N14  C15  aromatic  1.325  0.020  1.325
 3C5  C08  C07  aromatic  1.394  0.020  1.394
 3C5  C05  C06  aromatic  1.386  0.020  1.386
 3C5  C07  C06  aromatic  1.388  0.020  1.388
 3C5  C01  H1   single    0.970  0.020  1.090
 3C5  C01  H2   single    0.970  0.020  1.090
 3C5  C01  H3   single    0.970  0.020  1.090
 3C5  N02  H4   single    0.890  0.020  1.040
 3C5  C03  H6   single    0.970  0.020  1.090
 3C5  C03  H7   single    0.970  0.020  1.090
 3C5  C09  H8   single    0.930  0.020  1.080
 3C5  C07  H9   single    0.930  0.020  1.080
 3C5  C06  H10  single    0.930  0.020  1.080
 3C5  C05  H11  single    0.930  0.020  1.080
 3C5  C15  H12  single    0.930  0.020  1.080
 3C5  C13  H13  single    0.930  0.020  1.080
 3C5  C12  H14  single    0.930  0.020  1.080
 3C5  C11  H15  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
 3C5  C11  C10  C15  116.87  3.000
 3C5  C15  C10  C08  121.11  3.000
 3C5  C11  C10  C08  122.02  3.000
 3C5  H3   C01  H2   107.36  3.000
 3C5  H3   C01  H1   107.56  3.000
 3C5  H2   C01  H1   107.88  3.000
 3C5  H3   C01  N02  109.88  3.000
 3C5  H2   C01  N02  114.19  3.000
 3C5  H1   C01  N02  109.74  3.000
 3C5  H4   N02  C03  108.97  3.000
 3C5  H4   N02  C01  109.16  3.000
 3C5  C03  N02  C01  112.42  3.000
 3C5  C05  C04  C09  118.78  3.000
 3C5  C05  C04  C03  120.70  3.000
 3C5  C09  C04  C03  120.51  3.000
 3C5  H8   C09  C08  119.42  3.000
 3C5  H8   C09  C04  118.96  3.000
 3C5  C08  C09  C04  121.60  3.000
 3C5  C07  C08  C09  118.67  3.000
 3C5  C07  C08  C10  120.73  3.000
 3C5  C09  C08  C10  120.60  3.000
 3C5  H9   C07  C06  119.62  3.000
 3C5  H9   C07  C08  120.18  3.000
 3C5  C06  C07  C08  120.19  3.000
 3C5  H10  C06  C05  119.85  3.000
 3C5  H10  C06  C07  119.67  3.000
 3C5  C05  C06  C07  120.48  3.000
 3C5  H11  C05  C06  120.08  3.000
 3C5  H11  C05  C04  119.64  3.000
 3C5  C06  C05  C04  120.28  3.000
 3C5  H12  C15  N14  116.09  3.000
 3C5  H12  C15  C10  119.77  3.000
 3C5  N14  C15  C10  124.13  3.000
 3C5  C13  N14  C15  118.05  3.000
 3C5  H13  C13  C12  120.39  3.000
 3C5  H13  C13  N14  116.70  3.000
 3C5  C12  C13  N14  122.92  3.000
 3C5  H14  C12  C11  121.07  3.000
 3C5  H14  C12  C13  120.31  3.000
 3C5  C11  C12  C13  118.62  3.000
 3C5  H15  C11  C12  120.13  3.000
 3C5  H15  C11  C10  120.44  3.000
 3C5  C12  C11  C10  119.41  3.000
 3C5  H7   C03  H6   105.77  3.000
 3C5  H7   C03  C04  109.24  3.000
 3C5  H6   C03  C04  109.04  3.000
 3C5  H7   C03  N02  113.08  3.000
 3C5  H6   C03  N02  107.79  3.000
 3C5  C04  C03  N02  111.68  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
 3C5  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 3C5  CONST_02  C04  C09  C08  C10   180.00   0.0  0
 3C5  CONST_03  C06  C07  C08  C10   180.00   0.0  0
 3C5  CONST_04  C13  N14  C15  C10     0.00   0.0  0
 3C5  CONST_05  C07  C08  C09  C04     0.00   0.0  0
 3C5  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 3C5  CONST_07  C06  C05  C04  C09     0.00   0.0  0
 3C5  CONST_10  C06  C07  C08  C09     0.00   0.0  0
 3C5  CONST_11  C05  C04  C09  C08     0.00   0.0  0
 3C5  CONST_12  C12  C11  C10  C08   180.00   0.0  0
 3C5  CONST_13  N14  C15  C10  C08   180.00   0.0  0
 3C5  CONST_14  C05  C06  C07  C08     0.00   0.0  0
 3C5  CONST_17  C12  C11  C10  C15     0.00   0.0  0
 3C5  CONST_18  C12  C13  N14  C15     0.00   0.0  0
 3C5  CONST_19  C11  C12  C13  N14     0.00   0.0  0
 3C5  CONST_20  C11  C10  C15  N14     0.00   0.0  0
 3C5  CONST_21  C08  C09  C04  C03   180.00   0.0  0
 3C5  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 3C5  CONST_23  H14  C12  C11  C10   180.00   0.0  0
 3C5  CONST_24  H8   C09  C08  C10     0.00   0.0  0
 3C5  CONST_25  H9   C07  C08  C10     0.00   0.0  0
 3C5  CONST_26  H10  C06  C05  C04   180.00   0.0  0
 3C5  CONST_27  H11  C05  C04  C09   180.00   0.0  0
 3C5  CONST_28  H15  C11  C10  C08     0.00   0.0  0
 3C5  CONST_29  H12  C15  C10  C08     0.00   0.0  0
 3C5  CONST_30  H13  C13  N14  C15   180.00   0.0  0
 3C5  Var_01    C09  C04  C03  N02  -132.73  30.0  2
 3C5  Var_02    C04  C03  N02  C01  -179.13  30.0  1
 3C5  Var_03    H1   C01  N02  C03  -176.76  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
 3C5  plan-1  C10  0.020
 3C5  plan-1  C04  0.020
 3C5  plan-1  C09  0.020
 3C5  plan-1  C08  0.020
 3C5  plan-1  C07  0.020
 3C5  plan-1  C06  0.020
 3C5  plan-1  C05  0.020
 3C5  plan-1  H8   0.020
 3C5  plan-1  H9   0.020
 3C5  plan-1  H10  0.020
 3C5  plan-1  H11  0.020
 3C5  plan-1  C03  0.020
 3C5  plan-2  C10  0.020
 3C5  plan-2  C08  0.020
 3C5  plan-2  C15  0.020
 3C5  plan-2  N14  0.020
 3C5  plan-2  C13  0.020
 3C5  plan-2  C12  0.020
 3C5  plan-2  C11  0.020
 3C5  plan-2  H12  0.020
 3C5  plan-2  H13  0.020
 3C5  plan-2  H14  0.020
 3C5  plan-2  H15  0.020

