# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:00:47 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-[(S)-(3'-methoxybiphenyl-3-yl)(pyridin-4-yl)methyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(c2)[C@H](NC(N)=N)c3ccncc3
#
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
 GMF  GMF  1-[(S)-(3'-methoxybiphenyl-3-yl)(pyridin-4-yl)methyl]guanidine  ligand  45  25  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GMF
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
 GMF  N1    N  N     0  -0.702   4.3351   3.3265  -0.3218
 GMF  N2    N  NH1   0  -0.627   3.5497   1.2517   0.2363
 GMF  C3    C  CH1   0  -0.242   2.3827   0.4517   0.5437
 GMF  N3    N  NH2   0  -0.823   2.8187   3.0717   1.4782
 GMF  C4    C  C     0   0.521   3.6009   2.6149   0.4493
 GMF  N4    N  N     0  -0.407   3.5598  -3.6551  -0.0254
 GMF  C5    C  CR6   0   0.232   2.7616  -1.0008   0.3380
 GMF  C6    C  CR16  0  -0.382   3.1746  -1.7815   1.4091
 GMF  C7    C  CR16  0  -0.058   3.5573  -3.0942   1.1780
 GMF  C8    C  CR16  0  -0.056   3.1664  -2.9056  -1.0486
 GMF  C9    C  CR16  0  -0.355   2.7556  -1.5873  -0.9213
 GMF  C10   C  CR6   0   0.164   1.1294   0.8131  -0.2319
 GMF  C11   C  CR16  0  -0.323   1.1741   1.5226  -1.4248
 GMF  C12   C  CR16  0  -0.225  -0.0026   1.7979  -2.1106
 GMF  C13   C  CR16  0  -0.321  -1.2230   1.3705  -1.6146
 GMF  C14   C  CR6   0   0.107  -1.2879   0.6571  -0.4158
 GMF  C15   C  CR16  0  -0.361  -0.0997   0.3891   0.2601
 GMF  C30   C  CR6   0   0.407  -4.8206  -0.6625  -0.2151
 GMF  C16   C  CR6   0   0.106  -2.5836   0.2044   0.1320
 GMF  C17   C  CR16  0  -0.336  -2.8164   0.2151   1.5107
 GMF  C18   C  CR16  0  -0.226  -4.0358  -0.2095   2.0062
 GMF  C1    C  CH3   0  -0.437  -6.9837  -1.5221  -0.6811
 GMF  C19   C  CR16  0  -0.394  -5.0459  -0.6514   1.1590
 GMF  C20   C  CR16  0  -0.414  -3.5906  -0.2364  -0.7185
 GMF  H1    H  H     0   0.319   4.3659   4.2887  -0.0055
 GMF  H11C  H  HCH3  0   0.229  -6.9004  -2.4031  -0.0392
 GMF  H12C  H  HCH3  0   0.228  -7.5290  -0.7432  -0.1420
 GMF  H13C  H  HCH3  0   0.260  -7.5480  -1.7923  -1.5702
 GMF  H2    H  HNH1  0   0.386   4.0398   0.9861  -0.6055
 GMF  H3    H  HCH1  0   0.277   2.1544   0.5604   1.6078
 GMF  H31N  H  HNH2  0   0.393   2.9987   4.0189   1.7697
 GMF  H32N  H  HNH2  0   0.393   2.6682   2.4575   2.2626
 GMF  H7    H  HCR6  0   0.267   3.8750  -3.7183   2.0061
 GMF  H8    H  HCR6  0   0.267   3.1731  -3.3759  -2.0257
 GMF  H6    H  HCR6  0   0.271   3.1950  -1.3812   2.4149
 GMF  H9    H  HCR6  0   0.272   2.4309  -1.0424  -1.7986
 GMF  H11   H  HCR6  0   0.251   2.1176   1.8723  -1.8239
 GMF  H15   H  HCR6  0   0.250  -0.1274  -0.1777   1.1851
 GMF  H12   H  HCR6  0   0.258   0.0337   2.3598  -3.0349
 GMF  H13   H  HCR6  0   0.255  -2.1319   1.6146  -2.1498
 GMF  H17   H  HCR6  0   0.252  -2.0550   0.5747   2.1905
 GMF  H20   H  HCR6  0   0.259  -3.4270  -0.2721  -1.7892
 GMF  H18   H  HCR6  0   0.261  -4.2161  -0.1936   3.0733
 GMF  H19   H  HCR6  0   0.280  -5.9851  -0.9779   1.5834
 GMF  O1    O  O2    0  -0.473  -5.7209  -1.0713  -1.1291

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
 GMF  N1   C4    double    1.281  0.020  1.281
 GMF  O1   C30   single    1.347  0.020  1.347
 GMF  O1   C1    single    1.414  0.020  1.414
 GMF  N2   C3    single    1.448  0.020  1.448
 GMF  N2   C4    single    1.381  0.020  1.381
 GMF  C3   C5    single    1.515  0.020  1.515
 GMF  C3   C10   single    1.518  0.020  1.518
 GMF  N3   C4    single    1.371  0.020  1.371
 GMF  N4   C7    aromatic  1.328  0.020  1.328
 GMF  N4   C8    aromatic  1.328  0.020  1.328
 GMF  C5   C6    aromatic  1.388  0.020  1.388
 GMF  C5   C9    aromatic  1.389  0.020  1.389
 GMF  C6   C7    aromatic  1.387  0.020  1.387
 GMF  C8   C9    aromatic  1.387  0.020  1.387
 GMF  C10  C11   aromatic  1.389  0.020  1.389
 GMF  C10  C15   aromatic  1.390  0.020  1.390
 GMF  C11  C12   aromatic  1.389  0.020  1.389
 GMF  C12  C13   aromatic  1.385  0.020  1.385
 GMF  C13  C14   aromatic  1.397  0.020  1.397
 GMF  C14  C15   aromatic  1.393  0.020  1.393
 GMF  C14  C16   single    1.478  0.020  1.478
 GMF  C16  C17   aromatic  1.398  0.020  1.398
 GMF  C16  C20   aromatic  1.390  0.020  1.390
 GMF  C17  C18   aromatic  1.383  0.020  1.383
 GMF  C30  C19   aromatic  1.392  0.020  1.392
 GMF  C30  C20   aromatic  1.396  0.020  1.396
 GMF  C18  C19   aromatic  1.390  0.020  1.390
 GMF  N1   H1    single    0.890  0.020  1.040
 GMF  C1   H11C  single    0.970  0.020  1.090
 GMF  C1   H12C  single    0.970  0.020  1.090
 GMF  C1   H13C  single    0.970  0.020  1.090
 GMF  N2   H2    single    0.890  0.020  1.040
 GMF  C3   H3    single    0.970  0.020  1.090
 GMF  N3   H31N  single    0.890  0.020  1.040
 GMF  N3   H32N  single    0.890  0.020  1.040
 GMF  C7   H7    single    0.930  0.020  1.080
 GMF  C8   H8    single    0.930  0.020  1.080
 GMF  C6   H6    single    0.930  0.020  1.080
 GMF  C9   H9    single    0.930  0.020  1.080
 GMF  C11  H11   single    0.930  0.020  1.080
 GMF  C15  H15   single    0.930  0.020  1.080
 GMF  C12  H12   single    0.930  0.020  1.080
 GMF  C13  H13   single    0.930  0.020  1.080
 GMF  C17  H17   single    0.930  0.020  1.080
 GMF  C20  H20   single    0.930  0.020  1.080
 GMF  C18  H18   single    0.930  0.020  1.080
 GMF  C19  H19   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
 GMF  H1    N1   C4    110.92  3.000
 GMF  H2    N2   C4    111.74  3.000
 GMF  H2    N2   C3    115.02  3.000
 GMF  C4    N2   C3    122.86  3.000
 GMF  H3    C3   C10   107.53  3.000
 GMF  H3    C3   C5    106.24  3.000
 GMF  C10   C3   C5    111.44  3.000
 GMF  H3    C3   N2    108.66  3.000
 GMF  C10   C3   N2    115.19  3.000
 GMF  C5    C3   N2    107.41  3.000
 GMF  H32N  N3   H31N  112.00  3.000
 GMF  H32N  N3   C4    117.80  3.000
 GMF  H31N  N3   C4    115.38  3.000
 GMF  N3    C4   N2    115.07  3.000
 GMF  N3    C4   N1    126.43  3.000
 GMF  N2    C4   N1    118.49  3.000
 GMF  C8    N4   C7    117.35  3.000
 GMF  C9    C5   C6    117.60  3.000
 GMF  C9    C5   C3    121.78  3.000
 GMF  C6    C5   C3    120.58  3.000
 GMF  H6    C6   C7    119.97  3.000
 GMF  H6    C6   C5    120.96  3.000
 GMF  C7    C6   C5    119.07  3.000
 GMF  H7    C7   C6    119.89  3.000
 GMF  H7    C7   N4    116.65  3.000
 GMF  C6    C7   N4    123.47  3.000
 GMF  H8    C8   C9    119.80  3.000
 GMF  H8    C8   N4    116.59  3.000
 GMF  C9    C8   N4    123.61  3.000
 GMF  H9    C9   C8    119.54  3.000
 GMF  H9    C9   C5    121.56  3.000
 GMF  C8    C9   C5    118.90  3.000
 GMF  C15   C10  C11   119.23  3.000
 GMF  C15   C10  C3    118.47  3.000
 GMF  C11   C10  C3    122.28  3.000
 GMF  H11   C11  C12   119.49  3.000
 GMF  H11   C11  C10   120.65  3.000
 GMF  C12   C11  C10   119.86  3.000
 GMF  H12   C12  C13   119.71  3.000
 GMF  H12   C12  C11   119.73  3.000
 GMF  C13   C12  C11   120.55  3.000
 GMF  H13   C13  C14   120.03  3.000
 GMF  H13   C13  C12   119.55  3.000
 GMF  C14   C13  C12   120.40  3.000
 GMF  C16   C14  C15   120.60  3.000
 GMF  C16   C14  C13   121.03  3.000
 GMF  C15   C14  C13   118.37  3.000
 GMF  H15   C15  C14   119.49  3.000
 GMF  H15   C15  C10   118.91  3.000
 GMF  C14   C15  C10   121.58  3.000
 GMF  C20   C30  C19   119.74  3.000
 GMF  C20   C30  O1    115.92  3.000
 GMF  C19   C30  O1    124.34  3.000
 GMF  C20   C16  C17   119.02  3.000
 GMF  C20   C16  C14   120.37  3.000
 GMF  C17   C16  C14   120.61  3.000
 GMF  H17   C17  C18   119.82  3.000
 GMF  H17   C17  C16   120.32  3.000
 GMF  C18   C17  C16   119.85  3.000
 GMF  H18   C18  C19   118.98  3.000
 GMF  H18   C18  C17   119.70  3.000
 GMF  C19   C18  C17   121.32  3.000
 GMF  H13C  C1   H12C  108.75  3.000
 GMF  H13C  C1   H11C  108.64  3.000
 GMF  H12C  C1   H11C  108.82  3.000
 GMF  H13C  C1   O1    106.48  3.000
 GMF  H12C  C1   O1    112.01  3.000
 GMF  H11C  C1   O1    112.02  3.000
 GMF  H19   C19  C18   119.20  3.000
 GMF  H19   C19  C30   121.70  3.000
 GMF  C18   C19  C30   119.10  3.000
 GMF  H20   C20  C16   120.37  3.000
 GMF  H20   C20  C30   118.64  3.000
 GMF  C16   C20  C30   120.97  3.000
 GMF  C1    O1   C30   118.62  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
 GMF  CONST_01  C5    C6   C7   N4     0.00   0.0  0
 GMF  CONST_02  C5    C9   C8   N4     0.00   0.0  0
 GMF  CONST_03  C8    C9   C5   C6     0.00   0.0  0
 GMF  CONST_04  C8    N4   C7   C6     0.00   0.0  0
 GMF  CONST_05  C9    C8   N4   C7     0.00   0.0  0
 GMF  CONST_06  C9    C5   C6   C7     0.00   0.0  0
 GMF  CONST_07  C13   C12  C11  C10    0.00   0.0  0
 GMF  CONST_08  C13   C14  C15  C10    0.00   0.0  0
 GMF  CONST_09  C16   C14  C15  C10  180.00   0.0  0
 GMF  CONST_10  C14   C15  C10  C11    0.00   0.0  0
 GMF  CONST_11  C14   C13  C12  C11    0.00   0.0  0
 GMF  CONST_12  C15   C10  C11  C12    0.00   0.0  0
 GMF  CONST_13  C15   C14  C13  C12    0.00   0.0  0
 GMF  CONST_14  C16   C14  C13  C12  180.00   0.0  0
 GMF  CONST_17  C18   C17  C16  C14  180.00   0.0  0
 GMF  CONST_18  C30   C20  C16  C14  180.00   0.0  0
 GMF  CONST_21  C17   C18  C19  C30    0.00   0.0  0
 GMF  CONST_22  C17   C16  C20  C30    0.00   0.0  0
 GMF  CONST_23  C19   C18  C17  C16    0.00   0.0  0
 GMF  CONST_24  C19   C30  C20  C16    0.00   0.0  0
 GMF  CONST_25  C20   C16  C17  C18    0.00   0.0  0
 GMF  CONST_26  C20   C30  C19  C18    0.00   0.0  0
 GMF  CONST_27  C18   C19  C30  O1   180.00   0.0  0
 GMF  CONST_28  C16   C20  C30  O1   180.00   0.0  0
 GMF  CONST_29  C7    C6   C5   C3   180.00   0.0  0
 GMF  CONST_30  C8    C9   C5   C3   180.00   0.0  0
 GMF  CONST_31  C12   C11  C10  C3   180.00   0.0  0
 GMF  CONST_32  C14   C15  C10  C3   180.00   0.0  0
 GMF  CONST_33  H6    C6   C7   N4   180.00   0.0  0
 GMF  CONST_34  H9    C9   C8   N4   180.00   0.0  0
 GMF  CONST_35  H7    C7   C6   C5   180.00   0.0  0
 GMF  CONST_36  H8    C8   C9   C5   180.00   0.0  0
 GMF  CONST_37  H12   C12  C11  C10  180.00   0.0  0
 GMF  CONST_38  H15   C15  C10  C11  180.00   0.0  0
 GMF  CONST_39  H13   C13  C12  C11  180.00   0.0  0
 GMF  CONST_40  H11   C11  C12  C13  180.00   0.0  0
 GMF  CONST_41  H17   C17  C16  C14    0.00   0.0  0
 GMF  CONST_42  H20   C20  C16  C14    0.00   0.0  0
 GMF  CONST_43  H18   C18  C19  C30  180.00   0.0  0
 GMF  CONST_44  H19   C19  C18  C17  180.00   0.0  0
 GMF  CONST_47  H2    N2   C4   N1     0.00   0.0  0
 GMF  CONST_48  H31N  N3   C4   N1     0.00   0.0  0
 GMF  CONST_50  H1    N1   C4   N2   180.00   0.0  0
 GMF  Var_01    C19   C30  O1   C1     0.01  30.0  2
 GMF  Var_02    H11C  C1   O1   C30  -61.80  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
 GMF  chir_01  C3  N2  C5  C10  positiv

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
 GMF  plan-1  C3    0.020
 GMF  plan-1  N4    0.020
 GMF  plan-1  C5    0.020
 GMF  plan-1  C6    0.020
 GMF  plan-1  C7    0.020
 GMF  plan-1  C8    0.020
 GMF  plan-1  C9    0.020
 GMF  plan-1  H7    0.020
 GMF  plan-1  H8    0.020
 GMF  plan-1  H6    0.020
 GMF  plan-1  H9    0.020
 GMF  plan-2  C3    0.020
 GMF  plan-2  C10   0.020
 GMF  plan-2  C11   0.020
 GMF  plan-2  C12   0.020
 GMF  plan-2  C13   0.020
 GMF  plan-2  C14   0.020
 GMF  plan-2  C15   0.020
 GMF  plan-2  C16   0.020
 GMF  plan-2  H11   0.020
 GMF  plan-2  H15   0.020
 GMF  plan-2  H12   0.020
 GMF  plan-2  H13   0.020
 GMF  plan-3  C14   0.020
 GMF  plan-3  C30   0.020
 GMF  plan-3  C16   0.020
 GMF  plan-3  C17   0.020
 GMF  plan-3  C18   0.020
 GMF  plan-3  C19   0.020
 GMF  plan-3  C20   0.020
 GMF  plan-3  H17   0.020
 GMF  plan-3  H20   0.020
 GMF  plan-3  H18   0.020
 GMF  plan-3  H19   0.020
 GMF  plan-3  O1    0.020
 GMF  plan-4  N1    0.020
 GMF  plan-4  N2    0.020
 GMF  plan-4  C3    0.020
 GMF  plan-4  N3    0.020
 GMF  plan-4  C4    0.020
 GMF  plan-4  H1    0.020
 GMF  plan-4  H2    0.020
 GMF  plan-4  H31N  0.020
 GMF  plan-4  H32N  0.020

