# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:08:21 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)c1[nH]c(cn1)c2ccccc2F
#
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
 M9D  M9D  (1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethan-1-amine  ligand  27  15  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M9D
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
 M9D  C10  C  CR16  0  -0.252  -4.1341   0.2788   0.0574
 M9D  C13  C  CR15  0  -0.254   0.5966  -1.9681   0.0341
 M9D  C01  C  CH3   0  -0.662   4.1101   0.3710   0.9728
 M9D  C02  C  CH1   0  -0.177   3.5487   0.0377  -0.4080
 M9D  C03  C  CR5   0   0.443   2.2012  -0.6015  -0.2749
 M9D  C05  C  CR5   0   0.314   0.0115  -0.7311  -0.0884
 M9D  C06  C  CR6   0  -0.154  -1.3954  -0.3572  -0.0557
 M9D  C07  C  CR6   0   0.516  -1.8491   0.9013   0.3266
 M9D  C09  C  CR16  0  -0.397  -3.1864   1.2369   0.3851
 M9D  C11  C  CR16  0  -0.251  -3.7251  -0.9926  -0.3261
 M9D  C12  C  CR16  0  -0.310  -2.3765  -1.2987  -0.3873
 M9D  F08  F  F     0  -0.313  -0.9457   1.8386   0.6694
 M9D  N04  N  NR15  0  -0.646   1.0674   0.1230  -0.2781
 M9D  N14  N  N     0  -0.454   1.9501  -1.8750  -0.0844
 M9D  N15  N  NH2   0  -0.804   3.4079   1.2598  -1.1862
 M9D  H1   H  HCR6  0   0.270  -5.1855   0.5286   0.1002
 M9D  H2   H  HCR5  0   0.257   0.1046  -2.9130   0.2109
 M9D  H9   H  HCH3  0   0.228   3.4739   1.0964   1.4817
 M9D  H10  H  HCH3  0   0.239   4.1759  -0.5244   1.5893
 M9D  H11  H  HCH1  0   0.235   4.2115  -0.7037  -0.8732
 M9D  H12  H  HCR6  0   0.282  -3.4776   2.2331   0.6914
 M9D  H13  H  HCR6  0   0.264  -4.4576  -1.7437  -0.5894
 M9D  H14  H  HCR6  0   0.265  -2.0666  -2.2836  -0.7114
 M9D  H29  H  HNR5  0   0.408   1.0402   1.1156  -0.4524
 M9D  H31  H  HNH2  0   0.359   4.2741   1.7824  -1.1558
 M9D  H3   H  HNH2  0   0.355   3.2517   1.0346  -2.1611
 M9D  H8   H  HCH3  0   0.239   5.1128   0.7932   0.8866

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
 M9D  C10  C11  aromatic  1.390  0.020  1.390
 M9D  C10  C09  aromatic  1.387  0.020  1.387
 M9D  C13  C05  aromatic  1.374  0.020  1.374
 M9D  C13  N14  aromatic  1.362  0.020  1.362
 M9D  C01  C02  single    1.527  0.020  1.527
 M9D  C02  C03  single    1.497  0.020  1.497
 M9D  C02  N15  single    1.456  0.020  1.456
 M9D  C03  N04  aromatic  1.345  0.020  1.345
 M9D  C03  N14  aromatic  1.312  0.020  1.312
 M9D  C05  C06  single    1.456  0.020  1.456
 M9D  C05  N04  aromatic  1.371  0.020  1.371
 M9D  C06  C12  aromatic  1.400  0.020  1.400
 M9D  C06  C07  aromatic  1.391  0.020  1.391
 M9D  C07  C09  aromatic  1.380  0.020  1.380
 M9D  C07  F08  single    1.346  0.020  1.346
 M9D  C11  C12  aromatic  1.384  0.020  1.384
 M9D  C10  H1   single    0.930  0.020  1.080
 M9D  C13  H2   single    0.930  0.020  1.080
 M9D  C01  H8   single    0.970  0.020  1.090
 M9D  C01  H9   single    0.970  0.020  1.090
 M9D  C01  H10  single    0.970  0.020  1.090
 M9D  C02  H11  single    0.970  0.020  1.090
 M9D  C09  H12  single    0.930  0.020  1.080
 M9D  C11  H13  single    0.930  0.020  1.080
 M9D  C12  H14  single    0.930  0.020  1.080
 M9D  N04  H29  single    0.860  0.020  1.020
 M9D  N15  H31  single    0.890  0.020  1.040
 M9D  N15  H3   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
 M9D  H1   C10  C11  120.56  3.000
 M9D  H1   C10  C09  119.69  3.000
 M9D  C11  C10  C09  119.75  3.000
 M9D  H2   C13  N14  121.79  3.000
 M9D  H2   C13  C05  127.48  3.000
 M9D  N14  C13  C05  110.73  3.000
 M9D  H10  C01  H9   108.54  3.000
 M9D  H10  C01  H8   107.89  3.000
 M9D  H9   C01  H8   108.39  3.000
 M9D  H10  C01  C02  110.76  3.000
 M9D  H9   C01  C02  110.63  3.000
 M9D  H8   C01  C02  110.53  3.000
 M9D  H11  C02  N15  113.50  3.000
 M9D  H11  C02  C03  107.02  3.000
 M9D  N15  C02  C03  108.59  3.000
 M9D  H11  C02  C01  107.97  3.000
 M9D  N15  C02  C01  109.62  3.000
 M9D  C03  C02  C01  110.10  3.000
 M9D  N14  C03  N04  111.21  3.000
 M9D  N14  C03  C02  126.84  3.000
 M9D  N04  C03  C02  121.89  3.000
 M9D  N04  C05  C06  125.96  3.000
 M9D  N04  C05  C13  104.19  3.000
 M9D  C06  C05  C13  129.84  3.000
 M9D  C12  C06  C07  116.42  3.000
 M9D  C07  C06  C05  123.61  3.000
 M9D  C12  C06  C05  119.95  3.000
 M9D  F08  C07  C09  118.05  3.000
 M9D  F08  C07  C06  118.75  3.000
 M9D  C09  C07  C06  123.20  3.000
 M9D  H12  C09  C07  119.78  3.000
 M9D  H12  C09  C10  121.26  3.000
 M9D  C07  C09  C10  118.96  3.000
 M9D  H13  C11  C12  119.70  3.000
 M9D  H13  C11  C10  120.22  3.000
 M9D  C12  C11  C10  120.08  3.000
 M9D  H14  C12  C11  119.57  3.000
 M9D  H14  C12  C06  118.84  3.000
 M9D  C11  C12  C06  121.58  3.000
 M9D  H29  N04  C05  128.05  3.000
 M9D  H29  N04  C03  123.60  3.000
 M9D  C05  N04  C03  108.25  3.000
 M9D  C03  N14  C13  105.62  3.000
 M9D  H3   N15  H31  106.01  3.000
 M9D  H3   N15  C02  110.05  3.000
 M9D  H31  N15  C02  109.55  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
 M9D  CONST_01  C06  C12  C11  C10    0.00  0.0  0
 M9D  CONST_02  C06  C07  C09  C10    0.00  0.0  0
 M9D  CONST_05  C03  N04  C05  C13    0.00  0.0  0
 M9D  CONST_06  N04  C03  N14  C13    0.00  0.0  0
 M9D  CONST_07  C06  C05  N04  C03  180.00  0.0  0
 M9D  CONST_08  C05  C13  N14  C03    0.00  0.0  0
 M9D  CONST_09  C11  C12  C06  C05  180.00  0.0  0
 M9D  CONST_10  C09  C07  C06  C05  180.00  0.0  0
 M9D  CONST_11  N14  C03  N04  C05    0.00  0.0  0
 M9D  CONST_12  N14  C13  C05  C06  180.00  0.0  0
 M9D  CONST_14  C11  C12  C06  C07    0.00  0.0  0
 M9D  CONST_15  C11  C10  C09  C07    0.00  0.0  0
 M9D  CONST_16  C12  C11  C10  C09    0.00  0.0  0
 M9D  CONST_17  C12  C06  C07  C09    0.00  0.0  0
 M9D  CONST_19  N14  C13  C05  N04    0.00  0.0  0
 M9D  CONST_20  F08  C07  C09  C10  180.00  0.0  0
 M9D  CONST_21  C02  C03  N14  C13  180.00  0.0  0
 M9D  CONST_22  C05  N04  C03  C02  180.00  0.0  0
 M9D  CONST_23  F08  C07  C06  C05    0.00  0.0  0
 M9D  CONST_24  F08  C07  C06  C12  180.00  0.0  0
 M9D  CONST_25  H14  C12  C11  C10  180.00  0.0  0
 M9D  CONST_26  H29  N04  C05  C13  180.00  0.0  0
 M9D  CONST_27  H2   C13  N14  C03  180.00  0.0  0
 M9D  CONST_28  H13  C11  C12  C06  180.00  0.0  0
 M9D  CONST_29  H12  C09  C07  C06  180.00  0.0  0
 M9D  CONST_30  H1   C10  C09  C07  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
 M9D  chir_01  C02  C01  C03  N15  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
 M9D  plan-1  C13  0.020
 M9D  plan-1  C02  0.020
 M9D  plan-1  C03  0.020
 M9D  plan-1  C05  0.020
 M9D  plan-1  C06  0.020
 M9D  plan-1  N04  0.020
 M9D  plan-1  N14  0.020
 M9D  plan-1  H2   0.020
 M9D  plan-1  H29  0.020
 M9D  plan-2  C10  0.020
 M9D  plan-2  C05  0.020
 M9D  plan-2  C06  0.020
 M9D  plan-2  C07  0.020
 M9D  plan-2  C09  0.020
 M9D  plan-2  C11  0.020
 M9D  plan-2  C12  0.020
 M9D  plan-2  F08  0.020
 M9D  plan-2  H1   0.020
 M9D  plan-2  H12  0.020
 M9D  plan-2  H13  0.020
 M9D  plan-2  H14  0.020

