FMO DATABASE

FMODB ID: 22G7R

Calculation Name: 5DUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUK

Chain ID: A

ChEMBL ID:

UniProt ID: M7T6A0

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343490.960672
FMO2-HF: Nuclear repulsion	317831.198455
FMO2-HF: Total energy	-25659.762217
FMO2-MP2: Total energy	-25734.854155

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:12:ASP)

Summations of interaction energy for fragment #1(A:12:ASP)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-93.977	-89.15	0.197	-2.026	-2.999	0.015

Interaction energy analysis for fragmet #1(A:12:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.922 / q_NPA : -0.959

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	14	ARG	1	0.862	0.940	3.668	-38.822	-36.740	0.004	-0.912	-1.175	0.005
4	A	15	ARG	1	0.931	0.958	3.205	-47.064	-45.170	0.192	-0.882	-1.204	0.009
5	A	16	GLU	-1	-0.867	-0.937	4.169	44.273	45.124	0.001	-0.232	-0.620	0.001
6	A	17	ILE	0	-0.024	-0.005	5.875	-5.775	-5.775	0.000	0.000	0.000	0.000
7	A	18	TYR	0	-0.028	-0.020	8.068	-2.758	-2.758	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.953	0.968	8.257	-29.149	-29.149	0.000	0.000	0.000	0.000
9	A	20	HIS	0	-0.019	-0.028	10.018	-1.347	-1.347	0.000	0.000	0.000	0.000
10	A	21	ILE	0	-0.002	0.003	11.957	-1.834	-1.834	0.000	0.000	0.000	0.000
11	A	22	VAL	0	-0.052	-0.016	13.255	-1.420	-1.420	0.000	0.000	0.000	0.000
12	A	23	LYS	1	0.938	0.956	13.919	-20.972	-20.972	0.000	0.000	0.000	0.000
13	A	24	SER	0	-0.017	0.015	15.824	-1.350	-1.350	0.000	0.000	0.000	0.000
14	A	25	PRO	0	-0.002	-0.007	17.653	0.257	0.257	0.000	0.000	0.000	0.000
15	A	26	GLY	0	-0.005	-0.003	19.512	-0.492	-0.492	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.019	0.014	16.136	-0.480	-0.480	0.000	0.000	0.000	0.000
17	A	28	HIS	0	-0.055	-0.036	19.657	0.098	0.098	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-0.857	-0.938	17.368	16.944	16.944	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.976	0.966	17.095	-12.671	-12.671	0.000	0.000	0.000	0.000
20	A	31	GLN	0	-0.073	-0.052	18.063	0.442	0.442	0.000	0.000	0.000	0.000
21	A	32	LEU	0	0.063	0.043	12.916	0.525	0.525	0.000	0.000	0.000	0.000
22	A	33	ALA	0	0.002	0.001	13.107	1.410	1.410	0.000	0.000	0.000	0.000
23	A	34	LYS	1	0.918	0.973	13.828	-15.347	-15.347	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.923	-0.953	14.160	18.632	18.632	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.025	-0.012	8.638	1.202	1.202	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.935	-0.946	9.184	27.508	27.508	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.029	-0.001	8.046	2.240	2.240	0.000	0.000	0.000	0.000
28	A	39	PRO	0	0.025	-0.001	10.628	-2.419	-2.419	0.000	0.000	0.000	0.000
29	A	40	LEU	0	0.062	0.018	12.786	0.962	0.962	0.000	0.000	0.000	0.000
30	A	41	SER	0	0.026	0.006	14.975	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	42	THR	0	-0.007	0.000	8.332	-0.354	-0.354	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.022	0.004	10.703	1.285	1.285	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.046	0.032	11.736	0.136	0.136	0.000	0.000	0.000	0.000
34	A	45	TYR	0	0.009	0.012	8.932	0.163	0.163	0.000	0.000	0.000	0.000
35	A	46	HIS	0	0.005	-0.009	6.342	-0.429	-0.429	0.000	0.000	0.000	0.000
36	A	47	LEU	0	0.039	0.018	10.462	-0.118	-0.118	0.000	0.000	0.000	0.000
37	A	48	HIS	0	0.049	0.029	13.423	-1.013	-1.013	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.095	-0.044	10.331	-0.946	-0.946	0.000	0.000	0.000	0.000
39	A	50	LEU	0	-0.009	-0.022	9.332	-0.456	-0.456	0.000	0.000	0.000	0.000
40	A	51	GLU	-1	-0.868	-0.928	13.066	15.271	15.271	0.000	0.000	0.000	0.000
41	A	52	ARG	1	0.929	0.977	14.199	-17.926	-17.926	0.000	0.000	0.000	0.000
42	A	53	ARG	1	0.839	0.912	13.019	-17.189	-17.189	0.000	0.000	0.000	0.000
43	A	54	GLU	-1	-0.912	-0.944	16.204	13.002	13.002	0.000	0.000	0.000	0.000
44	A	55	LEU	0	-0.076	-0.033	11.864	0.203	0.203	0.000	0.000	0.000	0.000
45	A	56	ILE	0	-0.044	-0.021	13.525	0.380	0.380	0.000	0.000	0.000	0.000
46	A	57	MET	0	0.002	-0.003	16.396	-0.620	-0.620	0.000	0.000	0.000	0.000
47	A	58	MET	0	0.033	0.024	19.888	0.146	0.146	0.000	0.000	0.000	0.000
48	A	59	LYS	1	0.939	0.954	21.957	-12.527	-12.527	0.000	0.000	0.000	0.000
49	A	60	SER	0	0.008	0.007	25.017	0.246	0.246	0.000	0.000	0.000	0.000
50	A	61	ASP	-1	-0.784	-0.903	26.677	11.333	11.333	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.878	-0.947	28.525	9.875	9.875	0.000	0.000	0.000	0.000
52	A	63	ARG	1	0.868	0.941	29.142	-10.872	-10.872	0.000	0.000	0.000	0.000
53	A	64	TYR	0	-0.053	-0.024	28.031	0.049	0.049	0.000	0.000	0.000	0.000
54	A	65	ALA	0	-0.009	0.017	31.598	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	66	ARG	1	0.927	0.956	33.861	-9.215	-9.215	0.000	0.000	0.000	0.000
56	A	67	TYR	0	0.022	0.015	36.824	-0.095	-0.095	0.000	0.000	0.000	0.000
57	A	68	TYR	0	-0.008	-0.015	38.071	0.026	0.026	0.000	0.000	0.000	0.000
58	A	69	ALA	0	0.018	0.020	43.146	-0.025	-0.025	0.000	0.000	0.000	0.000
59	A	70	THR	0	0.011	0.005	45.392	0.066	0.066	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.979	0.993	46.640	-6.906	-6.906	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:12:ASP)