FMO DATABASE

FMODB ID: K9933

Calculation Name: 4D2K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D2K

Chain ID: A

ChEMBL ID:

UniProt ID: Q7K304

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-563107.143633
FMO2-HF: Nuclear repulsion	530954.279631
FMO2-HF: Total energy	-32152.864002
FMO2-MP2: Total energy	-32248.779511

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
30.829	33.378	0.188	-1.29	-1.447	0.005

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.968 / q_NPA : 0.970

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

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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	9	LYS	1	0.841	0.909	3.808	26.184	27.909	-0.023	-0.856	-0.846	0.002
4	A	10	ARG	1	0.911	0.962	3.206	21.050	21.874	0.211	-0.434	-0.601	0.003
5	A	11	PRO	0	-0.015	0.004	6.675	2.367	2.367	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.029	0.018	9.507	-0.585	-0.585	0.000	0.000	0.000	0.000
7	A	13	LYS	1	0.909	0.964	12.058	16.450	16.450	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.003	0.010	15.847	0.120	0.120	0.000	0.000	0.000	0.000
9	A	15	TRP	0	0.042	-0.001	18.190	0.306	0.306	0.000	0.000	0.000	0.000
10	A	16	ASP	-1	-0.743	-0.861	21.760	-10.164	-10.164	0.000	0.000	0.000	0.000
11	A	17	SER	0	0.022	-0.022	24.831	-0.043	-0.043	0.000	0.000	0.000	0.000
12	A	18	TRP	0	-0.012	0.005	26.676	0.147	0.147	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.748	0.866	24.627	10.585	10.585	0.000	0.000	0.000	0.000
14	A	20	ASN	0	-0.010	0.000	26.275	0.096	0.096	0.000	0.000	0.000	0.000
15	A	21	VAL	0	-0.038	-0.012	24.476	-0.199	-0.199	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.860	0.914	22.311	10.666	10.666	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.870	0.927	20.092	11.637	11.637	0.000	0.000	0.000	0.000
18	A	24	GLY	0	0.009	0.019	16.388	-0.334	-0.334	0.000	0.000	0.000	0.000
19	A	25	VAL	0	-0.034	-0.015	13.310	0.321	0.321	0.000	0.000	0.000	0.000
20	A	26	VAL	0	0.019	-0.009	9.681	-1.006	-1.006	0.000	0.000	0.000	0.000
21	A	27	VAL	0	-0.023	-0.009	9.636	0.544	0.544	0.000	0.000	0.000	0.000
22	A	28	GLY	0	-0.011	-0.009	6.798	-2.027	-2.027	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.045	-0.040	6.859	-0.484	-0.484	0.000	0.000	0.000	0.000
24	A	30	PHE	0	0.088	0.059	9.598	0.216	0.216	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.789	-0.888	12.445	-16.277	-16.277	0.000	0.000	0.000	0.000
26	A	32	GLU	-1	-0.787	-0.891	11.261	-19.874	-19.874	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.014	-0.007	12.355	0.278	0.278	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.025	0.020	14.093	0.681	0.681	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.036	-0.015	17.279	0.564	0.564	0.000	0.000	0.000	0.000
30	A	36	ARG	1	0.868	0.928	15.069	16.515	16.515	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.024	0.023	17.466	0.293	0.293	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.854	0.907	18.750	11.835	11.835	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.807	-0.894	20.169	-12.930	-12.930	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.797	0.897	18.764	14.128	14.128	0.000	0.000	0.000	0.000
35	A	41	LEU	0	-0.036	-0.021	21.291	0.306	0.306	0.000	0.000	0.000	0.000
36	A	42	GLY	0	-0.021	0.009	24.191	0.406	0.406	0.000	0.000	0.000	0.000
37	A	43	VAL	0	-0.056	-0.025	24.835	0.415	0.415	0.000	0.000	0.000	0.000
38	A	44	PRO	0	0.031	0.013	25.932	-0.282	-0.282	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.045	0.008	24.454	-0.108	-0.108	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.002	0.006	24.803	-0.312	-0.312	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.783	-0.846	27.095	-9.264	-9.264	0.000	0.000	0.000	0.000
42	A	48	PRO	0	0.014	0.016	25.185	-0.438	-0.438	0.000	0.000	0.000	0.000
43	A	49	VAL	0	-0.020	-0.023	21.614	0.207	0.207	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.853	0.933	22.145	9.827	9.827	0.000	0.000	0.000	0.000
45	A	51	VAL	0	0.007	0.002	16.443	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.010	0.007	19.520	0.002	0.002	0.000	0.000	0.000	0.000
47	A	53	LEU	0	0.003	-0.004	15.387	-0.501	-0.501	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.870	-0.931	18.785	-11.210	-11.210	0.000	0.000	0.000	0.000
49	A	55	CYS	0	-0.036	-0.013	19.684	0.257	0.257	0.000	0.000	0.000	0.000
50	A	56	ASP	-1	-0.786	-0.880	21.162	-11.988	-11.988	0.000	0.000	0.000	0.000
51	A	57	GLY	0	0.015	0.005	22.687	0.297	0.297	0.000	0.000	0.000	0.000
52	A	58	THR	0	-0.055	-0.042	19.018	0.197	0.197	0.000	0.000	0.000	0.000
53	A	59	GLN	0	-0.076	-0.060	19.909	-0.168	-0.168	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.036	-0.016	13.786	-0.398	-0.398	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.904	-0.950	17.125	-11.223	-11.223	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.799	-0.890	14.602	-14.789	-14.789	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.017	-0.012	11.262	-0.633	-0.633	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.809	-0.890	10.031	-18.572	-18.572	0.000	0.000	0.000	0.000
59	A	65	TYR	0	0.066	0.027	10.421	-1.147	-1.147	0.000	0.000	0.000	0.000
60	A	66	PHE	0	-0.014	0.014	7.363	-0.787	-0.787	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.768	0.865	5.941	19.463	19.463	0.000	0.000	0.000	0.000
62	A	68	THR	0	-0.074	-0.042	6.325	-2.043	-2.043	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.015	0.011	8.835	-0.051	-0.051	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.039	0.023	7.534	-2.237	-2.237	0.000	0.000	0.000	0.000
65	A	71	ASN	0	0.030	0.000	6.187	0.950	0.950	0.000	0.000	0.000	0.000
66	A	72	ASN	0	-0.090	-0.068	8.868	1.989	1.989	0.000	0.000	0.000	0.000
67	A	73	THR	0	0.054	0.018	11.269	1.292	1.292	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.041	-0.019	13.432	-0.203	-0.203	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.014	0.015	13.243	0.181	0.181	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.005	0.002	17.587	0.205	0.205	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.023	-0.007	20.482	-0.200	-0.200	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.038	-0.015	21.933	0.406	0.406	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.872	0.894	25.238	9.292	9.292	0.000	0.000	0.000	0.000
74	A	80	GLN	0	-0.047	-0.045	27.689	0.331	0.331	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.014	0.013	30.681	0.171	0.171	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.807	-0.865	28.075	-9.487	-9.487	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.959	0.961	28.618	8.213	8.213	0.000	0.000	0.000	0.000
78	A	84	TRP	0	0.001	0.018	23.759	0.191	0.191	0.000	0.000	0.000	0.000
79	A	85	LEU	0	-0.001	0.002	27.226	0.304	0.304	0.000	0.000	0.000	0.000
80	A	86	GLU	-1	-0.847	-0.915	27.832	-9.024	-9.024	0.000	0.000	0.000	0.000
81	A	87	HIS	0	-0.074	-0.033	28.001	-0.053	-0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)