FMO DATABASE

FMODB ID: MV23Z

Calculation Name: 4JVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JVW

Chain ID: A

ChEMBL ID:

UniProt ID: P01872

Base Structure: X-ray

Registration Date: 2023-06-26

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-804498.657031
FMO2-HF: Nuclear repulsion	762567.208687
FMO2-HF: Total energy	-41931.448344
FMO2-MP2: Total energy	-42054.318531

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:449:LYS)

Summations of interaction energy for fragment #1(A:449:LYS)

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.
-193.172	-189.705	23.209	-13.989	-12.687	-0.137

Interaction energy analysis for fragmet #1(A:449:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.915

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	451	PRO	0	0.031	0.020	3.781	-2.497	0.532	-0.034	-1.548	-1.447	0.005
4	A	452	PRO	0	-0.024	0.004	6.267	1.978	1.978	0.000	0.000	0.000	0.000
5	A	453	ALA	0	-0.006	0.004	9.356	0.722	0.722	0.000	0.000	0.000	0.000
6	A	454	VAL	0	-0.008	-0.017	12.673	0.095	0.095	0.000	0.000	0.000	0.000
7	A	455	TYR	0	-0.033	-0.024	15.215	0.373	0.373	0.000	0.000	0.000	0.000
8	A	456	LEU	0	-0.013	0.004	19.081	-0.123	-0.123	0.000	0.000	0.000	0.000
9	A	457	LEU	0	-0.029	-0.021	21.796	0.377	0.377	0.000	0.000	0.000	0.000
10	A	458	PRO	0	0.040	0.018	25.016	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	459	PRO	0	0.019	0.016	28.378	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	460	ALA	0	0.012	0.018	31.011	0.132	0.132	0.000	0.000	0.000	0.000
13	A	461	ARG	1	0.937	0.943	32.772	7.941	7.941	0.000	0.000	0.000	0.000
14	A	462	GLU	-1	-0.887	-0.946	35.504	-8.123	-8.123	0.000	0.000	0.000	0.000
15	A	463	GLN	0	0.032	0.014	33.015	0.013	0.013	0.000	0.000	0.000	0.000
16	A	464	LEU	0	0.043	0.021	34.222	0.193	0.193	0.000	0.000	0.000	0.000
17	A	465	ASN	0	-0.047	-0.033	37.780	0.184	0.184	0.000	0.000	0.000	0.000
18	A	466	LEU	0	-0.044	-0.020	39.191	0.208	0.208	0.000	0.000	0.000	0.000
19	A	467	ARG	1	0.769	0.880	41.141	7.310	7.310	0.000	0.000	0.000	0.000
20	A	468	GLU	-1	-0.904	-0.944	39.649	-7.573	-7.573	0.000	0.000	0.000	0.000
21	A	469	SER	0	-0.026	-0.010	35.065	-0.133	-0.133	0.000	0.000	0.000	0.000
22	A	470	ALA	0	-0.031	-0.016	32.991	0.099	0.099	0.000	0.000	0.000	0.000
23	A	471	THR	0	-0.028	-0.020	28.246	-0.036	-0.036	0.000	0.000	0.000	0.000
24	A	472	VAL	0	-0.005	0.012	25.335	0.010	0.010	0.000	0.000	0.000	0.000
25	A	473	THR	0	0.016	-0.001	22.418	-0.217	-0.217	0.000	0.000	0.000	0.000
26	A	474	CYS	0	-0.086	-0.009	18.466	-0.567	-0.567	0.000	0.000	0.000	0.000
27	A	475	LEU	0	-0.012	-0.008	18.180	-0.307	-0.307	0.000	0.000	0.000	0.000
28	A	476	VAL	0	0.009	0.004	12.023	-0.257	-0.257	0.000	0.000	0.000	0.000
29	A	477	LYS	1	0.871	0.895	12.408	16.577	16.577	0.000	0.000	0.000	0.000
30	A	478	GLY	0	0.093	0.061	9.529	-0.793	-0.793	0.000	0.000	0.000	0.000
31	A	479	PHE	0	-0.024	0.008	6.226	-1.274	-1.274	0.000	0.000	0.000	0.000
32	A	480	SER	0	-0.004	-0.009	2.799	0.668	1.159	0.165	-0.193	-0.464	0.000
33	A	481	PRO	0	0.033	0.016	2.317	-8.169	-5.426	3.035	-2.328	-3.450	-0.024
34	A	482	ALA	0	0.019	-0.004	5.043	1.372	1.376	-0.001	-0.004	0.002	0.000
35	A	483	ASP	-1	-0.921	-0.952	7.559	-28.380	-28.380	0.000	0.000	0.000	0.000
36	A	484	ILE	0	-0.030	-0.013	8.135	-2.489	-2.489	0.000	0.000	0.000	0.000
37	A	485	SER	0	-0.017	0.015	10.738	2.103	2.103	0.000	0.000	0.000	0.000
38	A	486	VAL	0	0.017	-0.008	13.906	-0.371	-0.371	0.000	0.000	0.000	0.000
39	A	487	GLN	0	0.019	0.022	16.293	1.209	1.209	0.000	0.000	0.000	0.000
40	A	488	TRP	0	0.018	0.011	19.555	0.051	0.051	0.000	0.000	0.000	0.000
41	A	489	LEU	0	-0.026	0.002	22.576	0.104	0.104	0.000	0.000	0.000	0.000
42	A	490	GLN	0	-0.029	-0.045	24.452	-0.129	-0.129	0.000	0.000	0.000	0.000
43	A	491	ARG	1	0.828	0.865	28.053	9.087	9.087	0.000	0.000	0.000	0.000
44	A	492	GLY	0	-0.005	0.008	27.331	0.121	0.121	0.000	0.000	0.000	0.000
45	A	493	GLN	0	-0.010	-0.001	26.780	-0.047	-0.047	0.000	0.000	0.000	0.000
46	A	494	LEU	0	-0.003	-0.002	20.715	0.046	0.046	0.000	0.000	0.000	0.000
47	A	495	LEU	0	-0.018	-0.010	24.476	0.423	0.423	0.000	0.000	0.000	0.000
48	A	496	PRO	0	0.009	0.006	24.817	-0.515	-0.515	0.000	0.000	0.000	0.000
49	A	497	GLN	0	0.025	-0.010	21.239	0.175	0.175	0.000	0.000	0.000	0.000
50	A	498	GLU	-1	-0.894	-0.942	25.151	-11.032	-11.032	0.000	0.000	0.000	0.000
51	A	499	LYS	1	0.880	0.938	27.873	10.399	10.399	0.000	0.000	0.000	0.000
52	A	500	TYR	0	-0.036	-0.007	21.110	-0.150	-0.150	0.000	0.000	0.000	0.000
53	A	501	VAL	0	0.021	0.019	24.328	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	502	THR	0	0.004	0.003	17.907	0.180	0.180	0.000	0.000	0.000	0.000
55	A	503	SER	0	-0.029	0.005	18.890	0.366	0.366	0.000	0.000	0.000	0.000
56	A	504	ALA	0	0.019	0.014	16.981	-0.893	-0.893	0.000	0.000	0.000	0.000
57	A	505	PRO	0	0.001	-0.008	11.985	0.648	0.648	0.000	0.000	0.000	0.000
58	A	506	MET	0	-0.052	-0.009	14.082	0.877	0.877	0.000	0.000	0.000	0.000
59	A	507	PRO	0	0.016	-0.003	12.442	-0.916	-0.916	0.000	0.000	0.000	0.000
60	A	508	GLU	-1	-0.813	-0.901	11.834	-17.769	-17.769	0.000	0.000	0.000	0.000
61	A	509	PRO	0	-0.018	-0.012	13.727	0.045	0.045	0.000	0.000	0.000	0.000
62	A	510	GLY	0	-0.015	-0.005	16.193	0.299	0.299	0.000	0.000	0.000	0.000
63	A	511	ALA	0	-0.028	-0.006	10.812	0.125	0.125	0.000	0.000	0.000	0.000
64	A	512	PRO	0	0.046	0.018	11.134	-1.104	-1.104	0.000	0.000	0.000	0.000
65	A	513	GLY	0	0.006	0.001	8.240	-0.518	-0.518	0.000	0.000	0.000	0.000
66	A	514	PHE	0	-0.051	-0.014	5.669	-3.278	-3.278	0.000	0.000	0.000	0.000
67	A	515	TYR	0	-0.030	-0.011	7.460	1.476	1.476	0.000	0.000	0.000	0.000
68	A	516	PHE	0	-0.042	-0.019	10.205	-0.202	-0.202	0.000	0.000	0.000	0.000
69	A	517	THR	0	0.017	-0.012	12.871	0.511	0.511	0.000	0.000	0.000	0.000
70	A	518	HIS	0	0.012	0.007	15.627	0.021	0.021	0.000	0.000	0.000	0.000
71	A	519	SER	0	0.023	0.007	18.790	0.102	0.102	0.000	0.000	0.000	0.000
72	A	520	ILE	0	-0.018	-0.012	21.049	0.186	0.186	0.000	0.000	0.000	0.000
73	A	521	LEU	0	0.042	0.029	24.617	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	522	THR	0	-0.029	-0.011	27.077	0.201	0.201	0.000	0.000	0.000	0.000
75	A	523	VAL	0	0.013	0.030	30.793	0.054	0.054	0.000	0.000	0.000	0.000
76	A	524	THR	0	0.037	0.012	33.382	0.171	0.171	0.000	0.000	0.000	0.000
77	A	525	GLU	-1	-0.884	-0.957	36.100	-7.915	-7.915	0.000	0.000	0.000	0.000
78	A	526	GLU	-1	-0.799	-0.894	37.639	-7.337	-7.337	0.000	0.000	0.000	0.000
79	A	527	GLU	-1	-0.851	-0.901	33.438	-9.303	-9.303	0.000	0.000	0.000	0.000
80	A	528	TRP	0	0.054	0.033	29.225	-0.172	-0.172	0.000	0.000	0.000	0.000
81	A	529	ASN	0	-0.002	0.001	34.886	-0.086	-0.086	0.000	0.000	0.000	0.000
82	A	530	SER	0	-0.118	-0.068	37.211	0.102	0.102	0.000	0.000	0.000	0.000
83	A	531	GLY	0	-0.008	-0.004	35.287	0.092	0.092	0.000	0.000	0.000	0.000
84	A	532	GLU	-1	-0.809	-0.832	31.778	-9.553	-9.553	0.000	0.000	0.000	0.000
85	A	533	THR	0	-0.032	-0.009	28.309	-0.112	-0.112	0.000	0.000	0.000	0.000
86	A	534	TYR	0	-0.058	-0.066	26.520	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	535	THR	0	0.038	0.020	21.182	0.052	0.052	0.000	0.000	0.000	0.000
88	A	537	VAL	0	-0.003	-0.019	17.000	-0.392	-0.392	0.000	0.000	0.000	0.000
89	A	538	VAL	0	0.005	-0.017	11.502	-0.145	-0.145	0.000	0.000	0.000	0.000
90	A	539	GLY	0	0.016	0.017	11.813	-0.307	-0.307	0.000	0.000	0.000	0.000
91	A	540	HIS	0	0.014	-0.031	3.754	-1.040	-0.869	0.000	-0.021	-0.150	0.000
92	A	541	GLU	-1	-0.799	-0.890	1.615	-127.657	-131.285	19.333	-9.536	-6.168	-0.117
93	A	542	ALA	0	-0.031	-0.007	2.332	-4.898	-4.340	0.710	-0.324	-0.944	-0.001
94	A	543	LEU	0	-0.054	-0.016	4.113	4.575	4.674	0.001	-0.035	-0.066	0.000
95	A	544	PRO	0	-0.003	-0.002	7.879	-0.525	-0.525	0.000	0.000	0.000	0.000
96	A	545	HIS	0	0.003	-0.008	9.905	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	546	LEU	0	-0.018	0.013	8.647	1.468	1.468	0.000	0.000	0.000	0.000
98	A	547	VAL	0	0.023	-0.008	10.718	-0.782	-0.782	0.000	0.000	0.000	0.000
99	A	548	THR	0	-0.056	-0.007	12.580	1.155	1.155	0.000	0.000	0.000	0.000
100	A	549	GLU	-1	-0.845	-0.936	14.418	-15.199	-15.199	0.000	0.000	0.000	0.000
101	A	550	ARG	1	0.812	0.903	14.464	17.354	17.354	0.000	0.000	0.000	0.000
102	A	551	THR	0	0.027	-0.002	20.218	-0.103	-0.103	0.000	0.000	0.000	0.000
103	A	552	VAL	0	-0.059	-0.023	23.934	0.063	0.063	0.000	0.000	0.000	0.000
104	A	553	ASP	-1	-0.753	-0.881	26.711	-9.660	-9.660	0.000	0.000	0.000	0.000
105	A	554	LYS	1	0.868	0.929	30.447	7.884	7.884	0.000	0.000	0.000	0.000
106	A	555	SER	0	-0.060	-0.036	32.679	0.251	0.251	0.000	0.000	0.000	0.000
107	A	556	THR	0	-0.055	-0.016	27.207	-0.153	-0.153	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:449:LYS)