FMO DATABASE

FMODB ID: 5223Z

Calculation Name: 4CVD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CVD

Chain ID: A

ChEMBL ID:

UniProt ID: P19385

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	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	48
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-214909.097336
FMO2-HF: Nuclear repulsion	196653.773505
FMO2-HF: Total energy	-18255.323831
FMO2-MP2: Total energy	-18309.677574

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:253:LEU)

Summations of interaction energy for fragment #1(A:253:LEU)

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.
-10.677	-3.388	1.789	-2.652	-6.424	0

Interaction energy analysis for fragmet #1(A:253:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.018

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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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	255	THR	0	0.006	0.006	3.797	-2.763	-0.986	-0.015	-0.764	-0.998	0.004
4	A	256	VAL	0	0.059	0.035	2.613	-2.219	-1.188	0.372	-0.369	-1.033	-0.001
5	A	257	ALA	0	0.031	0.018	3.580	-0.700	-0.023	0.005	-0.308	-0.374	0.001
6	A	258	ASN	0	0.011	-0.014	5.446	0.027	0.027	0.000	0.000	0.000	0.000
7	A	259	GLU	-1	-0.862	-0.922	7.268	0.667	0.667	0.000	0.000	0.000	0.000
8	A	260	VAL	0	-0.033	-0.021	7.442	-0.038	-0.038	0.000	0.000	0.000	0.000
9	A	261	ILE	0	-0.053	-0.021	9.464	0.032	0.032	0.000	0.000	0.000	0.000
10	A	262	GLN	0	-0.086	-0.038	11.409	0.106	0.106	0.000	0.000	0.000	0.000
11	A	263	GLY	0	0.025	0.020	12.726	0.022	0.022	0.000	0.000	0.000	0.000
12	A	264	LEU	0	-0.066	-0.035	11.196	0.005	0.005	0.000	0.000	0.000	0.000
13	A	265	TRP	0	-0.035	-0.029	8.011	-0.114	-0.114	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.051	0.042	12.297	-0.042	-0.042	0.000	0.000	0.000	0.000
15	A	267	ASN	0	0.002	-0.014	14.489	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	268	GLY	0	-0.021	-0.019	15.779	0.005	0.005	0.000	0.000	0.000	0.000
17	A	269	GLN	0	-0.010	-0.016	14.379	-0.047	-0.047	0.000	0.000	0.000	0.000
18	A	270	GLU	-1	-0.876	-0.927	14.892	-0.162	-0.162	0.000	0.000	0.000	0.000
19	A	271	ARG	1	0.895	0.945	8.860	0.684	0.684	0.000	0.000	0.000	0.000
20	A	272	TYR	0	-0.051	-0.042	10.227	-0.112	-0.112	0.000	0.000	0.000	0.000
21	A	273	ASP	-1	-0.851	-0.927	11.024	-0.335	-0.335	0.000	0.000	0.000	0.000
22	A	274	SER	0	-0.012	-0.015	12.524	0.023	0.023	0.000	0.000	0.000	0.000
23	A	275	LEU	0	-0.041	-0.022	5.931	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	276	ALA	0	0.018	0.008	8.680	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	277	ASN	0	-0.069	-0.024	10.301	0.032	0.032	0.000	0.000	0.000	0.000
26	A	278	ALA	0	-0.048	-0.021	9.105	0.051	0.051	0.000	0.000	0.000	0.000
27	A	279	GLY	0	-0.020	0.003	9.004	0.075	0.075	0.000	0.000	0.000	0.000
28	A	280	TYR	0	-0.059	-0.029	3.044	-0.806	-0.194	0.073	-0.142	-0.542	0.000
29	A	281	ASP	-1	-0.836	-0.926	4.063	-1.335	-1.256	-0.001	-0.019	-0.060	0.000
30	A	282	PRO	0	-0.011	-0.024	4.477	-0.625	-0.501	-0.001	-0.008	-0.115	0.000
31	A	283	GLN	0	-0.015	-0.012	6.659	0.017	0.017	0.000	0.000	0.000	0.000
32	A	284	ALA	0	0.029	0.031	2.616	-0.650	-0.143	0.428	-0.191	-0.744	0.000
33	A	285	VAL	0	-0.021	-0.013	2.493	-2.726	-1.171	0.855	-0.692	-1.719	-0.004
34	A	286	GLN	0	0.036	0.044	3.751	0.352	0.451	0.008	-0.005	-0.101	0.000
35	A	287	ASP	-1	-0.870	-0.934	5.431	-0.989	-0.989	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.812	0.899	3.297	0.084	0.868	0.066	-0.153	-0.697	0.000
37	A	289	VAL	0	-0.005	-0.015	5.285	0.427	0.471	-0.001	-0.001	-0.041	0.000
38	A	290	ASN	0	-0.044	-0.022	7.666	0.301	0.301	0.000	0.000	0.000	0.000
39	A	291	GLU	-1	-0.851	-0.908	7.663	-0.292	-0.292	0.000	0.000	0.000	0.000
40	A	292	ILE	0	-0.042	-0.026	6.570	0.142	0.142	0.000	0.000	0.000	0.000
41	A	293	LEU	0	-0.047	-0.034	10.376	0.107	0.107	0.000	0.000	0.000	0.000
42	A	294	ASN	0	-0.081	-0.031	12.976	0.063	0.063	0.000	0.000	0.000	0.000
43	A	295	ALA	0	0.019	0.016	13.352	0.034	0.034	0.000	0.000	0.000	0.000
44	A	296	ARG	1	0.885	0.963	14.935	0.123	0.123	0.000	0.000	0.000	0.000
45	A	297	GLU	-1	-0.861	-0.916	16.515	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	298	ILE	0	-0.062	-0.049	19.879	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	299	ALA	0	-0.045	-0.013	19.923	0.015	0.015	0.000	0.000	0.000	0.000
48	A	300	ASP	-1	-0.979	-0.989	21.983	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:253:LEU)