FMO DATABASE

FMODB ID: 821NY

Calculation Name: 1MVF-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MVF

Chain ID: D

ChEMBL ID:

UniProt ID: P0AE72

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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-171748.955172
FMO2-HF: Nuclear repulsion	154976.261942
FMO2-HF: Total energy	-16772.69323
FMO2-MP2: Total energy	-16821.874444

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(D:4:SER)

Summations of interaction energy for fragment #1(D:4:SER)

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.
-2.156	-0.042	-0.031	-1.047	-1.036	0.002

Interaction energy analysis for fragmet #1(D:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.002

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	D	6	VAL	0	0.048	0.053	3.801	-0.244	1.724	-0.029	-1.039	-0.901	0.002
4	D	7	LYS	1	0.858	0.914	6.266	0.362	0.362	0.000	0.000	0.000	0.000
5	D	8	ARG	1	0.955	0.978	8.940	-0.096	-0.096	0.000	0.000	0.000	0.000
6	D	9	TRP	0	0.017	0.013	12.415	0.086	0.086	0.000	0.000	0.000	0.000
7	D	10	GLY	0	0.031	0.011	13.939	-0.022	-0.022	0.000	0.000	0.000	0.000
8	D	11	ASN	0	0.021	0.004	17.473	-0.033	-0.033	0.000	0.000	0.000	0.000
9	D	12	SER	0	0.004	0.002	15.836	-0.033	-0.033	0.000	0.000	0.000	0.000
10	D	13	PRO	0	-0.012	0.002	12.034	0.047	0.047	0.000	0.000	0.000	0.000
11	D	14	ALA	0	0.047	0.024	10.191	0.033	0.033	0.000	0.000	0.000	0.000
12	D	15	VAL	0	0.024	-0.001	4.220	-0.262	-0.208	-0.001	-0.007	-0.046	0.000
13	D	16	ARG	1	0.943	0.980	5.859	-2.102	-2.102	0.000	0.000	0.000	0.000
14	D	17	ILE	0	0.066	0.030	5.457	0.863	0.863	0.000	0.000	0.000	0.000
15	D	18	PRO	0	-0.013	0.003	4.976	-0.342	-0.250	-0.001	-0.001	-0.089	0.000
16	D	19	ALA	0	0.081	0.020	7.587	-0.346	-0.346	0.000	0.000	0.000	0.000
17	D	20	THR	0	0.033	0.015	9.421	-0.031	-0.031	0.000	0.000	0.000	0.000
18	D	21	LEU	0	0.004	0.000	6.598	-0.111	-0.111	0.000	0.000	0.000	0.000
19	D	22	MET	0	-0.009	0.011	10.424	-0.113	-0.113	0.000	0.000	0.000	0.000
20	D	23	GLN	0	0.001	-0.003	12.922	-0.079	-0.079	0.000	0.000	0.000	0.000
21	D	24	ALA	0	-0.051	-0.016	12.902	-0.072	-0.072	0.000	0.000	0.000	0.000
22	D	25	LEU	0	-0.036	-0.019	12.668	-0.075	-0.075	0.000	0.000	0.000	0.000
23	D	26	ASN	0	-0.069	-0.029	15.917	-0.028	-0.028	0.000	0.000	0.000	0.000
24	D	27	LEU	0	0.008	0.006	13.501	-0.015	-0.015	0.000	0.000	0.000	0.000
25	D	28	ASN	0	-0.096	-0.053	16.788	0.064	0.064	0.000	0.000	0.000	0.000
26	D	29	ILE	0	-0.052	-0.045	15.540	0.013	0.013	0.000	0.000	0.000	0.000
27	D	30	ASP	-1	-0.921	-0.965	18.077	0.247	0.247	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.835	-0.888	18.265	0.227	0.227	0.000	0.000	0.000	0.000
29	D	32	GLU	-1	-0.939	-0.972	18.179	0.137	0.137	0.000	0.000	0.000	0.000
30	D	33	VAL	0	-0.060	-0.046	14.285	0.007	0.007	0.000	0.000	0.000	0.000
31	D	34	LYS	1	0.789	0.882	17.272	-0.047	-0.047	0.000	0.000	0.000	0.000
32	D	35	ILE	0	-0.026	-0.026	13.115	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	36	ASP	-1	-0.850	-0.917	14.885	-0.160	-0.160	0.000	0.000	0.000	0.000
34	D	37	LEU	0	-0.098	-0.044	14.751	-0.060	-0.060	0.000	0.000	0.000	0.000
35	D	38	VAL	0	0.060	0.028	15.849	0.027	0.027	0.000	0.000	0.000	0.000
36	D	39	ASP	-1	-0.857	-0.923	16.123	-0.363	-0.363	0.000	0.000	0.000	0.000
37	D	40	GLY	0	-0.027	-0.017	16.061	-0.046	-0.046	0.000	0.000	0.000	0.000
38	D	41	LYS	1	0.811	0.903	11.767	0.341	0.341	0.000	0.000	0.000	0.000
39	D	42	LEU	0	-0.022	-0.006	9.071	0.074	0.074	0.000	0.000	0.000	0.000
40	D	43	ILE	0	-0.018	-0.014	10.805	-0.023	-0.023	0.000	0.000	0.000	0.000
41	D	44	ILE	0	0.005	-0.006	9.078	0.029	0.029	0.000	0.000	0.000	0.000
42	D	45	GLU	-1	-0.853	-0.906	12.827	0.027	0.027	0.000	0.000	0.000	0.000
43	D	46	PRO	0	0.069	0.034	15.646	-0.005	-0.005	0.000	0.000	0.000	0.000
44	D	47	VAL	0	-0.038	0.001	18.143	-0.031	-0.031	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:4:SER)