FMO DATABASE

FMODB ID: N9M2Q

Calculation Name: 3B1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B1S

Chain ID: A

ChEMBL ID:

UniProt ID: O67813

Base Structure: X-ray

Registration Date: 2023-09-20

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	32
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-105039.83322
FMO2-HF: Nuclear repulsion	91813.807218
FMO2-HF: Total energy	-13226.026002
FMO2-MP2: Total energy	-13262.593081

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:232:PRO)

Summations of interaction energy for fragment #1(A:232:PRO)

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.
0.923	4.51	0.915	-1.398	-3.101	0.004

Interaction energy analysis for fragmet #1(A:232:PRO)

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 : 0.008

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	234	VAL	0	0.091	0.037	3.844	-0.640	0.885	-0.008	-0.638	-0.879	0.002
4	A	235	LYS	1	0.991	1.009	2.409	-2.386	-0.856	0.921	-0.639	-1.811	0.002
5	A	236	SER	0	0.011	-0.025	3.551	0.622	1.154	0.002	-0.121	-0.411	0.000
6	A	237	ARG	1	0.967	1.011	5.422	1.075	1.075	0.000	0.000	0.000	0.000
7	A	238	ILE	0	0.060	0.019	6.981	0.229	0.229	0.000	0.000	0.000	0.000
8	A	239	LYS	1	0.955	0.975	5.361	0.804	0.804	0.000	0.000	0.000	0.000
9	A	240	ALA	0	-0.047	-0.013	9.275	0.102	0.102	0.000	0.000	0.000	0.000
10	A	241	ARG	1	0.993	1.000	11.195	0.368	0.368	0.000	0.000	0.000	0.000
11	A	242	MET	0	0.036	0.015	10.630	0.063	0.063	0.000	0.000	0.000	0.000
12	A	243	ARG	1	0.937	0.971	9.259	0.536	0.536	0.000	0.000	0.000	0.000
13	A	244	GLU	-1	-0.953	-0.983	15.051	-0.242	-0.242	0.000	0.000	0.000	0.000
14	A	245	LEU	0	-0.018	-0.023	16.361	0.027	0.027	0.000	0.000	0.000	0.000
15	A	246	ALA	0	0.000	0.006	18.124	0.023	0.023	0.000	0.000	0.000	0.000
16	A	247	LYS	1	0.986	0.983	19.443	0.184	0.184	0.000	0.000	0.000	0.000
17	A	248	SER	0	0.005	-0.003	21.409	0.012	0.012	0.000	0.000	0.000	0.000
18	A	249	ARG	1	0.950	0.987	21.573	0.112	0.112	0.000	0.000	0.000	0.000
19	A	250	MET	0	0.031	0.007	23.687	0.008	0.008	0.000	0.000	0.000	0.000
20	A	251	MET	0	-0.048	-0.024	24.676	0.008	0.008	0.000	0.000	0.000	0.000
21	A	252	ALA	0	0.021	0.020	27.555	0.005	0.005	0.000	0.000	0.000	0.000
22	A	253	GLU	-1	-0.845	-0.908	28.878	-0.059	-0.059	0.000	0.000	0.000	0.000
23	A	254	VAL	0	-0.001	0.009	29.488	0.004	0.004	0.000	0.000	0.000	0.000
24	A	255	PRO	0	-0.081	-0.039	32.109	0.004	0.004	0.000	0.000	0.000	0.000
25	A	256	LYS	1	0.868	0.919	32.976	0.063	0.063	0.000	0.000	0.000	0.000
26	A	257	ALA	0	-0.053	-0.008	34.135	0.002	0.002	0.000	0.000	0.000	0.000
27	A	258	THR	0	0.027	0.013	36.024	0.001	0.001	0.000	0.000	0.000	0.000
28	A	259	VAL	0	-0.001	-0.014	37.329	0.002	0.002	0.000	0.000	0.000	0.000
29	A	260	VAL	0	-0.019	-0.003	33.160	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	261	ILE	0	-0.004	0.004	34.237	0.002	0.002	0.000	0.000	0.000	0.000
31	A	262	THR	0	-0.006	0.000	33.265	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	263	ASN	0	0.005	0.004	32.263	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:232:PRO)