FMO DATABASE

FMODB ID: YQ5M2

Calculation Name: 7KDT-B-EM89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7KDT

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2021-02-15

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	38
LigandCharge
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-137434.262567
FMO2-HF: Nuclear repulsion	122922.618472
FMO2-HF: Total energy	-14511.644095
FMO2-MP2: Total energy	-14554.277231

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(B:39:PRO )

Summations of interaction energy for fragment #1(B:39: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.
14.048	16.263	0.08	-1.122	-1.173	-0.007

Interaction energy analysis for fragmet #1(B:39:PRO )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / 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	B	41	VAL	0	0.009	0.004	3.113	-6.510	-4.400	0.081	-1.118	-1.073	-0.007
4	B	42	TYR	0	0.030	0.018	4.751	1.660	1.765	-0.001	-0.004	-0.100	0.000
5	B	43	PRO	0	0.044	0.020	8.818	-0.025	-0.025	0.000	0.000	0.000	0.000
6	B	44	ILE	0	0.007	-0.004	11.951	-0.456	-0.456	0.000	0.000	0.000	0.000
7	B	45	ILE	0	0.016	0.016	13.715	1.507	1.507	0.000	0.000	0.000	0.000
8	B	46	LEU	0	0.017	0.013	15.952	0.189	0.189	0.000	0.000	0.000	0.000
9	B	47	ARG	1	0.934	0.979	18.623	14.866	14.866	0.000	0.000	0.000	0.000
10	B	48	LEU	0	0.048	0.012	21.158	-0.130	-0.130	0.000	0.000	0.000	0.000
11	B	49	GLY	0	0.022	0.009	24.495	0.145	0.145	0.000	0.000	0.000	0.000
12	B	50	SER	0	-0.029	0.002	22.357	0.255	0.255	0.000	0.000	0.000	0.000
13	B	51	PRO	0	0.047	0.022	23.497	-0.248	-0.248	0.000	0.000	0.000	0.000
14	B	52	LEU	0	0.063	0.020	18.041	-0.499	-0.499	0.000	0.000	0.000	0.000
15	B	53	SER	0	0.029	0.011	18.754	-0.819	-0.819	0.000	0.000	0.000	0.000
16	B	54	LEU	0	0.026	0.011	18.602	-0.654	-0.654	0.000	0.000	0.000	0.000
17	B	55	ASN	0	0.005	-0.008	17.208	-0.887	-0.887	0.000	0.000	0.000	0.000
18	B	56	MET	0	-0.004	-0.006	12.394	-1.366	-1.366	0.000	0.000	0.000	0.000
19	B	57	ALA	0	0.034	0.036	13.660	-1.294	-1.294	0.000	0.000	0.000	0.000
20	B	58	ARG	1	0.891	0.936	14.059	16.012	16.012	0.000	0.000	0.000	0.000
21	B	59	LYS	1	0.939	0.966	9.099	27.065	27.065	0.000	0.000	0.000	0.000
22	B	60	THR	0	-0.012	-0.006	9.262	-2.891	-2.891	0.000	0.000	0.000	0.000
23	B	61	LEU	0	0.008	0.004	10.290	-1.291	-1.291	0.000	0.000	0.000	0.000
24	B	62	ASN	0	0.023	0.015	8.554	1.296	1.296	0.000	0.000	0.000	0.000
25	B	63	SER	0	-0.048	-0.021	6.395	-2.133	-2.133	0.000	0.000	0.000	0.000
26	B	64	LEU	0	0.015	-0.002	7.771	0.057	0.057	0.000	0.000	0.000	0.000
27	B	65	GLU	-1	-0.897	-0.956	11.022	-19.684	-19.684	0.000	0.000	0.000	0.000
28	B	66	ASP	-1	-0.881	-0.912	6.345	-36.182	-36.182	0.000	0.000	0.000	0.000
29	B	67	LYS	1	0.852	0.911	5.349	37.094	37.094	0.000	0.000	0.000	0.000
30	B	68	ALA	0	0.023	0.021	10.348	1.215	1.215	0.000	0.000	0.000	0.000
31	B	69	PHE	0	-0.016	-0.012	13.026	1.137	1.137	0.000	0.000	0.000	0.000
32	B	70	GLN	0	-0.025	-0.014	9.127	-1.666	-1.666	0.000	0.000	0.000	0.000
33	B	71	LEU	0	-0.038	-0.011	12.621	0.679	0.679	0.000	0.000	0.000	0.000
34	B	72	THR	0	0.002	-0.001	15.634	0.819	0.819	0.000	0.000	0.000	0.000
35	B	73	PRO	0	0.043	0.001	18.939	-0.084	-0.084	0.000	0.000	0.000	0.000
36	B	74	ILE	0	-0.025	0.004	21.600	0.172	0.172	0.000	0.000	0.000	0.000
37	B	75	ALA	0	-0.059	-0.026	17.480	0.105	0.105	0.000	0.000	0.000	0.000
38	B	76	VAL	-1	-0.962	-0.960	18.880	-13.406	-13.406	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:39:PRO )