FMO DATABASE

FMODB ID: N3YQQ

Calculation Name: 7KVR-B-Xray89

Preferred Name:

Target Type:

Ligand Name: n~4~,n~4~-dimethylpyridine-2,4-diamine

ligand 3-letter code: X4V

PDB ID: 7KVR

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 main protease 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	50
LigandResidueName	X4V
LigandFragmentNumber	3
LigandCharge	X4V=1
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-17371.216798
FMO2-HF: Nuclear repulsion	11119.817593
FMO2-HF: Total energy	-6251.399205
FMO2-MP2: Total energy	-6265.18415

3D Structure

Snapshot

Ligand structure

X4V

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.
10.944	19.902	12.695	-5.004	-16.650	0.036

Interactive mode: IFIE and PIEDA for fragment #3(B:703:X4V )

Summations of interaction energy for fragment #3(B:703:X4V )

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.
10.944	19.902	12.695	-5.004	-16.65	-0.036

Interaction energy analysis for fragmet #3(B:703:X4V )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.964 / q_NPA : 0.987

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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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].
1	B	701	PEG	0	0.000	0.000	36.194	0.070	0.070	0.000	0.000	0.000	0.000
2	B	702	DMS	0	0.037	0.035	27.420	0.256	0.256	0.000	0.000	0.000	0.000
4	B	704	DMS	0	-0.013	-0.003	25.490	0.069	0.069	0.000	0.000	0.000	0.000
5	B	705	DMS	0	0.000	0.000	20.497	-0.437	-0.437	0.000	0.000	0.000	0.000
6	B	801	HOH	0	0.000	0.000	27.515	-0.165	-0.165	0.000	0.000	0.000	0.000
7	B	802	HOH	0	0.025	0.021	42.631	0.050	0.050	0.000	0.000	0.000	0.000
8	B	803	HOH	0	-0.029	-0.023	43.021	-0.029	-0.029	0.000	0.000	0.000	0.000
9	B	804	HOH	0	0.015	0.004	2.508	-9.149	-8.063	1.687	-1.101	-1.672	-0.015
10	B	805	HOH	0	-0.012	-0.017	2.587	-9.336	-8.385	1.439	-1.009	-1.380	-0.014
11	B	806	HOH	0	-0.017	-0.019	26.174	-0.185	-0.185	0.000	0.000	0.000	0.000
12	B	807	HOH	0	0.000	0.000	29.345	-0.018	-0.018	0.000	0.000	0.000	0.000
13	B	808	HOH	0	0.038	0.027	3.886	-3.404	-3.262	0.003	-0.046	-0.100	0.000
14	B	809	HOH	0	0.000	0.000	18.246	-0.050	-0.050	0.000	0.000	0.000	0.000
15	B	810	HOH	0	0.000	0.000	22.694	-0.182	-0.182	0.000	0.000	0.000	0.000
16	B	811	HOH	0	0.023	0.021	21.477	0.253	0.253	0.000	0.000	0.000	0.000
17	B	812	HOH	0	0.003	0.002	43.935	-0.029	-0.029	0.000	0.000	0.000	0.000
18	B	813	HOH	0	0.004	0.004	22.212	0.019	0.019	0.000	0.000	0.000	0.000
19	B	814	HOH	0	0.000	0.000	16.389	-0.358	-0.358	0.000	0.000	0.000	0.000
20	B	815	HOH	0	0.000	0.000	13.303	-0.440	-0.440	0.000	0.000	0.000	0.000
21	B	816	HOH	0	0.000	0.000	29.620	-0.088	-0.088	0.000	0.000	0.000	0.000
22	B	817	HOH	0	0.026	0.022	8.951	-0.266	-0.266	0.000	0.000	0.000	0.000
23	B	818	HOH	0	0.023	0.019	18.112	-0.015	-0.015	0.000	0.000	0.000	0.000
24	B	819	HOH	0	-0.037	-0.035	31.966	0.044	0.044	0.000	0.000	0.000	0.000
25	B	820	HOH	0	0.025	0.024	15.479	0.374	0.374	0.000	0.000	0.000	0.000
26	B	821	HOH	0	0.023	0.021	36.823	-0.042	-0.042	0.000	0.000	0.000	0.000
27	B	822	HOH	0	-0.006	-0.005	9.833	-0.552	-0.552	0.000	0.000	0.000	0.000
28	B	823	HOH	0	0.000	0.000	10.429	-0.967	-0.967	0.000	0.000	0.000	0.000
29	B	824	HOH	0	0.000	0.000	11.616	-0.282	-0.282	0.000	0.000	0.000	0.000
30	B	825	HOH	0	0.000	0.000	22.251	-0.207	-0.207	0.000	0.000	0.000	0.000
31	B	826	HOH	0	0.026	0.021	4.996	-3.386	-3.359	0.000	-0.001	-0.027	0.000
32	B	827	HOH	0	0.000	0.000	16.056	-0.357	-0.357	0.000	0.000	0.000	0.000
33	B	828	HOH	0	0.000	0.000	18.839	-0.309	-0.309	0.000	0.000	0.000	0.000
34	B	829	HOH	0	0.030	0.022	28.717	-0.157	-0.157	0.000	0.000	0.000	0.000
35	B	830	HOH	0	0.004	0.003	18.117	0.300	0.300	0.000	0.000	0.000	0.000
36	B	831	HOH	0	0.000	0.000	11.127	-0.725	-0.725	0.000	0.000	0.000	0.000
37	B	832	HOH	0	0.006	0.007	9.877	0.584	0.584	0.000	0.000	0.000	0.000
38	B	833	HOH	0	-0.003	-0.003	22.287	-0.221	-0.221	0.000	0.000	0.000	0.000
39	B	834	HOH	0	-0.023	-0.021	35.876	0.045	0.045	0.000	0.000	0.000	0.000
40	B	836	HOH	0	0.000	0.000	12.845	-0.601	-0.601	0.000	0.000	0.000	0.000
41	B	837	HOH	0	-0.001	-0.001	20.326	0.139	0.139	0.000	0.000	0.000	0.000
42	B	838	HOH	0	-0.023	-0.021	23.912	0.164	0.164	0.000	0.000	0.000	0.000
43	B	839	HOH	0	0.024	0.022	25.259	-0.196	-0.196	0.000	0.000	0.000	0.000
44	B	840	HOH	0	-0.026	-0.022	7.468	-1.722	-1.722	0.000	0.000	0.000	0.000
45	B	841	HOH	0	0.001	-0.002	17.099	-0.038	-0.038	0.000	0.000	0.000	0.000
46	B	842	HOH	0	-0.027	-0.022	20.505	0.252	0.252	0.000	0.000	0.000	0.000
47	B	843	HOH	0	-0.024	-0.022	22.593	-0.178	-0.178	0.000	0.000	0.000	0.000
48	B	844	HOH	0	-0.027	-0.022	16.471	-0.427	-0.427	0.000	0.000	0.000	0.000
49	B	845	HOH	0	-0.001	-0.002	10.781	-0.215	-0.215	0.000	0.000	0.000	0.000
50	B	703	X4V	1	0.969	0.978	2.393	43.058	49.810	9.566	-2.847	-13.471	-0.007

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Interactive mode: IFIE and PIEDA for fragment #3(B:703:X4V )