FMO DATABASE

FMODB ID: VRVY1

Calculation Name: 1A92-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A92

Chain ID: A

ChEMBL ID:

UniProt ID: P25989

Base Structure: X-ray

Registration Date: 2023-03-13

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-220035.811816
FMO2-HF: Nuclear repulsion	199664.461391
FMO2-HF: Total energy	-20371.350425
FMO2-MP2: Total energy	-20432.739917

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-2.91	0.144	4.209	-3.576	-3.687	0.008

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.112 / q_NPA : 0.051

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	14	GLU	-1	-0.907	-0.941	3.431	-2.770	-0.256	0.011	-1.321	-1.204	0.006
4	A	15	ASP	-1	-0.818	-0.896	1.777	-6.571	-6.596	4.194	-2.061	-2.107	0.002
5	A	16	ILE	0	-0.013	-0.015	3.411	2.096	2.661	0.004	-0.194	-0.376	0.000
6	A	17	LEU	0	-0.026	-0.010	5.727	1.281	1.281	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.873	-0.926	7.265	-0.886	-0.886	0.000	0.000	0.000	0.000
8	A	19	GLN	0	-0.070	-0.035	5.765	1.050	1.050	0.000	0.000	0.000	0.000
9	A	20	TRP	0	-0.010	-0.004	9.660	0.434	0.434	0.000	0.000	0.000	0.000
10	A	21	VAL	0	-0.002	-0.012	11.567	0.257	0.257	0.000	0.000	0.000	0.000
11	A	22	SER	0	-0.016	-0.022	11.993	0.239	0.239	0.000	0.000	0.000	0.000
12	A	23	GLY	0	-0.010	-0.002	13.659	0.136	0.136	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.829	0.910	15.509	0.674	0.674	0.000	0.000	0.000	0.000
14	A	25	LYS	1	0.956	0.981	17.133	0.499	0.499	0.000	0.000	0.000	0.000
15	A	26	LYS	1	0.896	0.942	18.153	0.421	0.421	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.015	0.003	19.485	0.058	0.058	0.000	0.000	0.000	0.000
17	A	28	GLU	-1	-0.795	-0.894	21.372	-0.404	-0.404	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-0.908	-0.944	22.172	-0.320	-0.320	0.000	0.000	0.000	0.000
19	A	30	LEU	0	0.012	0.002	22.235	0.037	0.037	0.000	0.000	0.000	0.000
20	A	31	GLU	-1	-0.852	-0.907	25.439	-0.274	-0.274	0.000	0.000	0.000	0.000
21	A	32	ARG	1	0.786	0.874	26.404	0.277	0.277	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.782	-0.883	28.209	-0.202	-0.202	0.000	0.000	0.000	0.000
23	A	34	LEU	0	0.019	0.016	29.569	0.021	0.021	0.000	0.000	0.000	0.000
24	A	35	ARG	1	0.871	0.923	28.651	0.257	0.257	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.869	0.931	31.766	0.198	0.198	0.000	0.000	0.000	0.000
26	A	37	LEU	0	0.008	0.004	33.839	0.012	0.012	0.000	0.000	0.000	0.000
27	A	38	LYS	1	0.976	0.983	33.041	0.188	0.188	0.000	0.000	0.000	0.000
28	A	39	LYS	1	0.965	0.987	37.302	0.150	0.150	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.962	0.992	38.677	0.123	0.123	0.000	0.000	0.000	0.000
30	A	41	ILE	0	0.001	-0.008	38.849	0.006	0.006	0.000	0.000	0.000	0.000
31	A	42	LYS	1	0.817	0.895	41.367	0.109	0.109	0.000	0.000	0.000	0.000
32	A	43	LYS	1	0.879	0.921	43.306	0.093	0.093	0.000	0.000	0.000	0.000
33	A	44	LEU	0	-0.005	-0.007	43.088	0.004	0.004	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.799	-0.891	44.292	-0.094	-0.094	0.000	0.000	0.000	0.000
35	A	46	GLU	-1	-0.838	-0.891	46.804	-0.093	-0.093	0.000	0.000	0.000	0.000
36	A	47	ASP	-1	-0.847	-0.899	48.918	-0.081	-0.081	0.000	0.000	0.000	0.000
37	A	48	ASN	0	-0.088	-0.040	49.133	0.006	0.006	0.000	0.000	0.000	0.000
38	A	49	PRO	0	0.109	0.043	50.902	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	50	TRP	0	0.014	0.017	50.177	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	51	LEU	0	0.001	-0.010	46.629	0.000	0.000	0.000	0.000	0.000	0.000
41	A	52	GLY	0	0.004	0.006	49.018	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	53	ASN	0	0.008	-0.006	50.745	0.000	0.000	0.000	0.000	0.000	0.000
43	A	54	ILE	0	-0.015	0.002	47.613	0.001	0.001	0.000	0.000	0.000	0.000
44	A	55	LYS	1	0.804	0.880	44.404	0.096	0.096	0.000	0.000	0.000	0.000
45	A	56	GLY	0	0.036	0.026	47.851	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	57	ILE	0	-0.014	-0.006	50.448	0.001	0.001	0.000	0.000	0.000	0.000
47	A	58	ILE	0	-0.056	-0.029	43.979	0.000	0.000	0.000	0.000	0.000	0.000
48	A	59	GLY	0	-0.033	-0.023	46.260	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	60	LYS	1	0.901	0.956	47.143	0.066	0.066	0.000	0.000	0.000	0.000
50	A	61	TYR	0	0.005	0.021	47.559	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)