FMO DATABASE

FMODB ID: R8G88

Calculation Name: 1ZVA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZVA

Chain ID: A

ChEMBL ID:

UniProt ID: Q3I5J5

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-366078.760348
FMO2-HF: Nuclear repulsion	338895.663206
FMO2-HF: Total energy	-27183.097143
FMO2-MP2: Total energy	-27263.984203

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:1:ALA)

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

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.
-6.101	-3.126	0.053	-1.298	-1.732	0.003

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.027

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].
3	A	3	GLY	0	0.011	0.013	3.346	-2.107	-0.181	0.012	-0.957	-0.982	0.003
4	A	4	LYS	1	0.884	0.933	3.144	-2.692	-2.033	0.041	-0.198	-0.502	0.000
5	A	5	LEU	0	0.097	0.052	3.797	-0.594	-0.204	0.000	-0.143	-0.248	0.000
6	A	6	GLN	0	-0.018	-0.019	5.619	0.157	0.157	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.835	-0.903	8.241	0.375	0.375	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.036	0.029	8.244	-0.038	-0.038	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.029	0.012	9.688	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.021	-0.004	11.782	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.041	-0.033	13.240	-0.055	-0.055	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.014	-0.009	13.098	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.022	0.025	15.678	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.041	-0.027	17.550	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.005	0.017	18.976	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.035	0.017	19.372	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.011	-0.008	21.324	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.032	-0.021	23.441	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.005	-0.001	22.357	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.034	0.019	24.887	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.893	0.960	26.456	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.072	-0.031	28.157	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.068	0.041	27.886	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.042	-0.030	30.925	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.096	-0.052	33.262	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.012	-0.017	32.979	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.043	0.008	34.909	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.027	0.045	36.780	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.006	0.007	39.082	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.010	-0.013	37.835	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.030	-0.038	39.677	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.018	0.021	41.596	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.005	0.001	44.276	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.006	0.006	41.631	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.016	0.012	45.486	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.836	-0.900	47.039	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.026	-0.014	48.000	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.046	-0.036	47.585	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.038	-0.008	50.238	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.037	-0.020	52.795	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.779	0.867	51.849	0.009	0.009	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.002	0.016	53.538	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.030	-0.014	50.079	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.850	-0.887	50.082	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.013	-0.006	47.297	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.025	-0.041	46.815	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.031	-0.010	44.318	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.027	0.017	42.295	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.019	-0.003	41.067	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.009	0.003	39.679	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.015	0.001	37.194	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.006	0.005	36.203	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.011	-0.015	35.757	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.056	-0.022	33.400	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.066	0.030	31.753	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.008	0.004	30.848	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.914	0.961	29.440	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.813	-0.918	27.313	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.025	0.013	26.128	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.895	-0.941	25.438	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.887	0.931	23.131	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.004	-0.002	21.578	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.050	-0.009	20.925	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.813	-0.904	19.204	-0.039	-0.039	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.031	-0.008	17.221	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.013	-0.012	15.994	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.864	0.938	15.627	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.019	-0.019	13.236	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.036	-0.015	11.352	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	70	ASN	0	0.002	0.011	10.675	-0.113	-0.113	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.872	-0.952	11.047	-0.157	-0.157	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.087	-0.047	7.081	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.070	-0.037	5.877	-0.362	-0.362	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.086	-0.034	7.708	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.987	-0.985	7.898	-0.121	-0.121	0.000	0.000	0.000	0.000

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