FMO DATABASE

FMODB ID: M3JRZ

Calculation Name: 1KVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KVE

Chain ID: A

ChEMBL ID:

UniProt ID: P19972

Base Structure: X-ray

Registration Date: 2023-06-19

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-258234.0287
FMO2-HF: Nuclear repulsion	235674.052294
FMO2-HF: Total energy	-22559.976406
FMO2-MP2: Total energy	-22624.509979

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:19:TRP)

Summations of interaction energy for fragment #1(A:19:TRP)

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.
-7.296	-1.82	1.017	-2.129	-4.363	-0.002

Interaction energy analysis for fragmet #1(A:19:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.004

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	21	LEU	0	0.067	0.035	3.819	-1.448	0.959	-0.027	-1.251	-1.129	0.004
4	A	22	ARG	1	0.968	0.989	6.737	-0.904	-0.904	0.000	0.000	0.000	0.000
5	A	23	TRP	0	-0.011	-0.009	9.676	-0.051	-0.051	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.934	0.952	12.911	-0.258	-0.258	0.000	0.000	0.000	0.000
7	A	25	MET	0	0.008	0.015	16.692	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	26	GLN	0	0.019	0.014	19.325	0.028	0.028	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.988	0.980	21.123	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	28	SER	0	0.035	0.025	22.784	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	29	THR	0	-0.046	-0.033	24.538	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	30	THR	0	0.057	0.029	26.481	0.003	0.003	0.000	0.000	0.000	0.000
13	A	31	ILE	0	-0.004	0.000	28.546	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	32	ALA	0	0.050	0.024	27.465	0.001	0.001	0.000	0.000	0.000	0.000
15	A	33	ALA	0	-0.040	-0.015	28.844	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	34	ILE	0	-0.009	-0.001	23.629	0.001	0.001	0.000	0.000	0.000	0.000
17	A	35	ALA	0	-0.014	-0.005	27.465	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	36	GLY	0	0.055	0.032	26.330	0.000	0.000	0.000	0.000	0.000	0.000
19	A	37	CYS	0	-0.107	-0.057	18.703	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	38	SER	0	0.019	0.008	25.092	0.000	0.000	0.000	0.000	0.000	0.000
21	A	39	GLY	0	0.024	0.008	22.438	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	40	ALA	0	-0.017	0.002	20.716	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	41	ALA	0	-0.029	-0.019	16.459	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	42	THR	0	0.032	0.005	18.537	0.008	0.008	0.000	0.000	0.000	0.000
25	A	43	PHE	0	0.012	0.018	13.138	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	44	GLY	0	0.022	-0.009	13.934	0.018	0.018	0.000	0.000	0.000	0.000
27	A	45	GLY	0	-0.001	0.002	14.609	0.027	0.027	0.000	0.000	0.000	0.000
28	A	46	LEU	0	-0.049	-0.007	15.989	0.024	0.024	0.000	0.000	0.000	0.000
29	A	47	ALA	0	0.017	0.004	19.396	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.036	0.028	21.463	0.004	0.004	0.000	0.000	0.000	0.000
31	A	49	GLY	0	0.006	-0.017	22.514	0.007	0.007	0.000	0.000	0.000	0.000
32	A	50	ILE	0	0.056	0.016	23.132	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	51	VAL	0	0.035	0.017	18.774	0.000	0.000	0.000	0.000	0.000	0.000
34	A	52	GLY	0	0.073	0.041	18.730	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	54	ILE	0	0.011	0.010	16.960	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.007	-0.003	14.606	0.002	0.002	0.000	0.000	0.000	0.000
37	A	56	ALA	0	0.001	-0.007	14.124	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	57	GLY	0	0.029	0.019	15.698	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	58	ILE	0	-0.023	-0.023	10.907	0.001	0.001	0.000	0.000	0.000	0.000
40	A	59	LEU	0	-0.023	-0.004	9.799	0.010	0.010	0.000	0.000	0.000	0.000
41	A	60	ALA	0	0.033	0.024	11.203	0.024	0.024	0.000	0.000	0.000	0.000
42	A	61	ILE	0	-0.012	0.001	11.399	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	62	LEU	0	-0.050	-0.038	6.498	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	63	GLN	0	0.016	0.003	7.574	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	64	GLY	0	-0.007	0.009	9.594	-0.057	-0.057	0.000	0.000	0.000	0.000
46	A	65	PHE	0	-0.042	-0.046	7.539	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	66	GLU	-1	-0.854	-0.920	5.624	-0.104	-0.104	0.000	0.000	0.000	0.000
48	A	67	VAL	0	-0.015	-0.010	6.615	-0.301	-0.301	0.000	0.000	0.000	0.000
49	A	68	ASN	0	-0.017	-0.008	8.942	0.010	0.010	0.000	0.000	0.000	0.000
50	A	69	TRP	0	-0.018	0.011	3.018	-3.740	-0.861	1.045	-0.866	-3.057	-0.006
51	A	70	HIS	0	-0.062	-0.022	4.427	-0.696	-0.506	-0.001	-0.012	-0.177	0.000
52	A	71	ASN	0	-0.069	-0.035	6.894	0.113	0.113	0.000	0.000	0.000	0.000
53	A	72	GLY	0	0.022	0.025	9.422	0.107	0.107	0.000	0.000	0.000	0.000
54	A	73	GLY	0	-0.025	-0.026	11.084	0.000	0.000	0.000	0.000	0.000	0.000
55	A	74	GLY	0	0.000	-0.006	11.615	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	75	GLY	0	-0.025	-0.019	13.642	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.912	-0.938	14.856	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	77	ARG	1	0.860	0.929	11.933	0.182	0.182	0.000	0.000	0.000	0.000
59	A	78	SER	0	-0.018	-0.018	16.097	0.013	0.013	0.000	0.000	0.000	0.000
60	A	79	ASN	0	0.021	-0.001	17.256	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	80	PRO	0	-0.001	0.013	19.335	0.010	0.010	0.000	0.000	0.000	0.000
62	A	81	VAL	0	0.033	0.025	20.945	-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:19:TRP)