FMO DATABASE

FMODB ID: J3749

Calculation Name: 1KVE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KVE

Chain ID: B

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	OptH
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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-382748.652389
FMO2-HF: Nuclear repulsion	354296.155955
FMO2-HF: Total energy	-28452.496433
FMO2-MP2: Total energy	-28532.700042

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:146:GLY)

Summations of interaction energy for fragment #1(B:146: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.
-0.422	1.149	-0.008	-0.84	-0.723	0.003

Interaction energy analysis for fragmet #1(B:146:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.001

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	148	ALA	0	0.004	0.004	3.797	-0.376	1.110	-0.007	-0.804	-0.675	0.003
4	B	149	THR	0	-0.024	-0.016	4.417	-0.549	-0.464	-0.001	-0.036	-0.048	0.000
5	B	150	THR	0	-0.028	-0.005	6.127	0.663	0.663	0.000	0.000	0.000	0.000
6	B	151	ILE	0	-0.039	-0.016	9.768	-0.033	-0.033	0.000	0.000	0.000	0.000
7	B	152	TRP	0	0.012	0.002	12.445	0.105	0.105	0.000	0.000	0.000	0.000
8	B	153	GLY	0	0.013	0.000	15.877	0.034	0.034	0.000	0.000	0.000	0.000
9	B	154	VAL	0	-0.028	-0.002	19.264	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	155	GLY	0	0.006	-0.019	22.103	0.017	0.017	0.000	0.000	0.000	0.000
11	B	156	ALA	0	0.013	0.007	25.296	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	157	ASP	-1	-0.886	-0.962	29.059	-0.105	-0.105	0.000	0.000	0.000	0.000
13	B	158	GLH	0	-0.104	-0.066	31.475	0.002	0.002	0.000	0.000	0.000	0.000
14	B	159	ALA	0	-0.024	-0.015	34.025	0.007	0.007	0.000	0.000	0.000	0.000
15	B	160	ILE	0	0.025	0.021	35.158	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	161	ASH	0	-0.097	-0.104	34.947	0.008	0.008	0.000	0.000	0.000	0.000
17	B	162	LYS	1	0.921	0.950	35.525	0.072	0.072	0.000	0.000	0.000	0.000
18	B	163	GLY	0	0.028	0.034	36.314	0.002	0.002	0.000	0.000	0.000	0.000
19	B	164	THR	0	-0.044	-0.031	30.792	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	165	PRO	0	0.051	0.041	28.739	0.008	0.008	0.000	0.000	0.000	0.000
21	B	166	SER	0	0.053	0.024	30.471	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	167	LYS	1	1.012	0.997	22.955	0.018	0.018	0.000	0.000	0.000	0.000
23	B	168	ASN	0	0.003	-0.015	26.745	0.004	0.004	0.000	0.000	0.000	0.000
24	B	169	ASP	-1	-0.883	-0.924	27.762	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	170	LEU	0	0.006	-0.014	24.533	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	171	GLN	0	-0.029	-0.019	22.890	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	172	ASN	0	0.000	0.005	22.789	0.020	0.020	0.000	0.000	0.000	0.000
28	B	173	MET	0	0.009	0.017	23.784	0.006	0.006	0.000	0.000	0.000	0.000
29	B	174	SER	0	-0.010	-0.009	19.353	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	175	ALA	0	-0.027	-0.024	18.925	0.005	0.005	0.000	0.000	0.000	0.000
31	B	176	ASP	-1	-0.909	-0.933	19.443	0.049	0.049	0.000	0.000	0.000	0.000
32	B	177	LEU	0	0.075	0.036	17.870	0.013	0.013	0.000	0.000	0.000	0.000
33	B	178	ALA	0	-0.007	0.009	14.917	0.000	0.000	0.000	0.000	0.000	0.000
34	B	179	LYS	1	0.910	0.957	15.303	-0.100	-0.100	0.000	0.000	0.000	0.000
35	B	180	ASN	0	-0.054	-0.066	17.470	0.052	0.052	0.000	0.000	0.000	0.000
36	B	181	GLY	0	0.012	0.023	18.395	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	182	PHE	0	-0.054	-0.041	12.617	0.004	0.004	0.000	0.000	0.000	0.000
38	B	183	LYS	1	0.880	0.966	13.497	-0.078	-0.078	0.000	0.000	0.000	0.000
39	B	184	GLY	0	-0.025	-0.015	10.603	0.070	0.070	0.000	0.000	0.000	0.000
40	B	185	HIS	0	-0.033	-0.007	9.094	0.199	0.199	0.000	0.000	0.000	0.000
41	B	186	GLN	0	-0.045	-0.056	5.749	0.028	0.028	0.000	0.000	0.000	0.000
42	B	187	GLY	0	0.002	-0.003	10.048	0.120	0.120	0.000	0.000	0.000	0.000
43	B	188	VAL	0	-0.023	-0.017	13.743	-0.085	-0.085	0.000	0.000	0.000	0.000
44	B	189	ALA	0	-0.008	0.011	16.778	0.047	0.047	0.000	0.000	0.000	0.000
45	B	190	CYS	0	-0.070	-0.031	19.358	-0.034	-0.034	0.000	0.000	0.000	0.000
46	B	191	SER	0	-0.009	-0.006	22.803	0.021	0.021	0.000	0.000	0.000	0.000
47	B	192	THR	0	0.098	0.003	24.697	-0.018	-0.018	0.000	0.000	0.000	0.000
48	B	193	VAL	0	-0.067	-0.022	26.186	0.012	0.012	0.000	0.000	0.000	0.000
49	B	194	LYS	1	0.967	0.977	28.520	0.044	0.044	0.000	0.000	0.000	0.000
50	B	195	ASP	-1	-0.878	-0.888	31.954	-0.043	-0.043	0.000	0.000	0.000	0.000
51	B	196	GLY	0	0.013	-0.006	34.693	0.001	0.001	0.000	0.000	0.000	0.000
52	B	197	ASN	0	-0.044	-0.043	35.515	0.000	0.000	0.000	0.000	0.000	0.000
53	B	198	LYS	1	0.896	0.969	36.716	0.052	0.052	0.000	0.000	0.000	0.000
54	B	199	ASP	-1	-0.781	-0.890	33.531	-0.063	-0.063	0.000	0.000	0.000	0.000
55	B	200	VAL	0	-0.063	-0.033	31.976	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	201	TYR	0	-0.002	0.011	26.128	-0.013	-0.013	0.000	0.000	0.000	0.000
57	B	202	MET	0	0.003	0.034	27.417	0.003	0.003	0.000	0.000	0.000	0.000
58	B	203	ILE	0	-0.019	-0.022	21.062	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	204	LYS	1	0.938	0.990	19.475	0.350	0.350	0.000	0.000	0.000	0.000
60	B	205	PHE	0	-0.035	-0.034	16.656	-0.031	-0.031	0.000	0.000	0.000	0.000
61	B	206	SER	0	-0.003	-0.012	14.204	0.055	0.055	0.000	0.000	0.000	0.000
62	B	207	LEU	0	-0.017	-0.005	8.185	-0.094	-0.094	0.000	0.000	0.000	0.000
63	B	208	ALA	0	0.048	0.013	9.927	0.148	0.148	0.000	0.000	0.000	0.000
64	B	209	GLY	0	0.083	0.039	7.258	-0.261	-0.261	0.000	0.000	0.000	0.000
65	B	210	GLY	0	-0.059	-0.022	8.322	-0.335	-0.335	0.000	0.000	0.000	0.000
66	B	211	SER	0	0.044	0.016	9.427	0.063	0.063	0.000	0.000	0.000	0.000
67	B	212	ASN	0	-0.063	-0.039	10.999	0.153	0.153	0.000	0.000	0.000	0.000
68	B	213	ASP	-1	-0.847	-0.919	14.835	-0.499	-0.499	0.000	0.000	0.000	0.000
69	B	214	PRO	0	-0.060	-0.016	15.736	0.028	0.028	0.000	0.000	0.000	0.000
70	B	215	GLY	0	0.025	0.027	17.924	0.050	0.050	0.000	0.000	0.000	0.000
71	B	216	GLY	0	-0.017	-0.029	21.231	0.000	0.000	0.000	0.000	0.000	0.000
72	B	217	SER	0	-0.017	-0.021	23.651	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	218	PRO	0	-0.003	0.015	24.224	-0.009	-0.009	0.000	0.000	0.000	0.000
74	B	220	SER	0	-0.012	-0.015	25.478	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	221	ASP	-1	-0.968	-0.981	26.478	-0.069	-0.069	0.000	0.000	0.000	0.000
76	B	222	ASP	-1	-0.834	-0.846	28.484	-0.084	-0.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:146:GLY)