FMO DATABASE

FMODB ID: LJ9Q9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-383807.298078
FMO2-HF: Nuclear repulsion	355354.00031
FMO2-HF: Total energy	-28453.297768
FMO2-MP2: Total energy	-28533.425422

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.
0.662	2.288	0	-0.885	-0.742	0.002

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 : 0.028 / q_NPA : 0.007

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].	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	-0.005	0.012	3.580	-0.139	1.487	-0.885	-0.742	0.002
4	B	149	THR	0	-0.032	-0.024	5.116	0.294	0.294	0.000	0.000	0.000
5	B	150	THR	0	-0.057	-0.024	6.226	0.556	0.556	0.000	0.000	0.000
6	B	151	ILE	0	-0.028	-0.001	9.664	-0.012	-0.012	0.000	0.000	0.000
7	B	152	TRP	0	-0.002	-0.003	12.364	0.123	0.123	0.000	0.000	0.000
8	B	153	GLY	0	0.037	-0.002	15.925	0.035	0.035	0.000	0.000	0.000
9	B	154	VAL	0	-0.011	0.016	19.377	0.020	0.020	0.000	0.000	0.000
10	B	155	GLY	0	0.025	-0.010	22.195	0.018	0.018	0.000	0.000	0.000
11	B	156	ALA	0	-0.037	-0.017	25.417	-0.003	-0.003	0.000	0.000	0.000
12	B	157	ASP	-1	-0.904	-0.963	29.214	-0.113	-0.113	0.000	0.000	0.000
13	B	158	GLH	0	-0.104	-0.077	31.523	0.002	0.002	0.000	0.000	0.000
14	B	159	ALA	0	0.001	-0.004	34.667	0.008	0.008	0.000	0.000	0.000
15	B	160	ILE	0	0.009	0.012	35.807	0.001	0.001	0.000	0.000	0.000
16	B	161	ASH	0	-0.045	-0.058	34.942	0.010	0.010	0.000	0.000	0.000
17	B	162	LYS	1	0.913	0.941	36.181	0.088	0.088	0.000	0.000	0.000
18	B	163	GLY	0	0.030	0.041	36.563	0.002	0.002	0.000	0.000	0.000
19	B	164	THR	0	-0.044	-0.038	30.709	-0.010	-0.010	0.000	0.000	0.000
20	B	165	PRO	0	0.020	0.031	28.766	0.008	0.008	0.000	0.000	0.000
21	B	166	SER	0	0.010	-0.038	30.223	-0.004	-0.004	0.000	0.000	0.000
22	B	167	LYS	1	0.925	0.943	23.385	0.069	0.069	0.000	0.000	0.000
23	B	168	ASN	0	-0.005	-0.011	26.349	0.000	0.000	0.000	0.000	0.000
24	B	169	ASP	-1	-0.801	-0.858	27.052	-0.040	-0.040	0.000	0.000	0.000
25	B	170	LEU	0	0.044	0.018	24.382	-0.002	-0.002	0.000	0.000	0.000
26	B	171	GLN	0	0.009	0.023	22.374	-0.014	-0.014	0.000	0.000	0.000
27	B	172	ASN	0	0.005	0.007	22.383	0.014	0.014	0.000	0.000	0.000
28	B	173	MET	0	0.010	0.003	23.590	0.007	0.007	0.000	0.000	0.000
29	B	174	SER	0	-0.013	-0.017	18.901	-0.014	-0.014	0.000	0.000	0.000
30	B	175	ALA	0	-0.016	-0.009	18.702	-0.002	-0.002	0.000	0.000	0.000
31	B	176	ASP	-1	-0.813	-0.894	19.399	0.040	0.040	0.000	0.000	0.000
32	B	177	LEU	0	0.062	0.030	18.020	0.015	0.015	0.000	0.000	0.000
33	B	178	ALA	0	-0.008	0.002	15.003	-0.007	-0.007	0.000	0.000	0.000
34	B	179	LYS	1	0.797	0.886	15.651	-0.031	-0.031	0.000	0.000	0.000
35	B	180	ASN	0	-0.012	-0.018	17.947	0.051	0.051	0.000	0.000	0.000
36	B	181	GLY	0	0.007	0.009	18.625	0.004	0.004	0.000	0.000	0.000
37	B	182	PHE	0	-0.004	-0.007	12.846	0.012	0.012	0.000	0.000	0.000
38	B	183	LYS	1	0.824	0.927	13.587	-0.013	-0.013	0.000	0.000	0.000
39	B	184	GLY	0	-0.005	-0.002	11.122	0.082	0.082	0.000	0.000	0.000
40	B	185	HIS	0	-0.051	-0.015	9.139	0.162	0.162	0.000	0.000	0.000
41	B	186	GLN	0	-0.016	-0.031	6.327	-0.312	-0.312	0.000	0.000	0.000
42	B	187	GLY	0	-0.011	-0.007	9.976	0.131	0.131	0.000	0.000	0.000
43	B	188	VAL	0	-0.035	-0.022	13.661	-0.088	-0.088	0.000	0.000	0.000
44	B	189	ALA	0	-0.005	0.000	16.765	0.048	0.048	0.000	0.000	0.000
45	B	190	CYS	0	-0.077	-0.028	19.581	-0.020	-0.020	0.000	0.000	0.000
46	B	191	SER	0	-0.003	-0.010	23.047	0.015	0.015	0.000	0.000	0.000
47	B	192	THR	0	0.030	-0.023	24.894	-0.016	-0.016	0.000	0.000	0.000
48	B	193	VAL	0	-0.038	-0.001	26.397	0.011	0.011	0.000	0.000	0.000
49	B	194	LYS	1	0.856	0.907	28.751	0.064	0.064	0.000	0.000	0.000
50	B	195	ASP	-1	-0.830	-0.862	32.044	-0.064	-0.064	0.000	0.000	0.000
51	B	196	GLY	0	0.025	0.007	34.903	0.004	0.004	0.000	0.000	0.000
52	B	197	ASN	0	0.007	-0.017	35.750	-0.002	-0.002	0.000	0.000	0.000
53	B	198	LYS	1	0.817	0.920	37.042	0.064	0.064	0.000	0.000	0.000
54	B	199	ASP	-1	-0.712	-0.811	33.585	-0.074	-0.074	0.000	0.000	0.000
55	B	200	VAL	0	-0.038	-0.014	32.204	0.001	0.001	0.000	0.000	0.000
56	B	201	TYR	0	0.020	0.005	26.104	-0.010	-0.010	0.000	0.000	0.000
57	B	202	MET	0	0.006	0.035	27.601	-0.001	-0.001	0.000	0.000	0.000
58	B	203	ILE	0	-0.024	-0.032	21.480	-0.015	-0.015	0.000	0.000	0.000
59	B	204	LYS	1	0.859	0.937	19.801	0.322	0.322	0.000	0.000	0.000
60	B	205	PHE	0	-0.007	-0.005	17.098	-0.041	-0.041	0.000	0.000	0.000
61	B	206	SER	0	0.001	-0.010	14.456	0.055	0.055	0.000	0.000	0.000
62	B	207	LEU	0	-0.013	0.002	8.283	-0.093	-0.093	0.000	0.000	0.000
63	B	208	ALA	0	0.043	0.010	9.314	0.159	0.159	0.000	0.000	0.000
64	B	209	GLY	0	0.042	0.017	6.914	-0.326	-0.326	0.000	0.000	0.000
65	B	210	GLY	0	-0.046	-0.018	7.832	-0.093	-0.093	0.000	0.000	0.000
66	B	211	SER	0	0.017	0.014	9.382	0.181	0.181	0.000	0.000	0.000
67	B	212	ASN	0	-0.020	-0.021	10.995	0.143	0.143	0.000	0.000	0.000
68	B	213	ASP	-1	-0.829	-0.914	14.801	-0.490	-0.490	0.000	0.000	0.000
69	B	214	PRO	0	-0.052	-0.015	15.650	0.029	0.029	0.000	0.000	0.000
70	B	215	GLY	0	0.014	0.018	17.815	0.054	0.054	0.000	0.000	0.000
71	B	216	GLY	0	-0.008	-0.011	21.525	0.009	0.009	0.000	0.000	0.000
72	B	217	SER	0	-0.010	-0.016	24.182	-0.008	-0.008	0.000	0.000	0.000
73	B	218	PRO	0	0.024	0.028	24.333	-0.015	-0.015	0.000	0.000	0.000
74	B	220	SER	0	-0.042	-0.055	25.367	-0.013	-0.013	0.000	0.000	0.000
75	B	221	ASP	-1	-0.949	-0.972	26.473	-0.073	-0.073	0.000	0.000	0.000
76	B	222	ASP	-1	-0.858	-0.872	28.547	-0.091	-0.091	0.000	0.000	0.000

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