FMO DATABASE

FMODB ID: 3Q8KL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-382927.572723
FMO2-HF: Nuclear repulsion	354474.607334
FMO2-HF: Total energy	-28452.965389
FMO2-MP2: Total energy	-28533.168474

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.
-0.339	1.227	-0.008	-0.841	-0.717	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 : 0.021 / q_NPA : 0.003

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	-0.001	0.001	3.797	-0.384	1.095	-0.007	-0.800	-0.672	0.003
4	B	149	THR	0	-0.022	-0.024	4.316	-0.317	-0.230	-0.001	-0.041	-0.045	0.000
5	B	150	THR	0	-0.040	-0.009	6.093	0.666	0.666	0.000	0.000	0.000	0.000
6	B	151	ILE	0	-0.047	-0.011	9.746	-0.033	-0.033	0.000	0.000	0.000	0.000
7	B	152	TRP	0	0.013	0.002	12.440	0.108	0.108	0.000	0.000	0.000	0.000
8	B	153	GLY	0	0.020	0.007	15.872	0.035	0.035	0.000	0.000	0.000	0.000
9	B	154	VAL	0	-0.031	-0.001	19.259	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	155	GLY	0	0.007	-0.018	22.098	0.018	0.018	0.000	0.000	0.000	0.000
11	B	156	ALA	0	0.005	0.005	25.292	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	157	ASP	-1	-0.916	-0.964	29.055	-0.097	-0.097	0.000	0.000	0.000	0.000
13	B	158	GLH	0	-0.112	-0.079	31.203	0.002	0.002	0.000	0.000	0.000	0.000
14	B	159	ALA	0	-0.006	-0.013	34.020	0.006	0.006	0.000	0.000	0.000	0.000
15	B	160	ILE	0	0.019	0.016	35.153	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	161	ASH	0	-0.063	-0.085	34.936	0.009	0.009	0.000	0.000	0.000	0.000
17	B	162	LYS	1	0.918	0.953	35.539	0.068	0.068	0.000	0.000	0.000	0.000
18	B	163	GLY	0	0.022	0.031	36.337	0.001	0.001	0.000	0.000	0.000	0.000
19	B	164	THR	0	-0.048	-0.035	30.810	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	165	PRO	0	0.021	0.030	28.862	0.007	0.007	0.000	0.000	0.000	0.000
21	B	166	SER	0	0.007	-0.028	30.507	0.000	0.000	0.000	0.000	0.000	0.000
22	B	167	LYS	1	0.958	0.964	23.123	-0.013	-0.013	0.000	0.000	0.000	0.000
23	B	168	ASN	0	0.004	-0.018	26.796	0.006	0.006	0.000	0.000	0.000	0.000
24	B	169	ASP	-1	-0.799	-0.856	27.785	0.005	0.005	0.000	0.000	0.000	0.000
25	B	170	LEU	0	0.029	0.004	24.546	0.000	0.000	0.000	0.000	0.000	0.000
26	B	171	GLN	0	0.012	0.018	22.942	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	172	ASN	0	-0.004	0.004	22.787	0.022	0.022	0.000	0.000	0.000	0.000
28	B	173	MET	0	0.010	0.011	23.782	0.008	0.008	0.000	0.000	0.000	0.000
29	B	174	SER	0	-0.022	-0.025	19.329	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	175	ALA	0	-0.025	-0.018	18.922	0.007	0.007	0.000	0.000	0.000	0.000
31	B	176	ASP	-1	-0.886	-0.931	19.442	0.072	0.072	0.000	0.000	0.000	0.000
32	B	177	LEU	0	0.074	0.030	17.687	0.014	0.014	0.000	0.000	0.000	0.000
33	B	178	ALA	0	-0.018	0.005	14.961	0.001	0.001	0.000	0.000	0.000	0.000
34	B	179	LYS	1	0.895	0.945	15.302	-0.112	-0.112	0.000	0.000	0.000	0.000
35	B	180	ASN	0	-0.022	-0.033	17.470	0.053	0.053	0.000	0.000	0.000	0.000
36	B	181	GLY	0	0.012	0.017	18.394	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	182	PHE	0	-0.030	-0.028	12.665	0.006	0.006	0.000	0.000	0.000	0.000
38	B	183	LYS	1	0.836	0.942	13.497	-0.072	-0.072	0.000	0.000	0.000	0.000
39	B	184	GLY	0	-0.019	-0.010	10.602	0.068	0.068	0.000	0.000	0.000	0.000
40	B	185	HIS	0	-0.037	-0.010	9.094	0.195	0.195	0.000	0.000	0.000	0.000
41	B	186	GLN	0	-0.030	-0.043	6.439	-0.195	-0.195	0.000	0.000	0.000	0.000
42	B	187	GLY	0	-0.001	-0.004	10.047	0.114	0.114	0.000	0.000	0.000	0.000
43	B	188	VAL	0	-0.026	-0.018	13.742	-0.082	-0.082	0.000	0.000	0.000	0.000
44	B	189	ALA	0	-0.014	0.004	16.776	0.046	0.046	0.000	0.000	0.000	0.000
45	B	190	CYS	0	-0.066	-0.024	19.356	-0.034	-0.034	0.000	0.000	0.000	0.000
46	B	191	SER	0	0.006	-0.007	22.900	0.020	0.020	0.000	0.000	0.000	0.000
47	B	192	THR	0	0.079	-0.005	24.694	-0.018	-0.018	0.000	0.000	0.000	0.000
48	B	193	VAL	0	-0.055	-0.009	26.196	0.012	0.012	0.000	0.000	0.000	0.000
49	B	194	LYS	1	0.883	0.921	28.517	0.041	0.041	0.000	0.000	0.000	0.000
50	B	195	ASP	-1	-0.816	-0.848	31.950	-0.035	-0.035	0.000	0.000	0.000	0.000
51	B	196	GLY	0	0.006	-0.008	34.689	0.001	0.001	0.000	0.000	0.000	0.000
52	B	197	ASN	0	0.001	-0.018	35.512	0.000	0.000	0.000	0.000	0.000	0.000
53	B	198	LYS	1	0.818	0.913	36.896	0.043	0.043	0.000	0.000	0.000	0.000
54	B	199	ASP	-1	-0.733	-0.825	33.464	-0.053	-0.053	0.000	0.000	0.000	0.000
55	B	200	VAL	0	-0.029	-0.014	31.943	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	201	TYR	0	0.010	0.008	26.115	-0.012	-0.012	0.000	0.000	0.000	0.000
57	B	202	MET	0	0.014	0.041	27.415	0.003	0.003	0.000	0.000	0.000	0.000
58	B	203	ILE	0	-0.027	-0.029	21.202	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	204	LYS	1	0.870	0.955	19.544	0.330	0.330	0.000	0.000	0.000	0.000
60	B	205	PHE	0	-0.032	-0.031	16.704	-0.030	-0.030	0.000	0.000	0.000	0.000
61	B	206	SER	0	0.004	-0.009	14.222	0.054	0.054	0.000	0.000	0.000	0.000
62	B	207	LEU	0	-0.017	-0.009	7.881	-0.088	-0.088	0.000	0.000	0.000	0.000
63	B	208	ALA	0	0.041	0.011	9.941	0.147	0.147	0.000	0.000	0.000	0.000
64	B	209	GLY	0	0.075	0.040	7.244	-0.257	-0.257	0.000	0.000	0.000	0.000
65	B	210	GLY	0	-0.055	-0.023	8.319	-0.342	-0.342	0.000	0.000	0.000	0.000
66	B	211	SER	0	0.032	0.015	9.320	0.107	0.107	0.000	0.000	0.000	0.000
67	B	212	ASN	0	-0.040	-0.031	10.937	0.154	0.154	0.000	0.000	0.000	0.000
68	B	213	ASP	-1	-0.840	-0.917	14.772	-0.482	-0.482	0.000	0.000	0.000	0.000
69	B	214	PRO	0	-0.050	-0.014	15.735	0.026	0.026	0.000	0.000	0.000	0.000
70	B	215	GLY	0	0.027	0.030	17.919	0.049	0.049	0.000	0.000	0.000	0.000
71	B	216	GLY	0	0.007	-0.008	21.227	0.002	0.002	0.000	0.000	0.000	0.000
72	B	217	SER	0	-0.009	-0.024	23.647	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	218	PRO	0	0.006	0.021	24.211	-0.010	-0.010	0.000	0.000	0.000	0.000
74	B	220	SER	0	-0.051	-0.056	25.474	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	221	ASP	-1	-0.951	-0.974	26.436	-0.058	-0.058	0.000	0.000	0.000	0.000
76	B	222	ASP	-1	-0.846	-0.860	28.481	-0.074	-0.074	0.000	0.000	0.000	0.000

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