FMO DATABASE

FMODB ID: 9Y5Q2

Calculation Name: 1KVE-B-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	76
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-382728.470933
FMO2-HF: Nuclear repulsion	354276.223863
FMO2-HF: Total energy	-28452.24707
FMO2-MP2: Total energy	-28532.445008

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.
-0.801	0.767	-0.004	-0.85	-0.713	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 : 0.018 / 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	0.000	0.002	3.797	-0.368	1.114	-0.004	-0.812	-0.665	0.003
4	B	149	THR	0	-0.022	-0.015	4.373	-0.547	-0.461	0.000	-0.038	-0.048	0.000
5	B	150	THR	0	-0.022	-0.002	6.102	0.683	0.683	0.000	0.000	0.000	0.000
6	B	151	ILE	0	-0.050	-0.022	9.752	-0.022	-0.022	0.000	0.000	0.000	0.000
7	B	152	TRP	0	0.015	0.004	12.441	0.100	0.100	0.000	0.000	0.000	0.000
8	B	153	GLY	0	0.017	0.002	15.873	0.038	0.038	0.000	0.000	0.000	0.000
9	B	154	VAL	0	-0.035	-0.005	19.260	-0.004	-0.004	0.000	0.000	0.000	0.000
10	B	155	GLY	0	0.010	-0.016	22.099	0.018	0.018	0.000	0.000	0.000	0.000
11	B	156	ALA	0	0.009	0.005	25.293	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	157	ASP	-1	-0.890	-0.964	29.056	-0.097	-0.097	0.000	0.000	0.000	0.000
13	B	158	GLH	0	-0.105	-0.066	31.472	0.001	0.001	0.000	0.000	0.000	0.000
14	B	159	ALA	0	-0.023	-0.015	34.021	0.007	0.007	0.000	0.000	0.000	0.000
15	B	160	ILE	0	0.017	0.017	35.154	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	161	ASH	0	-0.090	-0.100	34.959	0.008	0.008	0.000	0.000	0.000	0.000
17	B	162	LYS	1	0.915	0.948	35.535	0.068	0.068	0.000	0.000	0.000	0.000
18	B	163	GLY	0	0.028	0.034	36.331	0.002	0.002	0.000	0.000	0.000	0.000
19	B	164	THR	0	-0.044	-0.031	30.810	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	165	PRO	0	0.053	0.042	28.763	0.008	0.008	0.000	0.000	0.000	0.000
21	B	166	SER	0	0.052	0.024	30.497	0.000	0.000	0.000	0.000	0.000	0.000
22	B	167	LYS	1	1.010	0.996	22.987	0.006	0.006	0.000	0.000	0.000	0.000
23	B	168	ASN	0	0.002	-0.016	26.782	0.006	0.006	0.000	0.000	0.000	0.000
24	B	169	ASP	-1	-0.878	-0.922	27.785	0.004	0.004	0.000	0.000	0.000	0.000
25	B	170	LEU	0	0.008	-0.013	24.563	0.000	0.000	0.000	0.000	0.000	0.000
26	B	171	GLN	0	-0.031	-0.020	22.930	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	172	ASN	0	0.001	0.005	22.787	0.023	0.023	0.000	0.000	0.000	0.000
28	B	173	MET	0	0.018	0.022	23.782	0.007	0.007	0.000	0.000	0.000	0.000
29	B	174	SER	0	-0.010	-0.009	19.350	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	175	ALA	0	-0.032	-0.028	18.923	0.009	0.009	0.000	0.000	0.000	0.000
31	B	176	ASP	-1	-0.901	-0.929	19.442	0.068	0.068	0.000	0.000	0.000	0.000
32	B	177	LEU	0	0.086	0.042	17.868	0.014	0.014	0.000	0.000	0.000	0.000
33	B	178	ALA	0	-0.008	0.009	14.915	0.004	0.004	0.000	0.000	0.000	0.000
34	B	179	LYS	1	0.904	0.954	15.302	-0.113	-0.113	0.000	0.000	0.000	0.000
35	B	180	ASN	0	-0.052	-0.066	17.470	0.054	0.054	0.000	0.000	0.000	0.000
36	B	181	GLY	0	0.026	0.031	18.394	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	182	PHE	0	-0.042	-0.031	12.615	0.010	0.010	0.000	0.000	0.000	0.000
38	B	183	LYS	1	0.879	0.966	13.497	-0.087	-0.087	0.000	0.000	0.000	0.000
39	B	184	GLY	0	-0.012	-0.012	10.604	0.078	0.078	0.000	0.000	0.000	0.000
40	B	185	HIS	1	0.826	0.914	9.094	-0.222	-0.222	0.000	0.000	0.000	0.000
41	B	186	GLN	0	0.004	-0.024	5.745	0.058	0.058	0.000	0.000	0.000	0.000
42	B	187	GLY	0	0.002	-0.005	10.048	0.119	0.119	0.000	0.000	0.000	0.000
43	B	188	VAL	0	-0.016	-0.012	13.742	-0.085	-0.085	0.000	0.000	0.000	0.000
44	B	189	ALA	0	-0.017	0.005	16.776	0.047	0.047	0.000	0.000	0.000	0.000
45	B	219	CYS	0	-0.077	-0.036	19.356	-0.035	-0.035	0.000	0.000	0.000	0.000
46	B	191	SER	0	-0.013	-0.008	22.800	0.021	0.021	0.000	0.000	0.000	0.000
47	B	192	THR	0	0.127	0.020	24.694	-0.020	-0.020	0.000	0.000	0.000	0.000
48	B	193	VAL	0	-0.086	-0.033	26.183	0.012	0.012	0.000	0.000	0.000	0.000
49	B	194	LYS	1	0.977	0.983	28.517	0.036	0.036	0.000	0.000	0.000	0.000
50	B	195	ASP	-1	-0.894	-0.899	31.951	-0.036	-0.036	0.000	0.000	0.000	0.000
51	B	196	GLY	0	-0.001	-0.014	34.690	0.001	0.001	0.000	0.000	0.000	0.000
52	B	197	ASN	0	-0.040	-0.040	35.512	0.000	0.000	0.000	0.000	0.000	0.000
53	B	198	LYS	1	0.892	0.968	36.712	0.046	0.046	0.000	0.000	0.000	0.000
54	B	199	ASP	-1	-0.744	-0.866	33.528	-0.056	-0.056	0.000	0.000	0.000	0.000
55	B	200	VAL	0	-0.084	-0.044	31.972	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	201	TYR	0	-0.010	0.006	26.124	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	202	MET	0	0.018	0.043	27.414	0.002	0.002	0.000	0.000	0.000	0.000
58	B	203	ILE	0	-0.027	-0.027	21.058	-0.019	-0.019	0.000	0.000	0.000	0.000
59	B	204	LYS	1	0.936	0.990	19.472	0.334	0.334	0.000	0.000	0.000	0.000
60	B	205	PHE	0	-0.036	-0.034	16.653	-0.034	-0.034	0.000	0.000	0.000	0.000
61	B	206	SER	0	0.004	-0.009	14.192	0.051	0.051	0.000	0.000	0.000	0.000
62	B	207	LEU	0	-0.025	-0.010	8.181	-0.093	-0.093	0.000	0.000	0.000	0.000
63	B	208	ALA	0	0.043	0.010	9.927	0.145	0.145	0.000	0.000	0.000	0.000
64	B	209	GLY	0	0.079	0.036	7.256	-0.268	-0.268	0.000	0.000	0.000	0.000
65	B	210	GLY	0	-0.055	-0.020	8.320	-0.340	-0.340	0.000	0.000	0.000	0.000
66	B	211	SER	0	0.043	0.016	9.374	0.062	0.062	0.000	0.000	0.000	0.000
67	B	212	ASN	0	-0.061	-0.038	10.953	0.159	0.159	0.000	0.000	0.000	0.000
68	B	213	ASP	-1	-0.846	-0.918	14.788	-0.482	-0.482	0.000	0.000	0.000	0.000
69	B	214	PRO	0	-0.063	-0.018	15.732	0.026	0.026	0.000	0.000	0.000	0.000
70	B	215	GLY	0	0.025	0.027	17.920	0.050	0.050	0.000	0.000	0.000	0.000
71	B	216	GLY	0	-0.017	-0.029	21.228	0.003	0.003	0.000	0.000	0.000	0.000
72	B	217	SER	0	-0.015	-0.021	23.648	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	218	PRO	0	-0.006	0.014	24.221	-0.009	-0.009	0.000	0.000	0.000	0.000
74	B	220	SER	0	-0.018	-0.020	25.475	-0.010	-0.010	0.000	0.000	0.000	0.000
75	B	221	ASP	-1	-1.003	-1.002	26.476	-0.058	-0.058	0.000	0.000	0.000	0.000
76	B	222	ASP	-2	-1.724	-1.788	28.481	-0.130	-0.130	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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