FMO DATABASE

FMODB ID: 7G5YK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-258652.690227
FMO2-HF: Nuclear repulsion	236092.413247
FMO2-HF: Total energy	-22560.27698
FMO2-MP2: Total energy	-22624.701259

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.
-8.538	-3.061	1.561	-2.133	-4.905	-0.004

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 : 0.014 / 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	A	21	LEU	0	0.062	0.028	3.863	-1.304	0.871	-0.021	-1.122	-1.032	0.005
4	A	22	ARG	1	0.955	0.983	6.995	-1.121	-1.121	0.000	0.000	0.000	0.000
5	A	23	TRP	0	0.009	0.004	9.803	-0.103	-0.103	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.924	0.935	13.061	-0.321	-0.321	0.000	0.000	0.000	0.000
7	A	25	MET	0	0.019	0.017	16.902	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	26	GLN	0	0.030	0.029	19.466	0.024	0.024	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.987	0.984	21.300	-0.112	-0.112	0.000	0.000	0.000	0.000
10	A	28	SER	0	0.032	0.024	23.329	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	29	THR	0	-0.046	-0.025	24.543	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	30	THR	0	0.052	0.022	26.777	0.005	0.005	0.000	0.000	0.000	0.000
13	A	31	ILE	0	0.005	0.002	28.266	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	32	ALA	0	0.025	0.012	27.686	0.000	0.000	0.000	0.000	0.000	0.000
15	A	33	ALA	0	-0.033	-0.005	28.819	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	34	ILE	0	-0.012	-0.007	23.698	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	35	ALA	0	0.033	0.022	27.585	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	36	GLY	0	0.047	0.034	26.536	0.002	0.002	0.000	0.000	0.000	0.000
19	A	37	CYS	0	-0.089	-0.030	18.382	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	38	SER	0	0.016	0.005	25.476	0.000	0.000	0.000	0.000	0.000	0.000
21	A	39	GLY	0	0.018	-0.001	22.070	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	40	ALA	0	-0.028	-0.013	20.278	0.000	0.000	0.000	0.000	0.000	0.000
23	A	41	ALA	0	-0.015	-0.001	16.118	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	42	THR	0	0.026	-0.002	18.185	0.008	0.008	0.000	0.000	0.000	0.000
25	A	43	PHE	0	0.014	0.017	12.821	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	44	GLY	0	0.005	-0.017	14.302	0.018	0.018	0.000	0.000	0.000	0.000
27	A	45	GLY	0	0.005	0.011	14.803	0.024	0.024	0.000	0.000	0.000	0.000
28	A	46	LEU	0	-0.033	-0.001	16.072	0.014	0.014	0.000	0.000	0.000	0.000
29	A	47	ALA	0	0.028	0.009	19.402	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.033	0.021	21.400	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	49	GLY	0	0.011	-0.001	22.499	0.010	0.010	0.000	0.000	0.000	0.000
32	A	50	ILE	0	0.047	0.011	22.833	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	51	VAL	0	0.027	0.013	18.800	0.002	0.002	0.000	0.000	0.000	0.000
34	A	52	GLY	0	0.075	0.042	18.592	0.004	0.004	0.000	0.000	0.000	0.000
35	A	54	ILE	0	-0.006	0.004	16.998	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.002	0.000	14.406	0.004	0.004	0.000	0.000	0.000	0.000
37	A	56	ALA	0	0.005	0.000	13.823	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	57	GLY	0	0.023	0.010	15.174	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	58	ILE	0	-0.024	-0.019	10.892	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	59	LEU	0	-0.011	0.003	9.365	0.004	0.004	0.000	0.000	0.000	0.000
41	A	60	ALA	0	0.042	0.024	10.821	0.008	0.008	0.000	0.000	0.000	0.000
42	A	61	ILE	0	-0.032	-0.012	11.318	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	62	LEU	0	-0.047	-0.027	6.416	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	63	GLN	0	0.029	0.001	7.309	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	64	GLY	0	-0.017	0.001	9.162	-0.087	-0.087	0.000	0.000	0.000	0.000
46	A	65	PHE	0	-0.048	-0.043	7.279	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	66	GLU	-1	-0.840	-0.903	5.323	-0.211	-0.211	0.000	0.000	0.000	0.000
48	A	67	VAL	0	-0.024	-0.007	6.449	-0.327	-0.327	0.000	0.000	0.000	0.000
49	A	68	ASN	0	-0.018	-0.006	8.676	0.041	0.041	0.000	0.000	0.000	0.000
50	A	69	TRP	0	-0.007	0.001	2.974	-4.159	-1.187	1.581	-0.963	-3.590	-0.009
51	A	70	HIS	0	-0.066	-0.039	4.075	-1.141	-0.811	0.001	-0.048	-0.283	0.000
52	A	71	ASN	0	-0.078	-0.038	6.508	0.183	0.183	0.000	0.000	0.000	0.000
53	A	72	GLY	0	0.021	0.028	9.377	0.122	0.122	0.000	0.000	0.000	0.000
54	A	73	GLY	0	-0.009	-0.011	11.055	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	74	GLY	0	-0.009	-0.020	11.802	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	75	GLY	0	0.001	-0.001	13.301	0.004	0.004	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.919	-0.953	14.428	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	77	ARG	1	0.859	0.932	11.763	0.226	0.226	0.000	0.000	0.000	0.000
59	A	78	SER	0	-0.031	-0.017	15.836	0.019	0.019	0.000	0.000	0.000	0.000
60	A	79	ASN	0	0.022	-0.001	16.893	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	80	PRO	0	0.003	0.006	18.926	0.011	0.011	0.000	0.000	0.000	0.000
62	A	81	VAL	0	-0.021	-0.019	20.732	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:19:TRP)