FMO DATABASE

FMODB ID: 3QVZL

Calculation Name: 4E1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E1P

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP7

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:

Apendix: None

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-236149.154363
FMO2-HF: Nuclear repulsion	215683.069655
FMO2-HF: Total energy	-20466.084708
FMO2-MP2: Total energy	-20527.021091

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:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
-101.091	-99.873	11.599	-5.888	-6.927	-0.062

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.928 / q_NPA : 0.943

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].	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	6	THR	0	-0.038	-0.014	1.829	-35.565	-34.900	11.581	-5.643	-6.602	-0.061
4	A	7	VAL	0	0.037	0.021	3.716	5.903	6.456	0.018	-0.245	-0.325	-0.001
5	A	8	THR	0	-0.030	-0.020	6.711	-2.921	-2.921	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.033	0.029	9.193	0.918	0.918	0.000	0.000	0.000	0.000
7	A	10	VAL	0	-0.025	-0.008	11.688	-0.252	-0.252	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.723	-0.831	14.002	-14.737	-14.737	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.780	-0.905	17.456	-16.758	-16.758	0.000	0.000	0.000	0.000
10	A	13	PHE	0	-0.122	-0.050	19.810	0.727	0.727	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.831	-0.933	18.438	-16.444	-16.444	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.010	0.033	16.619	-0.204	-0.204	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.134	-0.095	14.897	-1.303	-1.303	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.061	-0.024	14.012	-1.267	-1.267	0.000	0.000	0.000	0.000
15	A	18	ALA	0	-0.039	-0.027	12.464	-0.686	-0.686	0.000	0.000	0.000	0.000
16	A	19	ALA	0	0.004	-0.008	14.041	1.417	1.417	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.886	-0.957	16.233	-17.855	-17.855	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.912	-0.960	18.906	-12.368	-12.368	0.000	0.000	0.000	0.000
19	A	22	THR	0	0.029	0.008	21.295	-0.402	-0.402	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.135	-0.067	23.123	0.641	0.641	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.897	-0.951	26.556	-10.413	-10.413	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.079	-0.050	27.575	0.381	0.381	0.000	0.000	0.000	0.000
23	A	26	GLY	0	0.048	0.022	31.929	-0.096	-0.096	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.051	-0.024	34.576	0.102	0.102	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.920	-0.955	36.819	-8.101	-8.101	0.000	0.000	0.000	0.000
26	A	29	GLY	0	-0.046	-0.023	39.274	0.076	0.076	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.046	-0.009	33.124	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.012	-0.016	31.709	0.101	0.101	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.054	-0.035	28.432	-0.126	-0.126	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.887	-0.945	24.791	-12.532	-12.532	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.056	-0.031	22.992	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.806	-0.875	18.612	-16.224	-16.224	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.058	-0.036	20.096	-0.101	-0.101	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.045	0.037	18.757	0.101	0.101	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.008	-0.007	19.915	0.972	0.972	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.887	0.940	22.367	13.610	13.610	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.045	-0.053	21.062	1.380	1.380	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.056	0.052	23.998	0.556	0.556	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.073	-0.044	25.749	0.752	0.752	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.923	0.966	26.992	11.567	11.567	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.059	0.051	27.620	0.446	0.446	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.881	0.922	27.310	11.800	11.800	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.078	-0.042	31.654	0.418	0.418	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.914	-0.955	31.736	-9.680	-9.680	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.001	-0.011	32.911	0.373	0.373	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.931	0.982	35.966	9.034	9.034	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.023	-0.018	37.825	0.236	0.236	0.000	0.000	0.000	0.000
48	A	51	TRP	0	0.028	0.007	38.123	0.337	0.337	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.012	-0.006	37.385	0.173	0.173	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.069	-0.031	40.677	0.160	0.160	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.015	0.003	43.360	0.189	0.189	0.000	0.000	0.000	0.000
52	A	55	GLY	0	-0.011	0.014	44.138	0.175	0.175	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.945	0.962	45.262	6.719	6.719	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.967	0.978	41.411	7.509	7.509	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.032	0.026	43.518	0.202	0.202	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)