FMO DATABASE

FMODB ID: LJ3G9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-236254.472817
FMO2-HF: Nuclear repulsion	215788.144702
FMO2-HF: Total energy	-20466.328115
FMO2-MP2: Total energy	-20527.26062

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.
-102.883	-100.397	11.02	-6.323	-7.182	-0.059

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 : 0.951 / q_NPA : 0.966

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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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	-0.013	1.807	-37.619	-35.720	11.005	-6.053	-6.850	-0.058
4	A	7	VAL	0	0.036	0.020	3.771	6.169	6.756	0.015	-0.270	-0.332	-0.001
5	A	8	THR	0	-0.020	-0.011	6.512	-3.117	-3.117	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.028	0.025	9.119	0.850	0.850	0.000	0.000	0.000	0.000
7	A	10	VAL	0	-0.026	-0.011	11.520	-0.170	-0.170	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.730	-0.835	13.959	-14.711	-14.711	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.781	-0.905	17.428	-16.507	-16.507	0.000	0.000	0.000	0.000
10	A	13	PHE	0	-0.124	-0.050	19.764	0.710	0.710	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.828	-0.925	18.441	-16.328	-16.328	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.014	0.016	16.597	-0.192	-0.192	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.121	-0.069	14.919	-1.369	-1.369	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.059	-0.025	14.040	-1.241	-1.241	0.000	0.000	0.000	0.000
15	A	18	ALA	0	-0.042	-0.029	12.495	-0.685	-0.685	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.011	-0.011	14.042	1.401	1.401	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.834	-0.911	16.209	-17.584	-17.584	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.869	-0.912	18.887	-12.125	-12.125	0.000	0.000	0.000	0.000
19	A	22	THR	0	0.032	0.005	21.053	-0.322	-0.322	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.129	-0.063	23.057	0.639	0.639	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.888	-0.945	26.504	-10.385	-10.385	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.072	-0.047	27.566	0.391	0.391	0.000	0.000	0.000	0.000
23	A	26	GLY	0	0.044	0.019	31.869	-0.104	-0.104	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.066	-0.027	34.466	0.101	0.101	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.912	-0.956	36.716	-8.187	-8.187	0.000	0.000	0.000	0.000
26	A	29	GLY	0	-0.048	-0.024	39.135	0.079	0.079	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.045	-0.007	33.021	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.001	-0.011	31.563	0.137	0.137	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.061	-0.037	28.416	-0.156	-0.156	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.898	-0.947	24.804	-12.540	-12.540	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.049	-0.029	23.013	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.800	-0.870	18.435	-16.516	-16.516	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.059	-0.035	20.053	-0.114	-0.114	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.034	0.022	18.639	0.096	0.096	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.026	-0.051	19.914	0.986	0.986	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.895	0.951	22.395	13.704	13.704	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.037	-0.049	21.111	1.327	1.327	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.054	0.049	23.994	0.546	0.546	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.088	-0.057	25.736	0.731	0.731	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.831	0.901	27.229	11.151	11.151	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.051	0.042	27.589	0.469	0.469	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.832	0.874	26.901	12.021	12.021	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.062	-0.035	31.650	0.423	0.423	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.859	-0.912	31.383	-9.814	-9.814	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.022	0.006	32.726	0.371	0.371	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.934	0.981	35.944	9.000	9.000	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.030	-0.023	37.812	0.182	0.182	0.000	0.000	0.000	0.000
48	A	51	TRP	0	0.031	0.012	38.052	0.345	0.345	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.006	-0.005	37.354	0.172	0.172	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.072	-0.030	40.647	0.161	0.161	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.015	0.003	43.340	0.190	0.190	0.000	0.000	0.000	0.000
52	A	55	GLY	0	-0.008	0.015	44.109	0.174	0.174	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.941	0.960	45.225	6.707	6.707	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.968	0.979	41.301	7.530	7.530	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.036	0.029	43.076	0.187	0.187	0.000	0.000	0.000	0.000

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