FMO DATABASE

FMODB ID: V57M1

Calculation Name: 2J8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J8B

Chain ID: A

ChEMBL ID:

UniProt ID: P13987

Base Structure: X-ray

Registration Date: 2023-09-20

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-542780.657694
FMO2-HF: Nuclear repulsion	508282.015528
FMO2-HF: Total energy	-34498.642166
FMO2-MP2: Total energy	-34590.206357

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-13.861	-17.369	20.548	-7.905	-9.136	0.021

Interaction energy analysis for fragmet #1(A:0:MET)

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 : 0.034

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	2	GLN	0	-0.012	-0.012	3.775	-0.144	2.073	-0.001	-1.072	-1.144	0.002
4	A	3	CYS	0	-0.009	-0.003	5.733	-0.361	-0.361	0.000	0.000	0.000	0.000
5	A	4	TYR	0	0.038	0.018	8.935	0.278	0.278	0.000	0.000	0.000	0.000
6	A	5	ASN	0	0.020	0.002	10.410	-0.204	-0.204	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.063	0.016	12.401	0.138	0.138	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.007	0.014	15.535	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	8	ASN	0	0.022	0.000	16.940	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.032	0.028	19.923	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.060	-0.047	19.965	0.040	0.040	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.011	0.004	21.731	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.809	-0.889	21.363	-0.165	-0.165	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.901	0.921	16.288	0.054	0.054	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.015	-0.016	12.579	0.054	0.054	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.014	0.020	9.915	-0.124	-0.124	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.021	-0.011	6.945	0.233	0.233	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.016	-0.041	2.229	-6.705	-14.874	19.077	-5.371	-5.538	0.036
19	A	19	CYS	0	0.005	0.023	3.689	-1.297	-0.595	0.029	-0.174	-0.557	0.000
20	A	20	SER	0	-0.005	-0.035	2.461	-4.920	-3.301	1.444	-1.288	-1.775	-0.017
21	A	21	SER	0	0.022	-0.010	4.350	-0.014	0.109	-0.001	0.000	-0.122	0.000
22	A	22	ASP	-1	-0.891	-0.901	6.128	-0.728	-0.728	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.059	-0.025	7.101	0.273	0.273	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.812	-0.900	7.210	-1.539	-1.539	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.031	-0.020	8.807	-0.073	-0.073	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.021	0.004	11.302	0.081	0.081	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.018	0.001	14.892	0.013	0.013	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.033	-0.035	17.626	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.838	0.935	21.123	0.288	0.288	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.057	0.023	24.489	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.036	0.026	27.389	0.012	0.012	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.023	-0.012	29.096	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.069	-0.031	25.216	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.001	0.000	20.633	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.068	-0.068	19.101	0.019	0.019	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.012	-0.019	14.958	0.010	0.010	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.838	0.907	12.887	0.411	0.411	0.000	0.000	0.000	0.000
38	A	40	TRP	0	-0.019	-0.043	10.082	0.191	0.191	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.879	0.918	11.262	0.517	0.517	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.038	-0.018	12.447	0.115	0.115	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.853	-0.900	15.502	-0.552	-0.552	0.000	0.000	0.000	0.000
42	A	44	HIS	0	0.004	-0.003	17.257	0.071	0.071	0.000	0.000	0.000	0.000
43	A	45	CYS	0	-0.077	0.005	15.136	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.035	-0.032	18.859	0.046	0.046	0.000	0.000	0.000	0.000
45	A	47	PHE	0	0.086	0.041	22.683	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.024	0.037	25.562	0.028	0.028	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.773	-0.869	21.166	-0.341	-0.341	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.004	-0.001	19.909	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.011	-0.010	22.094	0.018	0.018	0.000	0.000	0.000	0.000
50	A	52	THR	0	-0.040	-0.040	24.709	0.010	0.010	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.771	0.892	18.885	0.379	0.379	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.038	-0.015	19.280	0.009	0.009	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.846	0.923	22.818	0.224	0.224	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.777	-0.833	25.258	-0.170	-0.170	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.018	-0.030	27.568	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.962	-0.976	29.954	-0.167	-0.167	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.040	-0.020	24.261	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.017	-0.015	25.684	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	61	TYR	0	0.010	-0.008	20.520	0.011	0.011	0.000	0.000	0.000	0.000
60	A	62	TYR	0	0.055	0.025	16.640	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.026	0.036	11.047	0.144	0.144	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.899	0.940	8.987	1.466	1.466	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.878	0.919	8.308	1.909	1.909	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.734	-0.871	5.894	-3.114	-3.114	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.064	-0.026	8.547	0.304	0.304	0.000	0.000	0.000	0.000
66	A	70	ASN	0	-0.012	-0.010	12.432	0.052	0.052	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.043	0.014	14.805	0.065	0.065	0.000	0.000	0.000	0.000
68	A	72	ASN	0	0.037	-0.006	17.572	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.847	-0.944	21.196	-0.281	-0.281	0.000	0.000	0.000	0.000
70	A	74	GLN	0	-0.085	-0.023	16.942	0.043	0.043	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.063	-0.025	21.363	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.898	-0.937	23.996	-0.238	-0.238	0.000	0.000	0.000	0.000
73	A	77	ASN	0	-0.007	0.018	26.818	0.013	0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)