FMO DATABASE

FMODB ID: 2K1MR

Calculation Name: 1J1V-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J1V

Chain ID: A

ChEMBL ID:

UniProt ID: P03004

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-709331.085341
FMO2-HF: Nuclear repulsion	671682.28843
FMO2-HF: Total energy	-37648.796911
FMO2-MP2: Total energy	-37758.705125

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:374:VAL )

Summations of interaction energy for fragment #1(A:374:VAL )

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.
-13.028	-3.463	5.224	-4.627	-10.159	-0.013

Interaction energy analysis for fragmet #1(A:374:VAL )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.022

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	376	ILE	0	0.070	0.019	2.962	-2.060	0.454	0.244	-1.307	-1.451	0.000
4	A	377	ASP	-1	-0.892	-0.948	5.004	0.361	0.479	0.000	-0.003	-0.115	0.000
5	A	378	ASN	0	0.003	0.000	3.305	-0.891	-0.399	0.024	-0.103	-0.413	0.001
6	A	379	ILE	0	0.044	0.038	2.274	-0.828	-0.615	1.838	-0.432	-1.619	0.001
7	A	380	GLN	0	-0.068	-0.047	4.832	-0.119	-0.069	0.000	-0.009	-0.041	0.000
8	A	381	LYS	1	0.887	0.943	8.180	-0.436	-0.436	0.000	0.000	0.000	0.000
9	A	382	THR	0	0.064	0.037	6.184	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	383	VAL	0	-0.013	-0.007	7.731	-0.035	-0.035	0.000	0.000	0.000	0.000
11	A	384	ALA	0	-0.065	-0.037	10.153	0.001	0.001	0.000	0.000	0.000	0.000
12	A	385	GLU	-1	-0.906	-0.953	12.277	0.024	0.024	0.000	0.000	0.000	0.000
13	A	386	TYR	0	-0.049	-0.038	11.771	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	387	TYR	0	-0.070	-0.039	12.439	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	388	LYS	1	0.881	0.953	16.139	0.053	0.053	0.000	0.000	0.000	0.000
16	A	389	ILE	0	-0.066	-0.024	15.259	0.004	0.004	0.000	0.000	0.000	0.000
17	A	390	LYS	1	0.965	0.966	16.674	0.001	0.001	0.000	0.000	0.000	0.000
18	A	391	VAL	0	0.118	0.057	11.988	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	392	ALA	0	0.016	0.003	14.404	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	393	ASP	-1	-0.867	-0.935	17.303	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	394	LEU	0	-0.008	0.012	10.958	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	395	LEU	0	0.043	0.030	13.296	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	396	SER	0	0.028	0.030	16.333	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	397	LYS	1	1.022	1.019	19.397	0.019	0.019	0.000	0.000	0.000	0.000
25	A	398	ARG	1	0.932	0.978	21.936	0.041	0.041	0.000	0.000	0.000	0.000
26	A	399	ARG	1	1.045	0.998	21.377	0.069	0.069	0.000	0.000	0.000	0.000
27	A	400	SER	0	0.012	0.017	23.226	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	401	ARG	1	1.033	1.012	21.818	0.111	0.111	0.000	0.000	0.000	0.000
29	A	402	SER	0	0.043	0.021	20.446	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	403	VAL	0	0.038	0.009	18.427	0.000	0.000	0.000	0.000	0.000	0.000
31	A	404	ALA	0	-0.021	-0.016	17.200	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	405	ARG	1	0.950	0.989	17.050	0.150	0.150	0.000	0.000	0.000	0.000
33	A	406	PRO	0	0.056	0.049	14.171	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	407	ARG	1	0.816	0.897	12.618	0.075	0.075	0.000	0.000	0.000	0.000
35	A	408	GLN	0	-0.044	-0.038	12.560	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	409	MET	0	0.052	0.039	10.245	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	410	ALA	0	0.016	0.006	8.404	-0.083	-0.083	0.000	0.000	0.000	0.000
38	A	411	MET	0	-0.080	-0.039	7.992	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	412	ALA	0	0.033	0.005	9.986	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	413	LEU	0	0.034	0.021	5.185	-0.086	-0.086	0.000	0.000	0.000	0.000
41	A	414	ALA	0	-0.004	-0.003	5.195	-0.299	-0.299	0.000	0.000	0.000	0.000
42	A	415	LYS	1	0.899	0.968	6.143	0.309	0.309	0.000	0.000	0.000	0.000
43	A	416	GLU	-1	-0.922	-0.953	7.599	-0.770	-0.770	0.000	0.000	0.000	0.000
44	A	417	LEU	0	-0.034	-0.020	2.378	-1.845	-0.428	1.685	-0.671	-2.429	0.000
45	A	418	THR	0	-0.088	-0.054	2.413	-2.666	-0.890	0.600	-0.885	-1.492	-0.006
46	A	419	ASN	0	-0.001	-0.008	4.432	0.317	0.507	0.000	-0.024	-0.167	0.000
47	A	420	HIS	0	-0.029	-0.001	6.241	0.228	0.228	0.000	0.000	0.000	0.000
48	A	421	SER	0	-0.029	-0.011	9.320	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	422	LEU	0	0.011	-0.016	12.248	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	423	PRO	0	0.004	-0.028	14.292	0.009	0.009	0.000	0.000	0.000	0.000
51	A	424	GLU	-1	-0.775	-0.868	11.976	-0.207	-0.207	0.000	0.000	0.000	0.000
52	A	425	ILE	0	-0.012	-0.002	8.941	0.037	0.037	0.000	0.000	0.000	0.000
53	A	426	GLY	0	0.013	-0.011	11.214	0.037	0.037	0.000	0.000	0.000	0.000
54	A	427	ASP	-1	-0.894	-0.934	14.601	-0.053	-0.053	0.000	0.000	0.000	0.000
55	A	428	ALA	0	-0.033	-0.013	10.265	0.032	0.032	0.000	0.000	0.000	0.000
56	A	429	PHE	0	-0.032	-0.018	8.380	0.033	0.033	0.000	0.000	0.000	0.000
57	A	430	GLY	0	-0.013	-0.008	13.614	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	431	GLY	0	-0.023	0.011	16.518	0.004	0.004	0.000	0.000	0.000	0.000
59	A	432	ARG	1	0.699	0.815	16.012	0.100	0.100	0.000	0.000	0.000	0.000
60	A	433	ASP	-1	-0.752	-0.862	17.893	-0.125	-0.125	0.000	0.000	0.000	0.000
61	A	434	HIS	0	0.106	0.021	16.994	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	435	THR	0	-0.080	-0.040	17.702	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	436	THR	0	-0.033	-0.022	17.626	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	437	VAL	0	0.025	0.021	12.737	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	438	LEU	0	0.001	0.006	15.367	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	439	HIS	0	-0.055	-0.030	17.336	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	440	ALA	0	-0.034	-0.017	14.576	0.002	0.002	0.000	0.000	0.000	0.000
68	A	441	CYS	0	0.002	0.007	13.135	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	442	ARG	1	1.046	1.029	14.690	0.224	0.224	0.000	0.000	0.000	0.000
70	A	443	LYS	1	0.818	0.923	18.149	0.187	0.187	0.000	0.000	0.000	0.000
71	A	444	ILE	0	0.003	-0.011	12.662	0.018	0.018	0.000	0.000	0.000	0.000
72	A	445	GLU	-1	-0.922	-0.959	15.697	-0.336	-0.336	0.000	0.000	0.000	0.000
73	A	446	GLN	0	0.012	-0.003	17.047	0.012	0.012	0.000	0.000	0.000	0.000
74	A	447	LEU	0	-0.047	-0.039	18.079	0.016	0.016	0.000	0.000	0.000	0.000
75	A	448	ARG	1	0.942	0.985	13.755	0.421	0.421	0.000	0.000	0.000	0.000
76	A	449	GLU	-1	-0.992	-0.990	18.056	-0.214	-0.214	0.000	0.000	0.000	0.000
77	A	450	GLU	-1	-0.909	-0.944	21.488	-0.146	-0.146	0.000	0.000	0.000	0.000
78	A	451	SER	0	-0.045	-0.018	20.996	0.012	0.012	0.000	0.000	0.000	0.000
79	A	452	HIS	0	0.054	0.011	20.065	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	453	ASP	-1	-0.810	-0.898	19.526	-0.169	-0.169	0.000	0.000	0.000	0.000
81	A	454	ILE	0	-0.082	-0.033	15.819	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	455	LYS	1	0.900	0.938	15.242	0.199	0.199	0.000	0.000	0.000	0.000
83	A	456	GLU	-1	-0.918	-0.964	15.300	-0.237	-0.237	0.000	0.000	0.000	0.000
84	A	457	ASP	-1	-0.821	-0.885	13.477	-0.264	-0.264	0.000	0.000	0.000	0.000
85	A	458	PHE	0	-0.040	-0.030	10.094	-0.050	-0.050	0.000	0.000	0.000	0.000
86	A	459	SER	0	-0.006	-0.001	10.021	-0.129	-0.129	0.000	0.000	0.000	0.000
87	A	460	ASN	0	0.014	-0.003	10.683	-0.077	-0.077	0.000	0.000	0.000	0.000
88	A	461	LEU	0	-0.020	-0.019	7.581	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	462	ILE	0	0.008	0.009	5.862	-0.130	-0.130	0.000	0.000	0.000	0.000
90	A	463	ARG	1	0.928	0.973	6.243	0.153	0.153	0.000	0.000	0.000	0.000
91	A	464	THR	0	-0.029	-0.014	7.450	0.053	0.053	0.000	0.000	0.000	0.000
92	A	465	LEU	0	-0.047	-0.041	2.774	-0.925	0.053	0.528	-0.277	-1.228	0.000
93	A	466	SER	0	-0.132	-0.045	2.890	-2.785	-1.007	0.304	-0.902	-1.179	-0.009
94	A	467	SER	-1	-0.946	-0.959	4.372	0.303	0.342	0.001	-0.014	-0.025	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:374:VAL )