FMO DATABASE

FMODB ID: 1487Z

Calculation Name: 1J1V-A-Xray372

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: 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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-711795.587859
FMO2-HF: Nuclear repulsion	674145.330408
FMO2-HF: Total energy	-37650.257451
FMO2-MP2: Total energy	-37760.11719

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.
-13.499	-3.761	5.475	-4.814	-10.398	-0.024

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 : 0.021 / q_NPA : 0.010

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	0.020	3.038	-1.967	0.297	0.181	-1.196	-1.249	0.000
4	A	377	ASP	-1	-0.839	-0.898	5.178	0.526	0.654	-0.001	-0.003	-0.124	0.000
5	A	378	ASN	0	0.024	0.009	3.037	-2.034	-0.641	0.170	-0.558	-1.005	-0.005
6	A	379	ILE	0	0.050	0.046	2.234	-0.668	-0.763	2.396	-0.505	-1.795	0.001
7	A	380	GLN	0	-0.056	-0.049	4.815	-0.096	-0.037	-0.001	-0.011	-0.047	0.000
8	A	381	LYS	1	0.821	0.886	8.240	-0.479	-0.479	0.000	0.000	0.000	0.000
9	A	382	THR	0	0.019	0.005	5.922	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	383	VAL	0	-0.008	-0.009	7.429	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	384	ALA	0	-0.052	-0.031	10.010	0.005	0.005	0.000	0.000	0.000	0.000
12	A	385	GLU	-1	-0.831	-0.892	11.962	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	386	TYR	0	-0.004	-0.023	11.488	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	387	TYR	0	-0.090	-0.086	12.521	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	388	LYS	1	0.790	0.892	15.860	0.097	0.097	0.000	0.000	0.000	0.000
16	A	389	ILE	0	-0.055	-0.020	15.330	0.010	0.010	0.000	0.000	0.000	0.000
17	A	390	LYS	1	0.960	0.982	16.443	0.014	0.014	0.000	0.000	0.000	0.000
18	A	391	VAL	0	0.104	0.038	11.894	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	392	ALA	0	0.016	0.011	14.318	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	393	ASP	-1	-0.833	-0.925	17.652	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	394	LEU	0	-0.009	0.016	10.930	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	395	LEU	0	0.071	0.039	13.154	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	396	SER	0	0.008	0.022	15.988	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	397	LYS	1	1.004	1.002	19.182	0.012	0.012	0.000	0.000	0.000	0.000
25	A	398	ARG	1	0.877	0.938	21.432	0.044	0.044	0.000	0.000	0.000	0.000
26	A	399	ARG	1	1.046	1.007	21.233	0.064	0.064	0.000	0.000	0.000	0.000
27	A	400	SER	0	0.018	0.022	23.340	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	401	ARG	1	1.030	1.010	21.938	0.107	0.107	0.000	0.000	0.000	0.000
29	A	402	SER	0	0.048	0.020	20.558	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	403	VAL	0	0.006	0.006	18.244	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	404	ALA	0	-0.035	-0.017	17.072	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	405	ARG	1	0.918	0.962	17.081	0.157	0.157	0.000	0.000	0.000	0.000
33	A	406	PRO	0	0.066	0.044	13.945	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	407	ARG	1	0.792	0.888	12.530	0.077	0.077	0.000	0.000	0.000	0.000
35	A	408	GLN	0	-0.011	-0.003	12.729	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	409	MET	0	0.069	0.046	10.093	-0.061	-0.061	0.000	0.000	0.000	0.000
37	A	410	ALA	0	-0.003	0.000	8.415	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	411	MET	0	-0.051	-0.025	8.004	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	412	ALA	0	0.028	0.011	9.834	-0.056	-0.056	0.000	0.000	0.000	0.000
40	A	413	LEU	0	0.029	0.014	5.285	-0.084	-0.084	0.000	0.000	0.000	0.000
41	A	414	ALA	0	-0.013	-0.007	5.267	-0.292	-0.292	0.000	0.000	0.000	0.000
42	A	415	LYS	1	0.806	0.912	6.330	0.657	0.657	0.000	0.000	0.000	0.000
43	A	416	GLU	-1	-0.885	-0.942	7.590	-0.796	-0.796	0.000	0.000	0.000	0.000
44	A	417	LEU	0	-0.015	-0.010	2.552	-1.522	-0.205	0.847	-0.418	-1.746	-0.001
45	A	418	THR	0	-0.069	-0.039	2.693	-3.594	-1.529	0.591	-1.034	-1.622	-0.011
46	A	419	ASN	0	0.022	-0.012	4.664	0.313	0.472	-0.001	-0.012	-0.146	0.000
47	A	420	HIS	0	-0.074	-0.025	6.422	0.228	0.228	0.000	0.000	0.000	0.000
48	A	421	SER	0	-0.017	-0.046	9.507	-0.074	-0.074	0.000	0.000	0.000	0.000
49	A	422	LEU	0	0.018	-0.010	12.493	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	423	PRO	0	0.031	-0.007	14.400	0.006	0.006	0.000	0.000	0.000	0.000
51	A	424	GLU	-1	-0.728	-0.793	11.708	-0.152	-0.152	0.000	0.000	0.000	0.000
52	A	425	ILE	0	-0.011	-0.003	8.838	0.037	0.037	0.000	0.000	0.000	0.000
53	A	426	GLY	0	0.009	-0.006	11.272	0.027	0.027	0.000	0.000	0.000	0.000
54	A	427	ASP	-1	-0.900	-0.944	14.612	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	428	ALA	0	-0.002	0.000	10.097	0.026	0.026	0.000	0.000	0.000	0.000
56	A	429	PHE	0	-0.040	-0.012	8.425	0.029	0.029	0.000	0.000	0.000	0.000
57	A	430	GLY	0	-0.015	-0.001	13.325	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	431	GLY	0	-0.015	0.006	16.592	0.005	0.005	0.000	0.000	0.000	0.000
59	A	432	ARG	1	0.696	0.824	16.020	0.095	0.095	0.000	0.000	0.000	0.000
60	A	433	ASP	-1	-0.692	-0.820	17.933	-0.117	-0.117	0.000	0.000	0.000	0.000
61	A	434	HIS	0	-0.014	-0.029	16.916	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	435	THR	0	-0.025	-0.035	17.603	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	436	THR	0	-0.058	-0.028	17.463	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	437	VAL	0	0.025	0.012	12.507	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	438	LEU	0	0.023	0.024	15.161	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	439	HIS	0	-0.032	-0.023	17.357	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	440	ALA	0	-0.047	-0.027	14.479	0.001	0.001	0.000	0.000	0.000	0.000
68	A	441	CYS	0	-0.026	-0.001	13.303	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	442	ARG	1	1.056	1.029	14.669	0.224	0.224	0.000	0.000	0.000	0.000
70	A	443	LYS	1	0.796	0.895	18.033	0.189	0.189	0.000	0.000	0.000	0.000
71	A	444	ILE	0	0.011	-0.001	12.475	0.016	0.016	0.000	0.000	0.000	0.000
72	A	445	GLU	-1	-0.920	-0.971	15.507	-0.331	-0.331	0.000	0.000	0.000	0.000
73	A	446	GLN	0	-0.006	0.001	17.044	0.008	0.008	0.000	0.000	0.000	0.000
74	A	447	LEU	0	-0.006	-0.020	18.087	0.012	0.012	0.000	0.000	0.000	0.000
75	A	448	ARG	1	0.903	0.963	13.400	0.425	0.425	0.000	0.000	0.000	0.000
76	A	449	GLU	-1	-0.960	-0.964	17.759	-0.230	-0.230	0.000	0.000	0.000	0.000
77	A	450	GLU	-1	-0.882	-0.937	21.345	-0.156	-0.156	0.000	0.000	0.000	0.000
78	A	451	SER	0	-0.075	-0.044	20.666	0.009	0.009	0.000	0.000	0.000	0.000
79	A	452	HIS	0	0.071	0.016	20.060	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	453	ASP	-1	-0.791	-0.869	19.537	-0.182	-0.182	0.000	0.000	0.000	0.000
81	A	454	ILE	0	-0.035	-0.022	15.476	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	455	LYS	1	0.821	0.911	15.074	0.174	0.174	0.000	0.000	0.000	0.000
83	A	456	GLU	-1	-0.888	-0.925	15.362	-0.261	-0.261	0.000	0.000	0.000	0.000
84	A	457	ASP	-1	-0.767	-0.840	13.367	-0.288	-0.288	0.000	0.000	0.000	0.000
85	A	458	PHE	0	-0.037	-0.026	10.536	-0.054	-0.054	0.000	0.000	0.000	0.000
86	A	459	SER	0	-0.001	0.008	10.000	-0.134	-0.134	0.000	0.000	0.000	0.000
87	A	460	ASN	0	-0.022	-0.028	10.552	-0.089	-0.089	0.000	0.000	0.000	0.000
88	A	461	LEU	0	-0.013	-0.001	7.648	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	462	ILE	0	0.035	0.020	5.912	-0.175	-0.175	0.000	0.000	0.000	0.000
90	A	463	ARG	1	0.947	1.003	5.975	0.148	0.148	0.000	0.000	0.000	0.000
91	A	464	THR	0	-0.025	-0.020	7.580	0.062	0.062	0.000	0.000	0.000	0.000
92	A	465	LEU	0	-0.038	-0.025	2.628	-1.019	-0.047	0.812	-0.327	-1.457	0.000
93	A	466	SER	0	-0.074	-0.051	2.811	-2.318	-0.868	0.481	-0.741	-1.190	-0.008
94	A	467	SER	0	-0.100	-0.044	4.534	0.613	0.639	0.000	-0.009	-0.017	0.000

Top

Graph

Manual

About

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