FMO DATABASE

FMODB ID: VRJ51

Calculation Name: 1J1V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-710006.993184
FMO2-HF: Nuclear repulsion	672356.891702
FMO2-HF: Total energy	-37650.101482
FMO2-MP2: Total energy	-37759.984382

3D Structure Molmil

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.
-12.207	-3.095	5.667	-4.579	-10.2	-0.019

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 : 0.020 / q_NPA : 0.008

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	0.081	0.026	3.007	-2.024	0.474	0.185	-1.268	-1.416	-0.001
4	A	377	ASP	-1	-0.836	-0.894	5.115	0.433	0.559	-0.001	-0.003	-0.123	0.000
5	A	378	ASN	0	0.018	0.007	3.440	-1.040	-0.367	0.025	-0.191	-0.507	0.000
6	A	379	ILE	0	0.046	0.037	2.247	-0.683	-0.711	2.301	-0.490	-1.782	0.000
7	A	380	GLN	0	-0.062	-0.046	4.805	-0.111	-0.054	-0.001	-0.010	-0.046	0.000
8	A	381	LYS	1	0.820	0.888	8.129	-0.414	-0.414	0.000	0.000	0.000	0.000
9	A	382	THR	0	0.022	0.008	6.095	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	383	VAL	0	-0.004	-0.006	7.636	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	384	ALA	0	-0.057	-0.031	10.106	0.002	0.002	0.000	0.000	0.000	0.000
12	A	385	GLU	-1	-0.817	-0.894	12.242	-0.043	-0.043	0.000	0.000	0.000	0.000
13	A	386	TYR	0	-0.009	-0.018	11.688	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	387	TYR	0	-0.107	-0.085	12.595	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	388	LYS	1	0.772	0.874	16.081	0.070	0.070	0.000	0.000	0.000	0.000
16	A	389	ILE	0	-0.055	-0.017	15.353	0.006	0.006	0.000	0.000	0.000	0.000
17	A	390	LYS	1	0.971	0.980	16.625	0.010	0.010	0.000	0.000	0.000	0.000
18	A	391	VAL	0	0.109	0.046	12.075	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	392	ALA	0	0.012	0.006	14.401	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	393	ASP	-1	-0.862	-0.948	17.418	-0.043	-0.043	0.000	0.000	0.000	0.000
21	A	394	LEU	0	-0.008	0.007	11.013	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	395	LEU	0	0.043	0.028	13.222	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	396	SER	0	0.018	0.021	16.403	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	397	LYS	1	1.016	1.014	19.468	0.020	0.020	0.000	0.000	0.000	0.000
25	A	398	ARG	1	0.931	0.979	21.985	0.044	0.044	0.000	0.000	0.000	0.000
26	A	399	ARG	1	1.046	1.002	21.434	0.067	0.067	0.000	0.000	0.000	0.000
27	A	400	SER	0	0.024	0.024	23.279	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	401	ARG	1	1.032	1.012	21.851	0.107	0.107	0.000	0.000	0.000	0.000
29	A	402	SER	0	0.048	0.023	20.461	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	403	VAL	0	0.012	0.004	18.436	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	404	ALA	0	-0.028	-0.021	17.228	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	405	ARG	1	0.929	0.981	17.100	0.153	0.153	0.000	0.000	0.000	0.000
33	A	406	PRO	0	0.067	0.048	14.174	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	407	ARG	1	0.798	0.898	12.644	0.077	0.077	0.000	0.000	0.000	0.000
35	A	408	GLN	0	-0.008	-0.018	12.626	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	409	MET	0	0.055	0.037	10.231	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	410	ALA	0	0.006	0.003	8.446	-0.078	-0.078	0.000	0.000	0.000	0.000
38	A	411	MET	0	-0.073	-0.036	8.072	-0.054	-0.054	0.000	0.000	0.000	0.000
39	A	412	ALA	0	0.037	0.010	9.998	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	413	LEU	0	0.030	0.018	5.265	-0.083	-0.083	0.000	0.000	0.000	0.000
41	A	414	ALA	0	-0.006	-0.002	5.323	-0.284	-0.284	0.000	0.000	0.000	0.000
42	A	415	LYS	1	0.828	0.915	6.251	0.505	0.505	0.000	0.000	0.000	0.000
43	A	416	GLU	-1	-0.892	-0.934	7.658	-0.732	-0.732	0.000	0.000	0.000	0.000
44	A	417	LEU	0	-0.028	-0.018	2.302	-1.652	-0.401	1.480	-0.580	-2.150	-0.002
45	A	418	THR	0	-0.083	-0.041	2.555	-2.611	-0.894	0.380	-0.799	-1.298	-0.006
46	A	419	ASN	0	-0.004	-0.014	4.561	0.308	0.484	-0.001	-0.016	-0.160	0.000
47	A	420	HIS	0	-0.070	-0.032	6.558	0.211	0.211	0.000	0.000	0.000	0.000
48	A	421	SER	0	-0.030	-0.055	9.490	-0.044	-0.044	0.000	0.000	0.000	0.000
49	A	422	LEU	0	0.025	-0.011	12.407	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	423	PRO	0	0.022	-0.018	14.436	0.006	0.006	0.000	0.000	0.000	0.000
51	A	424	GLU	-1	-0.721	-0.784	11.789	-0.184	-0.184	0.000	0.000	0.000	0.000
52	A	425	ILE	0	-0.017	-0.007	8.928	0.028	0.028	0.000	0.000	0.000	0.000
53	A	426	GLY	0	0.017	-0.007	11.375	0.030	0.030	0.000	0.000	0.000	0.000
54	A	427	ASP	-1	-0.904	-0.938	14.751	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	428	ALA	0	-0.040	-0.018	10.385	0.029	0.029	0.000	0.000	0.000	0.000
56	A	429	PHE	0	-0.029	-0.016	8.593	0.028	0.028	0.000	0.000	0.000	0.000
57	A	430	GLY	0	-0.013	-0.009	13.724	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	431	GLY	0	-0.017	0.014	16.642	0.005	0.005	0.000	0.000	0.000	0.000
59	A	432	ARG	1	0.707	0.829	16.225	0.101	0.101	0.000	0.000	0.000	0.000
60	A	433	ASP	-1	-0.698	-0.830	18.041	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	434	HIS	0	0.011	-0.012	17.135	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	435	THR	0	-0.027	-0.037	17.854	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	436	THR	0	-0.050	-0.027	17.914	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	437	VAL	0	0.032	0.022	12.813	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	438	LEU	0	0.006	0.016	15.491	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	439	HIS	0	-0.048	-0.026	17.469	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	440	ALA	0	-0.045	-0.025	14.740	0.002	0.002	0.000	0.000	0.000	0.000
68	A	441	CYS	0	-0.024	-0.008	13.406	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	442	ARG	1	1.071	1.040	14.791	0.216	0.216	0.000	0.000	0.000	0.000
70	A	443	LYS	1	0.791	0.894	18.223	0.180	0.180	0.000	0.000	0.000	0.000
71	A	444	ILE	0	0.003	-0.012	12.635	0.015	0.015	0.000	0.000	0.000	0.000
72	A	445	GLU	-1	-0.922	-0.959	15.567	-0.324	-0.324	0.000	0.000	0.000	0.000
73	A	446	GLN	0	0.022	0.006	17.101	0.008	0.008	0.000	0.000	0.000	0.000
74	A	447	LEU	0	-0.020	-0.027	18.148	0.014	0.014	0.000	0.000	0.000	0.000
75	A	448	ARG	1	0.905	0.970	13.570	0.410	0.410	0.000	0.000	0.000	0.000
76	A	449	GLU	-1	-0.974	-0.985	18.063	-0.214	-0.214	0.000	0.000	0.000	0.000
77	A	450	GLU	-1	-0.911	-0.935	21.498	-0.146	-0.146	0.000	0.000	0.000	0.000
78	A	451	SER	0	-0.062	-0.028	20.900	0.010	0.010	0.000	0.000	0.000	0.000
79	A	452	HIS	0	0.069	0.021	20.040	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	453	ASP	-1	-0.798	-0.899	19.473	-0.170	-0.170	0.000	0.000	0.000	0.000
81	A	454	ILE	0	-0.038	-0.010	15.716	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	455	LYS	1	0.868	0.928	15.210	0.176	0.176	0.000	0.000	0.000	0.000
83	A	456	GLU	-1	-0.911	-0.956	15.249	-0.239	-0.239	0.000	0.000	0.000	0.000
84	A	457	ASP	-1	-0.773	-0.832	13.341	-0.262	-0.262	0.000	0.000	0.000	0.000
85	A	458	PHE	0	-0.040	-0.031	10.592	-0.051	-0.051	0.000	0.000	0.000	0.000
86	A	459	SER	0	-0.006	0.002	9.961	-0.127	-0.127	0.000	0.000	0.000	0.000
87	A	460	ASN	0	-0.002	-0.009	10.566	-0.076	-0.076	0.000	0.000	0.000	0.000
88	A	461	LEU	0	-0.003	-0.005	7.550	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	462	ILE	0	0.022	0.017	5.729	-0.144	-0.144	0.000	0.000	0.000	0.000
90	A	463	ARG	1	0.946	0.998	6.070	0.130	0.130	0.000	0.000	0.000	0.000
91	A	464	THR	0	-0.029	-0.017	7.641	0.047	0.047	0.000	0.000	0.000	0.000
92	A	465	LEU	0	-0.021	-0.023	2.647	-0.908	0.010	0.637	-0.292	-1.262	0.000
93	A	466	SER	0	-0.096	-0.043	2.711	-2.777	-1.076	0.661	-0.919	-1.444	-0.010
94	A	467	SER	0	-0.070	-0.028	4.287	0.584	0.607	0.001	-0.011	-0.012	0.000

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