FMO DATABASE

FMODB ID: V5NN1

Calculation Name: 2JA4-A-Xray372

Preferred Name: T-cell surface glycoprotein CD5

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2JA4

Chain ID: A

ChEMBL ID: CHEMBL3712888

UniProt ID: P06127

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-753458.904727
FMO2-HF: Nuclear repulsion	712169.849071
FMO2-HF: Total energy	-41289.055655
FMO2-MP2: Total energy	-41404.097199

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:269:ALA)

Summations of interaction energy for fragment #1(A:269:ALA)

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.
-1.051	1.89	0.009	-1.357	-1.592	0.004

Interaction energy analysis for fragmet #1(A:269:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.025

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	271	GLN	0	0.001	0.009	3.292	-1.445	1.496	0.009	-1.357	-1.592	0.004
4	A	272	PRO	0	0.063	0.034	5.781	0.419	0.419	0.000	0.000	0.000	0.000
5	A	273	LYS	1	0.955	0.997	6.155	0.195	0.195	0.000	0.000	0.000	0.000
6	A	274	VAL	0	0.004	0.006	10.198	0.001	0.001	0.000	0.000	0.000	0.000
7	A	275	GLN	0	0.039	0.030	13.248	0.002	0.002	0.000	0.000	0.000	0.000
8	A	276	SER	0	0.013	-0.014	15.800	0.011	0.011	0.000	0.000	0.000	0.000
9	A	277	ARG	1	0.828	0.913	18.797	0.083	0.083	0.000	0.000	0.000	0.000
10	A	278	LEU	0	0.011	0.037	22.304	0.004	0.004	0.000	0.000	0.000	0.000
11	A	279	VAL	0	-0.013	-0.010	25.652	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	280	GLY	0	-0.013	-0.018	28.788	0.005	0.005	0.000	0.000	0.000	0.000
13	A	281	GLY	0	0.019	0.011	31.170	0.004	0.004	0.000	0.000	0.000	0.000
14	A	282	SER	0	-0.123	-0.073	32.388	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	283	SER	0	0.027	0.005	32.226	0.000	0.000	0.000	0.000	0.000	0.000
16	A	284	ILE	0	0.023	-0.004	27.743	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	285	CYS	0	0.029	0.043	22.120	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	286	GLU	-1	-0.811	-0.895	27.973	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	287	GLY	0	0.063	0.024	28.924	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	288	THR	0	-0.063	-0.028	27.827	0.007	0.007	0.000	0.000	0.000	0.000
21	A	289	VAL	0	-0.005	-0.001	21.510	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	290	GLU	-1	-0.849	-0.927	23.266	-0.074	-0.074	0.000	0.000	0.000	0.000
23	A	291	VAL	0	0.011	-0.007	18.242	0.000	0.000	0.000	0.000	0.000	0.000
24	A	292	ARG	1	0.905	0.968	18.156	0.202	0.202	0.000	0.000	0.000	0.000
25	A	293	GLN	0	-0.010	-0.022	13.398	-0.058	-0.058	0.000	0.000	0.000	0.000
26	A	294	GLY	0	0.055	0.021	16.121	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	295	ALA	0	-0.052	-0.029	17.401	0.004	0.004	0.000	0.000	0.000	0.000
28	A	296	GLN	0	0.029	0.024	20.340	0.022	0.022	0.000	0.000	0.000	0.000
29	A	297	TRP	0	-0.070	-0.037	19.750	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	298	ALA	0	0.049	0.036	23.041	0.006	0.006	0.000	0.000	0.000	0.000
31	A	299	ALA	0	0.035	0.014	23.645	0.000	0.000	0.000	0.000	0.000	0.000
32	A	300	LEU	0	0.004	0.011	19.774	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	301	CYS	0	-0.133	-0.027	23.089	0.009	0.009	0.000	0.000	0.000	0.000
34	A	302	ASP	-1	-0.828	-0.923	22.380	0.045	0.045	0.000	0.000	0.000	0.000
35	A	303	SER	0	-0.044	-0.045	23.634	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	304	SER	0	-0.059	-0.016	23.307	0.006	0.006	0.000	0.000	0.000	0.000
37	A	305	SER	0	0.009	-0.010	25.157	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	306	ALA	0	0.012	0.016	27.056	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	307	ARG	1	0.920	0.963	26.565	-0.040	-0.040	0.000	0.000	0.000	0.000
40	A	308	SER	0	0.020	0.003	22.287	0.002	0.002	0.000	0.000	0.000	0.000
41	A	309	SER	0	0.026	0.010	24.067	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	310	LEU	0	-0.004	-0.017	17.747	0.000	0.000	0.000	0.000	0.000	0.000
43	A	311	ARG	1	0.809	0.887	17.491	-0.049	-0.049	0.000	0.000	0.000	0.000
44	A	312	TRP	0	0.039	0.021	18.983	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	313	GLU	-1	-0.805	-0.866	19.938	0.062	0.062	0.000	0.000	0.000	0.000
46	A	314	GLU	-1	-0.840	-0.914	13.184	0.129	0.129	0.000	0.000	0.000	0.000
47	A	315	VAL	0	0.022	0.009	17.428	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	316	CYS	0	-0.065	-0.021	19.139	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	317	ARG	1	0.962	0.978	18.106	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	318	GLU	-1	-0.938	-0.956	14.395	-0.069	-0.069	0.000	0.000	0.000	0.000
51	A	319	GLN	0	-0.084	-0.039	17.714	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	320	GLN	0	-0.041	-0.022	19.409	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	322	GLY	0	-0.010	0.010	23.365	0.004	0.004	0.000	0.000	0.000	0.000
54	A	323	SER	0	-0.020	-0.050	23.042	0.003	0.003	0.000	0.000	0.000	0.000
55	A	324	VAL	0	-0.052	-0.035	24.014	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	325	ASN	0	0.001	0.005	25.635	0.009	0.009	0.000	0.000	0.000	0.000
57	A	326	SER	0	-0.055	-0.034	29.408	0.002	0.002	0.000	0.000	0.000	0.000
58	A	327	TYR	0	0.044	0.015	26.981	0.000	0.000	0.000	0.000	0.000	0.000
59	A	328	ARG	1	0.942	0.983	29.084	0.004	0.004	0.000	0.000	0.000	0.000
60	A	329	VAL	0	0.003	-0.001	29.472	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	330	LEU	0	-0.029	0.002	30.368	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	331	ASP	-1	-0.836	-0.943	31.858	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	332	ALA	0	-0.050	-0.032	33.663	0.001	0.001	0.000	0.000	0.000	0.000
64	A	333	GLY	0	-0.009	-0.011	34.557	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	334	ASP	-1	-0.778	-0.828	35.293	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	335	PRO	0	-0.023	-0.025	34.700	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	336	THR	0	-0.067	-0.087	35.201	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	337	SER	0	0.031	0.042	31.471	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	338	ARG	1	0.900	0.942	29.289	0.058	0.058	0.000	0.000	0.000	0.000
70	A	339	GLY	0	-0.003	-0.023	26.305	0.001	0.001	0.000	0.000	0.000	0.000
71	A	340	LEU	0	0.014	0.006	20.568	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	341	PHE	0	-0.021	-0.011	20.988	0.012	0.012	0.000	0.000	0.000	0.000
73	A	342	CYS	0	-0.034	0.020	9.881	0.006	0.006	0.000	0.000	0.000	0.000
74	A	343	PRO	0	-0.025	-0.001	16.007	0.018	0.018	0.000	0.000	0.000	0.000
75	A	344	HIS	0	0.060	0.013	13.052	0.056	0.056	0.000	0.000	0.000	0.000
76	A	345	GLN	0	0.012	0.002	15.408	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	346	LYS	1	0.964	0.987	12.867	-0.273	-0.273	0.000	0.000	0.000	0.000
78	A	347	LEU	0	0.103	0.040	13.127	0.005	0.005	0.000	0.000	0.000	0.000
79	A	348	SER	0	-0.093	-0.050	9.633	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	349	GLN	0	-0.030	-0.031	8.486	0.012	0.012	0.000	0.000	0.000	0.000
81	A	351	HIS	1	0.829	0.892	6.072	0.171	0.171	0.000	0.000	0.000	0.000
82	A	352	GLU	-1	-0.899	-0.951	10.524	-0.269	-0.269	0.000	0.000	0.000	0.000
83	A	353	LEU	0	-0.045	-0.010	14.077	0.048	0.048	0.000	0.000	0.000	0.000
84	A	354	TRP	0	0.047	0.027	14.932	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	355	GLU	-1	-0.891	-0.953	20.762	-0.080	-0.080	0.000	0.000	0.000	0.000
86	A	356	ARG	1	0.894	0.961	24.393	0.011	0.011	0.000	0.000	0.000	0.000
87	A	357	ASN	0	-0.028	-0.041	26.602	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	358	SER	0	0.033	0.025	30.092	0.002	0.002	0.000	0.000	0.000	0.000
89	A	359	TYR	0	0.015	0.017	30.515	0.002	0.002	0.000	0.000	0.000	0.000
90	A	361	LYS	1	0.976	0.993	28.683	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	362	LYS	1	0.968	1.002	26.978	0.032	0.032	0.000	0.000	0.000	0.000
92	A	363	VAL	0	-0.023	-0.014	25.119	0.006	0.006	0.000	0.000	0.000	0.000
93	A	364	PHE	0	-0.003	0.014	27.230	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	365	VAL	0	-0.011	-0.024	24.223	0.008	0.008	0.000	0.000	0.000	0.000
95	A	366	THR	0	0.010	0.008	27.523	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	368	GLN	0	-0.017	-0.010	27.187	0.003	0.003	0.000	0.000	0.000	0.000
97	A	369	ASP	-1	-0.935	-0.969	27.315	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:269:ALA)