FMO DATABASE

FMODB ID: G6RR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-755448.46346
FMO2-HF: Nuclear repulsion	714158.066252
FMO2-HF: Total energy	-41290.397208
FMO2-MP2: Total energy	-41405.341536

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.
-1.09	2.905	-0.017	-2.118	-1.86	0.003

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 : 0.056 / q_NPA : 0.028

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	0.014	0.022	3.716	-1.864	2.131	-0.017	-2.118	-1.860	0.003
4	A	272	PRO	0	0.033	0.018	5.822	0.412	0.412	0.000	0.000	0.000	0.000
5	A	273	LYS	1	0.912	0.959	6.710	0.194	0.194	0.000	0.000	0.000	0.000
6	A	274	VAL	0	-0.007	0.010	9.982	0.009	0.009	0.000	0.000	0.000	0.000
7	A	275	GLN	0	0.008	0.013	13.196	0.018	0.018	0.000	0.000	0.000	0.000
8	A	276	SER	0	0.007	-0.026	15.719	0.009	0.009	0.000	0.000	0.000	0.000
9	A	277	ARG	1	0.811	0.897	18.668	0.105	0.105	0.000	0.000	0.000	0.000
10	A	278	LEU	0	0.023	0.024	22.255	0.005	0.005	0.000	0.000	0.000	0.000
11	A	279	VAL	0	-0.016	-0.006	25.607	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	280	GLY	0	0.004	-0.006	28.916	0.005	0.005	0.000	0.000	0.000	0.000
13	A	281	GLY	0	-0.006	0.006	31.476	0.004	0.004	0.000	0.000	0.000	0.000
14	A	282	SER	0	-0.088	-0.067	32.561	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	283	SER	0	0.027	0.010	31.660	0.000	0.000	0.000	0.000	0.000	0.000
16	A	284	ILE	0	0.009	-0.008	28.284	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	285	CYS	0	0.000	0.030	21.943	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	286	GLU	-1	-0.778	-0.857	28.014	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	287	GLY	0	0.039	0.013	28.910	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	288	THR	0	-0.040	-0.020	27.657	0.006	0.006	0.000	0.000	0.000	0.000
21	A	289	VAL	0	-0.009	-0.006	21.587	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	290	GLU	-1	-0.826	-0.898	23.204	-0.098	-0.098	0.000	0.000	0.000	0.000
23	A	291	VAL	0	-0.019	-0.021	18.164	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	292	ARG	1	0.893	0.951	17.692	0.229	0.229	0.000	0.000	0.000	0.000
25	A	293	GLN	0	0.026	-0.020	12.817	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	294	GLY	0	-0.035	-0.003	15.618	0.027	0.027	0.000	0.000	0.000	0.000
27	A	295	ALA	0	0.005	0.006	17.254	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	296	GLN	0	0.027	0.011	19.984	0.023	0.023	0.000	0.000	0.000	0.000
29	A	297	TRP	0	-0.032	-0.028	19.661	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	298	ALA	0	0.056	0.043	23.187	0.008	0.008	0.000	0.000	0.000	0.000
31	A	299	ALA	0	0.034	0.018	23.467	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	300	LEU	0	-0.020	-0.006	19.631	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	301	CYS	0	-0.109	0.001	23.031	0.012	0.012	0.000	0.000	0.000	0.000
34	A	302	ASP	-1	-0.800	-0.875	22.066	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	303	SER	0	-0.020	-0.016	23.588	0.000	0.000	0.000	0.000	0.000	0.000
36	A	304	SER	0	-0.027	-0.021	23.394	0.006	0.006	0.000	0.000	0.000	0.000
37	A	305	SER	0	0.002	-0.005	25.103	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	306	ALA	0	0.042	0.022	26.806	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	307	ARG	1	0.868	0.932	26.088	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	308	SER	0	0.066	0.017	22.426	0.006	0.006	0.000	0.000	0.000	0.000
41	A	309	SER	0	0.043	0.020	23.476	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	310	LEU	0	-0.003	0.005	16.913	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	311	ARG	1	0.829	0.885	17.030	0.016	0.016	0.000	0.000	0.000	0.000
44	A	312	TRP	0	0.020	0.008	18.811	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	313	GLU	-1	-0.692	-0.803	19.799	0.046	0.046	0.000	0.000	0.000	0.000
46	A	314	GLU	-1	-0.804	-0.866	13.624	0.060	0.060	0.000	0.000	0.000	0.000
47	A	315	VAL	0	0.029	0.006	17.419	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	316	CYS	0	-0.087	-0.021	19.234	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	317	ARG	1	0.878	0.929	17.852	-0.080	-0.080	0.000	0.000	0.000	0.000
50	A	318	GLU	-1	-0.946	-0.971	14.026	-0.099	-0.099	0.000	0.000	0.000	0.000
51	A	319	GLN	0	-0.068	-0.036	17.505	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	320	GLN	0	-0.035	-0.017	18.768	0.005	0.005	0.000	0.000	0.000	0.000
53	A	322	GLY	0	0.024	0.017	23.547	0.005	0.005	0.000	0.000	0.000	0.000
54	A	323	SER	0	-0.023	-0.054	22.823	0.001	0.001	0.000	0.000	0.000	0.000
55	A	324	VAL	0	-0.071	-0.054	24.058	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	325	ASN	0	-0.016	0.009	25.646	0.010	0.010	0.000	0.000	0.000	0.000
57	A	326	SER	0	-0.062	-0.035	29.101	0.002	0.002	0.000	0.000	0.000	0.000
58	A	327	TYR	0	0.063	0.019	26.146	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	328	ARG	1	0.880	0.969	29.003	0.022	0.022	0.000	0.000	0.000	0.000
60	A	329	VAL	0	0.027	0.013	28.468	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	330	LEU	0	-0.011	-0.008	30.387	0.001	0.001	0.000	0.000	0.000	0.000
62	A	331	ASP	-1	-0.787	-0.895	31.475	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	332	ALA	0	-0.041	-0.017	33.259	0.000	0.000	0.000	0.000	0.000	0.000
64	A	333	GLY	0	0.021	0.004	34.129	0.003	0.003	0.000	0.000	0.000	0.000
65	A	334	ASP	-1	-0.805	-0.871	35.023	-0.038	-0.038	0.000	0.000	0.000	0.000
66	A	335	PRO	0	-0.004	0.000	34.561	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	336	THR	0	-0.063	-0.065	35.191	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	337	SER	0	-0.018	0.000	31.638	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	338	ARG	1	0.805	0.883	28.761	0.089	0.089	0.000	0.000	0.000	0.000
70	A	339	GLY	0	0.019	-0.020	26.185	0.003	0.003	0.000	0.000	0.000	0.000
71	A	340	LEU	0	0.003	0.010	20.412	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	341	PHE	0	-0.001	-0.005	20.659	0.015	0.015	0.000	0.000	0.000	0.000
73	A	342	CYS	0	-0.025	0.013	9.034	-0.042	-0.042	0.000	0.000	0.000	0.000
74	A	343	PRO	0	-0.017	0.006	15.589	0.021	0.021	0.000	0.000	0.000	0.000
75	A	344	HIS	0	0.055	0.026	12.692	0.055	0.055	0.000	0.000	0.000	0.000
76	A	345	GLN	0	0.031	0.009	14.870	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	346	LYS	1	0.807	0.902	12.732	-0.125	-0.125	0.000	0.000	0.000	0.000
78	A	347	LEU	0	0.083	0.030	12.993	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	348	SER	0	-0.067	-0.058	9.970	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	349	GLN	0	0.027	0.003	8.331	-0.036	-0.036	0.000	0.000	0.000	0.000
81	A	351	HIS	1	0.888	0.924	5.764	0.498	0.498	0.000	0.000	0.000	0.000
82	A	352	GLU	-1	-0.904	-0.937	10.353	-0.355	-0.355	0.000	0.000	0.000	0.000
83	A	353	LEU	0	-0.028	-0.018	14.047	0.040	0.040	0.000	0.000	0.000	0.000
84	A	354	TRP	0	0.012	0.018	14.814	0.001	0.001	0.000	0.000	0.000	0.000
85	A	355	GLU	-1	-0.809	-0.904	20.724	-0.102	-0.102	0.000	0.000	0.000	0.000
86	A	356	ARG	1	0.850	0.928	23.470	0.050	0.050	0.000	0.000	0.000	0.000
87	A	357	ASN	0	0.013	-0.011	26.417	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	358	SER	0	0.066	0.049	29.964	0.002	0.002	0.000	0.000	0.000	0.000
89	A	359	TYR	0	0.003	0.000	30.282	0.000	0.000	0.000	0.000	0.000	0.000
90	A	361	LYS	1	0.880	0.923	27.528	0.008	0.008	0.000	0.000	0.000	0.000
91	A	362	LYS	1	0.884	0.953	26.904	0.053	0.053	0.000	0.000	0.000	0.000
92	A	363	VAL	0	-0.022	-0.017	24.649	0.008	0.008	0.000	0.000	0.000	0.000
93	A	364	PHE	0	0.010	0.016	27.164	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	365	VAL	0	-0.037	-0.028	23.974	0.008	0.008	0.000	0.000	0.000	0.000
95	A	366	THR	0	0.017	-0.013	27.247	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	368	GLN	0	0.006	0.005	26.770	0.001	0.001	0.000	0.000	0.000	0.000
97	A	369	ASP	-1	-0.912	-0.948	27.454	-0.016	-0.016	0.000	0.000	0.000	0.000

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