FMO DATABASE

FMODB ID: 17YYZ

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	OptHSide
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	-754186.211873
FMO2-HF: Nuclear repulsion	712896.263748
FMO2-HF: Total energy	-41289.948125
FMO2-MP2: Total energy	-41404.887364

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.
-0.684	2.179	-0.005	-1.339	-1.519	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 : 0.055 / q_NPA : 0.019

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	0.004	0.013	3.510	-1.177	1.686	-0.005	-1.339	-1.519	0.004
4	A	272	PRO	0	0.047	0.023	5.793	0.415	0.415	0.000	0.000	0.000	0.000
5	A	273	LYS	1	0.943	0.984	6.686	0.140	0.140	0.000	0.000	0.000	0.000
6	A	274	VAL	0	0.001	0.007	10.332	0.007	0.007	0.000	0.000	0.000	0.000
7	A	275	GLN	0	0.016	0.025	13.368	0.012	0.012	0.000	0.000	0.000	0.000
8	A	276	SER	0	0.016	-0.016	15.925	0.009	0.009	0.000	0.000	0.000	0.000
9	A	277	ARG	1	0.824	0.904	18.911	0.086	0.086	0.000	0.000	0.000	0.000
10	A	278	LEU	0	0.008	0.026	22.418	0.004	0.004	0.000	0.000	0.000	0.000
11	A	279	VAL	0	-0.017	-0.005	25.758	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	280	GLY	0	0.000	-0.011	28.900	0.005	0.005	0.000	0.000	0.000	0.000
13	A	281	GLY	0	0.019	0.017	31.275	0.004	0.004	0.000	0.000	0.000	0.000
14	A	282	SER	0	-0.124	-0.077	32.490	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	283	SER	0	0.022	0.002	32.116	0.000	0.000	0.000	0.000	0.000	0.000
16	A	284	ILE	0	0.030	0.002	28.129	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	285	CYS	0	0.028	0.043	22.203	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	286	GLU	-1	-0.786	-0.887	28.056	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	287	GLY	0	0.054	0.027	29.004	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	288	THR	0	-0.066	-0.034	27.912	0.007	0.007	0.000	0.000	0.000	0.000
21	A	289	VAL	0	-0.018	-0.003	21.573	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	290	GLU	-1	-0.821	-0.902	23.377	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	291	VAL	0	-0.001	-0.014	18.274	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	292	ARG	1	0.912	0.965	18.277	0.208	0.208	0.000	0.000	0.000	0.000
25	A	293	GLN	0	-0.046	-0.046	13.246	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	294	GLY	0	0.065	0.025	16.252	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	295	ALA	0	-0.050	-0.028	17.539	0.004	0.004	0.000	0.000	0.000	0.000
28	A	296	GLN	0	0.031	0.035	20.477	0.016	0.016	0.000	0.000	0.000	0.000
29	A	297	TRP	0	-0.060	-0.037	19.846	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	298	ALA	0	0.058	0.038	23.156	0.007	0.007	0.000	0.000	0.000	0.000
31	A	299	ALA	0	0.032	0.015	23.757	0.000	0.000	0.000	0.000	0.000	0.000
32	A	300	LEU	0	0.007	0.012	19.728	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	301	CYS	0	-0.124	-0.021	23.182	0.010	0.010	0.000	0.000	0.000	0.000
34	A	302	ASP	-1	-0.792	-0.875	22.356	0.034	0.034	0.000	0.000	0.000	0.000
35	A	303	SER	0	-0.038	-0.041	23.683	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	304	SER	0	-0.045	-0.028	23.387	0.005	0.005	0.000	0.000	0.000	0.000
37	A	305	SER	0	-0.002	-0.008	25.185	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	306	ALA	0	0.030	0.022	27.021	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	307	ARG	1	0.887	0.952	26.583	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	308	SER	0	0.035	0.000	22.586	0.003	0.003	0.000	0.000	0.000	0.000
41	A	309	SER	0	0.009	0.008	24.094	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	310	LEU	0	0.008	-0.006	17.292	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	311	ARG	1	0.805	0.874	17.546	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	312	TRP	0	0.038	0.016	19.040	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	313	GLU	-1	-0.718	-0.806	19.953	0.052	0.052	0.000	0.000	0.000	0.000
46	A	314	GLU	-1	-0.815	-0.882	13.536	0.117	0.117	0.000	0.000	0.000	0.000
47	A	315	VAL	0	0.025	0.010	17.482	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	316	CYS	0	-0.055	-0.011	19.217	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	317	ARG	1	0.886	0.927	18.175	-0.087	-0.087	0.000	0.000	0.000	0.000
50	A	318	GLU	-1	-0.936	-0.958	14.485	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	319	GLN	0	-0.098	-0.045	17.801	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	320	GLN	0	-0.044	-0.024	19.253	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	322	GLY	0	-0.003	0.021	23.427	0.005	0.005	0.000	0.000	0.000	0.000
54	A	323	SER	0	-0.024	-0.054	23.100	0.001	0.001	0.000	0.000	0.000	0.000
55	A	324	VAL	0	-0.047	-0.040	24.123	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	325	ASN	0	-0.043	-0.007	25.685	0.009	0.009	0.000	0.000	0.000	0.000
57	A	326	SER	0	-0.034	-0.021	29.500	0.003	0.003	0.000	0.000	0.000	0.000
58	A	327	TYR	0	0.056	0.021	26.833	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	328	ARG	1	0.932	0.979	29.141	0.009	0.009	0.000	0.000	0.000	0.000
60	A	329	VAL	0	0.012	0.004	28.967	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	330	LEU	0	-0.026	-0.001	30.819	0.000	0.000	0.000	0.000	0.000	0.000
62	A	331	ASP	-1	-0.801	-0.907	31.933	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	332	ALA	0	-0.045	-0.024	33.730	0.000	0.000	0.000	0.000	0.000	0.000
64	A	333	GLY	0	-0.003	-0.008	34.622	0.000	0.000	0.000	0.000	0.000	0.000
65	A	334	ASP	-1	-0.766	-0.848	35.306	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	335	PRO	0	-0.040	-0.025	34.777	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	336	THR	0	-0.055	-0.070	35.282	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	337	SER	0	0.012	0.031	31.889	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	338	ARG	1	0.829	0.896	28.942	0.066	0.066	0.000	0.000	0.000	0.000
70	A	339	GLY	0	-0.001	-0.018	26.406	0.001	0.001	0.000	0.000	0.000	0.000
71	A	340	LEU	0	0.012	0.006	20.632	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	341	PHE	0	-0.010	-0.012	21.217	0.012	0.012	0.000	0.000	0.000	0.000
73	A	342	CYS	0	-0.040	0.009	9.922	0.004	0.004	0.000	0.000	0.000	0.000
74	A	343	PRO	0	-0.037	-0.004	16.111	0.019	0.019	0.000	0.000	0.000	0.000
75	A	344	HIS	0	0.066	0.020	13.303	0.054	0.054	0.000	0.000	0.000	0.000
76	A	345	GLN	0	0.034	0.018	15.506	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	346	LYS	1	0.873	0.932	13.116	-0.201	-0.201	0.000	0.000	0.000	0.000
78	A	347	LEU	0	0.117	0.046	13.174	0.002	0.002	0.000	0.000	0.000	0.000
79	A	348	SER	0	-0.091	-0.058	9.816	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	349	GLN	0	0.004	-0.019	8.547	0.001	0.001	0.000	0.000	0.000	0.000
81	A	351	HIS	1	0.870	0.918	6.110	0.237	0.237	0.000	0.000	0.000	0.000
82	A	352	GLU	-1	-0.898	-0.952	10.622	-0.277	-0.277	0.000	0.000	0.000	0.000
83	A	353	LEU	0	-0.040	-0.004	14.093	0.047	0.047	0.000	0.000	0.000	0.000
84	A	354	TRP	0	0.050	0.026	14.841	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	355	GLU	-1	-0.836	-0.917	20.779	-0.077	-0.077	0.000	0.000	0.000	0.000
86	A	356	ARG	1	0.852	0.944	24.033	0.016	0.016	0.000	0.000	0.000	0.000
87	A	357	ASN	0	0.008	-0.021	26.685	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	358	SER	0	0.057	0.039	30.180	0.000	0.000	0.000	0.000	0.000	0.000
89	A	359	TYR	0	0.007	0.011	30.589	0.002	0.002	0.000	0.000	0.000	0.000
90	A	361	LYS	1	0.917	0.964	27.937	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	362	LYS	1	0.915	0.954	27.054	0.035	0.035	0.000	0.000	0.000	0.000
92	A	363	VAL	0	-0.027	-0.018	25.161	0.007	0.007	0.000	0.000	0.000	0.000
93	A	364	PHE	0	0.020	0.020	27.316	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	365	VAL	0	-0.027	-0.031	24.324	0.008	0.008	0.000	0.000	0.000	0.000
95	A	366	THR	0	0.002	-0.004	27.598	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	368	GLN	0	-0.013	-0.009	27.086	0.001	0.001	0.000	0.000	0.000	0.000
97	A	369	ASP	-1	-0.925	-0.967	27.384	-0.014	-0.014	0.000	0.000	0.000	0.000

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