FMO DATABASE

FMODB ID: 4952N

Calculation Name: 2X44-D-Xray372

Preferred Name: Cytotoxic T-lymphocyte protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2X44

Chain ID: D

ChEMBL ID: CHEMBL2364164

UniProt ID: P16410

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-802673.510227
FMO2-HF: Nuclear repulsion	755129.086815
FMO2-HF: Total energy	-47544.423412
FMO2-MP2: Total energy	-47675.975747

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(D:0:MET)

Summations of interaction energy for fragment #1(D:0:MET)

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.
-3.547	-0.804	0.195	-1.111	-1.828	-0.002

Interaction energy analysis for fragmet #1(D:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.007

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	D	2	ALA	0	0.032	0.018	3.256	-2.443	0.230	0.190	-1.117	-1.747	-0.002
4	D	3	MET	0	0.002	0.005	4.713	-0.795	-0.725	0.005	0.006	-0.081	0.000
5	D	4	HIS	0	-0.005	0.005	7.598	0.023	0.023	0.000	0.000	0.000	0.000
6	D	5	VAL	0	0.022	-0.001	10.011	-0.029	-0.029	0.000	0.000	0.000	0.000
7	D	6	ALA	0	-0.034	-0.001	12.626	-0.028	-0.028	0.000	0.000	0.000	0.000
8	D	7	GLN	0	0.066	0.011	15.944	-0.014	-0.014	0.000	0.000	0.000	0.000
9	D	8	PRO	0	-0.035	0.000	18.975	0.002	0.002	0.000	0.000	0.000	0.000
10	D	9	ALA	0	0.003	-0.001	21.980	-0.012	-0.012	0.000	0.000	0.000	0.000
11	D	10	VAL	0	0.002	-0.005	22.993	-0.014	-0.014	0.000	0.000	0.000	0.000
12	D	11	VAL	0	0.009	0.003	24.808	0.009	0.009	0.000	0.000	0.000	0.000
13	D	12	LEU	0	-0.026	-0.006	27.276	-0.008	-0.008	0.000	0.000	0.000	0.000
14	D	13	ALA	0	0.011	0.012	29.599	0.004	0.004	0.000	0.000	0.000	0.000
15	D	14	SER	0	-0.002	0.002	30.989	0.001	0.001	0.000	0.000	0.000	0.000
16	D	15	SER	0	0.031	0.006	34.370	-0.004	-0.004	0.000	0.000	0.000	0.000
17	D	16	ARG	1	0.928	0.968	35.306	0.022	0.022	0.000	0.000	0.000	0.000
18	D	17	GLY	0	0.040	0.026	32.713	-0.003	-0.003	0.000	0.000	0.000	0.000
19	D	18	ILE	0	-0.038	-0.020	29.812	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	19	ALA	0	0.016	-0.006	26.777	0.006	0.006	0.000	0.000	0.000	0.000
21	D	20	SER	0	0.003	-0.003	25.564	-0.005	-0.005	0.000	0.000	0.000	0.000
22	D	21	PHE	0	-0.039	-0.026	18.689	0.004	0.004	0.000	0.000	0.000	0.000
23	D	22	VAL	0	0.037	0.028	19.551	-0.006	-0.006	0.000	0.000	0.000	0.000
24	D	23	CYS	0	-0.076	-0.036	13.777	-0.048	-0.048	0.000	0.000	0.000	0.000
25	D	24	GLU	-1	-0.884	-0.939	16.186	0.151	0.151	0.000	0.000	0.000	0.000
26	D	25	TYR	0	0.020	-0.014	11.127	0.017	0.017	0.000	0.000	0.000	0.000
27	D	26	ALA	0	-0.003	0.008	12.079	-0.025	-0.025	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.054	-0.023	10.757	0.077	0.077	0.000	0.000	0.000	0.000
29	D	28	PRO	0	-0.022	-0.013	9.513	-0.025	-0.025	0.000	0.000	0.000	0.000
30	D	29	GLY	0	0.040	0.013	12.586	-0.053	-0.053	0.000	0.000	0.000	0.000
31	D	30	LYS	1	0.898	0.954	14.022	-0.234	-0.234	0.000	0.000	0.000	0.000
32	D	31	ALA	0	0.008	0.014	11.217	0.045	0.045	0.000	0.000	0.000	0.000
33	D	32	THR	0	-0.037	-0.039	12.817	-0.050	-0.050	0.000	0.000	0.000	0.000
34	D	33	GLU	-1	-0.868	-0.953	11.920	-0.138	-0.138	0.000	0.000	0.000	0.000
35	D	34	VAL	0	-0.043	-0.015	11.507	0.070	0.070	0.000	0.000	0.000	0.000
36	D	35	ARG	1	0.956	0.978	10.615	0.389	0.389	0.000	0.000	0.000	0.000
37	D	36	VAL	0	-0.008	0.011	10.992	-0.040	-0.040	0.000	0.000	0.000	0.000
38	D	37	THR	0	-0.012	-0.017	11.896	-0.040	-0.040	0.000	0.000	0.000	0.000
39	D	38	VAL	0	0.009	0.012	13.642	0.014	0.014	0.000	0.000	0.000	0.000
40	D	39	LEU	0	0.021	0.002	11.706	-0.032	-0.032	0.000	0.000	0.000	0.000
41	D	40	ARG	1	0.897	0.960	15.967	0.184	0.184	0.000	0.000	0.000	0.000
42	D	41	GLN	0	-0.027	-0.014	16.827	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	42	ALA	0	-0.005	-0.016	19.415	0.027	0.027	0.000	0.000	0.000	0.000
44	D	43	ASP	-1	-0.862	-0.928	22.909	-0.156	-0.156	0.000	0.000	0.000	0.000
45	D	44	SER	0	-0.064	-0.034	19.516	-0.004	-0.004	0.000	0.000	0.000	0.000
46	D	45	GLN	0	-0.035	-0.006	19.090	-0.052	-0.052	0.000	0.000	0.000	0.000
47	D	46	VAL	0	0.013	-0.007	14.246	0.017	0.017	0.000	0.000	0.000	0.000
48	D	47	THR	0	-0.050	-0.017	17.577	-0.015	-0.015	0.000	0.000	0.000	0.000
49	D	48	GLU	-1	-0.930	-0.962	14.663	-0.429	-0.429	0.000	0.000	0.000	0.000
50	D	49	VAL	0	-0.033	-0.026	17.387	0.021	0.021	0.000	0.000	0.000	0.000
51	D	50	CYS	0	-0.105	-0.054	18.445	0.031	0.031	0.000	0.000	0.000	0.000
52	D	51	ALA	0	0.028	0.012	15.231	-0.026	-0.026	0.000	0.000	0.000	0.000
53	D	52	ALA	0	0.007	0.010	15.943	0.023	0.023	0.000	0.000	0.000	0.000
54	D	53	THR	0	-0.013	-0.008	14.241	-0.039	-0.039	0.000	0.000	0.000	0.000
55	D	54	TYR	0	0.009	0.012	15.474	0.021	0.021	0.000	0.000	0.000	0.000
56	D	55	MET	0	0.051	0.022	15.872	0.019	0.019	0.000	0.000	0.000	0.000
57	D	56	MET	0	-0.006	0.011	15.529	0.005	0.005	0.000	0.000	0.000	0.000
58	D	57	GLY	0	-0.034	-0.014	17.279	0.011	0.011	0.000	0.000	0.000	0.000
59	D	58	ASN	0	-0.028	-0.018	20.727	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	59	GLU	-1	-0.800	-0.882	20.757	0.030	0.030	0.000	0.000	0.000	0.000
61	D	60	LEU	0	-0.075	-0.014	17.732	-0.008	-0.008	0.000	0.000	0.000	0.000
62	D	61	THR	0	-0.007	-0.025	20.949	0.007	0.007	0.000	0.000	0.000	0.000
63	D	62	PHE	0	-0.052	-0.021	18.367	-0.011	-0.011	0.000	0.000	0.000	0.000
64	D	63	LEU	0	0.006	-0.004	20.070	0.008	0.008	0.000	0.000	0.000	0.000
65	D	64	ASP	-1	-0.886	-0.944	23.792	-0.077	-0.077	0.000	0.000	0.000	0.000
66	D	65	ASP	-1	-0.969	-0.977	27.467	-0.079	-0.079	0.000	0.000	0.000	0.000
67	D	66	SER	0	-0.021	0.005	23.013	-0.012	-0.012	0.000	0.000	0.000	0.000
68	D	67	ILE	0	0.020	0.006	24.242	0.010	0.010	0.000	0.000	0.000	0.000
69	D	69	THR	0	0.055	0.031	23.888	0.001	0.001	0.000	0.000	0.000	0.000
70	D	70	GLY	0	-0.042	-0.034	21.520	-0.003	-0.003	0.000	0.000	0.000	0.000
71	D	71	THR	0	0.031	0.000	21.996	-0.001	-0.001	0.000	0.000	0.000	0.000
72	D	72	SER	0	-0.035	-0.004	18.199	0.012	0.012	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.035	0.006	20.156	0.000	0.000	0.000	0.000	0.000	0.000
74	D	74	GLY	0	-0.014	0.004	19.743	0.006	0.006	0.000	0.000	0.000	0.000
75	D	75	ASN	0	-0.060	-0.031	15.651	0.041	0.041	0.000	0.000	0.000	0.000
76	D	76	GLN	0	0.055	0.016	16.838	-0.007	-0.007	0.000	0.000	0.000	0.000
77	D	77	VAL	0	-0.011	0.006	15.902	-0.007	-0.007	0.000	0.000	0.000	0.000
78	D	78	ASN	0	0.017	-0.003	18.251	0.004	0.004	0.000	0.000	0.000	0.000
79	D	79	LEU	0	0.003	0.005	17.579	-0.009	-0.009	0.000	0.000	0.000	0.000
80	D	80	THR	0	-0.016	-0.011	21.918	0.010	0.010	0.000	0.000	0.000	0.000
81	D	81	ILE	0	0.023	0.007	21.714	-0.011	-0.011	0.000	0.000	0.000	0.000
82	D	82	GLN	0	-0.015	-0.005	25.820	0.013	0.013	0.000	0.000	0.000	0.000
83	D	83	GLY	0	0.014	0.004	28.973	-0.008	-0.008	0.000	0.000	0.000	0.000
84	D	84	LEU	0	-0.033	0.000	26.299	-0.004	-0.004	0.000	0.000	0.000	0.000
85	D	85	ARG	1	0.932	0.948	30.386	0.086	0.086	0.000	0.000	0.000	0.000
86	D	86	ALA	0	0.036	0.016	31.019	-0.004	-0.004	0.000	0.000	0.000	0.000
87	D	87	MET	0	-0.002	-0.006	30.189	0.002	0.002	0.000	0.000	0.000	0.000
88	D	88	ASP	-1	-0.804	-0.887	27.219	-0.108	-0.108	0.000	0.000	0.000	0.000
89	D	89	THR	0	-0.030	-0.001	26.286	-0.001	-0.001	0.000	0.000	0.000	0.000
90	D	90	GLY	0	0.003	-0.002	23.727	-0.010	-0.010	0.000	0.000	0.000	0.000
91	D	91	LEU	0	-0.013	0.008	17.984	0.014	0.014	0.000	0.000	0.000	0.000
92	D	92	TYR	0	-0.023	-0.044	18.923	-0.030	-0.030	0.000	0.000	0.000	0.000
93	D	93	ILE	0	-0.005	0.000	12.691	0.029	0.029	0.000	0.000	0.000	0.000
94	D	95	LYS	1	0.939	0.985	7.345	1.041	1.041	0.000	0.000	0.000	0.000
95	D	96	VAL	0	0.004	-0.008	9.284	-0.031	-0.031	0.000	0.000	0.000	0.000
96	D	97	GLU	-1	-0.933	-0.964	5.741	-1.095	-1.095	0.000	0.000	0.000	0.000
97	D	98	LEU	0	0.000	-0.006	6.697	0.123	0.123	0.000	0.000	0.000	0.000
98	D	99	MET	0	-0.038	-0.001	6.726	0.082	0.082	0.000	0.000	0.000	0.000
99	D	100	TYR	0	-0.002	-0.022	7.923	-0.072	-0.072	0.000	0.000	0.000	0.000
100	D	101	PRO	0	-0.004	0.002	10.174	0.051	0.051	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.019	0.004	11.428	0.152	0.152	0.000	0.000	0.000	0.000
102	D	103	PRO	0	-0.021	-0.010	11.159	-0.119	-0.119	0.000	0.000	0.000	0.000
103	D	104	TYR	0	0.010	0.006	14.236	-0.023	-0.023	0.000	0.000	0.000	0.000
104	D	105	TYR	0	-0.018	-0.006	15.440	0.010	0.010	0.000	0.000	0.000	0.000
105	D	106	LEU	0	0.017	0.014	20.206	-0.016	-0.016	0.000	0.000	0.000	0.000
106	D	107	GLY	0	-0.007	0.000	23.840	0.003	0.003	0.000	0.000	0.000	0.000
107	D	108	ILE	0	-0.010	-0.010	26.273	-0.009	-0.009	0.000	0.000	0.000	0.000
108	D	109	GLY	0	0.009	0.009	29.971	0.001	0.001	0.000	0.000	0.000	0.000
109	D	110	ASN	0	-0.008	-0.022	32.308	0.001	0.001	0.000	0.000	0.000	0.000
110	D	111	GLY	0	0.029	0.030	35.619	-0.006	-0.006	0.000	0.000	0.000	0.000
111	D	112	THR	0	-0.035	-0.024	36.985	0.001	0.001	0.000	0.000	0.000	0.000
112	D	113	GLN	0	-0.003	0.008	39.240	0.001	0.001	0.000	0.000	0.000	0.000
113	D	114	ILE	0	0.001	-0.001	39.819	-0.001	-0.001	0.000	0.000	0.000	0.000
114	D	115	TYR	0	-0.018	-0.012	43.881	-0.002	-0.002	0.000	0.000	0.000	0.000
115	D	116	VAL	0	-0.003	-0.013	46.731	0.000	0.000	0.000	0.000	0.000	0.000
116	D	117	ILE	0	-0.028	-0.014	49.177	-0.001	-0.001	0.000	0.000	0.000	0.000
117	D	118	ASP	-1	-0.909	-0.943	52.682	0.037	0.037	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.066	-0.029	54.686	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	120	GLU	-1	-0.962	-0.978	57.538	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:0:MET)