FMO DATABASE

FMODB ID: YZ452

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-804005.207742
FMO2-HF: Nuclear repulsion	756460.007927
FMO2-HF: Total energy	-47545.199816
FMO2-MP2: Total energy	-47676.725594

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.
-0.301	0.276	1.175	0.378	-2.13	-0.005

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 : -0.005

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

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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	0.019	3.598	0.003	0.536	1.171	0.344	-2.048	-0.005
4	D	3	MET	0	-0.012	0.006	4.598	-0.596	-0.552	0.004	0.034	-0.082	0.000
5	D	4	HIS	0	0.003	0.008	7.688	-0.078	-0.078	0.000	0.000	0.000	0.000
6	D	5	VAL	0	0.028	0.002	10.072	0.045	0.045	0.000	0.000	0.000	0.000
7	D	6	ALA	0	-0.039	-0.006	12.711	-0.071	-0.071	0.000	0.000	0.000	0.000
8	D	7	GLN	0	0.040	0.006	16.434	0.017	0.017	0.000	0.000	0.000	0.000
9	D	8	PRO	0	-0.036	-0.009	19.009	-0.012	-0.012	0.000	0.000	0.000	0.000
10	D	9	ALA	0	0.007	-0.002	21.596	-0.009	-0.009	0.000	0.000	0.000	0.000
11	D	10	VAL	0	-0.008	-0.006	22.593	-0.017	-0.017	0.000	0.000	0.000	0.000
12	D	11	VAL	0	0.001	0.000	24.779	0.011	0.011	0.000	0.000	0.000	0.000
13	D	12	LEU	0	-0.015	0.001	27.502	-0.010	-0.010	0.000	0.000	0.000	0.000
14	D	13	ALA	0	0.001	0.003	30.677	0.006	0.006	0.000	0.000	0.000	0.000
15	D	14	SER	0	-0.010	-0.020	31.731	-0.003	-0.003	0.000	0.000	0.000	0.000
16	D	15	SER	0	0.018	-0.005	34.884	-0.003	-0.003	0.000	0.000	0.000	0.000
17	D	16	ARG	1	0.925	0.970	35.836	-0.028	-0.028	0.000	0.000	0.000	0.000
18	D	17	GLY	0	0.070	0.041	33.755	-0.001	-0.001	0.000	0.000	0.000	0.000
19	D	18	ILE	0	-0.048	-0.019	30.141	-0.002	-0.002	0.000	0.000	0.000	0.000
20	D	19	ALA	0	0.032	0.027	27.526	0.001	0.001	0.000	0.000	0.000	0.000
21	D	20	SER	0	0.004	-0.015	26.019	-0.002	-0.002	0.000	0.000	0.000	0.000
22	D	21	PHE	0	-0.034	-0.022	19.214	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	22	VAL	0	0.004	0.005	20.384	0.003	0.003	0.000	0.000	0.000	0.000
24	D	23	CYS	0	-0.021	-0.013	14.178	-0.059	-0.059	0.000	0.000	0.000	0.000
25	D	24	GLU	-1	-0.839	-0.903	16.768	0.289	0.289	0.000	0.000	0.000	0.000
26	D	25	TYR	0	-0.025	-0.029	12.139	0.041	0.041	0.000	0.000	0.000	0.000
27	D	26	ALA	0	-0.004	0.000	12.315	-0.058	-0.058	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.014	-0.017	11.172	0.141	0.141	0.000	0.000	0.000	0.000
29	D	28	PRO	0	-0.021	-0.020	9.501	-0.087	-0.087	0.000	0.000	0.000	0.000
30	D	29	GLY	0	0.042	0.027	12.665	-0.096	-0.096	0.000	0.000	0.000	0.000
31	D	30	LYS	1	0.820	0.894	13.836	-0.359	-0.359	0.000	0.000	0.000	0.000
32	D	31	ALA	0	0.039	0.028	11.558	0.031	0.031	0.000	0.000	0.000	0.000
33	D	32	THR	0	-0.033	-0.028	12.672	-0.086	-0.086	0.000	0.000	0.000	0.000
34	D	33	GLU	-1	-0.824	-0.914	12.061	0.082	0.082	0.000	0.000	0.000	0.000
35	D	34	VAL	0	-0.043	-0.030	11.249	0.140	0.140	0.000	0.000	0.000	0.000
36	D	35	ARG	1	0.923	0.986	10.569	0.017	0.017	0.000	0.000	0.000	0.000
37	D	36	VAL	0	-0.006	0.008	11.203	0.056	0.056	0.000	0.000	0.000	0.000
38	D	37	THR	0	-0.007	-0.015	11.395	-0.074	-0.074	0.000	0.000	0.000	0.000
39	D	38	VAL	0	0.004	0.003	13.903	0.016	0.016	0.000	0.000	0.000	0.000
40	D	39	LEU	0	0.022	0.005	12.942	-0.038	-0.038	0.000	0.000	0.000	0.000
41	D	40	ARG	1	0.865	0.927	16.891	0.107	0.107	0.000	0.000	0.000	0.000
42	D	41	GLN	0	-0.055	-0.035	17.585	-0.015	-0.015	0.000	0.000	0.000	0.000
43	D	42	ALA	0	0.008	-0.004	20.266	0.024	0.024	0.000	0.000	0.000	0.000
44	D	43	ASP	-1	-0.872	-0.932	23.523	-0.119	-0.119	0.000	0.000	0.000	0.000
45	D	44	SER	0	-0.050	-0.024	20.164	-0.013	-0.013	0.000	0.000	0.000	0.000
46	D	45	GLN	0	-0.017	0.001	19.851	-0.043	-0.043	0.000	0.000	0.000	0.000
47	D	46	VAL	0	0.021	-0.001	15.205	0.017	0.017	0.000	0.000	0.000	0.000
48	D	47	THR	0	-0.059	-0.032	18.623	-0.009	-0.009	0.000	0.000	0.000	0.000
49	D	48	GLU	-1	-0.884	-0.947	14.358	-0.204	-0.204	0.000	0.000	0.000	0.000
50	D	49	VAL	0	-0.021	-0.024	17.689	0.005	0.005	0.000	0.000	0.000	0.000
51	D	50	CYS	0	-0.095	-0.026	19.020	0.021	0.021	0.000	0.000	0.000	0.000
52	D	51	ALA	0	0.005	0.002	15.336	0.001	0.001	0.000	0.000	0.000	0.000
53	D	52	ALA	0	0.026	0.017	16.081	-0.005	-0.005	0.000	0.000	0.000	0.000
54	D	53	THR	0	-0.032	-0.025	13.711	0.006	0.006	0.000	0.000	0.000	0.000
55	D	54	TYR	0	-0.012	-0.008	15.379	-0.015	-0.015	0.000	0.000	0.000	0.000
56	D	55	MET	0	0.049	0.025	15.611	0.049	0.049	0.000	0.000	0.000	0.000
57	D	56	MET	0	-0.028	0.018	15.213	0.003	0.003	0.000	0.000	0.000	0.000
58	D	57	GLY	0	0.010	0.013	17.188	0.006	0.006	0.000	0.000	0.000	0.000
59	D	58	ASN	0	-0.043	-0.025	20.511	-0.007	-0.007	0.000	0.000	0.000	0.000
60	D	59	GLU	-1	-0.746	-0.857	20.740	0.176	0.176	0.000	0.000	0.000	0.000
61	D	60	LEU	0	-0.060	-0.016	18.426	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	61	THR	0	-0.030	-0.027	20.779	-0.013	-0.013	0.000	0.000	0.000	0.000
63	D	62	PHE	0	-0.030	-0.011	18.938	0.004	0.004	0.000	0.000	0.000	0.000
64	D	63	LEU	0	0.003	-0.005	20.198	0.001	0.001	0.000	0.000	0.000	0.000
65	D	64	ASP	-1	-0.878	-0.949	23.990	-0.004	-0.004	0.000	0.000	0.000	0.000
66	D	65	ASP	-1	-0.965	-0.979	27.570	-0.014	-0.014	0.000	0.000	0.000	0.000
67	D	66	SER	0	-0.065	-0.025	24.119	-0.009	-0.009	0.000	0.000	0.000	0.000
68	D	67	ILE	0	0.013	0.002	24.777	0.008	0.008	0.000	0.000	0.000	0.000
69	D	69	THR	0	0.020	0.013	24.312	-0.002	-0.002	0.000	0.000	0.000	0.000
70	D	70	GLY	0	-0.008	-0.022	22.063	0.001	0.001	0.000	0.000	0.000	0.000
71	D	71	THR	0	-0.009	-0.014	22.438	-0.010	-0.010	0.000	0.000	0.000	0.000
72	D	72	SER	0	-0.041	-0.008	18.591	0.024	0.024	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.025	0.000	20.268	-0.011	-0.011	0.000	0.000	0.000	0.000
74	D	74	GLY	0	0.012	0.007	20.516	0.009	0.009	0.000	0.000	0.000	0.000
75	D	75	ASN	0	-0.022	-0.019	15.428	0.104	0.104	0.000	0.000	0.000	0.000
76	D	76	GLN	0	0.003	0.012	17.003	0.002	0.002	0.000	0.000	0.000	0.000
77	D	77	VAL	0	-0.003	0.007	15.505	0.008	0.008	0.000	0.000	0.000	0.000
78	D	78	ASN	0	-0.022	-0.023	18.392	0.003	0.003	0.000	0.000	0.000	0.000
79	D	79	LEU	0	0.036	0.024	17.923	-0.009	-0.009	0.000	0.000	0.000	0.000
80	D	80	THR	0	-0.015	-0.014	22.204	-0.004	-0.004	0.000	0.000	0.000	0.000
81	D	81	ILE	0	0.013	0.019	22.010	-0.003	-0.003	0.000	0.000	0.000	0.000
82	D	82	GLN	0	-0.011	-0.015	26.235	0.005	0.005	0.000	0.000	0.000	0.000
83	D	83	GLY	0	0.040	0.023	29.658	-0.006	-0.006	0.000	0.000	0.000	0.000
84	D	84	LEU	0	-0.062	-0.017	27.080	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	85	ARG	1	0.882	0.906	31.204	0.039	0.039	0.000	0.000	0.000	0.000
86	D	86	ALA	0	0.041	0.016	32.070	-0.003	-0.003	0.000	0.000	0.000	0.000
87	D	87	MET	0	0.015	0.021	31.691	0.001	0.001	0.000	0.000	0.000	0.000
88	D	88	ASP	-1	-0.787	-0.870	28.498	-0.050	-0.050	0.000	0.000	0.000	0.000
89	D	89	THR	0	-0.018	-0.014	27.146	0.004	0.004	0.000	0.000	0.000	0.000
90	D	90	GLY	0	-0.007	0.001	24.551	-0.013	-0.013	0.000	0.000	0.000	0.000
91	D	91	LEU	0	-0.002	0.022	18.167	0.016	0.016	0.000	0.000	0.000	0.000
92	D	92	TYR	0	-0.008	-0.026	19.771	-0.020	-0.020	0.000	0.000	0.000	0.000
93	D	93	ILE	0	-0.005	0.004	13.759	0.022	0.022	0.000	0.000	0.000	0.000
94	D	95	LYS	1	0.822	0.927	8.081	0.388	0.388	0.000	0.000	0.000	0.000
95	D	96	VAL	0	-0.008	-0.016	9.423	-0.061	-0.061	0.000	0.000	0.000	0.000
96	D	97	GLU	-1	-0.817	-0.891	6.165	-0.014	-0.014	0.000	0.000	0.000	0.000
97	D	98	LEU	0	0.017	0.000	6.699	-0.077	-0.077	0.000	0.000	0.000	0.000
98	D	99	MET	0	-0.045	-0.010	6.752	0.253	0.253	0.000	0.000	0.000	0.000
99	D	100	TYR	0	0.010	-0.022	7.993	-0.107	-0.107	0.000	0.000	0.000	0.000
100	D	101	PRO	0	0.003	0.000	10.517	0.017	0.017	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.014	0.000	10.826	0.166	0.166	0.000	0.000	0.000	0.000
102	D	103	PRO	0	-0.034	-0.010	10.591	-0.128	-0.128	0.000	0.000	0.000	0.000
103	D	104	TYR	0	0.017	0.010	13.538	-0.049	-0.049	0.000	0.000	0.000	0.000
104	D	105	TYR	0	-0.019	-0.013	14.974	0.027	0.027	0.000	0.000	0.000	0.000
105	D	106	LEU	0	0.001	0.006	19.894	-0.022	-0.022	0.000	0.000	0.000	0.000
106	D	107	GLY	0	0.003	0.008	23.565	0.005	0.005	0.000	0.000	0.000	0.000
107	D	108	ILE	0	-0.002	-0.009	26.233	-0.009	-0.009	0.000	0.000	0.000	0.000
108	D	109	GLY	0	0.014	0.016	29.932	0.001	0.001	0.000	0.000	0.000	0.000
109	D	110	ASN	0	-0.015	-0.027	32.233	-0.001	-0.001	0.000	0.000	0.000	0.000
110	D	111	GLY	0	0.061	0.045	35.731	-0.005	-0.005	0.000	0.000	0.000	0.000
111	D	112	THR	0	-0.059	-0.048	37.131	0.001	0.001	0.000	0.000	0.000	0.000
112	D	113	GLN	0	-0.007	0.013	39.155	0.001	0.001	0.000	0.000	0.000	0.000
113	D	114	ILE	0	0.008	-0.001	39.168	-0.002	-0.002	0.000	0.000	0.000	0.000
114	D	115	TYR	0	-0.010	-0.003	43.437	-0.001	-0.001	0.000	0.000	0.000	0.000
115	D	116	VAL	0	-0.013	-0.012	46.442	0.000	0.000	0.000	0.000	0.000	0.000
116	D	117	ILE	0	-0.037	-0.016	48.901	0.000	0.000	0.000	0.000	0.000	0.000
117	D	118	ASP	-1	-0.896	-0.941	52.445	0.031	0.031	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.069	-0.027	54.189	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	120	GLU	-1	-0.970	-0.984	57.078	0.023	0.023	0.000	0.000	0.000	0.000

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