FMO DATABASE

FMODB ID: 5247Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-803432.163754
FMO2-HF: Nuclear repulsion	755887.254776
FMO2-HF: Total energy	-47544.908978
FMO2-MP2: Total energy	-47676.425116

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.
-2.71	-0.604	0.811	-0.766	-2.15	-0.004

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 : -0.019 / q_NPA : -0.010

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	0.035	0.017	3.713	-1.614	0.484	0.802	-0.850	-2.049	-0.004
4	D	3	MET	0	-0.003	0.004	4.467	-0.813	-0.805	0.009	0.084	-0.101	0.000
5	D	4	HIS	0	0.002	0.008	7.536	-0.054	-0.054	0.000	0.000	0.000	0.000
6	D	5	VAL	0	0.022	-0.001	9.839	0.004	0.004	0.000	0.000	0.000	0.000
7	D	6	ALA	0	-0.036	0.001	12.493	-0.056	-0.056	0.000	0.000	0.000	0.000
8	D	7	GLN	0	0.054	-0.001	16.188	-0.002	-0.002	0.000	0.000	0.000	0.000
9	D	8	PRO	0	-0.031	-0.004	18.793	-0.005	-0.005	0.000	0.000	0.000	0.000
10	D	9	ALA	0	-0.003	0.000	21.725	-0.012	-0.012	0.000	0.000	0.000	0.000
11	D	10	VAL	0	-0.001	-0.007	22.753	-0.016	-0.016	0.000	0.000	0.000	0.000
12	D	11	VAL	0	0.010	0.004	24.777	0.011	0.011	0.000	0.000	0.000	0.000
13	D	12	LEU	0	-0.027	-0.005	27.374	-0.010	-0.010	0.000	0.000	0.000	0.000
14	D	13	ALA	0	0.011	0.012	29.881	0.005	0.005	0.000	0.000	0.000	0.000
15	D	14	SER	0	-0.004	-0.003	31.268	-0.001	-0.001	0.000	0.000	0.000	0.000
16	D	15	SER	0	0.029	0.005	34.573	-0.004	-0.004	0.000	0.000	0.000	0.000
17	D	16	ARG	1	0.925	0.965	35.566	0.006	0.006	0.000	0.000	0.000	0.000
18	D	17	GLY	0	0.042	0.027	33.015	-0.003	-0.003	0.000	0.000	0.000	0.000
19	D	18	ILE	0	-0.041	-0.024	29.834	-0.004	-0.004	0.000	0.000	0.000	0.000
20	D	19	ALA	0	0.020	0.002	27.009	0.005	0.005	0.000	0.000	0.000	0.000
21	D	20	SER	0	0.006	-0.006	25.477	-0.005	-0.005	0.000	0.000	0.000	0.000
22	D	21	PHE	0	-0.030	-0.021	18.796	0.001	0.001	0.000	0.000	0.000	0.000
23	D	22	VAL	0	0.007	0.009	19.723	-0.003	-0.003	0.000	0.000	0.000	0.000
24	D	23	CYS	0	-0.033	-0.015	13.817	-0.048	-0.048	0.000	0.000	0.000	0.000
25	D	24	GLU	-1	-0.856	-0.910	16.227	0.223	0.223	0.000	0.000	0.000	0.000
26	D	25	TYR	0	0.000	-0.019	11.343	0.030	0.030	0.000	0.000	0.000	0.000
27	D	26	ALA	0	-0.013	0.001	12.363	-0.043	-0.043	0.000	0.000	0.000	0.000
28	D	27	SER	0	-0.047	-0.037	10.944	0.124	0.124	0.000	0.000	0.000	0.000
29	D	28	PRO	0	-0.023	-0.016	9.403	-0.049	-0.049	0.000	0.000	0.000	0.000
30	D	29	GLY	0	0.049	0.016	12.585	-0.079	-0.079	0.000	0.000	0.000	0.000
31	D	30	LYS	1	0.865	0.953	14.023	-0.278	-0.278	0.000	0.000	0.000	0.000
32	D	31	ALA	0	0.000	0.012	11.200	0.038	0.038	0.000	0.000	0.000	0.000
33	D	32	THR	0	-0.023	-0.033	12.833	-0.056	-0.056	0.000	0.000	0.000	0.000
34	D	33	GLU	-1	-0.866	-0.954	11.626	-0.134	-0.134	0.000	0.000	0.000	0.000
35	D	34	VAL	0	-0.030	-0.019	11.186	0.095	0.095	0.000	0.000	0.000	0.000
36	D	35	ARG	1	0.955	0.994	10.448	0.301	0.301	0.000	0.000	0.000	0.000
37	D	36	VAL	0	-0.001	0.015	10.795	-0.005	-0.005	0.000	0.000	0.000	0.000
38	D	37	THR	0	-0.037	-0.024	11.780	-0.066	-0.066	0.000	0.000	0.000	0.000
39	D	38	VAL	0	0.010	0.012	13.751	0.024	0.024	0.000	0.000	0.000	0.000
40	D	39	LEU	0	0.030	0.009	12.294	-0.034	-0.034	0.000	0.000	0.000	0.000
41	D	40	ARG	1	0.876	0.938	16.368	0.162	0.162	0.000	0.000	0.000	0.000
42	D	41	GLN	0	-0.032	-0.016	17.042	-0.009	-0.009	0.000	0.000	0.000	0.000
43	D	42	ALA	0	0.015	-0.004	19.712	0.027	0.027	0.000	0.000	0.000	0.000
44	D	43	ASP	-1	-0.866	-0.928	23.211	-0.152	-0.152	0.000	0.000	0.000	0.000
45	D	44	SER	0	-0.066	-0.030	19.665	-0.009	-0.009	0.000	0.000	0.000	0.000
46	D	45	GLN	0	-0.048	-0.021	19.356	-0.050	-0.050	0.000	0.000	0.000	0.000
47	D	46	VAL	0	0.019	-0.003	14.611	0.019	0.019	0.000	0.000	0.000	0.000
48	D	47	THR	0	-0.054	-0.017	17.943	-0.016	-0.016	0.000	0.000	0.000	0.000
49	D	48	GLU	-1	-0.899	-0.956	14.473	-0.379	-0.379	0.000	0.000	0.000	0.000
50	D	49	VAL	0	-0.033	-0.029	17.868	0.018	0.018	0.000	0.000	0.000	0.000
51	D	50	CYS	0	-0.100	-0.036	18.515	0.029	0.029	0.000	0.000	0.000	0.000
52	D	51	ALA	0	0.030	0.011	15.245	-0.017	-0.017	0.000	0.000	0.000	0.000
53	D	52	ALA	0	0.012	0.012	16.023	0.014	0.014	0.000	0.000	0.000	0.000
54	D	53	THR	0	-0.002	-0.008	13.945	-0.027	-0.027	0.000	0.000	0.000	0.000
55	D	54	TYR	0	-0.009	0.001	15.368	-0.003	-0.003	0.000	0.000	0.000	0.000
56	D	55	MET	0	0.046	0.021	15.510	0.026	0.026	0.000	0.000	0.000	0.000
57	D	56	MET	0	-0.021	-0.004	15.289	0.007	0.007	0.000	0.000	0.000	0.000
58	D	57	GLY	0	-0.012	-0.002	17.079	0.005	0.005	0.000	0.000	0.000	0.000
59	D	58	ASN	0	-0.029	-0.021	20.474	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	59	GLU	-1	-0.750	-0.861	20.503	0.081	0.081	0.000	0.000	0.000	0.000
61	D	60	LEU	0	-0.069	-0.008	17.584	-0.007	-0.007	0.000	0.000	0.000	0.000
62	D	61	THR	0	-0.024	-0.033	20.690	0.001	0.001	0.000	0.000	0.000	0.000
63	D	62	PHE	0	-0.040	-0.020	18.395	-0.007	-0.007	0.000	0.000	0.000	0.000
64	D	63	LEU	0	0.000	-0.004	19.964	0.005	0.005	0.000	0.000	0.000	0.000
65	D	64	ASP	-1	-0.901	-0.955	23.835	-0.062	-0.062	0.000	0.000	0.000	0.000
66	D	65	ASP	-1	-0.959	-0.972	27.499	-0.060	-0.060	0.000	0.000	0.000	0.000
67	D	66	SER	0	-0.044	-0.005	23.868	-0.013	-0.013	0.000	0.000	0.000	0.000
68	D	67	ILE	0	0.017	0.001	24.241	0.009	0.009	0.000	0.000	0.000	0.000
69	D	69	THR	0	0.025	0.013	24.004	0.000	0.000	0.000	0.000	0.000	0.000
70	D	70	GLY	0	-0.020	-0.020	21.305	-0.001	-0.001	0.000	0.000	0.000	0.000
71	D	71	THR	0	0.006	-0.015	21.798	-0.005	-0.005	0.000	0.000	0.000	0.000
72	D	72	SER	0	-0.039	0.001	18.046	0.019	0.019	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.022	0.006	20.018	-0.003	-0.003	0.000	0.000	0.000	0.000
74	D	74	GLY	0	-0.003	0.006	19.746	0.007	0.007	0.000	0.000	0.000	0.000
75	D	75	ASN	0	-0.036	-0.009	15.227	0.061	0.061	0.000	0.000	0.000	0.000
76	D	76	GLN	0	0.043	0.002	16.906	-0.008	-0.008	0.000	0.000	0.000	0.000
77	D	77	VAL	0	-0.008	0.004	15.443	-0.006	-0.006	0.000	0.000	0.000	0.000
78	D	78	ASN	0	-0.014	-0.023	18.175	0.004	0.004	0.000	0.000	0.000	0.000
79	D	79	LEU	0	0.017	0.019	17.519	-0.011	-0.011	0.000	0.000	0.000	0.000
80	D	80	THR	0	-0.005	-0.012	21.794	0.005	0.005	0.000	0.000	0.000	0.000
81	D	81	ILE	0	0.015	0.009	21.634	-0.009	-0.009	0.000	0.000	0.000	0.000
82	D	82	GLN	0	-0.003	0.000	25.951	0.011	0.011	0.000	0.000	0.000	0.000
83	D	83	GLY	0	0.027	0.012	29.066	-0.007	-0.007	0.000	0.000	0.000	0.000
84	D	84	LEU	0	-0.038	-0.001	26.679	-0.006	-0.006	0.000	0.000	0.000	0.000
85	D	85	ARG	1	0.927	0.946	30.763	0.075	0.075	0.000	0.000	0.000	0.000
86	D	86	ALA	0	0.049	0.024	31.373	-0.004	-0.004	0.000	0.000	0.000	0.000
87	D	87	MET	0	-0.005	0.005	30.919	0.002	0.002	0.000	0.000	0.000	0.000
88	D	88	ASP	-1	-0.819	-0.907	27.589	-0.094	-0.094	0.000	0.000	0.000	0.000
89	D	89	THR	0	-0.025	-0.018	26.625	0.002	0.002	0.000	0.000	0.000	0.000
90	D	90	GLY	0	0.002	0.008	24.016	-0.012	-0.012	0.000	0.000	0.000	0.000
91	D	91	LEU	0	-0.020	0.008	17.901	0.016	0.016	0.000	0.000	0.000	0.000
92	D	92	TYR	0	-0.006	-0.022	19.241	-0.028	-0.028	0.000	0.000	0.000	0.000
93	D	93	ILE	0	-0.013	0.001	13.049	0.030	0.030	0.000	0.000	0.000	0.000
94	D	95	LYS	1	0.836	0.926	7.512	0.775	0.775	0.000	0.000	0.000	0.000
95	D	96	VAL	0	0.005	-0.012	9.229	-0.055	-0.055	0.000	0.000	0.000	0.000
96	D	97	GLU	-1	-0.848	-0.908	5.902	-0.697	-0.697	0.000	0.000	0.000	0.000
97	D	98	LEU	0	0.010	0.002	6.469	0.056	0.056	0.000	0.000	0.000	0.000
98	D	99	MET	0	-0.042	-0.009	6.732	0.071	0.071	0.000	0.000	0.000	0.000
99	D	100	TYR	0	0.005	-0.025	7.912	-0.045	-0.045	0.000	0.000	0.000	0.000
100	D	101	PRO	0	0.004	0.004	10.156	0.027	0.027	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.011	-0.003	11.332	0.153	0.153	0.000	0.000	0.000	0.000
102	D	103	PRO	0	-0.020	-0.005	11.137	-0.112	-0.112	0.000	0.000	0.000	0.000
103	D	104	TYR	0	0.012	0.007	14.226	-0.030	-0.030	0.000	0.000	0.000	0.000
104	D	105	TYR	0	-0.021	-0.009	15.327	0.014	0.014	0.000	0.000	0.000	0.000
105	D	106	LEU	0	0.009	0.011	20.206	-0.018	-0.018	0.000	0.000	0.000	0.000
106	D	107	GLY	0	0.001	0.004	23.840	0.005	0.005	0.000	0.000	0.000	0.000
107	D	108	ILE	0	-0.009	-0.008	26.273	-0.011	-0.011	0.000	0.000	0.000	0.000
108	D	109	GLY	0	0.010	0.010	29.971	0.001	0.001	0.000	0.000	0.000	0.000
109	D	110	ASN	0	-0.014	-0.026	32.308	0.000	0.000	0.000	0.000	0.000	0.000
110	D	111	GLY	0	0.030	0.030	35.624	-0.007	-0.007	0.000	0.000	0.000	0.000
111	D	112	THR	0	-0.029	-0.020	37.301	0.002	0.002	0.000	0.000	0.000	0.000
112	D	113	GLN	0	-0.006	0.006	39.240	0.000	0.000	0.000	0.000	0.000	0.000
113	D	114	ILE	0	-0.004	-0.005	39.619	-0.001	-0.001	0.000	0.000	0.000	0.000
114	D	115	TYR	0	-0.011	-0.009	43.881	-0.002	-0.002	0.000	0.000	0.000	0.000
115	D	116	VAL	0	-0.005	-0.012	46.681	0.000	0.000	0.000	0.000	0.000	0.000
116	D	117	ILE	0	-0.029	-0.017	49.177	-0.001	-0.001	0.000	0.000	0.000	0.000
117	D	118	ASP	-1	-0.889	-0.936	52.711	0.037	0.037	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.083	-0.031	54.635	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	120	GLU	-1	-0.960	-0.980	57.559	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)