FMO DATABASE

FMODB ID: G6761

Calculation Name: 1QA9-A-Xray372

Preferred Name: T-cell surface antigen CD2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1QA9

Chain ID: A

ChEMBL ID: CHEMBL2040

UniProt ID: P06729

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817817.192111
FMO2-HF: Nuclear repulsion	776400.938551
FMO2-HF: Total energy	-41416.25356
FMO2-MP2: Total energy	-41539.428757

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:4:THR)

Summations of interaction energy for fragment #1(A:4:THR)

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.
-1.778	1.179	0.025	-1.311	-1.67	0.003

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / 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	A	6	ALA	0	0.002	-0.004	3.536	-2.049	0.601	0.022	-1.260	-1.411	0.003
4	A	7	LEU	0	0.003	0.010	5.190	0.256	0.341	-0.001	-0.007	-0.077	0.000
5	A	8	GLU	-1	-0.908	-0.986	8.483	0.168	0.168	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.090	-0.033	10.042	0.009	0.009	0.000	0.000	0.000	0.000
7	A	10	TRP	0	-0.011	0.003	13.470	0.016	0.016	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.019	0.010	16.523	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	12	ALA	0	-0.017	0.004	19.260	0.002	0.002	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.047	0.017	22.642	0.000	0.000	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.026	-0.003	24.296	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	15	GLN	0	-0.043	-0.020	24.991	0.000	0.000	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.851	-0.912	24.309	0.014	0.014	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.027	-0.013	17.383	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	ASN	0	0.000	-0.013	19.987	0.001	0.001	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.001	0.013	13.443	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.865	-0.939	16.445	0.041	0.041	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.020	-0.023	13.711	0.005	0.005	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.011	-0.023	12.712	0.007	0.007	0.000	0.000	0.000	0.000
20	A	23	SER	0	0.026	0.044	15.690	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	24	PHE	0	-0.048	-0.027	16.749	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.010	-0.017	18.465	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.036	0.003	22.076	0.007	0.007	0.000	0.000	0.000	0.000
24	A	27	SER	0	0.006	0.004	23.836	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.838	-0.925	25.885	0.043	0.043	0.000	0.000	0.000	0.000
26	A	29	ASP	-1	-0.960	-0.965	24.691	0.068	0.068	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.064	-0.026	20.727	0.007	0.007	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.879	-0.956	22.500	0.050	0.050	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.856	-0.933	20.472	0.057	0.057	0.000	0.000	0.000	0.000
30	A	33	ILE	0	-0.012	0.019	18.072	0.012	0.012	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.961	0.964	15.974	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	35	TRP	0	0.025	0.026	13.476	0.008	0.008	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.982	-1.010	13.008	0.027	0.027	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.866	0.940	12.993	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.048	-0.063	9.872	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	39	SER	0	0.004	-0.024	12.387	0.012	0.012	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.881	-0.946	14.777	0.025	0.025	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.894	0.970	14.765	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.935	0.942	16.386	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.858	0.953	17.754	-0.039	-0.039	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.050	0.044	16.797	0.000	0.000	0.000	0.000	0.000	0.000
42	A	45	ALA	0	0.006	0.007	19.532	0.000	0.000	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.036	-0.041	19.709	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	47	PHE	0	-0.022	0.000	21.531	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.931	0.956	23.032	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.926	0.959	25.308	-0.054	-0.054	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.972	-0.974	27.391	0.036	0.036	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.874	0.920	28.897	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.930	-0.942	30.070	0.025	0.025	0.000	0.000	0.000	0.000
50	A	53	THR	0	-0.057	-0.028	25.044	0.002	0.002	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.014	0.018	22.480	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.973	0.957	24.247	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.958	-0.971	22.339	0.020	0.020	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.975	0.979	23.660	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.948	-0.969	25.781	0.018	0.018	0.000	0.000	0.000	0.000
56	A	59	THR	0	0.002	0.002	23.724	0.000	0.000	0.000	0.000	0.000	0.000
57	A	60	TYR	0	0.006	-0.004	19.905	0.000	0.000	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.957	-0.986	23.048	0.021	0.021	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.001	0.000	20.470	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	LEU	0	-0.020	-0.007	22.526	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.967	0.974	22.827	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.007	-0.021	21.310	0.002	0.002	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.041	0.011	19.174	0.005	0.005	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.084	0.053	18.046	0.003	0.003	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.024	0.012	16.956	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.924	0.960	19.176	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.006	-0.001	17.135	0.000	0.000	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.895	0.934	21.653	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	72	HIS	0	-0.028	-0.025	24.856	0.001	0.001	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.003	0.016	19.605	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.920	0.959	22.237	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	75	THR	0	0.047	-0.005	21.381	0.000	0.000	0.000	0.000	0.000	0.000
73	A	76	ASP	-1	-0.904	-0.942	20.100	0.028	0.028	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.912	-0.954	18.677	0.020	0.020	0.000	0.000	0.000	0.000
75	A	78	GLN	0	0.055	0.081	14.789	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.785	-0.847	12.966	0.031	0.031	0.000	0.000	0.000	0.000
77	A	80	ILE	0	0.022	0.005	7.266	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	81	TYR	0	-0.104	-0.080	10.417	0.005	0.005	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.965	0.988	8.589	-0.102	-0.102	0.000	0.000	0.000	0.000
80	A	83	VAL	0	0.000	0.002	10.131	0.014	0.014	0.000	0.000	0.000	0.000
81	A	84	SER	0	-0.055	-0.038	11.512	0.032	0.032	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.063	0.047	13.754	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.038	-0.025	14.818	0.014	0.014	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.719	-0.866	19.103	0.088	0.088	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.035	-0.035	22.260	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.877	0.926	24.138	-0.071	-0.071	0.000	0.000	0.000	0.000
87	A	90	GLY	0	-0.039	0.008	22.128	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.922	0.953	19.784	-0.104	-0.104	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.040	-0.019	13.262	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.038	-0.007	16.544	0.013	0.013	0.000	0.000	0.000	0.000
91	A	94	LEU	0	-0.026	-0.027	12.537	0.017	0.017	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.904	-0.953	8.746	0.263	0.263	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.887	0.949	7.612	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.007	0.000	3.403	-0.321	-0.099	0.004	-0.044	-0.182	0.000
95	A	98	PHE	0	-0.033	-0.021	7.005	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.882	-0.946	7.886	0.151	0.151	0.000	0.000	0.000	0.000
97	A	100	LEU	0	-0.009	0.007	9.666	0.022	0.022	0.000	0.000	0.000	0.000
98	A	101	LYS	1	0.943	0.980	10.378	-0.163	-0.163	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.007	0.001	14.712	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	103	GLN	0	-0.027	-0.018	18.507	0.002	0.002	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.942	-0.972	20.723	0.025	0.025	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.934	0.967	24.006	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)