FMO DATABASE

FMODB ID: 85K5Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-819018.413144
FMO2-HF: Nuclear repulsion	777600.786316
FMO2-HF: Total energy	-41417.626828
FMO2-MP2: Total energy	-41540.771982

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.
-1.292	1.853	0.012	-1.492	-1.665	0.004

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 : 0.075 / q_NPA : 0.017

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	6	ALA	0	0.012	-0.009	3.513	-0.832	2.024	0.011	-1.450	-1.417	0.004
4	A	7	LEU	0	0.007	0.010	5.161	0.164	0.258	-0.001	-0.008	-0.085	0.000
5	A	8	GLU	-1	-0.903	-0.963	8.198	-0.712	-0.712	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.068	-0.034	9.907	0.205	0.205	0.000	0.000	0.000	0.000
7	A	10	TRP	0	-0.010	0.004	12.964	0.054	0.054	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.026	0.007	16.467	0.037	0.037	0.000	0.000	0.000	0.000
9	A	12	ALA	0	-0.033	0.000	19.243	0.003	0.003	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.045	0.019	22.628	0.009	0.009	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.016	0.004	24.279	0.013	0.013	0.000	0.000	0.000	0.000
12	A	15	GLN	0	-0.046	-0.024	24.966	0.001	0.001	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.836	-0.913	24.335	-0.177	-0.177	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.037	-0.020	17.541	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	18	ASN	0	0.003	-0.010	19.987	0.019	0.019	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.015	0.008	14.143	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.879	-0.946	16.444	-0.214	-0.214	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.014	-0.019	13.593	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	22	PRO	0	0.016	-0.013	12.531	0.037	0.037	0.000	0.000	0.000	0.000
20	A	23	SER	0	0.008	0.041	15.684	0.002	0.002	0.000	0.000	0.000	0.000
21	A	24	PHE	0	-0.061	-0.038	16.684	0.032	0.032	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.008	-0.016	18.458	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.038	-0.002	22.069	0.010	0.010	0.000	0.000	0.000	0.000
24	A	27	SER	0	-0.032	-0.043	23.829	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.838	-0.915	25.878	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	29	ASP	-1	-0.896	-0.921	24.365	0.007	0.007	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.026	-0.006	20.608	0.004	0.004	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.829	-0.914	22.488	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.800	-0.875	19.878	-0.070	-0.070	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.011	0.014	17.999	0.002	0.002	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.927	0.957	15.973	0.080	0.080	0.000	0.000	0.000	0.000
32	A	35	TRP	0	0.040	0.022	13.431	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.973	-1.004	13.018	-0.161	-0.161	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.843	0.907	12.994	0.206	0.206	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.039	-0.053	9.645	0.035	0.035	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.002	-0.011	12.391	0.068	0.068	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.858	-0.920	14.783	-0.188	-0.188	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.891	0.966	14.591	0.149	0.149	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.936	0.949	16.389	0.132	0.132	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.860	0.943	17.753	0.080	0.080	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.036	0.029	17.547	0.015	0.015	0.000	0.000	0.000	0.000
42	A	45	ALA	0	0.017	0.013	19.527	0.015	0.015	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.055	-0.053	19.707	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	47	PHE	0	-0.019	-0.001	21.523	0.005	0.005	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.808	0.892	22.963	0.037	0.037	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.886	0.932	25.304	0.021	0.021	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.956	-0.966	27.385	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.890	0.928	28.844	0.035	0.035	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.939	-0.946	30.277	-0.058	-0.058	0.000	0.000	0.000	0.000
50	A	53	THR	0	-0.046	-0.030	24.987	0.000	0.000	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.016	0.021	22.591	0.001	0.001	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.932	0.942	24.252	0.104	0.104	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.878	-0.915	22.673	-0.148	-0.148	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.901	0.934	22.681	0.174	0.174	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.908	-0.956	25.782	-0.124	-0.124	0.000	0.000	0.000	0.000
56	A	59	THR	0	0.035	0.014	24.029	0.000	0.000	0.000	0.000	0.000	0.000
57	A	60	TYR	0	0.022	0.010	20.779	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.838	-0.928	23.039	-0.107	-0.107	0.000	0.000	0.000	0.000
59	A	62	LEU	0	0.009	0.004	20.186	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	63	LEU	0	-0.019	-0.004	22.519	0.016	0.016	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.956	0.972	22.823	0.078	0.078	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.003	-0.013	21.331	0.004	0.004	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.037	0.010	19.171	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.070	0.054	18.042	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.026	0.008	17.195	0.026	0.026	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.885	0.944	19.176	0.129	0.129	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.023	-0.013	17.256	0.014	0.014	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.785	0.881	21.655	0.125	0.125	0.000	0.000	0.000	0.000
69	A	72	HIS	0	-0.026	-0.021	24.858	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.004	0.015	19.683	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.823	0.890	22.150	0.204	0.204	0.000	0.000	0.000	0.000
72	A	75	THR	0	0.029	0.001	21.357	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	76	ASP	-1	-0.892	-0.943	20.080	-0.189	-0.189	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.904	-0.933	18.647	-0.248	-0.248	0.000	0.000	0.000	0.000
75	A	78	GLN	0	0.041	0.042	14.865	-0.065	-0.065	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.755	-0.842	13.241	-0.376	-0.376	0.000	0.000	0.000	0.000
77	A	80	ILE	0	-0.002	-0.008	7.104	-0.115	-0.115	0.000	0.000	0.000	0.000
78	A	81	TYR	0	-0.046	-0.023	10.413	0.130	0.130	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.833	0.922	8.099	0.022	0.022	0.000	0.000	0.000	0.000
80	A	83	VAL	0	0.026	0.011	10.130	0.076	0.076	0.000	0.000	0.000	0.000
81	A	84	SER	0	-0.060	-0.057	11.506	0.017	0.017	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.024	0.028	13.749	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.010	-0.009	14.959	0.020	0.020	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.748	-0.881	19.096	0.030	0.030	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.056	-0.042	22.252	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.889	0.931	24.134	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	90	GLY	0	-0.030	0.010	22.122	0.005	0.005	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.937	0.966	19.738	-0.086	-0.086	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.051	-0.036	12.646	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.020	-0.009	16.537	0.025	0.025	0.000	0.000	0.000	0.000
91	A	94	LEU	0	-0.011	-0.011	12.253	0.020	0.020	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.807	-0.875	8.227	-0.034	-0.034	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.849	0.937	7.143	0.860	0.860	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.006	-0.006	3.562	-0.256	-0.061	0.002	-0.034	-0.163	0.000
95	A	98	PHE	0	-0.007	-0.010	7.003	-0.188	-0.188	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.838	-0.912	7.584	-1.204	-1.204	0.000	0.000	0.000	0.000
97	A	100	LEU	0	0.006	0.013	9.639	0.062	0.062	0.000	0.000	0.000	0.000
98	A	101	LYS	1	0.866	0.929	9.370	0.981	0.981	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.020	-0.019	14.702	0.020	0.020	0.000	0.000	0.000	0.000
100	A	103	GLN	0	0.000	-0.005	18.496	0.038	0.038	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.926	-0.965	20.659	-0.202	-0.202	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.912	0.959	24.004	0.191	0.191	0.000	0.000	0.000	0.000

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