FMO DATABASE

FMODB ID: 17QQZ

Calculation Name: 1QA9-B-Xray372

Preferred Name: T-cell surface antigen CD2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1QA9

Chain ID: B

ChEMBL ID: CHEMBL2040

UniProt ID: P06729

Base Structure: X-ray

Registration Date: 2023-09-20

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-717508.49369
FMO2-HF: Nuclear repulsion	679084.919022
FMO2-HF: Total energy	-38423.574668
FMO2-MP2: Total energy	-38536.507403

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(B:1:SER)

Summations of interaction energy for fragment #1(B:1:SER)

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.
-2.171	-0.173	-0.009	-0.818	-1.172	0.005

Interaction energy analysis for fragmet #1(B:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.002

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	B	3	GLN	0	-0.014	-0.016	3.801	-0.305	1.328	-0.007	-0.790	-0.837	0.005
4	B	4	GLN	0	0.007	-0.001	6.042	0.004	0.004	0.000	0.000	0.000	0.000
5	B	5	ILE	0	-0.041	-0.011	9.204	-0.205	-0.205	0.000	0.000	0.000	0.000
6	B	6	TYR	0	0.052	0.036	12.193	0.086	0.086	0.000	0.000	0.000	0.000
7	B	7	GLY	0	-0.003	-0.009	15.681	-0.074	-0.074	0.000	0.000	0.000	0.000
8	B	8	VAL	0	-0.069	-0.003	18.709	0.033	0.033	0.000	0.000	0.000	0.000
9	B	9	LYS	1	1.064	1.041	22.463	-0.106	-0.106	0.000	0.000	0.000	0.000
10	B	10	TYR	0	-0.070	-0.040	25.144	-0.001	-0.001	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.006	0.020	23.897	-0.014	-0.014	0.000	0.000	0.000	0.000
12	B	12	ASN	0	-0.070	-0.018	21.615	0.012	0.012	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.010	0.004	15.238	0.005	0.005	0.000	0.000	0.000	0.000
14	B	14	THR	0	0.012	-0.013	15.380	0.024	0.024	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.065	-0.016	11.668	-0.020	-0.020	0.000	0.000	0.000	0.000
16	B	16	HIS	0	0.047	-0.002	11.257	-0.050	-0.050	0.000	0.000	0.000	0.000
17	B	17	VAL	0	0.003	0.007	9.808	-0.278	-0.278	0.000	0.000	0.000	0.000
18	B	18	PRO	0	-0.017	-0.003	7.466	0.231	0.231	0.000	0.000	0.000	0.000
19	B	19	SER	0	0.020	0.033	10.734	-0.059	-0.059	0.000	0.000	0.000	0.000
20	B	20	ASN	0	-0.022	-0.034	13.613	0.122	0.122	0.000	0.000	0.000	0.000
21	B	21	GLN	0	0.015	0.013	16.987	0.045	0.045	0.000	0.000	0.000	0.000
22	B	22	PRO	0	-0.042	-0.013	17.673	-0.042	-0.042	0.000	0.000	0.000	0.000
23	B	23	LEU	0	0.064	0.016	14.525	0.050	0.050	0.000	0.000	0.000	0.000
24	B	24	LYS	1	0.829	0.931	18.437	0.343	0.343	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.882	-0.956	19.387	-0.283	-0.283	0.000	0.000	0.000	0.000
26	B	26	VAL	0	-0.037	-0.003	14.920	-0.057	-0.057	0.000	0.000	0.000	0.000
27	B	27	LEU	0	-0.004	0.002	15.635	0.080	0.080	0.000	0.000	0.000	0.000
28	B	28	TRP	0	-0.008	-0.006	11.041	-0.059	-0.059	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.954	0.958	13.833	0.235	0.235	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.905	0.983	13.718	-0.129	-0.129	0.000	0.000	0.000	0.000
31	B	31	GLN	0	0.058	0.037	13.534	-0.016	-0.016	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.909	0.937	14.557	-0.214	-0.214	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.910	-0.935	17.206	0.013	0.013	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.923	0.962	17.636	0.131	0.131	0.000	0.000	0.000	0.000
35	B	35	VAL	0	-0.025	0.006	17.108	0.025	0.025	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.027	-0.035	18.810	0.021	0.021	0.000	0.000	0.000	0.000
37	B	37	GLU	-1	-0.860	-0.933	18.720	-0.223	-0.223	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.064	-0.027	20.341	0.022	0.022	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.820	-0.921	21.745	-0.196	-0.196	0.000	0.000	0.000	0.000
40	B	40	ASN	0	0.008	-0.001	24.346	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	41	SER	0	-0.123	-0.053	25.333	0.001	0.001	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.908	-0.961	25.881	-0.127	-0.127	0.000	0.000	0.000	0.000
43	B	43	PHE	0	-0.072	-0.030	21.455	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	44	ARG	1	1.001	0.998	24.082	0.136	0.136	0.000	0.000	0.000	0.000
45	B	45	ALA	0	-0.006	0.026	23.398	-0.013	-0.013	0.000	0.000	0.000	0.000
46	B	46	PHE	0	-0.048	-0.034	22.887	0.026	0.026	0.000	0.000	0.000	0.000
47	B	47	SER	0	-0.010	-0.018	24.553	0.008	0.008	0.000	0.000	0.000	0.000
48	B	48	SER	0	0.024	0.000	24.913	-0.015	-0.015	0.000	0.000	0.000	0.000
49	B	49	PHE	0	0.044	0.026	19.702	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	50	LYS	1	0.980	1.006	24.240	0.057	0.057	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.065	-0.032	27.227	0.015	0.015	0.000	0.000	0.000	0.000
52	B	52	ARG	1	0.778	0.857	22.285	0.033	0.033	0.000	0.000	0.000	0.000
53	B	53	VAL	0	-0.009	0.002	20.859	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	54	TYR	0	-0.021	-0.006	21.447	0.004	0.004	0.000	0.000	0.000	0.000
55	B	55	LEU	0	0.004	0.003	16.989	-0.024	-0.024	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.819	-0.912	18.034	-0.439	-0.439	0.000	0.000	0.000	0.000
57	B	57	THR	0	-0.067	-0.029	19.029	-0.035	-0.035	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.916	0.935	19.948	0.350	0.350	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.011	-0.024	15.568	-0.023	-0.023	0.000	0.000	0.000	0.000
60	B	60	GLY	0	0.046	0.031	14.699	-0.088	-0.088	0.000	0.000	0.000	0.000
61	B	61	SER	0	0.074	0.052	14.120	-0.088	-0.088	0.000	0.000	0.000	0.000
62	B	62	LEU	0	-0.016	0.010	14.760	0.092	0.092	0.000	0.000	0.000	0.000
63	B	63	THR	0	-0.029	-0.003	16.188	-0.022	-0.022	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.006	0.022	17.082	0.023	0.023	0.000	0.000	0.000	0.000
65	B	65	TYR	0	0.027	-0.025	20.513	0.000	0.000	0.000	0.000	0.000	0.000
66	B	66	ASN	0	0.020	0.016	23.712	0.012	0.012	0.000	0.000	0.000	0.000
67	B	67	LEU	0	-0.035	-0.016	19.678	0.006	0.006	0.000	0.000	0.000	0.000
68	B	68	THR	0	0.041	0.003	23.454	0.013	0.013	0.000	0.000	0.000	0.000
69	B	69	SER	0	0.030	0.004	22.459	0.002	0.002	0.000	0.000	0.000	0.000
70	B	70	SER	0	-0.054	-0.042	22.059	0.020	0.020	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.838	-0.899	19.467	0.003	0.003	0.000	0.000	0.000	0.000
72	B	72	GLU	-1	-0.948	-0.943	16.558	0.328	0.328	0.000	0.000	0.000	0.000
73	B	73	ASP	-1	-0.790	-0.897	15.412	0.319	0.319	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.980	-0.986	9.129	1.052	1.052	0.000	0.000	0.000	0.000
75	B	75	TYR	0	-0.093	-0.101	10.841	-0.115	-0.115	0.000	0.000	0.000	0.000
76	B	76	GLU	-1	-0.885	-0.944	9.071	-0.392	-0.392	0.000	0.000	0.000	0.000
77	B	77	MET	0	-0.077	-0.015	9.464	0.145	0.145	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.907	-0.948	10.108	-0.510	-0.510	0.000	0.000	0.000	0.000
79	B	79	SER	0	-0.006	-0.045	12.526	0.045	0.045	0.000	0.000	0.000	0.000
80	B	80	PRO	0	0.109	0.060	14.068	-0.065	-0.065	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.091	-0.008	16.274	0.002	0.002	0.000	0.000	0.000	0.000
82	B	82	ILE	0	-0.042	0.020	10.420	-0.082	-0.082	0.000	0.000	0.000	0.000
83	B	83	THR	0	-0.071	-0.093	8.730	0.121	0.121	0.000	0.000	0.000	0.000
84	B	84	ASP	-1	-0.938	-0.990	7.048	-1.159	-1.159	0.000	0.000	0.000	0.000
85	B	85	SER	0	-0.018	-0.017	6.582	-0.461	-0.461	0.000	0.000	0.000	0.000
86	B	86	MET	0	0.007	0.036	4.646	-1.082	-0.860	-0.001	-0.017	-0.204	0.000
87	B	87	LYS	1	0.939	0.965	4.571	0.330	0.473	-0.001	-0.011	-0.131	0.000
88	B	88	PHE	0	-0.004	0.007	5.827	0.012	0.012	0.000	0.000	0.000	0.000
89	B	89	PHE	0	0.062	0.034	8.309	0.206	0.206	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.069	-0.028	10.398	-0.046	-0.046	0.000	0.000	0.000	0.000
91	B	91	TYR	0	0.045	0.001	11.554	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	92	VAL	0	-0.081	-0.039	15.989	-0.058	-0.058	0.000	0.000	0.000	0.000
93	B	93	GLY	0	0.065	0.021	19.572	0.016	0.016	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.920	-0.971	21.054	0.182	0.182	0.000	0.000	0.000	0.000
95	B	95	SER	0	-0.031	-0.012	24.663	-0.017	-0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:SER)