FMO DATABASE

FMODB ID: N969Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-820489.699758
FMO2-HF: Nuclear repulsion	779071.34611
FMO2-HF: Total energy	-41418.353648
FMO2-MP2: Total energy	-41541.482545

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.
-0.185	2.078	0	-1.074	-1.189	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 : 0.071 / q_NPA : 0.016

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	0.021	0.014	3.700	0.045	2.167	0.001	-1.055	-1.068	0.003
4	A	7	LEU	0	-0.028	-0.017	5.446	-0.044	-0.044	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.868	-0.923	8.353	-0.672	-0.672	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.048	-0.032	9.912	0.184	0.184	0.000	0.000	0.000	0.000
7	A	10	TRP	0	-0.026	-0.021	13.020	0.067	0.067	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.032	0.010	16.439	0.031	0.031	0.000	0.000	0.000	0.000
9	A	12	ALA	0	-0.049	-0.019	19.746	0.002	0.002	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.025	0.013	22.825	0.004	0.004	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.013	-0.004	24.640	0.013	0.013	0.000	0.000	0.000	0.000
12	A	15	GLN	0	-0.060	-0.031	25.113	0.002	0.002	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.818	-0.918	24.701	-0.175	-0.175	0.000	0.000	0.000	0.000
14	A	17	ILE	0	-0.041	-0.015	18.362	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	18	ASN	0	-0.033	-0.037	20.768	0.025	0.025	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.003	0.015	14.890	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.826	-0.916	17.148	-0.232	-0.232	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.006	-0.013	14.389	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.008	-0.010	13.182	0.038	0.038	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.021	-0.003	15.780	0.008	0.008	0.000	0.000	0.000	0.000
21	A	24	PHE	0	-0.013	-0.008	17.061	0.034	0.034	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.017	-0.012	18.985	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.027	-0.003	22.526	0.008	0.008	0.000	0.000	0.000	0.000
24	A	27	SER	0	-0.038	-0.047	24.461	0.002	0.002	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.837	-0.922	26.341	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	29	ASP	-1	-0.869	-0.897	24.599	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.046	-0.009	20.795	0.004	0.004	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.835	-0.905	23.022	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.837	-0.903	19.841	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.030	0.019	18.578	0.001	0.001	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.909	0.955	16.088	0.104	0.104	0.000	0.000	0.000	0.000
32	A	35	TRP	0	0.039	0.004	13.814	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.952	-0.984	13.516	-0.172	-0.172	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.812	0.910	13.600	0.209	0.209	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.023	-0.041	9.751	0.034	0.034	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.053	-0.048	12.636	0.052	0.052	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.866	-0.925	15.123	-0.188	-0.188	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.905	0.967	14.509	0.161	0.161	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.941	0.965	16.240	0.144	0.144	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.894	0.951	17.945	0.083	0.083	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.023	0.010	17.806	0.017	0.017	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.008	-0.008	19.736	0.015	0.015	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.047	-0.032	19.882	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	47	PHE	0	0.011	0.016	21.993	0.006	0.006	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.768	0.859	22.925	0.049	0.049	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.849	0.918	25.821	0.036	0.036	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.916	-0.951	27.861	-0.042	-0.042	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.875	0.927	29.284	0.042	0.042	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.915	-0.944	30.320	-0.067	-0.067	0.000	0.000	0.000	0.000
50	A	53	THR	0	-0.023	-0.019	25.182	0.000	0.000	0.000	0.000	0.000	0.000
51	A	54	PHE	0	-0.012	0.007	22.886	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.838	0.902	24.405	0.113	0.113	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.866	-0.907	22.873	-0.150	-0.150	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.868	0.911	22.824	0.177	0.177	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.803	-0.914	26.405	-0.123	-0.123	0.000	0.000	0.000	0.000
56	A	59	THR	0	-0.003	0.006	24.370	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	TYR	0	0.041	0.039	21.524	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.768	-0.897	23.375	-0.114	-0.114	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.005	0.015	20.244	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	63	LEU	0	-0.022	0.001	22.849	0.018	0.018	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.974	0.968	23.611	0.089	0.089	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.001	-0.015	21.486	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	GLY	0	0.046	0.024	19.818	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.014	0.035	18.608	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.036	-0.011	17.756	0.030	0.030	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.885	0.949	19.355	0.127	0.127	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.025	-0.020	17.899	0.012	0.012	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.775	0.883	22.308	0.130	0.130	0.000	0.000	0.000	0.000
69	A	72	HIS	0	-0.028	-0.028	25.174	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.015	0.014	20.096	0.002	0.002	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.824	0.889	22.660	0.205	0.205	0.000	0.000	0.000	0.000
72	A	75	THR	0	0.029	-0.005	21.414	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	76	ASP	-1	-0.888	-0.940	19.967	-0.186	-0.186	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.833	-0.904	19.095	-0.239	-0.239	0.000	0.000	0.000	0.000
75	A	78	GLN	0	0.041	0.048	15.211	-0.077	-0.077	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.771	-0.851	13.328	-0.373	-0.373	0.000	0.000	0.000	0.000
77	A	80	ILE	0	0.009	0.005	6.964	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	81	TYR	0	-0.024	-0.019	10.357	0.123	0.123	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.811	0.894	8.643	0.066	0.066	0.000	0.000	0.000	0.000
80	A	83	VAL	0	0.009	0.001	10.443	0.085	0.085	0.000	0.000	0.000	0.000
81	A	84	SER	0	-0.056	-0.053	11.317	0.003	0.003	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.011	0.014	13.876	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	86	TYR	0	-0.007	-0.006	15.366	0.017	0.017	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.748	-0.883	19.212	0.013	0.013	0.000	0.000	0.000	0.000
85	A	88	THR	0	-0.031	-0.030	22.517	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.860	0.924	24.384	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	90	GLY	0	-0.018	0.007	22.034	0.005	0.005	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.928	0.970	19.245	-0.075	-0.075	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.042	-0.046	12.552	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	93	VAL	0	-0.029	-0.011	16.549	0.028	0.028	0.000	0.000	0.000	0.000
91	A	94	LEU	0	-0.020	-0.013	12.716	0.019	0.019	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.745	-0.818	8.468	-0.116	-0.116	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.811	0.896	7.118	1.132	1.132	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.021	0.006	3.849	-0.194	-0.053	-0.001	-0.019	-0.121	0.000
95	A	98	PHE	0	-0.016	-0.001	7.574	-0.180	-0.180	0.000	0.000	0.000	0.000
96	A	99	ASP	-1	-0.844	-0.898	7.739	-1.022	-1.022	0.000	0.000	0.000	0.000
97	A	100	LEU	0	0.009	0.010	9.747	0.041	0.041	0.000	0.000	0.000	0.000
98	A	101	LYS	1	0.853	0.924	9.513	0.925	0.925	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.025	-0.025	14.910	0.020	0.020	0.000	0.000	0.000	0.000
100	A	103	GLN	0	0.010	0.007	18.751	0.042	0.042	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.893	-0.954	20.850	-0.196	-0.196	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.890	0.951	24.210	0.189	0.189	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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