FMO DATABASE

FMODB ID: G6MM1

Calculation Name: 1QA9-B-Xray372

Preferred Name: T-cell surface antigen CD2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-717722.377019
FMO2-HF: Nuclear repulsion	679297.578774
FMO2-HF: Total energy	-38424.798245
FMO2-MP2: Total energy	-38537.66693

3D Structure Molmil

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.
-1.194	0.476	-0.014	-0.606	-1.05	0.003

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 : 0.004 / q_NPA : -0.013

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	B	3	GLN	0	-0.036	-0.019	3.801	1.262	2.539	-0.012	-0.568	-0.697	0.003
4	B	4	GLN	0	0.012	-0.001	6.107	0.046	0.046	0.000	0.000	0.000	0.000
5	B	5	ILE	0	-0.032	-0.013	9.262	-0.126	-0.126	0.000	0.000	0.000	0.000
6	B	6	TYR	0	0.049	0.035	12.254	0.073	0.073	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.008	-0.008	15.746	-0.068	-0.068	0.000	0.000	0.000	0.000
8	B	8	VAL	0	-0.073	-0.001	18.769	0.036	0.036	0.000	0.000	0.000	0.000
9	B	9	LYS	1	1.043	1.035	22.523	-0.066	-0.066	0.000	0.000	0.000	0.000
10	B	10	TYR	0	-0.054	-0.034	25.203	0.003	0.003	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.011	0.023	23.949	-0.012	-0.012	0.000	0.000	0.000	0.000
12	B	12	ASN	0	-0.079	-0.039	21.702	0.007	0.007	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.018	0.015	15.401	0.007	0.007	0.000	0.000	0.000	0.000
14	B	14	THR	0	0.010	-0.015	15.489	0.022	0.022	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.060	-0.017	11.613	-0.026	-0.026	0.000	0.000	0.000	0.000
16	B	16	HIS	0	0.034	0.002	11.344	-0.049	-0.049	0.000	0.000	0.000	0.000
17	B	17	VAL	0	0.029	0.012	9.653	-0.290	-0.290	0.000	0.000	0.000	0.000
18	B	18	PRO	0	-0.008	0.003	7.446	0.257	0.257	0.000	0.000	0.000	0.000
19	B	19	SER	0	0.002	-0.001	10.703	-0.047	-0.047	0.000	0.000	0.000	0.000
20	B	20	ASN	0	-0.027	-0.037	13.571	0.114	0.114	0.000	0.000	0.000	0.000
21	B	21	GLN	0	0.021	0.027	16.939	0.051	0.051	0.000	0.000	0.000	0.000
22	B	22	PRO	0	-0.018	-0.007	17.623	-0.041	-0.041	0.000	0.000	0.000	0.000
23	B	23	LEU	0	0.045	0.015	13.776	0.055	0.055	0.000	0.000	0.000	0.000
24	B	24	LYS	1	0.801	0.903	18.401	0.369	0.369	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.878	-0.949	19.366	-0.321	-0.321	0.000	0.000	0.000	0.000
26	B	26	VAL	0	-0.057	-0.005	14.672	-0.061	-0.061	0.000	0.000	0.000	0.000
27	B	27	LEU	0	0.009	0.007	15.621	0.083	0.083	0.000	0.000	0.000	0.000
28	B	28	TRP	0	-0.010	-0.015	11.096	-0.083	-0.083	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.836	0.886	13.682	0.437	0.437	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.829	0.920	13.725	-0.071	-0.071	0.000	0.000	0.000	0.000
31	B	31	GLN	0	0.006	-0.002	12.865	0.022	0.022	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.910	0.944	14.564	-0.126	-0.126	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.908	-0.927	17.205	-0.059	-0.059	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.820	0.885	17.638	0.186	0.186	0.000	0.000	0.000	0.000
35	B	35	VAL	0	-0.029	-0.001	17.220	0.028	0.028	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.029	-0.032	18.797	0.030	0.030	0.000	0.000	0.000	0.000
37	B	37	GLU	-1	-0.785	-0.864	18.708	-0.285	-0.285	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.062	-0.038	20.268	0.026	0.026	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.848	-0.923	21.731	-0.232	-0.232	0.000	0.000	0.000	0.000
40	B	40	ASN	0	-0.003	-0.013	24.335	0.007	0.007	0.000	0.000	0.000	0.000
41	B	41	SER	0	-0.090	-0.031	25.300	0.004	0.004	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.906	-0.962	25.847	-0.152	-0.152	0.000	0.000	0.000	0.000
43	B	43	PHE	0	-0.067	-0.025	21.183	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.978	0.996	24.067	0.178	0.178	0.000	0.000	0.000	0.000
45	B	45	ALA	0	0.003	0.018	23.384	-0.017	-0.017	0.000	0.000	0.000	0.000
46	B	46	PHE	0	-0.019	-0.025	23.120	0.029	0.029	0.000	0.000	0.000	0.000
47	B	47	SER	0	-0.001	-0.018	24.680	0.002	0.002	0.000	0.000	0.000	0.000
48	B	48	SER	0	0.049	0.014	24.796	-0.012	-0.012	0.000	0.000	0.000	0.000
49	B	49	PHE	0	0.035	0.020	19.990	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	50	LYS	1	1.001	1.016	24.223	0.089	0.089	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.076	-0.039	27.206	0.013	0.013	0.000	0.000	0.000	0.000
52	B	52	ARG	1	0.817	0.870	22.838	0.088	0.088	0.000	0.000	0.000	0.000
53	B	53	VAL	0	-0.031	-0.005	20.749	-0.008	-0.008	0.000	0.000	0.000	0.000
54	B	54	TYR	0	-0.038	-0.015	21.156	0.026	0.026	0.000	0.000	0.000	0.000
55	B	55	LEU	0	0.012	0.005	17.022	-0.029	-0.029	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.800	-0.905	18.095	-0.443	-0.443	0.000	0.000	0.000	0.000
57	B	57	THR	0	-0.042	-0.014	18.975	-0.042	-0.042	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.905	0.944	19.814	0.385	0.385	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.052	0.030	14.287	-0.015	-0.015	0.000	0.000	0.000	0.000
60	B	60	GLY	0	0.065	0.037	14.636	-0.096	-0.096	0.000	0.000	0.000	0.000
61	B	61	SER	0	0.003	0.011	14.086	-0.090	-0.090	0.000	0.000	0.000	0.000
62	B	62	LEU	0	-0.009	0.010	14.696	0.097	0.097	0.000	0.000	0.000	0.000
63	B	63	THR	0	-0.022	0.007	16.207	-0.021	-0.021	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.009	0.022	17.152	0.027	0.027	0.000	0.000	0.000	0.000
65	B	65	TYR	0	0.035	-0.014	20.544	0.003	0.003	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.015	-0.010	23.748	0.014	0.014	0.000	0.000	0.000	0.000
67	B	67	LEU	0	-0.030	0.004	19.766	0.003	0.003	0.000	0.000	0.000	0.000
68	B	68	THR	0	-0.011	-0.040	23.438	0.017	0.017	0.000	0.000	0.000	0.000
69	B	69	SER	0	0.032	0.008	22.639	0.003	0.003	0.000	0.000	0.000	0.000
70	B	70	SER	0	-0.032	-0.013	22.184	0.024	0.024	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.803	-0.872	19.509	-0.062	-0.062	0.000	0.000	0.000	0.000
72	B	72	GLU	-1	-0.890	-0.932	16.984	0.210	0.210	0.000	0.000	0.000	0.000
73	B	73	ASP	-1	-0.756	-0.857	15.440	0.167	0.167	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.873	-0.918	8.908	0.474	0.474	0.000	0.000	0.000	0.000
75	B	75	TYR	0	-0.087	-0.098	10.876	-0.061	-0.061	0.000	0.000	0.000	0.000
76	B	76	GLU	-1	-0.815	-0.879	8.397	-0.721	-0.721	0.000	0.000	0.000	0.000
77	B	77	MET	0	-0.065	-0.014	9.429	0.149	0.149	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.776	-0.868	10.114	-0.608	-0.608	0.000	0.000	0.000	0.000
79	B	79	SER	0	-0.021	-0.055	12.533	0.061	0.061	0.000	0.000	0.000	0.000
80	B	80	PRO	0	0.109	0.063	14.070	-0.067	-0.067	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.094	-0.016	16.275	0.008	0.008	0.000	0.000	0.000	0.000
82	B	82	ILE	0	-0.046	-0.030	10.142	-0.068	-0.068	0.000	0.000	0.000	0.000
83	B	83	THR	0	-0.061	-0.066	8.946	0.161	0.161	0.000	0.000	0.000	0.000
84	B	84	ASP	-1	-0.953	-0.981	7.181	-1.248	-1.248	0.000	0.000	0.000	0.000
85	B	85	SER	0	-0.039	-0.032	6.594	-0.498	-0.498	0.000	0.000	0.000	0.000
86	B	86	MET	0	0.027	0.039	4.636	-1.341	-1.105	-0.001	-0.025	-0.210	0.000
87	B	87	LYS	1	0.810	0.887	4.492	0.869	1.026	-0.001	-0.013	-0.143	0.000
88	B	88	PHE	0	-0.014	0.000	5.840	-0.209	-0.209	0.000	0.000	0.000	0.000
89	B	89	PHE	0	0.045	0.021	8.309	0.249	0.249	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.076	-0.024	10.544	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	91	TYR	0	0.018	0.005	11.696	0.019	0.019	0.000	0.000	0.000	0.000
92	B	92	VAL	0	-0.066	-0.047	16.414	-0.046	-0.046	0.000	0.000	0.000	0.000
93	B	93	GLY	0	0.064	0.020	19.844	0.020	0.020	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.928	-0.977	21.305	0.141	0.141	0.000	0.000	0.000	0.000
95	B	95	SER	0	-0.028	-0.010	25.041	-0.018	-0.018	0.000	0.000	0.000	0.000

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