FMO DATABASE

FMODB ID: 8511Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-719251.987158
FMO2-HF: Nuclear repulsion	680826.386764
FMO2-HF: Total energy	-38425.600394
FMO2-MP2: Total energy	-38538.382451

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.
-2.042	0.167	-0.012	-0.919	-1.278	0.004

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 : 0.044 / q_NPA : 0.021

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	-0.020	-0.011	3.880	-0.232	1.490	-0.009	-0.831	-0.882	0.004
4	B	4	GLN	0	0.012	0.013	6.010	0.442	0.442	0.000	0.000	0.000	0.000
5	B	5	ILE	0	-0.024	-0.006	9.053	0.009	0.009	0.000	0.000	0.000	0.000
6	B	6	TYR	0	0.016	0.008	11.965	0.073	0.073	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.021	0.006	15.384	-0.029	-0.029	0.000	0.000	0.000	0.000
8	B	8	VAL	0	-0.058	-0.025	18.366	0.028	0.028	0.000	0.000	0.000	0.000
9	B	9	LYS	1	0.976	0.990	22.132	0.073	0.073	0.000	0.000	0.000	0.000
10	B	10	TYR	0	-0.032	-0.028	24.836	0.008	0.008	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.018	0.028	23.888	0.000	0.000	0.000	0.000	0.000	0.000
12	B	12	ASN	0	-0.065	-0.043	21.506	0.016	0.016	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.022	0.017	15.240	0.004	0.004	0.000	0.000	0.000	0.000
14	B	14	THR	0	-0.020	-0.018	15.002	0.033	0.033	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.030	-0.004	11.376	-0.048	-0.048	0.000	0.000	0.000	0.000
16	B	16	HIS	0	0.016	-0.010	11.263	0.014	0.014	0.000	0.000	0.000	0.000
17	B	17	VAL	0	0.043	0.020	9.369	-0.248	-0.248	0.000	0.000	0.000	0.000
18	B	18	PRO	0	-0.042	-0.009	7.685	0.185	0.185	0.000	0.000	0.000	0.000
19	B	19	SER	0	0.010	-0.008	10.483	0.018	0.018	0.000	0.000	0.000	0.000
20	B	20	ASN	0	-0.044	-0.046	13.258	0.077	0.077	0.000	0.000	0.000	0.000
21	B	21	GLN	0	0.036	0.043	16.724	0.011	0.011	0.000	0.000	0.000	0.000
22	B	22	PRO	0	-0.031	-0.016	17.417	-0.028	-0.028	0.000	0.000	0.000	0.000
23	B	23	LEU	0	0.049	0.025	13.275	0.026	0.026	0.000	0.000	0.000	0.000
24	B	24	LYS	1	0.827	0.897	17.870	0.196	0.196	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.891	-0.932	19.256	-0.175	-0.175	0.000	0.000	0.000	0.000
26	B	26	VAL	0	-0.043	-0.007	14.709	-0.032	-0.032	0.000	0.000	0.000	0.000
27	B	27	LEU	0	-0.014	-0.002	15.503	0.050	0.050	0.000	0.000	0.000	0.000
28	B	28	TRP	0	-0.013	-0.005	10.931	-0.094	-0.094	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.828	0.879	13.585	0.394	0.394	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.825	0.908	14.024	0.085	0.085	0.000	0.000	0.000	0.000
31	B	31	GLN	0	-0.028	-0.035	12.489	0.054	0.054	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.908	0.964	14.240	0.004	0.004	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.905	-0.929	17.089	-0.122	-0.122	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.815	0.884	17.742	0.149	0.149	0.000	0.000	0.000	0.000
35	B	35	VAL	0	-0.029	-0.001	17.039	0.018	0.018	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.027	-0.038	18.518	0.030	0.030	0.000	0.000	0.000	0.000
37	B	37	GLU	-1	-0.771	-0.872	18.324	-0.238	-0.238	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.037	-0.020	20.176	0.017	0.017	0.000	0.000	0.000	0.000
39	B	39	GLU	-1	-0.867	-0.922	21.728	-0.146	-0.146	0.000	0.000	0.000	0.000
40	B	40	ASN	0	0.004	-0.007	23.805	0.010	0.010	0.000	0.000	0.000	0.000
41	B	41	SER	0	-0.030	-0.019	24.597	0.008	0.008	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.900	-0.931	25.960	-0.124	-0.124	0.000	0.000	0.000	0.000
43	B	43	PHE	0	-0.044	-0.029	21.095	-0.012	-0.012	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.868	0.940	23.661	0.149	0.149	0.000	0.000	0.000	0.000
45	B	45	ALA	0	0.022	0.007	22.941	-0.022	-0.022	0.000	0.000	0.000	0.000
46	B	46	PHE	0	-0.018	-0.013	22.569	0.027	0.027	0.000	0.000	0.000	0.000
47	B	47	SER	0	0.017	-0.009	24.307	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	48	SER	0	0.011	0.008	24.348	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	49	PHE	0	0.059	0.026	20.007	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	50	LYS	1	0.961	0.992	23.887	0.110	0.110	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.023	-0.019	27.037	0.006	0.006	0.000	0.000	0.000	0.000
52	B	52	ARG	1	0.779	0.878	22.878	0.180	0.180	0.000	0.000	0.000	0.000
53	B	53	VAL	0	-0.012	-0.005	20.628	-0.018	-0.018	0.000	0.000	0.000	0.000
54	B	54	TYR	0	-0.048	-0.025	20.629	0.033	0.033	0.000	0.000	0.000	0.000
55	B	55	LEU	0	0.006	0.010	16.655	-0.035	-0.035	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.781	-0.891	17.721	-0.283	-0.283	0.000	0.000	0.000	0.000
57	B	57	THR	0	-0.019	-0.005	18.556	-0.017	-0.017	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.885	0.942	19.605	0.266	0.266	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.061	0.040	14.172	0.026	0.026	0.000	0.000	0.000	0.000
60	B	60	GLY	0	0.069	0.041	14.325	-0.074	-0.074	0.000	0.000	0.000	0.000
61	B	61	SER	0	0.001	0.011	13.706	-0.075	-0.075	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.011	0.019	14.259	0.087	0.087	0.000	0.000	0.000	0.000
63	B	63	THR	0	-0.021	-0.004	15.906	-0.041	-0.041	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.009	0.011	16.901	0.032	0.032	0.000	0.000	0.000	0.000
65	B	65	TYR	0	0.034	-0.004	20.417	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.009	-0.009	23.702	0.013	0.013	0.000	0.000	0.000	0.000
67	B	67	LEU	0	-0.043	0.002	19.395	0.005	0.005	0.000	0.000	0.000	0.000
68	B	68	THR	0	-0.008	-0.040	23.460	0.023	0.023	0.000	0.000	0.000	0.000
69	B	69	SER	0	0.016	-0.008	22.534	0.016	0.016	0.000	0.000	0.000	0.000
70	B	70	SER	0	-0.008	0.002	22.248	0.009	0.009	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.817	-0.864	19.553	-0.186	-0.186	0.000	0.000	0.000	0.000
72	B	72	GLU	-1	-0.824	-0.895	17.255	-0.133	-0.133	0.000	0.000	0.000	0.000
73	B	73	ASP	-1	-0.792	-0.881	15.338	-0.088	-0.088	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.846	-0.892	8.543	-0.069	-0.069	0.000	0.000	0.000	0.000
75	B	75	TYR	0	-0.064	-0.070	10.903	0.066	0.066	0.000	0.000	0.000	0.000
76	B	76	GLU	-1	-0.830	-0.875	7.714	-0.879	-0.879	0.000	0.000	0.000	0.000
77	B	77	MET	0	-0.059	-0.025	9.232	0.147	0.147	0.000	0.000	0.000	0.000
78	B	78	GLU	-1	-0.753	-0.852	9.922	-0.469	-0.469	0.000	0.000	0.000	0.000
79	B	79	SER	0	-0.013	-0.041	12.552	0.038	0.038	0.000	0.000	0.000	0.000
80	B	80	PRO	0	0.045	0.027	14.268	-0.013	-0.013	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.100	-0.047	15.895	0.028	0.028	0.000	0.000	0.000	0.000
82	B	82	ILE	0	-0.036	-0.007	9.628	-0.031	-0.031	0.000	0.000	0.000	0.000
83	B	83	THR	0	-0.054	-0.042	8.222	0.092	0.092	0.000	0.000	0.000	0.000
84	B	84	ASP	-1	-0.872	-0.925	6.853	-0.350	-0.350	0.000	0.000	0.000	0.000
85	B	85	SER	0	-0.071	-0.066	6.152	-0.193	-0.193	0.000	0.000	0.000	0.000
86	B	86	MET	0	-0.005	0.004	4.358	-1.340	-1.008	-0.001	-0.042	-0.289	0.000
87	B	87	LYS	1	0.796	0.879	4.360	1.065	1.297	-0.001	-0.038	-0.193	0.000
88	B	88	PHE	0	-0.006	-0.019	5.685	-0.858	-0.935	-0.001	-0.008	0.086	0.000
89	B	89	PHE	0	0.017	0.010	8.446	0.275	0.275	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.048	-0.012	10.744	-0.044	-0.044	0.000	0.000	0.000	0.000
91	B	91	TYR	0	0.020	-0.005	11.980	0.068	0.068	0.000	0.000	0.000	0.000
92	B	92	VAL	0	-0.083	-0.055	16.330	-0.032	-0.032	0.000	0.000	0.000	0.000
93	B	93	GLY	0	0.061	0.035	19.838	0.025	0.025	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.909	-0.968	21.473	-0.072	-0.072	0.000	0.000	0.000	0.000
95	B	95	SER	0	-0.050	-0.017	25.270	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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