FMO DATABASE

FMODB ID: QY8QY

Calculation Name: 1XIW-B-Xray372

Preferred Name: T cell surface glycoprotein CD3

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 1XIW

Chain ID: B

ChEMBL ID: CHEMBL2364168

UniProt ID: P04234

Base Structure: X-ray

Registration Date: 2023-06-21

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-399538.576533
FMO2-HF: Nuclear repulsion	371911.616492
FMO2-HF: Total energy	-27626.960041
FMO2-MP2: Total energy	-27704.420288

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:MET)

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

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.
-5.185	-1.376	3.145	-3.225	-3.729	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.023

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	ILE	0	0.008	-0.005	3.553	-2.518	0.435	-0.009	-1.445	-1.500	0.006
4	B	4	PRO	0	-0.025	0.000	5.419	0.480	0.480	0.000	0.000	0.000	0.000
5	B	5	ILE	0	0.016	0.004	7.835	-0.068	-0.068	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.826	-0.882	11.371	-0.409	-0.409	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.777	-0.854	14.145	-0.141	-0.141	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.027	-0.011	16.697	0.030	0.030	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.890	-0.937	19.790	-0.136	-0.136	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.885	-0.941	23.184	-0.142	-0.142	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.861	0.919	21.209	0.227	0.227	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.013	0.015	16.371	0.003	0.003	0.000	0.000	0.000	0.000
13	B	13	PHE	0	-0.011	-0.003	15.571	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	14	VAL	0	-0.020	0.013	11.169	-0.029	-0.029	0.000	0.000	0.000	0.000
15	B	15	ASN	0	-0.023	-0.022	10.647	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.031	0.020	6.467	0.046	0.046	0.000	0.000	0.000	0.000
17	B	17	ASN	0	0.020	0.012	6.365	0.230	0.230	0.000	0.000	0.000	0.000
18	B	18	THR	0	0.011	0.001	9.980	0.183	0.183	0.000	0.000	0.000	0.000
19	B	19	SER	0	-0.011	-0.011	12.306	-0.045	-0.045	0.000	0.000	0.000	0.000
20	B	20	ILE	0	0.001	-0.010	11.889	-0.148	-0.148	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.038	-0.007	12.310	0.158	0.158	0.000	0.000	0.000	0.000
22	B	22	TRP	0	-0.016	0.001	13.634	-0.086	-0.086	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.058	-0.036	13.323	0.008	0.008	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.907	-0.959	16.501	-0.288	-0.288	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.048	0.028	18.268	-0.034	-0.034	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.004	-0.015	20.340	0.004	0.004	0.000	0.000	0.000	0.000
27	B	27	VAL	0	0.020	0.018	19.795	-0.040	-0.040	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.025	0.017	20.204	-0.036	-0.036	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.034	-0.016	21.506	0.023	0.023	0.000	0.000	0.000	0.000
30	B	30	LEU	0	-0.004	-0.004	17.397	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.013	0.003	19.276	0.043	0.043	0.000	0.000	0.000	0.000
32	B	32	SER	0	0.005	-0.029	18.978	-0.041	-0.041	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.894	-0.934	18.889	-0.327	-0.327	0.000	0.000	0.000	0.000
34	B	34	ILE	0	-0.054	-0.016	17.907	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	35	THR	0	-0.007	-0.003	13.305	-0.015	-0.015	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.827	0.879	13.818	0.446	0.446	0.000	0.000	0.000	0.000
37	B	37	LEU	0	-0.034	-0.002	15.317	0.046	0.046	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.794	-0.896	16.853	-0.295	-0.295	0.000	0.000	0.000	0.000
39	B	39	LEU	0	-0.037	-0.030	15.902	0.019	0.019	0.000	0.000	0.000	0.000
40	B	40	GLY	0	0.008	0.010	19.901	0.030	0.030	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.861	0.901	21.913	0.139	0.139	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.966	0.954	21.475	0.119	0.119	0.000	0.000	0.000	0.000
43	B	43	ILE	0	-0.079	-0.042	22.893	0.005	0.005	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.055	-0.023	25.488	0.012	0.012	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.797	-0.869	23.278	-0.129	-0.129	0.000	0.000	0.000	0.000
46	B	46	PRO	0	0.013	0.030	19.660	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	47	ARG	1	0.808	0.872	19.029	0.167	0.167	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.039	0.027	17.609	0.022	0.022	0.000	0.000	0.000	0.000
49	B	49	ILE	0	-0.034	0.001	12.784	-0.040	-0.040	0.000	0.000	0.000	0.000
50	B	50	TYR	0	0.002	-0.019	11.920	0.058	0.058	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.902	0.941	8.811	0.997	0.997	0.000	0.000	0.000	0.000
52	B	53	ASN	0	0.034	0.003	7.125	-0.564	-0.564	0.000	0.000	0.000	0.000
53	B	62	GLU	-1	-0.869	-0.918	4.861	-1.384	-1.384	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.059	-0.046	2.062	-2.943	-2.198	3.155	-1.764	-2.136	-0.006
55	B	64	THR	0	0.014	-0.018	4.710	1.031	1.142	-0.001	-0.016	-0.093	0.000
56	B	65	VAL	0	-0.033	-0.008	7.580	-0.073	-0.073	0.000	0.000	0.000	0.000
57	B	66	GLN	0	0.031	0.019	9.745	0.081	0.081	0.000	0.000	0.000	0.000
58	B	67	VAL	0	-0.047	-0.018	13.269	0.067	0.067	0.000	0.000	0.000	0.000
59	B	68	HIS	0	0.036	-0.007	15.109	0.004	0.004	0.000	0.000	0.000	0.000
60	B	69	TYR	0	-0.020	-0.026	16.360	0.023	0.023	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.920	0.946	20.560	0.051	0.051	0.000	0.000	0.000	0.000
62	B	71	MET	0	-0.029	-0.032	21.691	0.018	0.018	0.000	0.000	0.000	0.000
63	B	72	CYS	0	-0.105	-0.040	25.596	0.012	0.012	0.000	0.000	0.000	0.000
64	B	73	GLN	0	0.019	0.012	29.205	0.002	0.002	0.000	0.000	0.000	0.000
65	B	74	SER	0	0.046	0.036	27.899	0.006	0.006	0.000	0.000	0.000	0.000

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