FMO DATABASE

FMODB ID: R91R8

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	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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-399176.255038
FMO2-HF: Nuclear repulsion	371549.679976
FMO2-HF: Total energy	-27626.575062
FMO2-MP2: Total energy	-27704.066204

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.
-5.782	-3.297	3.716	-2.9	-3.301	-0.01

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 : -0.005 / q_NPA : -0.007

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	ILE	0	0.010	-0.005	3.493	-1.714	0.100	0.010	-0.764	-1.060	0.000
4	B	4	PRO	0	-0.042	-0.006	5.475	0.501	0.501	0.000	0.000	0.000	0.000
5	B	5	ILE	0	0.028	0.010	7.788	-0.006	-0.006	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.851	-0.899	11.301	-0.539	-0.539	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.803	-0.876	14.089	-0.039	-0.039	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.026	-0.012	17.045	0.009	0.009	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.926	-0.951	19.852	-0.150	-0.150	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.932	-0.972	23.171	-0.107	-0.107	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.873	0.936	21.075	0.188	0.188	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.007	0.014	16.258	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	13	PHE	0	0.007	0.007	15.426	0.004	0.004	0.000	0.000	0.000	0.000
14	B	14	VAL	0	-0.025	0.007	10.986	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	15	ASN	0	0.028	0.006	10.510	0.038	0.038	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.035	0.014	6.470	-0.219	-0.219	0.000	0.000	0.000	0.000
17	B	17	ASN	0	0.019	0.007	6.058	0.277	0.277	0.000	0.000	0.000	0.000
18	B	18	THR	0	0.016	0.008	10.019	0.222	0.222	0.000	0.000	0.000	0.000
19	B	19	SER	0	-0.024	-0.019	12.221	0.015	0.015	0.000	0.000	0.000	0.000
20	B	20	ILE	0	0.017	0.004	11.884	-0.117	-0.117	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.030	-0.004	12.319	0.108	0.108	0.000	0.000	0.000	0.000
22	B	22	TRP	0	-0.020	-0.003	13.612	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.062	-0.036	13.354	0.015	0.015	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.905	-0.966	16.470	0.104	0.104	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.037	0.025	18.239	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.008	-0.016	20.331	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	27	VAL	0	0.022	0.016	19.774	-0.018	-0.018	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.018	0.015	20.188	-0.028	-0.028	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.025	-0.011	21.295	0.016	0.016	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.004	-0.002	17.257	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.017	0.001	19.020	0.031	0.031	0.000	0.000	0.000	0.000
32	B	32	SER	0	0.003	-0.032	18.749	-0.046	-0.046	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.882	-0.928	18.718	-0.374	-0.374	0.000	0.000	0.000	0.000
34	B	34	ILE	0	-0.071	-0.019	17.666	-0.026	-0.026	0.000	0.000	0.000	0.000
35	B	35	THR	0	0.000	-0.001	13.453	-0.039	-0.039	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.816	0.873	13.586	0.548	0.548	0.000	0.000	0.000	0.000
37	B	37	LEU	0	-0.025	-0.005	15.069	0.050	0.050	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.803	-0.905	16.769	-0.222	-0.222	0.000	0.000	0.000	0.000
39	B	39	LEU	0	-0.041	-0.034	15.949	0.029	0.029	0.000	0.000	0.000	0.000
40	B	40	GLY	0	-0.012	-0.013	19.875	0.034	0.034	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.964	0.971	21.861	0.083	0.083	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.998	0.974	21.480	0.080	0.080	0.000	0.000	0.000	0.000
43	B	43	ILE	0	-0.068	-0.040	22.802	0.015	0.015	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.074	-0.035	25.393	0.009	0.009	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.827	-0.899	23.176	0.017	0.017	0.000	0.000	0.000	0.000
46	B	46	PRO	0	-0.004	0.025	19.533	0.008	0.008	0.000	0.000	0.000	0.000
47	B	47	ARG	1	0.852	0.901	19.031	-0.021	-0.021	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.042	0.028	17.613	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	49	ILE	0	-0.025	0.006	13.030	0.028	0.028	0.000	0.000	0.000	0.000
50	B	50	TYR	0	0.001	-0.015	11.894	-0.022	-0.022	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.947	0.982	8.598	0.038	0.038	0.000	0.000	0.000	0.000
52	B	53	ASN	0	0.033	0.009	7.108	-0.274	-0.274	0.000	0.000	0.000	0.000
53	B	62	GLU	-1	-0.936	-0.990	5.190	-0.313	-0.313	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.026	-0.003	1.913	-3.655	-3.079	3.707	-2.118	-2.165	-0.010
55	B	64	THR	0	-0.002	-0.023	4.675	-0.440	-0.345	-0.001	-0.018	-0.076	0.000
56	B	65	VAL	0	-0.028	-0.005	7.857	0.231	0.231	0.000	0.000	0.000	0.000
57	B	66	GLN	0	0.031	0.019	9.748	-0.013	-0.013	0.000	0.000	0.000	0.000
58	B	67	VAL	0	-0.044	-0.018	13.270	0.040	0.040	0.000	0.000	0.000	0.000
59	B	68	HIS	0	0.027	-0.010	15.109	0.005	0.005	0.000	0.000	0.000	0.000
60	B	69	TYR	0	-0.029	-0.026	16.254	0.015	0.015	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.924	0.952	20.432	-0.079	-0.079	0.000	0.000	0.000	0.000
62	B	71	MET	0	-0.022	-0.027	21.632	0.007	0.007	0.000	0.000	0.000	0.000
63	B	72	CYS	0	-0.095	-0.032	25.458	0.004	0.004	0.000	0.000	0.000	0.000
64	B	73	GLN	0	0.014	0.010	29.064	0.000	0.000	0.000	0.000	0.000	0.000
65	B	74	SER	0	0.031	0.028	27.737	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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