FMO DATABASE

FMODB ID: K9RN3

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-399551.862843
FMO2-HF: Nuclear repulsion	371924.762258
FMO2-HF: Total energy	-27627.100585
FMO2-MP2: Total energy	-27704.563582

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.
-6.781	-2.983	3.104	-3.101	-3.8	-0.006

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 : 0.069 / q_NPA : 0.035

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	0.028	0.004	3.316	-3.251	-0.426	0.036	-1.441	-1.419	0.003
4	B	4	PRO	0	-0.046	-0.009	5.275	0.642	0.642	0.000	0.000	0.000	0.000
5	B	5	ILE	0	0.009	0.003	7.755	-0.052	-0.052	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.816	-0.875	11.194	-0.527	-0.527	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.799	-0.874	13.788	-0.131	-0.131	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.021	-0.004	16.622	0.025	0.025	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.873	-0.938	19.783	-0.150	-0.150	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.861	-0.922	23.549	-0.134	-0.134	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.872	0.932	21.347	0.248	0.248	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.022	0.021	16.399	0.005	0.005	0.000	0.000	0.000	0.000
13	B	13	PHE	0	-0.019	-0.010	15.503	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	14	VAL	0	0.001	0.013	10.941	-0.029	-0.029	0.000	0.000	0.000	0.000
15	B	15	ASN	0	-0.029	-0.022	10.550	0.012	0.012	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.035	0.014	6.297	0.011	0.011	0.000	0.000	0.000	0.000
17	B	17	ASN	0	0.013	0.008	6.612	0.240	0.240	0.000	0.000	0.000	0.000
18	B	18	THR	0	0.000	-0.002	10.198	0.181	0.181	0.000	0.000	0.000	0.000
19	B	19	SER	0	0.001	0.002	12.668	-0.032	-0.032	0.000	0.000	0.000	0.000
20	B	20	ILE	0	0.018	0.004	11.875	-0.163	-0.163	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.030	-0.011	11.901	0.168	0.168	0.000	0.000	0.000	0.000
22	B	22	TRP	0	-0.004	-0.002	13.431	-0.091	-0.091	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.063	-0.033	13.038	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.914	-0.961	16.341	-0.258	-0.258	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.047	0.021	18.322	-0.030	-0.030	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.012	-0.017	20.268	0.004	0.004	0.000	0.000	0.000	0.000
27	B	27	VAL	0	0.028	0.026	19.717	-0.042	-0.042	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.032	0.020	19.977	-0.041	-0.041	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.050	-0.026	21.140	0.028	0.028	0.000	0.000	0.000	0.000
30	B	30	LEU	0	-0.010	-0.010	17.520	-0.026	-0.026	0.000	0.000	0.000	0.000
31	B	31	LEU	0	-0.014	-0.009	18.968	0.045	0.045	0.000	0.000	0.000	0.000
32	B	32	SER	0	0.022	-0.009	18.842	-0.047	-0.047	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.901	-0.945	18.796	-0.388	-0.388	0.000	0.000	0.000	0.000
34	B	34	ILE	0	-0.055	-0.018	17.895	0.006	0.006	0.000	0.000	0.000	0.000
35	B	35	THR	0	-0.021	-0.013	13.140	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.835	0.888	13.296	0.528	0.528	0.000	0.000	0.000	0.000
37	B	37	LEU	0	-0.025	-0.003	15.294	0.042	0.042	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.797	-0.879	16.676	-0.312	-0.312	0.000	0.000	0.000	0.000
39	B	39	LEU	0	-0.020	-0.019	15.710	0.019	0.019	0.000	0.000	0.000	0.000
40	B	40	GLY	0	0.019	0.015	19.848	0.032	0.032	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.820	0.878	21.963	0.143	0.143	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.892	0.920	21.607	0.124	0.124	0.000	0.000	0.000	0.000
43	B	43	ILE	0	-0.038	-0.026	22.914	0.006	0.006	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.046	-0.017	25.597	0.012	0.012	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.802	-0.874	23.396	-0.107	-0.107	0.000	0.000	0.000	0.000
46	B	46	PRO	0	-0.013	0.014	19.505	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	47	ARG	1	0.818	0.881	19.247	0.143	0.143	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.042	0.031	17.791	0.015	0.015	0.000	0.000	0.000	0.000
49	B	49	ILE	0	-0.040	-0.005	12.402	-0.024	-0.024	0.000	0.000	0.000	0.000
50	B	50	TYR	0	-0.008	-0.029	11.838	0.046	0.046	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.873	0.915	8.693	0.997	0.997	0.000	0.000	0.000	0.000
52	B	53	ASN	0	0.005	-0.007	7.058	-0.519	-0.519	0.000	0.000	0.000	0.000
53	B	62	GLU	-1	-0.793	-0.852	5.188	-1.584	-1.584	0.000	0.000	0.000	0.000
54	B	63	SER	0	-0.050	-0.042	1.997	-3.847	-3.025	3.069	-1.622	-2.269	-0.009
55	B	64	THR	0	-0.001	-0.040	4.289	1.182	1.333	-0.001	-0.038	-0.112	0.000
56	B	65	VAL	0	-0.056	-0.023	6.875	-0.121	-0.121	0.000	0.000	0.000	0.000
57	B	66	GLN	0	0.025	0.019	9.407	0.092	0.092	0.000	0.000	0.000	0.000
58	B	67	VAL	0	-0.015	-0.008	12.913	0.064	0.064	0.000	0.000	0.000	0.000
59	B	68	HIS	0	0.026	-0.008	15.112	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	69	TYR	0	-0.032	-0.030	16.617	0.032	0.032	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.929	0.948	20.783	0.031	0.031	0.000	0.000	0.000	0.000
62	B	71	MET	0	0.016	0.002	21.727	0.021	0.021	0.000	0.000	0.000	0.000
63	B	72	CYS	0	-0.095	-0.039	25.712	0.011	0.011	0.000	0.000	0.000	0.000
64	B	73	GLN	0	0.035	0.021	29.203	0.004	0.004	0.000	0.000	0.000	0.000
65	B	74	SER	0	-0.019	0.006	27.447	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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