FMO DATABASE

FMODB ID: 8983Y

Calculation Name: 2W2W-L-Xray372

Preferred Name: Phospholipase C-gamma-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2W2W

Chain ID: L

ChEMBL ID: CHEMBL4100

UniProt ID: P16885

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-480934.686407
FMO2-HF: Nuclear repulsion	450902.091843
FMO2-HF: Total energy	-30032.594564
FMO2-MP2: Total energy	-30120.833763

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(L:7:LYS)

Summations of interaction energy for fragment #1(L:7:LYS)

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.
-101.735	-98.903	12.93	-7.241	-8.522	-0.069

Interaction energy analysis for fragmet #1(L:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.932 / q_NPA : 0.962

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	L	9	GLN	0	-0.042	-0.046	1.818	-48.534	-48.323	12.415	-6.219	-6.407	-0.061
4	L	10	GLY	0	0.023	0.025	4.233	3.927	4.040	-0.001	-0.038	-0.075	0.000
5	L	11	GLU	-1	-0.981	-0.977	7.591	-22.570	-22.570	0.000	0.000	0.000	0.000
6	L	12	LEU	0	-0.029	-0.024	10.126	1.516	1.516	0.000	0.000	0.000	0.000
7	L	25	HIS	1	0.901	0.937	12.580	20.893	20.893	0.000	0.000	0.000	0.000
8	L	26	PHE	0	0.016	0.008	4.650	-1.123	-1.060	-0.001	-0.002	-0.060	0.000
9	L	27	CYS	0	-0.026	-0.012	7.403	2.122	2.122	0.000	0.000	0.000	0.000
10	L	28	ALA	0	-0.024	-0.020	2.551	-9.586	-9.145	0.371	-0.234	-0.578	-0.002
11	L	29	ILE	0	0.026	0.018	3.492	9.544	9.943	0.000	-0.065	-0.334	0.000
12	L	30	ALA	0	-0.021	-0.002	3.023	-11.437	-9.888	0.147	-0.676	-1.020	-0.006
13	L	31	ASP	-1	-0.895	-0.947	4.893	-24.644	-24.588	-0.001	-0.007	-0.048	0.000
14	L	32	ALA	0	0.004	0.007	7.900	0.042	0.042	0.000	0.000	0.000	0.000
15	L	33	LYS	1	0.802	0.884	8.523	24.842	24.842	0.000	0.000	0.000	0.000
16	L	34	LEU	0	0.022	0.018	7.608	-4.623	-4.623	0.000	0.000	0.000	0.000
17	L	35	SER	0	0.019	0.007	6.625	2.007	2.007	0.000	0.000	0.000	0.000
18	L	36	PHE	0	0.001	-0.007	8.182	-2.390	-2.390	0.000	0.000	0.000	0.000
19	L	37	SER	0	0.016	0.026	10.174	1.298	1.298	0.000	0.000	0.000	0.000
20	L	38	ASP	-1	-0.789	-0.872	11.781	-17.785	-17.785	0.000	0.000	0.000	0.000
21	L	52	SER	0	0.026	0.009	14.456	-0.099	-0.099	0.000	0.000	0.000	0.000
22	L	53	LEU	0	-0.038	-0.034	7.030	0.071	0.071	0.000	0.000	0.000	0.000
23	L	54	CYS	0	-0.015	-0.031	9.317	-3.648	-3.648	0.000	0.000	0.000	0.000
24	L	55	ARG	1	0.847	0.933	11.341	18.555	18.555	0.000	0.000	0.000	0.000
25	L	56	GLY	0	0.027	0.013	12.919	1.755	1.755	0.000	0.000	0.000	0.000
26	L	57	ILE	0	-0.009	-0.013	10.391	-2.454	-2.454	0.000	0.000	0.000	0.000
27	L	58	LEU	0	-0.020	0.005	12.037	2.018	2.018	0.000	0.000	0.000	0.000
28	L	59	ASP	-1	-0.727	-0.856	12.233	-21.983	-21.983	0.000	0.000	0.000	0.000
29	L	60	LEU	0	0.037	0.017	9.688	1.588	1.588	0.000	0.000	0.000	0.000
30	L	61	ASN	0	-0.056	-0.033	13.920	1.292	1.292	0.000	0.000	0.000	0.000
31	L	62	THR	0	-0.089	-0.046	16.230	1.099	1.099	0.000	0.000	0.000	0.000
32	L	63	TYR	0	-0.007	0.003	16.470	0.572	0.572	0.000	0.000	0.000	0.000
33	L	64	ASN	0	0.042	-0.003	17.794	-0.436	-0.436	0.000	0.000	0.000	0.000
34	L	65	VAL	0	-0.007	0.015	14.429	-0.059	-0.059	0.000	0.000	0.000	0.000
35	L	66	VAL	0	-0.016	0.008	17.632	0.535	0.535	0.000	0.000	0.000	0.000
36	L	67	LYS	1	0.923	0.964	18.717	14.474	14.474	0.000	0.000	0.000	0.000
37	L	68	ALA	0	0.009	0.008	20.822	0.681	0.681	0.000	0.000	0.000	0.000
38	L	69	PRO	0	-0.020	-0.005	23.938	-0.132	-0.132	0.000	0.000	0.000	0.000
39	L	70	GLN	0	-0.019	-0.016	25.847	0.091	0.091	0.000	0.000	0.000	0.000
40	L	71	GLY	0	0.045	0.044	24.402	0.129	0.129	0.000	0.000	0.000	0.000
41	L	72	LYS	1	0.818	0.865	24.159	12.916	12.916	0.000	0.000	0.000	0.000
42	L	73	ASN	0	-0.016	-0.016	25.032	-0.368	-0.368	0.000	0.000	0.000	0.000
43	L	74	GLN	0	0.003	0.002	26.268	-0.320	-0.320	0.000	0.000	0.000	0.000
44	L	75	LYS	1	0.956	0.999	19.855	15.601	15.601	0.000	0.000	0.000	0.000
45	L	76	SER	0	0.011	-0.003	23.619	0.110	0.110	0.000	0.000	0.000	0.000
46	L	77	PHE	0	-0.003	0.002	19.586	0.352	0.352	0.000	0.000	0.000	0.000
47	L	78	VAL	0	0.018	0.008	18.654	-0.732	-0.732	0.000	0.000	0.000	0.000
48	L	79	PHE	0	-0.036	-0.014	12.267	0.698	0.698	0.000	0.000	0.000	0.000
49	L	80	ILE	0	-0.003	-0.009	18.098	-0.294	-0.294	0.000	0.000	0.000	0.000
50	L	81	LEU	0	-0.010	-0.003	13.732	0.391	0.391	0.000	0.000	0.000	0.000
51	L	91	VAL	0	0.034	0.024	16.267	0.183	0.183	0.000	0.000	0.000	0.000
52	L	92	GLU	-1	-0.880	-0.935	18.562	-13.689	-13.689	0.000	0.000	0.000	0.000
53	L	93	PHE	0	0.026	0.023	12.714	-0.336	-0.336	0.000	0.000	0.000	0.000
54	L	94	ALA	0	0.033	-0.006	16.266	0.963	0.963	0.000	0.000	0.000	0.000
55	L	95	THR	0	-0.025	0.004	13.718	-0.990	-0.990	0.000	0.000	0.000	0.000
56	L	96	ASP	-1	-0.895	-0.955	16.333	-16.178	-16.178	0.000	0.000	0.000	0.000
57	L	97	LYS	1	0.820	0.898	15.919	20.621	20.621	0.000	0.000	0.000	0.000
58	L	98	VAL	0	0.014	0.004	17.519	-0.834	-0.834	0.000	0.000	0.000	0.000
59	L	99	GLU	-1	-0.837	-0.949	15.003	-17.103	-17.103	0.000	0.000	0.000	0.000
60	L	100	GLU	-1	-0.774	-0.866	12.775	-22.335	-22.335	0.000	0.000	0.000	0.000
61	L	101	LEU	0	-0.024	0.004	12.855	-1.211	-1.211	0.000	0.000	0.000	0.000
62	L	102	PHE	0	-0.037	-0.043	14.310	-0.097	-0.097	0.000	0.000	0.000	0.000
63	L	103	GLU	-1	-0.849	-0.898	7.931	-29.369	-29.369	0.000	0.000	0.000	0.000
64	L	104	TRP	0	-0.009	-0.004	6.528	-3.185	-3.185	0.000	0.000	0.000	0.000
65	L	105	PHE	0	-0.031	-0.025	10.861	0.557	0.557	0.000	0.000	0.000	0.000
66	L	106	GLN	0	-0.038	-0.029	10.717	1.829	1.829	0.000	0.000	0.000	0.000
67	L	107	SER	0	0.041	0.019	6.609	-0.582	-0.582	0.000	0.000	0.000	0.000
68	L	108	ILE	0	-0.011	-0.004	8.420	0.250	0.250	0.000	0.000	0.000	0.000
69	L	109	ARG	1	0.958	0.977	10.641	17.479	17.479	0.000	0.000	0.000	0.000
70	L	110	GLU	-1	-0.967	-0.960	9.783	-20.158	-20.158	0.000	0.000	0.000	0.000
71	L	111	ILE	0	-0.005	-0.008	6.772	-0.609	-0.609	0.000	0.000	0.000	0.000
72	L	112	THR	0	-0.048	-0.022	11.416	0.641	0.641	0.000	0.000	0.000	0.000
73	L	113	TRP	0	-0.079	-0.032	14.577	1.536	1.536	0.000	0.000	0.000	0.000
74	L	114	LYS	1	0.959	0.995	12.239	14.980	14.980	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:7:LYS)