FMO DATABASE

FMODB ID: G5L91

Calculation Name: 2W2W-L-Xray372

Preferred Name: Phospholipase C-gamma-2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-480832.306514
FMO2-HF: Nuclear repulsion	450800.377235
FMO2-HF: Total energy	-30031.929279
FMO2-MP2: Total energy	-30120.221968

3D Structure Molmil

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.
-98.644	-95.537	11.216	-6.088	-8.235	-0.065

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 : 0.923 / q_NPA : 0.946

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	L	9	GLN	0	-0.039	-0.052	1.925	-45.909	-45.654	10.658	-4.950	-5.964	-0.055
4	L	10	GLY	0	0.004	0.020	3.999	3.784	3.981	0.000	-0.083	-0.114	0.000
5	L	11	GLU	-1	-0.945	-0.963	7.321	-22.955	-22.955	0.000	0.000	0.000	0.000
6	L	12	LEU	0	-0.009	-0.005	10.046	1.266	1.266	0.000	0.000	0.000	0.000
7	L	25	HIS	1	0.913	0.951	12.430	21.129	21.129	0.000	0.000	0.000	0.000
8	L	26	PHE	0	0.017	0.008	3.991	-1.346	-1.236	-0.001	-0.014	-0.095	0.000
9	L	27	CYS	0	-0.016	-0.010	7.211	2.228	2.228	0.000	0.000	0.000	0.000
10	L	28	ALA	0	-0.036	-0.025	2.570	-10.257	-9.750	0.381	-0.259	-0.629	-0.003
11	L	29	ILE	0	0.041	0.023	3.567	9.934	10.345	0.000	-0.060	-0.351	0.000
12	L	30	ALA	0	-0.019	0.000	2.946	-11.096	-9.517	0.179	-0.717	-1.041	-0.007
13	L	31	ASP	-1	-0.904	-0.952	4.940	-24.280	-24.232	-0.001	-0.005	-0.041	0.000
14	L	32	ALA	0	0.021	0.016	7.972	0.102	0.102	0.000	0.000	0.000	0.000
15	L	33	LYS	1	0.811	0.899	8.498	24.457	24.457	0.000	0.000	0.000	0.000
16	L	34	LEU	0	0.029	0.019	7.627	-4.583	-4.583	0.000	0.000	0.000	0.000
17	L	35	SER	0	-0.045	-0.016	6.272	3.033	3.033	0.000	0.000	0.000	0.000
18	L	36	PHE	0	0.028	0.009	8.093	-2.326	-2.326	0.000	0.000	0.000	0.000
19	L	37	SER	0	0.011	0.022	10.094	1.191	1.191	0.000	0.000	0.000	0.000
20	L	38	ASP	-1	-0.841	-0.923	11.639	-17.530	-17.530	0.000	0.000	0.000	0.000
21	L	52	SER	0	0.000	-0.004	14.305	-0.525	-0.525	0.000	0.000	0.000	0.000
22	L	53	LEU	0	0.034	0.002	7.129	0.315	0.315	0.000	0.000	0.000	0.000
23	L	54	CYS	0	-0.031	-0.034	9.245	-3.577	-3.577	0.000	0.000	0.000	0.000
24	L	55	ARG	1	0.871	0.951	11.313	18.525	18.525	0.000	0.000	0.000	0.000
25	L	56	GLY	0	0.026	0.013	12.886	1.795	1.795	0.000	0.000	0.000	0.000
26	L	57	ILE	0	0.000	-0.008	10.159	-2.490	-2.490	0.000	0.000	0.000	0.000
27	L	58	LEU	0	-0.037	-0.006	11.974	2.027	2.027	0.000	0.000	0.000	0.000
28	L	59	ASP	-1	-0.793	-0.898	12.234	-21.270	-21.270	0.000	0.000	0.000	0.000
29	L	60	LEU	0	0.029	-0.003	9.735	1.459	1.459	0.000	0.000	0.000	0.000
30	L	61	ASN	0	-0.002	0.001	13.858	0.905	0.905	0.000	0.000	0.000	0.000
31	L	62	THR	0	-0.091	-0.030	16.216	1.174	1.174	0.000	0.000	0.000	0.000
32	L	63	TYR	0	-0.019	-0.011	16.389	0.855	0.855	0.000	0.000	0.000	0.000
33	L	64	ASN	0	0.042	-0.004	17.812	-0.515	-0.515	0.000	0.000	0.000	0.000
34	L	65	VAL	0	0.000	0.016	14.445	-0.089	-0.089	0.000	0.000	0.000	0.000
35	L	66	VAL	0	-0.027	0.005	17.614	0.578	0.578	0.000	0.000	0.000	0.000
36	L	67	LYS	1	0.932	0.962	18.697	13.700	13.700	0.000	0.000	0.000	0.000
37	L	68	ALA	0	0.000	0.004	20.801	0.678	0.678	0.000	0.000	0.000	0.000
38	L	69	PRO	0	-0.042	-0.012	23.916	-0.141	-0.141	0.000	0.000	0.000	0.000
39	L	70	GLN	0	0.036	0.012	25.825	-0.159	-0.159	0.000	0.000	0.000	0.000
40	L	71	GLY	0	0.031	0.042	24.261	0.117	0.117	0.000	0.000	0.000	0.000
41	L	72	LYS	1	0.866	0.914	24.107	12.803	12.803	0.000	0.000	0.000	0.000
42	L	73	ASN	0	-0.019	-0.009	24.880	-0.640	-0.640	0.000	0.000	0.000	0.000
43	L	74	GLN	0	0.011	0.002	26.099	-0.330	-0.330	0.000	0.000	0.000	0.000
44	L	75	LYS	1	0.968	0.997	20.426	14.961	14.961	0.000	0.000	0.000	0.000
45	L	76	SER	0	0.030	-0.003	23.647	0.228	0.228	0.000	0.000	0.000	0.000
46	L	77	PHE	0	0.000	0.015	19.275	0.407	0.407	0.000	0.000	0.000	0.000
47	L	78	VAL	0	0.020	0.008	18.515	-0.752	-0.752	0.000	0.000	0.000	0.000
48	L	79	PHE	0	-0.035	-0.020	12.310	0.720	0.720	0.000	0.000	0.000	0.000
49	L	80	ILE	0	-0.017	-0.014	18.023	-0.215	-0.215	0.000	0.000	0.000	0.000
50	L	81	LEU	0	0.024	0.020	13.658	0.200	0.200	0.000	0.000	0.000	0.000
51	L	91	VAL	0	0.041	0.026	16.188	0.165	0.165	0.000	0.000	0.000	0.000
52	L	92	GLU	-1	-0.944	-0.995	18.534	-13.705	-13.705	0.000	0.000	0.000	0.000
53	L	93	PHE	0	0.012	0.015	13.152	-0.449	-0.449	0.000	0.000	0.000	0.000
54	L	94	ALA	0	0.003	-0.027	16.083	1.042	1.042	0.000	0.000	0.000	0.000
55	L	95	THR	0	-0.025	0.005	13.768	-0.774	-0.774	0.000	0.000	0.000	0.000
56	L	96	ASP	-1	-0.910	-0.954	16.127	-17.167	-17.167	0.000	0.000	0.000	0.000
57	L	97	LYS	1	0.830	0.906	15.953	20.492	20.492	0.000	0.000	0.000	0.000
58	L	98	VAL	0	0.026	0.008	17.373	-0.818	-0.818	0.000	0.000	0.000	0.000
59	L	99	GLU	-1	-0.865	-0.960	14.757	-16.545	-16.545	0.000	0.000	0.000	0.000
60	L	100	GLU	-1	-0.806	-0.887	12.650	-22.507	-22.507	0.000	0.000	0.000	0.000
61	L	101	LEU	0	-0.034	0.000	12.934	-1.063	-1.063	0.000	0.000	0.000	0.000
62	L	102	PHE	0	-0.029	-0.041	14.389	-0.056	-0.056	0.000	0.000	0.000	0.000
63	L	103	GLU	-1	-0.902	-0.940	7.703	-27.588	-27.588	0.000	0.000	0.000	0.000
64	L	104	TRP	0	-0.012	-0.010	6.100	-3.000	-3.000	0.000	0.000	0.000	0.000
65	L	105	PHE	0	-0.014	-0.025	10.838	0.555	0.555	0.000	0.000	0.000	0.000
66	L	106	GLN	0	-0.083	-0.052	10.997	1.802	1.802	0.000	0.000	0.000	0.000
67	L	107	SER	0	0.040	0.023	6.586	-0.221	-0.221	0.000	0.000	0.000	0.000
68	L	108	ILE	0	-0.015	-0.004	8.404	0.221	0.221	0.000	0.000	0.000	0.000
69	L	109	ARG	1	0.994	0.997	10.624	16.614	16.614	0.000	0.000	0.000	0.000
70	L	110	GLU	-1	-0.966	-0.956	9.677	-19.285	-19.285	0.000	0.000	0.000	0.000
71	L	111	ILE	0	-0.001	-0.008	6.994	-0.551	-0.551	0.000	0.000	0.000	0.000
72	L	112	THR	0	-0.046	-0.020	11.409	0.562	0.562	0.000	0.000	0.000	0.000
73	L	113	TRP	0	-0.066	-0.024	14.567	1.467	1.467	0.000	0.000	0.000	0.000
74	L	114	LYS	1	0.947	0.986	12.238	14.579	14.579	0.000	0.000	0.000	0.000

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