FMO DATABASE

FMODB ID: NNV5Q

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	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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-483215.323912
FMO2-HF: Nuclear repulsion	453182.468599
FMO2-HF: Total energy	-30032.855313
FMO2-MP2: Total energy	-30121.069412

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.
-129.195	-124.694	18.65	-11.285	-11.864	-0.117

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 : 0.910 / q_NPA : 0.951

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	-0.017	-0.018	1.731	-68.662	-68.466	16.121	-8.427	-7.890	-0.090
4	L	10	GLY	0	0.014	0.018	4.336	5.901	5.985	0.000	-0.028	-0.055	0.000
5	L	11	GLU	-1	-0.970	-0.973	7.870	-23.246	-23.246	0.000	0.000	0.000	0.000
6	L	12	LEU	0	-0.061	-0.044	9.950	1.578	1.578	0.000	0.000	0.000	0.000
7	L	25	HIS	1	0.917	0.946	12.387	21.262	21.262	0.000	0.000	0.000	0.000
8	L	26	PHE	0	0.052	0.034	5.005	-1.384	-1.384	0.000	0.000	0.000	0.000
9	L	27	CYS	0	-0.045	-0.026	7.395	2.610	2.610	0.000	0.000	0.000	0.000
10	L	28	ALA	0	-0.023	-0.021	2.073	-8.095	-8.113	1.355	-0.500	-0.837	-0.002
11	L	29	ILE	0	0.019	0.012	2.752	12.225	13.047	0.032	-0.245	-0.609	-0.001
12	L	30	ALA	0	-0.021	-0.012	2.603	-26.335	-23.026	1.142	-2.058	-2.393	-0.024
13	L	31	ASP	-1	-0.893	-0.948	4.249	-25.728	-25.620	0.000	-0.027	-0.080	0.000
14	L	32	ALA	0	0.011	0.007	7.441	0.839	0.839	0.000	0.000	0.000	0.000
15	L	33	LYS	1	0.794	0.890	8.042	26.455	26.455	0.000	0.000	0.000	0.000
16	L	34	LEU	0	0.036	0.024	7.164	-5.502	-5.502	0.000	0.000	0.000	0.000
17	L	35	SER	0	0.012	0.008	6.021	2.551	2.551	0.000	0.000	0.000	0.000
18	L	36	PHE	0	-0.002	-0.010	7.408	-3.388	-3.388	0.000	0.000	0.000	0.000
19	L	37	SER	0	0.062	0.026	9.860	1.410	1.410	0.000	0.000	0.000	0.000
20	L	38	ASP	-1	-0.821	-0.872	11.673	-17.681	-17.681	0.000	0.000	0.000	0.000
21	L	52	SER	0	0.036	0.016	14.106	-0.076	-0.076	0.000	0.000	0.000	0.000
22	L	53	LEU	0	-0.028	-0.026	7.143	0.047	0.047	0.000	0.000	0.000	0.000
23	L	54	CYS	0	-0.023	-0.023	9.425	-3.302	-3.302	0.000	0.000	0.000	0.000
24	L	55	ARG	1	0.819	0.909	11.151	19.487	19.487	0.000	0.000	0.000	0.000
25	L	56	GLY	0	0.003	-0.002	12.637	1.890	1.890	0.000	0.000	0.000	0.000
26	L	57	ILE	0	-0.001	-0.013	9.930	-2.639	-2.639	0.000	0.000	0.000	0.000
27	L	58	LEU	0	-0.019	0.008	11.515	2.208	2.208	0.000	0.000	0.000	0.000
28	L	59	ASP	-1	-0.742	-0.859	11.834	-23.466	-23.466	0.000	0.000	0.000	0.000
29	L	60	LEU	0	0.036	0.019	9.441	1.705	1.705	0.000	0.000	0.000	0.000
30	L	61	ASN	0	-0.053	-0.038	13.519	1.612	1.612	0.000	0.000	0.000	0.000
31	L	62	THR	0	-0.093	-0.048	16.284	1.174	1.174	0.000	0.000	0.000	0.000
32	L	63	TYR	0	0.015	0.008	15.939	0.499	0.499	0.000	0.000	0.000	0.000
33	L	64	ASN	0	0.049	0.013	17.376	-0.290	-0.290	0.000	0.000	0.000	0.000
34	L	65	VAL	0	-0.007	0.026	14.207	0.044	0.044	0.000	0.000	0.000	0.000
35	L	66	VAL	0	-0.001	0.011	17.368	0.595	0.595	0.000	0.000	0.000	0.000
36	L	67	LYS	1	0.886	0.947	18.007	14.951	14.951	0.000	0.000	0.000	0.000
37	L	68	ALA	0	-0.001	0.006	20.452	0.699	0.699	0.000	0.000	0.000	0.000
38	L	69	PRO	0	-0.018	-0.008	23.560	-0.132	-0.132	0.000	0.000	0.000	0.000
39	L	70	GLN	0	-0.028	-0.017	25.568	0.194	0.194	0.000	0.000	0.000	0.000
40	L	71	GLY	0	0.043	0.038	23.893	0.146	0.146	0.000	0.000	0.000	0.000
41	L	72	LYS	1	0.820	0.871	23.453	13.298	13.298	0.000	0.000	0.000	0.000
42	L	73	ASN	0	0.004	-0.013	24.483	-0.246	-0.246	0.000	0.000	0.000	0.000
43	L	74	GLN	0	0.007	0.004	25.684	-0.355	-0.355	0.000	0.000	0.000	0.000
44	L	75	LYS	1	0.922	0.989	19.924	15.838	15.838	0.000	0.000	0.000	0.000
45	L	76	SER	0	0.032	0.002	23.579	0.087	0.087	0.000	0.000	0.000	0.000
46	L	77	PHE	0	-0.001	-0.001	19.083	0.218	0.218	0.000	0.000	0.000	0.000
47	L	78	VAL	0	0.010	0.002	18.234	-0.671	-0.671	0.000	0.000	0.000	0.000
48	L	79	PHE	0	-0.029	-0.013	11.745	0.790	0.790	0.000	0.000	0.000	0.000
49	L	80	ILE	0	0.003	0.002	17.722	-0.257	-0.257	0.000	0.000	0.000	0.000
50	L	81	LEU	0	-0.012	-0.012	13.032	0.639	0.639	0.000	0.000	0.000	0.000
51	L	91	VAL	0	0.031	0.022	15.989	0.197	0.197	0.000	0.000	0.000	0.000
52	L	92	GLU	-1	-0.891	-0.930	17.745	-14.187	-14.187	0.000	0.000	0.000	0.000
53	L	93	PHE	0	0.016	0.009	12.379	-0.470	-0.470	0.000	0.000	0.000	0.000
54	L	94	ALA	0	0.014	-0.006	15.959	0.801	0.801	0.000	0.000	0.000	0.000
55	L	95	THR	0	-0.017	0.010	13.671	-1.167	-1.167	0.000	0.000	0.000	0.000
56	L	96	ASP	-1	-0.869	-0.939	16.348	-15.958	-15.958	0.000	0.000	0.000	0.000
57	L	97	LYS	1	0.815	0.904	15.941	20.505	20.505	0.000	0.000	0.000	0.000
58	L	98	VAL	0	0.023	0.017	17.268	-0.816	-0.816	0.000	0.000	0.000	0.000
59	L	99	GLU	-1	-0.814	-0.934	14.334	-17.545	-17.545	0.000	0.000	0.000	0.000
60	L	100	GLU	-1	-0.763	-0.874	12.349	-22.426	-22.426	0.000	0.000	0.000	0.000
61	L	101	LEU	0	-0.036	-0.002	12.538	-1.432	-1.432	0.000	0.000	0.000	0.000
62	L	102	PHE	0	-0.019	-0.028	14.262	-0.070	-0.070	0.000	0.000	0.000	0.000
63	L	103	GLU	-1	-0.838	-0.892	7.645	-30.037	-30.037	0.000	0.000	0.000	0.000
64	L	104	TRP	0	0.010	0.003	6.236	-2.979	-2.979	0.000	0.000	0.000	0.000
65	L	105	PHE	0	-0.001	-0.014	10.598	0.222	0.222	0.000	0.000	0.000	0.000
66	L	106	GLN	0	-0.030	-0.020	10.802	1.916	1.916	0.000	0.000	0.000	0.000
67	L	107	SER	0	0.019	0.001	6.558	-0.679	-0.679	0.000	0.000	0.000	0.000
68	L	108	ILE	0	-0.014	-0.002	8.328	-0.609	-0.609	0.000	0.000	0.000	0.000
69	L	109	ARG	1	0.898	0.948	10.471	18.188	18.188	0.000	0.000	0.000	0.000
70	L	110	GLU	-1	-0.902	-0.940	9.793	-20.299	-20.299	0.000	0.000	0.000	0.000
71	L	111	ILE	0	-0.011	0.021	6.897	-0.321	-0.321	0.000	0.000	0.000	0.000
72	L	112	THR	0	-0.050	-0.046	11.348	0.981	0.981	0.000	0.000	0.000	0.000
73	L	113	TRP	0	-0.070	-0.026	14.487	1.638	1.638	0.000	0.000	0.000	0.000
74	L	114	LYS	1	0.912	0.954	12.313	15.855	15.855	0.000	0.000	0.000	0.000

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