FMO DATABASE

FMODB ID: M3Y1Z

Calculation Name: 2W4S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W4S

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-624397.474002
FMO2-HF: Nuclear repulsion	588588.471982
FMO2-HF: Total energy	-35809.002021
FMO2-MP2: Total energy	-35912.393033

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(A:387:ASP)

Summations of interaction energy for fragment #1(A:387:ASP)

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.
-64.276	-66.714	18.14	-7.153	-8.549	-0.001

Interaction energy analysis for fragmet #1(A:387:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.855 / q_NPA : -0.934

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	A	389	MET	0	0.023	0.012	3.845	-6.932	-4.901	0.005	-0.971	-1.065	0.005
4	A	390	GLU	-1	-0.896	-0.953	2.041	73.879	68.603	18.131	-5.873	-6.982	-0.007
5	A	391	SER	0	0.043	0.015	3.663	-12.460	-11.653	0.004	-0.309	-0.502	0.001
6	A	392	ILE	0	-0.044	-0.011	5.640	-6.392	-6.392	0.000	0.000	0.000	0.000
7	A	393	VAL	0	0.013	-0.003	7.313	-3.887	-3.887	0.000	0.000	0.000	0.000
8	A	394	LEU	0	-0.021	-0.002	7.000	-3.829	-3.829	0.000	0.000	0.000	0.000
9	A	395	ASN	0	0.015	-0.006	9.140	-3.689	-3.689	0.000	0.000	0.000	0.000
10	A	396	THR	0	-0.027	0.008	11.262	-2.993	-2.993	0.000	0.000	0.000	0.000
11	A	397	ILE	0	-0.005	-0.007	11.403	-1.901	-1.901	0.000	0.000	0.000	0.000
12	A	398	VAL	0	-0.061	-0.030	12.523	-1.423	-1.423	0.000	0.000	0.000	0.000
13	A	399	THR	0	0.021	0.006	14.858	-1.567	-1.567	0.000	0.000	0.000	0.000
14	A	400	GLY	0	-0.021	-0.015	16.729	-1.112	-1.112	0.000	0.000	0.000	0.000
15	A	401	LEU	0	-0.103	-0.067	16.821	-1.063	-1.063	0.000	0.000	0.000	0.000
16	A	402	GLN	0	-0.043	-0.007	19.006	-1.116	-1.116	0.000	0.000	0.000	0.000
17	A	403	GLU	-1	-0.854	-0.935	17.428	18.205	18.205	0.000	0.000	0.000	0.000
18	A	404	PRO	0	-0.002	0.012	16.455	-0.310	-0.310	0.000	0.000	0.000	0.000
19	A	405	LYS	1	0.835	0.883	15.700	-18.524	-18.524	0.000	0.000	0.000	0.000
20	A	406	LYS	1	0.978	1.018	9.884	-28.755	-28.755	0.000	0.000	0.000	0.000
21	A	407	GLU	-1	-0.823	-0.933	11.260	23.932	23.932	0.000	0.000	0.000	0.000
22	A	408	PHE	0	-0.021	-0.001	12.208	0.759	0.759	0.000	0.000	0.000	0.000
23	A	409	ILE	0	0.063	0.026	10.822	0.204	0.204	0.000	0.000	0.000	0.000
24	A	410	ALA	0	0.003	0.004	8.026	1.590	1.590	0.000	0.000	0.000	0.000
25	A	411	ARG	1	0.831	0.931	8.672	-18.668	-18.668	0.000	0.000	0.000	0.000
26	A	412	VAL	0	0.028	0.022	11.172	-0.608	-0.608	0.000	0.000	0.000	0.000
27	A	413	ILE	0	-0.036	-0.012	6.245	-1.042	-1.042	0.000	0.000	0.000	0.000
28	A	414	LYS	1	0.934	0.957	6.784	-36.345	-36.345	0.000	0.000	0.000	0.000
29	A	415	THR	0	-0.028	-0.002	8.400	-1.497	-1.497	0.000	0.000	0.000	0.000
30	A	416	ILE	0	-0.027	-0.007	11.794	-1.387	-1.387	0.000	0.000	0.000	0.000
31	A	417	GLY	0	0.055	0.035	8.349	-0.957	-0.957	0.000	0.000	0.000	0.000
32	A	418	SER	0	0.020	-0.018	5.787	-2.833	-2.833	0.000	0.000	0.000	0.000
33	A	419	GLN	0	0.016	0.009	8.461	-2.963	-2.963	0.000	0.000	0.000	0.000
34	A	420	ARG	1	1.019	1.008	11.511	-19.748	-19.748	0.000	0.000	0.000	0.000
35	A	421	SER	0	0.008	0.009	10.790	-1.286	-1.286	0.000	0.000	0.000	0.000
36	A	422	LEU	0	0.010	-0.001	11.227	-1.014	-1.014	0.000	0.000	0.000	0.000
37	A	423	GLN	0	0.019	0.019	13.691	-0.914	-0.914	0.000	0.000	0.000	0.000
38	A	424	LEU	0	-0.001	0.014	16.124	-1.062	-1.062	0.000	0.000	0.000	0.000
39	A	425	TYR	0	0.021	-0.001	15.663	-0.928	-0.928	0.000	0.000	0.000	0.000
40	A	426	GLU	-1	-0.927	-0.969	17.529	13.711	13.711	0.000	0.000	0.000	0.000
41	A	427	ASN	0	-0.037	-0.032	19.569	-1.478	-1.478	0.000	0.000	0.000	0.000
42	A	428	ALA	0	0.009	0.002	20.955	-0.715	-0.715	0.000	0.000	0.000	0.000
43	A	429	MET	0	-0.002	0.003	19.293	-0.606	-0.606	0.000	0.000	0.000	0.000
44	A	430	LYS	1	0.948	0.984	23.370	-13.272	-13.272	0.000	0.000	0.000	0.000
45	A	431	VAL	0	-0.003	0.009	25.598	-0.543	-0.543	0.000	0.000	0.000	0.000
46	A	432	GLU	-1	-0.876	-0.948	25.449	11.094	11.094	0.000	0.000	0.000	0.000
47	A	433	ASN	0	-0.024	-0.025	25.899	-0.445	-0.445	0.000	0.000	0.000	0.000
48	A	434	SER	0	-0.065	-0.013	29.201	-0.447	-0.447	0.000	0.000	0.000	0.000
49	A	435	GLY	0	-0.023	-0.009	31.471	-0.309	-0.309	0.000	0.000	0.000	0.000
50	A	436	GLY	0	-0.031	-0.009	29.731	-0.125	-0.125	0.000	0.000	0.000	0.000
51	A	437	LEU	0	0.020	-0.006	28.418	-0.176	-0.176	0.000	0.000	0.000	0.000
52	A	438	LEU	0	0.027	0.030	31.806	0.176	0.176	0.000	0.000	0.000	0.000
53	A	439	THR	0	-0.100	-0.069	31.939	0.269	0.269	0.000	0.000	0.000	0.000
54	A	440	ALA	0	0.004	-0.010	33.706	-0.184	-0.184	0.000	0.000	0.000	0.000
55	A	441	ASP	-1	-0.826	-0.898	35.465	8.531	8.531	0.000	0.000	0.000	0.000
56	A	442	MET	0	-0.054	-0.029	37.290	-0.244	-0.244	0.000	0.000	0.000	0.000
57	A	443	SER	0	-0.008	0.016	37.450	-0.083	-0.083	0.000	0.000	0.000	0.000
58	A	444	ARG	1	0.951	0.974	29.860	-10.131	-10.131	0.000	0.000	0.000	0.000
59	A	445	ARG	1	0.936	0.972	29.548	-10.283	-10.283	0.000	0.000	0.000	0.000
60	A	446	LYS	1	0.863	0.927	28.003	-10.710	-10.710	0.000	0.000	0.000	0.000
61	A	447	THR	0	0.049	0.027	25.431	-0.050	-0.050	0.000	0.000	0.000	0.000
62	A	448	ILE	0	0.128	0.059	21.727	0.043	0.043	0.000	0.000	0.000	0.000
63	A	449	GLY	0	0.039	0.025	21.267	0.412	0.412	0.000	0.000	0.000	0.000
64	A	450	GLY	0	-0.017	-0.014	22.294	0.254	0.254	0.000	0.000	0.000	0.000
65	A	451	VAL	0	-0.020	-0.005	24.272	-0.097	-0.097	0.000	0.000	0.000	0.000
66	A	452	PHE	0	0.037	0.013	15.257	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	453	CYS	0	-0.043	-0.024	20.866	0.405	0.405	0.000	0.000	0.000	0.000
68	A	454	TYR	0	-0.040	-0.016	22.062	-0.136	-0.136	0.000	0.000	0.000	0.000
69	A	455	LEU	0	0.059	0.016	21.626	-0.201	-0.201	0.000	0.000	0.000	0.000
70	A	456	LEU	0	-0.015	0.003	17.152	0.057	0.057	0.000	0.000	0.000	0.000
71	A	457	LYS	1	0.940	0.967	20.629	-11.222	-11.222	0.000	0.000	0.000	0.000
72	A	458	GLN	0	-0.011	-0.007	23.646	-0.408	-0.408	0.000	0.000	0.000	0.000
73	A	459	LEU	0	0.010	0.011	18.235	-0.095	-0.095	0.000	0.000	0.000	0.000
74	A	460	VAL	0	-0.029	-0.011	21.967	0.040	0.040	0.000	0.000	0.000	0.000
75	A	461	ALA	0	-0.069	-0.027	23.688	-0.316	-0.316	0.000	0.000	0.000	0.000
76	A	462	GLU	-1	-0.941	-0.966	24.485	10.925	10.925	0.000	0.000	0.000	0.000
77	A	463	ASP	-1	-0.946	-0.961	24.667	11.578	11.578	0.000	0.000	0.000	0.000
78	A	464	GLN	0	-0.106	-0.051	19.868	0.904	0.904	0.000	0.000	0.000	0.000
79	A	465	ILE	0	-0.061	-0.036	17.175	1.074	1.074	0.000	0.000	0.000	0.000
80	A	466	THR	0	0.045	0.017	19.873	-0.968	-0.968	0.000	0.000	0.000	0.000
81	A	467	ILE	0	0.053	0.002	21.040	0.485	0.485	0.000	0.000	0.000	0.000
82	A	468	GLN	0	-0.008	-0.006	19.276	0.670	0.670	0.000	0.000	0.000	0.000
83	A	469	GLU	-1	-0.791	-0.893	16.529	18.109	18.109	0.000	0.000	0.000	0.000
84	A	470	TRP	0	0.039	0.019	17.492	0.805	0.805	0.000	0.000	0.000	0.000
85	A	471	ASN	0	-0.020	-0.027	19.916	0.038	0.038	0.000	0.000	0.000	0.000
86	A	472	TYR	0	-0.020	-0.001	11.670	0.937	0.937	0.000	0.000	0.000	0.000
87	A	473	ILE	0	-0.002	-0.002	14.299	0.607	0.607	0.000	0.000	0.000	0.000
88	A	474	ARG	1	0.936	0.959	16.312	-13.343	-13.343	0.000	0.000	0.000	0.000
89	A	475	GLN	0	-0.057	0.002	18.262	-0.160	-0.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:387:ASP)