FMO DATABASE

FMODB ID: 7G7VK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-624328.139427
FMO2-HF: Nuclear repulsion	588518.599453
FMO2-HF: Total energy	-35809.539973
FMO2-MP2: Total energy	-35912.896451

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.
-93.622	-86.022	4.106	-5.745	-5.959	-0.008

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 : -0.870 / q_NPA : -0.945

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	A	389	MET	0	0.019	0.005	3.529	-7.164	-5.246	0.005	-0.864	-1.059	0.004
4	A	390	GLU	-1	-0.900	-0.952	2.076	44.439	49.118	4.096	-4.536	-4.238	-0.014
5	A	391	SER	0	0.038	0.019	3.705	-11.940	-11.029	0.006	-0.339	-0.578	0.002
6	A	392	ILE	0	0.004	0.006	5.540	-6.662	-6.570	-0.001	-0.006	-0.084	0.000
7	A	393	VAL	0	0.012	0.015	7.358	-3.867	-3.867	0.000	0.000	0.000	0.000
8	A	394	LEU	0	-0.015	0.001	6.732	-3.639	-3.639	0.000	0.000	0.000	0.000
9	A	395	ASN	0	0.028	0.001	9.007	-5.242	-5.242	0.000	0.000	0.000	0.000
10	A	396	THR	0	-0.026	0.006	11.295	-2.874	-2.874	0.000	0.000	0.000	0.000
11	A	397	ILE	0	0.000	-0.004	11.596	-1.859	-1.859	0.000	0.000	0.000	0.000
12	A	398	VAL	0	-0.075	-0.035	12.316	-1.374	-1.374	0.000	0.000	0.000	0.000
13	A	399	THR	0	0.029	0.002	14.787	-1.467	-1.467	0.000	0.000	0.000	0.000
14	A	400	GLY	0	-0.032	-0.012	16.759	-1.131	-1.131	0.000	0.000	0.000	0.000
15	A	401	LEU	0	-0.105	-0.070	17.000	-1.090	-1.090	0.000	0.000	0.000	0.000
16	A	402	GLN	0	-0.039	-0.013	18.946	-1.216	-1.216	0.000	0.000	0.000	0.000
17	A	403	GLU	-1	-0.861	-0.930	17.110	18.209	18.209	0.000	0.000	0.000	0.000
18	A	404	PRO	0	0.003	0.017	16.382	-0.370	-0.370	0.000	0.000	0.000	0.000
19	A	405	LYS	1	0.829	0.874	15.770	-18.390	-18.390	0.000	0.000	0.000	0.000
20	A	406	LYS	1	0.908	0.973	9.430	-28.552	-28.552	0.000	0.000	0.000	0.000
21	A	407	GLU	-1	-0.802	-0.913	11.258	23.102	23.102	0.000	0.000	0.000	0.000
22	A	408	PHE	0	-0.002	0.007	12.371	0.605	0.605	0.000	0.000	0.000	0.000
23	A	409	ILE	0	0.051	0.020	10.903	0.130	0.130	0.000	0.000	0.000	0.000
24	A	410	ALA	0	0.007	0.002	8.085	1.449	1.449	0.000	0.000	0.000	0.000
25	A	411	ARG	1	0.830	0.926	9.072	-18.373	-18.373	0.000	0.000	0.000	0.000
26	A	412	VAL	0	0.024	0.025	11.558	-0.618	-0.618	0.000	0.000	0.000	0.000
27	A	413	ILE	0	-0.026	-0.008	6.371	-0.717	-0.717	0.000	0.000	0.000	0.000
28	A	414	LYS	1	0.926	0.952	6.594	-36.764	-36.764	0.000	0.000	0.000	0.000
29	A	415	THR	0	-0.032	-0.011	9.032	-1.309	-1.309	0.000	0.000	0.000	0.000
30	A	416	ILE	0	-0.027	-0.009	12.048	-1.240	-1.240	0.000	0.000	0.000	0.000
31	A	417	GLY	0	0.068	0.040	8.358	-0.883	-0.883	0.000	0.000	0.000	0.000
32	A	418	SER	0	0.022	-0.006	5.816	-2.492	-2.492	0.000	0.000	0.000	0.000
33	A	419	GLN	0	0.018	0.009	8.491	-2.243	-2.243	0.000	0.000	0.000	0.000
34	A	420	ARG	1	1.003	0.998	11.089	-18.657	-18.657	0.000	0.000	0.000	0.000
35	A	421	SER	0	0.001	-0.004	10.853	-1.091	-1.091	0.000	0.000	0.000	0.000
36	A	422	LEU	0	0.009	0.001	11.144	-0.887	-0.887	0.000	0.000	0.000	0.000
37	A	423	GLN	0	0.000	0.008	13.729	-0.853	-0.853	0.000	0.000	0.000	0.000
38	A	424	LEU	0	0.013	0.028	16.149	-0.972	-0.972	0.000	0.000	0.000	0.000
39	A	425	TYR	0	0.015	-0.013	15.510	-0.544	-0.544	0.000	0.000	0.000	0.000
40	A	426	GLU	-1	-0.829	-0.902	17.561	12.834	12.834	0.000	0.000	0.000	0.000
41	A	427	ASN	0	-0.004	-0.023	19.608	-1.359	-1.359	0.000	0.000	0.000	0.000
42	A	428	ALA	0	0.009	0.005	20.943	-0.672	-0.672	0.000	0.000	0.000	0.000
43	A	429	MET	0	-0.009	0.000	19.119	-0.563	-0.563	0.000	0.000	0.000	0.000
44	A	430	LYS	1	0.844	0.918	22.544	-13.294	-13.294	0.000	0.000	0.000	0.000
45	A	431	VAL	0	-0.001	0.018	25.633	-0.532	-0.532	0.000	0.000	0.000	0.000
46	A	432	GLU	-1	-0.848	-0.915	25.672	10.739	10.739	0.000	0.000	0.000	0.000
47	A	433	ASN	0	-0.035	-0.032	25.821	-0.425	-0.425	0.000	0.000	0.000	0.000
48	A	434	SER	0	-0.062	-0.025	29.240	-0.408	-0.408	0.000	0.000	0.000	0.000
49	A	435	GLY	0	-0.023	-0.012	31.505	-0.304	-0.304	0.000	0.000	0.000	0.000
50	A	436	GLY	0	-0.007	-0.002	29.764	-0.126	-0.126	0.000	0.000	0.000	0.000
51	A	437	LEU	0	0.002	-0.011	28.967	-0.185	-0.185	0.000	0.000	0.000	0.000
52	A	438	LEU	0	0.065	0.047	31.829	0.183	0.183	0.000	0.000	0.000	0.000
53	A	439	THR	0	-0.064	-0.046	32.059	0.290	0.290	0.000	0.000	0.000	0.000
54	A	440	ALA	0	-0.007	-0.012	33.948	-0.185	-0.185	0.000	0.000	0.000	0.000
55	A	441	ASP	-1	-0.781	-0.844	35.760	8.475	8.475	0.000	0.000	0.000	0.000
56	A	442	MET	0	-0.060	-0.031	37.535	-0.239	-0.239	0.000	0.000	0.000	0.000
57	A	443	SER	0	-0.019	-0.020	37.796	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	444	ARG	1	0.911	0.951	29.824	-10.028	-10.028	0.000	0.000	0.000	0.000
59	A	445	ARG	1	0.894	0.953	29.472	-10.197	-10.197	0.000	0.000	0.000	0.000
60	A	446	LYS	1	0.812	0.887	28.301	-10.164	-10.164	0.000	0.000	0.000	0.000
61	A	447	THR	0	0.057	0.026	25.863	-0.068	-0.068	0.000	0.000	0.000	0.000
62	A	448	ILE	0	0.115	0.051	21.987	0.034	0.034	0.000	0.000	0.000	0.000
63	A	449	GLY	0	0.043	0.029	21.422	0.366	0.366	0.000	0.000	0.000	0.000
64	A	450	GLY	0	-0.004	-0.002	22.456	0.232	0.232	0.000	0.000	0.000	0.000
65	A	451	VAL	0	-0.024	-0.013	24.310	-0.113	-0.113	0.000	0.000	0.000	0.000
66	A	452	PHE	0	0.032	0.014	15.313	0.004	0.004	0.000	0.000	0.000	0.000
67	A	453	CYS	0	-0.049	-0.026	21.095	0.385	0.385	0.000	0.000	0.000	0.000
68	A	454	TYR	0	-0.030	-0.014	22.407	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	455	LEU	0	0.057	0.015	21.704	-0.168	-0.168	0.000	0.000	0.000	0.000
70	A	456	LEU	0	-0.001	0.005	17.481	0.040	0.040	0.000	0.000	0.000	0.000
71	A	457	LYS	1	0.944	0.966	20.879	-10.880	-10.880	0.000	0.000	0.000	0.000
72	A	458	GLN	0	-0.021	-0.013	24.060	-0.464	-0.464	0.000	0.000	0.000	0.000
73	A	459	LEU	0	0.017	0.016	18.310	-0.113	-0.113	0.000	0.000	0.000	0.000
74	A	460	VAL	0	-0.033	-0.013	22.316	0.029	0.029	0.000	0.000	0.000	0.000
75	A	461	ALA	0	-0.066	-0.026	24.022	-0.307	-0.307	0.000	0.000	0.000	0.000
76	A	462	GLU	-1	-0.943	-0.966	24.496	10.628	10.628	0.000	0.000	0.000	0.000
77	A	463	ASP	-1	-0.934	-0.955	24.779	11.311	11.311	0.000	0.000	0.000	0.000
78	A	464	GLN	0	-0.116	-0.055	20.025	0.876	0.876	0.000	0.000	0.000	0.000
79	A	465	ILE	0	-0.054	-0.033	17.304	1.044	1.044	0.000	0.000	0.000	0.000
80	A	466	THR	0	0.031	-0.018	20.184	-0.880	-0.880	0.000	0.000	0.000	0.000
81	A	467	ILE	0	0.044	-0.001	21.664	0.471	0.471	0.000	0.000	0.000	0.000
82	A	468	GLN	0	-0.013	-0.010	20.319	0.616	0.616	0.000	0.000	0.000	0.000
83	A	469	GLU	-1	-0.754	-0.848	17.091	17.149	17.149	0.000	0.000	0.000	0.000
84	A	470	TRP	0	0.035	0.018	18.029	0.758	0.758	0.000	0.000	0.000	0.000
85	A	471	ASN	0	-0.019	-0.024	20.376	0.087	0.087	0.000	0.000	0.000	0.000
86	A	472	TYR	0	-0.021	0.002	12.112	0.790	0.790	0.000	0.000	0.000	0.000
87	A	473	ILE	0	0.012	0.001	14.762	0.608	0.608	0.000	0.000	0.000	0.000
88	A	474	ARG	1	0.916	0.962	16.726	-12.947	-12.947	0.000	0.000	0.000	0.000
89	A	475	GLN	0	-0.056	0.002	18.518	-0.299	-0.299	0.000	0.000	0.000	0.000

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