FMO DATABASE

FMODB ID: ZV54N

Calculation Name: 2VWR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VWR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N448

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-633662.472832
FMO2-HF: Nuclear repulsion	598044.130177
FMO2-HF: Total energy	-35618.342655
FMO2-MP2: Total energy	-35723.954018

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:-1:SER)

Summations of interaction energy for fragment #1(A:-1:SER)

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.
-1.217	2.17	-0.016	-1.616	-1.754	0.002

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.005

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	336	GLU	-1	-0.826	-0.875	3.857	-1.527	0.946	-0.018	-1.335	-1.120	0.002
4	A	337	ILE	0	-0.032	-0.027	6.155	-0.269	-0.269	0.000	0.000	0.000	0.000
5	A	338	LEU	0	-0.007	0.008	9.286	0.202	0.202	0.000	0.000	0.000	0.000
6	A	339	GLN	0	-0.005	-0.004	12.546	-0.033	-0.033	0.000	0.000	0.000	0.000
7	A	340	VAL	0	-0.018	0.004	16.226	0.041	0.041	0.000	0.000	0.000	0.000
8	A	341	ALA	0	-0.064	-0.032	18.744	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	342	LEU	0	0.034	0.030	22.330	0.020	0.020	0.000	0.000	0.000	0.000
10	A	343	HIS	0	-0.037	-0.054	24.837	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	344	LYS	1	0.786	0.914	28.582	0.152	0.152	0.000	0.000	0.000	0.000
12	A	345	ARG	1	0.889	0.931	31.185	0.081	0.081	0.000	0.000	0.000	0.000
13	A	346	ASP	-1	-0.837	-0.915	34.409	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	347	SER	0	-0.037	-0.019	34.462	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	348	GLY	0	-0.009	-0.013	34.446	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	349	GLU	-1	-0.854	-0.923	31.505	-0.106	-0.106	0.000	0.000	0.000	0.000
17	A	350	GLN	0	-0.004	-0.007	29.955	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	351	LEU	0	0.029	0.002	24.128	0.005	0.005	0.000	0.000	0.000	0.000
19	A	352	GLY	0	0.015	0.018	25.726	0.003	0.003	0.000	0.000	0.000	0.000
20	A	353	ILE	0	0.022	0.005	21.070	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	354	LYS	1	0.799	0.893	22.782	0.199	0.199	0.000	0.000	0.000	0.000
22	A	355	LEU	0	0.007	0.008	20.173	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	356	VAL	0	-0.017	-0.012	18.774	0.035	0.035	0.000	0.000	0.000	0.000
24	A	357	ARG	1	0.880	0.904	19.074	0.254	0.254	0.000	0.000	0.000	0.000
25	A	358	ARG	1	0.837	0.909	11.218	0.949	0.949	0.000	0.000	0.000	0.000
26	A	359	THR	0	-0.039	-0.035	17.992	0.043	0.043	0.000	0.000	0.000	0.000
27	A	360	ASP	-1	-0.891	-0.932	14.867	-0.584	-0.584	0.000	0.000	0.000	0.000
28	A	361	GLU	-1	-0.820	-0.898	11.127	-1.424	-1.424	0.000	0.000	0.000	0.000
29	A	362	PRO	0	-0.031	-0.011	13.812	0.058	0.058	0.000	0.000	0.000	0.000
30	A	363	GLY	0	0.026	-0.001	14.564	-0.112	-0.112	0.000	0.000	0.000	0.000
31	A	364	VAL	0	-0.031	-0.004	16.552	0.064	0.064	0.000	0.000	0.000	0.000
32	A	365	PHE	0	-0.009	-0.007	11.880	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	366	ILE	0	0.008	0.014	16.165	0.086	0.086	0.000	0.000	0.000	0.000
34	A	367	LEU	0	-0.002	0.011	16.721	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	368	ASP	-1	-0.797	-0.886	18.847	-0.203	-0.203	0.000	0.000	0.000	0.000
36	A	369	LEU	0	0.021	0.010	19.778	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	370	LEU	0	-0.052	-0.026	23.048	0.016	0.016	0.000	0.000	0.000	0.000
38	A	371	GLU	-1	-0.880	-0.950	26.870	-0.068	-0.068	0.000	0.000	0.000	0.000
39	A	372	GLY	0	0.003	0.006	28.694	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	373	GLY	0	0.020	0.020	27.969	0.003	0.003	0.000	0.000	0.000	0.000
41	A	374	LEU	0	-0.002	-0.002	26.610	0.001	0.001	0.000	0.000	0.000	0.000
42	A	375	ALA	0	0.016	-0.003	21.669	0.005	0.005	0.000	0.000	0.000	0.000
43	A	376	ALA	0	-0.019	0.000	22.158	0.001	0.001	0.000	0.000	0.000	0.000
44	A	377	GLN	0	-0.081	-0.048	24.270	0.020	0.020	0.000	0.000	0.000	0.000
45	A	378	ASP	-1	-0.810	-0.873	20.496	-0.137	-0.137	0.000	0.000	0.000	0.000
46	A	379	GLY	0	0.014	0.008	20.771	0.014	0.014	0.000	0.000	0.000	0.000
47	A	380	ARG	1	0.808	0.877	16.517	0.146	0.146	0.000	0.000	0.000	0.000
48	A	381	LEU	0	-0.026	-0.006	15.485	-0.047	-0.047	0.000	0.000	0.000	0.000
49	A	382	SER	0	0.022	0.003	13.879	0.093	0.093	0.000	0.000	0.000	0.000
50	A	383	SER	0	-0.052	-0.032	15.773	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	384	ASN	0	-0.006	-0.020	11.140	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	385	ASP	-1	-0.753	-0.832	11.863	-0.764	-0.764	0.000	0.000	0.000	0.000
53	A	386	ARG	1	0.865	0.932	10.914	1.217	1.217	0.000	0.000	0.000	0.000
54	A	387	VAL	0	-0.001	-0.012	13.220	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	388	LEU	0	-0.036	-0.011	11.083	0.003	0.003	0.000	0.000	0.000	0.000
56	A	389	ALA	0	0.013	-0.004	15.290	0.052	0.052	0.000	0.000	0.000	0.000
57	A	390	ILE	0	0.036	0.019	18.825	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	391	ASN	0	-0.015	-0.011	21.825	0.009	0.009	0.000	0.000	0.000	0.000
59	A	392	GLY	0	0.003	0.009	21.964	0.018	0.018	0.000	0.000	0.000	0.000
60	A	393	HIS	0	-0.051	-0.017	22.866	0.007	0.007	0.000	0.000	0.000	0.000
61	A	394	ASP	-1	-0.829	-0.916	18.422	-0.532	-0.532	0.000	0.000	0.000	0.000
62	A	395	LEU	0	0.009	-0.009	18.791	0.031	0.031	0.000	0.000	0.000	0.000
63	A	396	LYS	1	0.847	0.929	13.667	0.566	0.566	0.000	0.000	0.000	0.000
64	A	397	TYR	0	-0.019	-0.017	14.903	-0.107	-0.107	0.000	0.000	0.000	0.000
65	A	398	GLY	0	0.007	0.025	18.593	0.049	0.049	0.000	0.000	0.000	0.000
66	A	399	THR	0	-0.026	-0.051	20.696	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	400	PRO	0	0.043	0.013	21.875	0.007	0.007	0.000	0.000	0.000	0.000
68	A	401	GLU	-1	-0.776	-0.838	23.879	-0.259	-0.259	0.000	0.000	0.000	0.000
69	A	402	LEU	0	0.022	0.021	24.237	0.013	0.013	0.000	0.000	0.000	0.000
70	A	403	ALA	0	0.024	0.003	22.729	0.010	0.010	0.000	0.000	0.000	0.000
71	A	404	ALA	0	-0.005	-0.002	24.712	0.016	0.016	0.000	0.000	0.000	0.000
72	A	405	GLN	0	-0.002	-0.005	27.813	0.007	0.007	0.000	0.000	0.000	0.000
73	A	406	ILE	0	-0.011	-0.001	24.402	0.013	0.013	0.000	0.000	0.000	0.000
74	A	407	ILE	0	-0.014	-0.015	24.068	0.011	0.011	0.000	0.000	0.000	0.000
75	A	408	GLN	0	-0.055	-0.025	28.179	0.019	0.019	0.000	0.000	0.000	0.000
76	A	409	ALA	0	-0.004	0.000	31.447	0.011	0.011	0.000	0.000	0.000	0.000
77	A	410	SER	0	-0.069	-0.020	28.997	0.004	0.004	0.000	0.000	0.000	0.000
78	A	411	GLY	0	0.039	0.019	31.046	0.009	0.009	0.000	0.000	0.000	0.000
79	A	412	GLU	-1	-0.770	-0.875	31.120	-0.121	-0.121	0.000	0.000	0.000	0.000
80	A	413	ARG	1	0.848	0.951	22.962	0.152	0.152	0.000	0.000	0.000	0.000
81	A	414	VAL	0	0.007	0.000	23.941	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	415	ASN	0	-0.020	-0.027	20.019	0.025	0.025	0.000	0.000	0.000	0.000
83	A	416	LEU	0	0.021	0.012	18.572	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	417	THR	0	-0.017	-0.016	14.641	0.036	0.036	0.000	0.000	0.000	0.000
85	A	418	ILE	0	-0.009	0.001	11.837	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	419	ALA	0	0.022	0.007	8.431	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	420	ARG	1	0.769	0.831	8.107	0.539	0.539	0.000	0.000	0.000	0.000
88	A	421	PRO	0	-0.020	-0.024	5.013	-0.335	-0.335	0.000	0.000	0.000	0.000
89	A	422	GLY	0	0.003	0.014	3.453	0.565	1.141	0.002	-0.213	-0.365	0.000
90	A	423	LYS	1	0.932	0.969	4.277	-0.308	-0.006	0.001	-0.067	-0.236	0.000
91	A	424	PRO	0	0.013	0.004	5.667	-0.646	-0.610	-0.001	-0.001	-0.033	0.000
92	A	425	GLU	-1	-0.917	-0.956	8.774	0.357	0.357	0.000	0.000	0.000	0.000
93	A	426	ILE	0	-0.069	-0.054	7.972	0.307	0.307	0.000	0.000	0.000	0.000
94	A	427	GLU	-1	-0.907	-0.933	10.881	0.404	0.404	0.000	0.000	0.000	0.000
95	A	428	LEU	0	-0.062	-0.027	13.099	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:SER)