FMO DATABASE

FMODB ID: 2N3VR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-631050.569303
FMO2-HF: Nuclear repulsion	595432.633833
FMO2-HF: Total energy	-35617.935469
FMO2-MP2: Total energy	-35723.472956

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.
-1.254	3.655	-0.027	-2.456	-2.423	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 : -0.013 / 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	-0.892	-0.920	3.757	-2.160	1.570	-0.037	-2.049	-1.643	0.002
4	A	337	ILE	0	-0.047	-0.024	6.229	-0.358	-0.358	0.000	0.000	0.000	0.000
5	A	338	LEU	0	0.016	0.014	9.364	0.172	0.172	0.000	0.000	0.000	0.000
6	A	339	GLN	0	-0.026	-0.018	12.508	-0.062	-0.062	0.000	0.000	0.000	0.000
7	A	340	VAL	0	0.000	0.006	16.191	0.047	0.047	0.000	0.000	0.000	0.000
8	A	341	ALA	0	-0.042	-0.014	18.669	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	342	LEU	0	0.006	0.007	22.364	0.014	0.014	0.000	0.000	0.000	0.000
10	A	343	HIS	0	-0.058	-0.066	24.945	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	344	LYS	1	0.816	0.945	28.673	0.114	0.114	0.000	0.000	0.000	0.000
12	A	345	ARG	1	0.945	0.959	31.276	0.038	0.038	0.000	0.000	0.000	0.000
13	A	346	ASP	-1	-0.850	-0.921	34.485	-0.064	-0.064	0.000	0.000	0.000	0.000
14	A	347	SER	0	-0.009	-0.029	34.592	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	348	GLY	0	-0.047	-0.021	34.688	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	349	GLU	-1	-0.841	-0.900	31.483	-0.072	-0.072	0.000	0.000	0.000	0.000
17	A	350	GLN	0	-0.037	-0.028	29.489	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	351	LEU	0	0.056	0.011	24.282	0.005	0.005	0.000	0.000	0.000	0.000
19	A	352	GLY	0	-0.002	0.005	25.992	0.006	0.006	0.000	0.000	0.000	0.000
20	A	353	ILE	0	0.014	0.003	20.701	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	354	LYS	1	0.882	0.967	22.438	0.172	0.172	0.000	0.000	0.000	0.000
22	A	355	LEU	0	-0.002	0.002	19.541	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	356	VAL	0	-0.015	-0.003	18.315	0.029	0.029	0.000	0.000	0.000	0.000
24	A	357	ARG	1	0.990	0.989	18.924	0.242	0.242	0.000	0.000	0.000	0.000
25	A	358	ARG	1	0.870	0.921	11.252	0.922	0.922	0.000	0.000	0.000	0.000
26	A	359	THR	0	-0.016	-0.022	18.140	0.010	0.010	0.000	0.000	0.000	0.000
27	A	360	ASP	-1	-0.928	-0.956	15.246	-0.634	-0.634	0.000	0.000	0.000	0.000
28	A	361	GLU	-1	-0.874	-0.917	11.036	-1.356	-1.356	0.000	0.000	0.000	0.000
29	A	362	PRO	0	-0.039	-0.012	13.450	0.069	0.069	0.000	0.000	0.000	0.000
30	A	363	GLY	0	0.002	-0.011	14.314	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	364	VAL	0	-0.018	0.009	16.203	0.053	0.053	0.000	0.000	0.000	0.000
32	A	365	PHE	0	-0.007	-0.012	11.349	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	366	ILE	0	0.016	0.013	15.637	0.082	0.082	0.000	0.000	0.000	0.000
34	A	367	LEU	0	-0.029	-0.001	16.360	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	368	ASP	-1	-0.849	-0.939	18.593	-0.194	-0.194	0.000	0.000	0.000	0.000
36	A	369	LEU	0	0.021	0.007	19.874	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	370	LEU	0	-0.054	-0.033	22.743	0.009	0.009	0.000	0.000	0.000	0.000
38	A	371	GLU	-1	-0.898	-0.956	26.520	-0.047	-0.047	0.000	0.000	0.000	0.000
39	A	372	GLY	0	0.010	0.004	28.134	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	373	GLY	0	0.018	0.025	27.895	0.003	0.003	0.000	0.000	0.000	0.000
41	A	374	LEU	0	0.015	0.003	26.671	0.005	0.005	0.000	0.000	0.000	0.000
42	A	375	ALA	0	-0.005	-0.008	21.851	0.008	0.008	0.000	0.000	0.000	0.000
43	A	376	ALA	0	-0.005	0.001	22.386	0.008	0.008	0.000	0.000	0.000	0.000
44	A	377	GLN	0	-0.102	-0.059	23.855	0.022	0.022	0.000	0.000	0.000	0.000
45	A	378	ASP	-1	-0.833	-0.895	20.740	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	379	GLY	0	0.007	0.011	20.819	0.021	0.021	0.000	0.000	0.000	0.000
47	A	380	ARG	1	0.799	0.886	16.500	0.027	0.027	0.000	0.000	0.000	0.000
48	A	381	LEU	0	-0.013	0.002	15.748	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	382	SER	0	0.043	0.018	13.705	0.071	0.071	0.000	0.000	0.000	0.000
50	A	383	SER	0	-0.041	-0.024	15.153	-0.085	-0.085	0.000	0.000	0.000	0.000
51	A	384	ASN	0	-0.025	-0.038	11.122	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	385	ASP	-1	-0.730	-0.818	11.251	-0.634	-0.634	0.000	0.000	0.000	0.000
53	A	386	ARG	1	0.899	0.935	10.784	1.125	1.125	0.000	0.000	0.000	0.000
54	A	387	VAL	0	-0.001	-0.013	12.937	0.017	0.017	0.000	0.000	0.000	0.000
55	A	388	LEU	0	-0.064	-0.033	10.786	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	389	ALA	0	0.026	0.010	15.218	0.035	0.035	0.000	0.000	0.000	0.000
57	A	390	ILE	0	0.031	0.017	18.587	0.002	0.002	0.000	0.000	0.000	0.000
58	A	391	ASN	0	-0.022	-0.007	21.614	0.009	0.009	0.000	0.000	0.000	0.000
59	A	392	GLY	0	-0.005	-0.001	21.690	0.014	0.014	0.000	0.000	0.000	0.000
60	A	393	HIS	0	-0.049	-0.011	22.616	0.004	0.004	0.000	0.000	0.000	0.000
61	A	394	ASP	-1	-0.880	-0.949	18.271	-0.441	-0.441	0.000	0.000	0.000	0.000
62	A	395	LEU	0	0.019	-0.006	18.617	0.024	0.024	0.000	0.000	0.000	0.000
63	A	396	LYS	1	0.943	0.999	12.514	0.623	0.623	0.000	0.000	0.000	0.000
64	A	397	TYR	0	-0.017	-0.026	15.280	-0.106	-0.106	0.000	0.000	0.000	0.000
65	A	398	GLY	0	0.008	0.023	18.858	0.043	0.043	0.000	0.000	0.000	0.000
66	A	399	THR	0	0.025	0.005	20.834	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	400	PRO	0	0.049	0.007	21.933	0.005	0.005	0.000	0.000	0.000	0.000
68	A	401	GLU	-1	-0.895	-0.947	23.828	-0.226	-0.226	0.000	0.000	0.000	0.000
69	A	402	LEU	0	-0.006	0.006	23.794	0.014	0.014	0.000	0.000	0.000	0.000
70	A	403	ALA	0	0.027	0.002	22.563	0.012	0.012	0.000	0.000	0.000	0.000
71	A	404	ALA	0	-0.010	-0.003	24.571	0.018	0.018	0.000	0.000	0.000	0.000
72	A	405	GLN	0	-0.005	-0.004	27.702	0.009	0.009	0.000	0.000	0.000	0.000
73	A	406	ILE	0	-0.014	-0.004	24.305	0.013	0.013	0.000	0.000	0.000	0.000
74	A	407	ILE	0	-0.018	-0.021	23.850	0.013	0.013	0.000	0.000	0.000	0.000
75	A	408	GLN	0	-0.049	-0.032	27.964	0.016	0.016	0.000	0.000	0.000	0.000
76	A	409	ALA	0	-0.003	0.010	31.239	0.010	0.010	0.000	0.000	0.000	0.000
77	A	410	SER	0	-0.070	-0.010	28.775	0.004	0.004	0.000	0.000	0.000	0.000
78	A	411	GLY	0	0.024	0.007	30.695	0.008	0.008	0.000	0.000	0.000	0.000
79	A	412	GLU	-1	-0.830	-0.922	30.819	-0.069	-0.069	0.000	0.000	0.000	0.000
80	A	413	ARG	1	0.966	1.019	22.822	0.086	0.086	0.000	0.000	0.000	0.000
81	A	414	VAL	0	0.008	-0.007	23.832	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	415	ASN	0	-0.035	-0.028	19.484	0.019	0.019	0.000	0.000	0.000	0.000
83	A	416	LEU	0	0.016	0.007	18.435	-0.021	-0.021	0.000	0.000	0.000	0.000
84	A	417	THR	0	-0.036	-0.016	13.943	0.037	0.037	0.000	0.000	0.000	0.000
85	A	418	ILE	0	-0.002	0.005	11.837	-0.056	-0.056	0.000	0.000	0.000	0.000
86	A	419	ALA	0	0.005	-0.010	8.256	0.028	0.028	0.000	0.000	0.000	0.000
87	A	420	ARG	1	0.843	0.885	7.981	0.066	0.066	0.000	0.000	0.000	0.000
88	A	421	PRO	0	-0.036	-0.035	4.751	-0.113	-0.063	-0.001	-0.032	-0.017	0.000
89	A	422	GLY	0	0.001	0.009	3.179	0.560	1.387	0.011	-0.331	-0.506	0.000
90	A	423	LYS	1	0.934	0.963	4.230	0.575	0.877	0.000	-0.044	-0.257	0.000
91	A	424	PRO	0	0.020	0.010	5.418	-0.423	-0.423	0.000	0.000	0.000	0.000
92	A	425	GLU	-1	-0.897	-0.939	8.727	0.302	0.302	0.000	0.000	0.000	0.000
93	A	426	ILE	0	-0.092	-0.061	7.921	0.147	0.147	0.000	0.000	0.000	0.000
94	A	427	GLU	-1	-0.913	-0.936	11.047	0.335	0.335	0.000	0.000	0.000	0.000
95	A	428	LEU	0	-0.054	-0.028	13.310	0.004	0.004	0.000	0.000	0.000	0.000

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