FMO DATABASE

FMODB ID: NN1KQ

Calculation Name: 1VR4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VR4

Chain ID: B

ChEMBL ID:

UniProt ID: Q81H14

Base Structure: X-ray

Registration Date: 2023-09-21

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479360.68905
FMO2-HF: Nuclear repulsion	447356.772628
FMO2-HF: Total energy	-32003.916422
FMO2-MP2: Total energy	-32093.239615

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-24.99	-13.557	14.397	-7.006	-18.821	-0.044

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.028

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	B	3	VAL	0	-0.011	-0.004	2.665	-2.924	-0.388	0.400	-0.982	-1.955	-0.001
4	B	4	THR	0	-0.036	-0.020	4.595	0.558	0.650	-0.001	-0.016	-0.074	0.000
5	B	5	THR	0	0.078	0.048	8.293	-0.071	-0.071	0.000	0.000	0.000	0.000
6	B	6	THR	0	-0.035	0.000	11.411	0.031	0.031	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.051	0.010	11.530	-0.142	-0.142	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.026	0.011	11.780	0.062	0.062	0.000	0.000	0.000	0.000
9	B	9	ILE	0	-0.025	-0.010	7.132	-0.027	-0.027	0.000	0.000	0.000	0.000
10	B	10	GLN	0	0.010	0.006	11.340	0.108	0.108	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.004	0.005	13.173	0.075	0.075	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.880	0.919	8.367	-0.296	-0.296	0.000	0.000	0.000	0.000
13	B	13	GLU	-1	-0.891	-0.928	11.914	-0.423	-0.423	0.000	0.000	0.000	0.000
14	B	14	ILE	0	-0.034	-0.012	9.795	-0.058	-0.058	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.021	-0.010	11.233	0.103	0.103	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.935	-0.972	10.382	-0.716	-0.716	0.000	0.000	0.000	0.000
17	B	17	TYR	0	-0.025	-0.027	9.562	-0.257	-0.257	0.000	0.000	0.000	0.000
18	B	18	ILE	0	-0.048	-0.017	6.481	0.088	0.088	0.000	0.000	0.000	0.000
19	B	19	ASP	-1	-0.851	-0.920	8.751	-0.498	-0.498	0.000	0.000	0.000	0.000
20	B	20	ILE	0	-0.063	-0.025	8.638	-0.285	-0.285	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.077	-0.046	5.716	0.028	0.028	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.024	-0.023	9.022	0.018	0.018	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.015	0.023	10.755	0.055	0.055	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.919	-0.967	12.179	-0.132	-0.132	0.000	0.000	0.000	0.000
25	B	25	ALA	0	0.006	0.030	15.735	0.040	0.040	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.020	-0.002	17.800	-0.027	-0.027	0.000	0.000	0.000	0.000
27	B	27	MET	0	-0.063	-0.012	21.572	0.017	0.017	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.035	0.018	24.029	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	29	ALA	0	-0.039	-0.014	27.775	0.001	0.001	0.000	0.000	0.000	0.000
30	B	51	GLU	-1	-0.903	-0.964	24.711	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	52	SER	0	-0.011	-0.022	22.626	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	53	LYS	1	0.992	0.995	21.556	-0.054	-0.054	0.000	0.000	0.000	0.000
33	B	54	LEU	0	0.021	0.011	20.086	0.006	0.006	0.000	0.000	0.000	0.000
34	B	55	LYS	1	0.827	0.893	14.941	-0.086	-0.086	0.000	0.000	0.000	0.000
35	B	56	GLU	-1	-0.895	-0.941	16.780	0.105	0.105	0.000	0.000	0.000	0.000
36	B	57	ALA	0	0.009	0.010	16.710	0.030	0.030	0.000	0.000	0.000	0.000
37	B	58	ARG	1	0.939	0.960	14.173	0.066	0.066	0.000	0.000	0.000	0.000
38	B	59	ASP	-1	-0.843	-0.919	12.478	0.117	0.117	0.000	0.000	0.000	0.000
39	B	60	ILE	0	0.033	0.017	11.901	0.097	0.097	0.000	0.000	0.000	0.000
40	B	61	ALA	0	0.026	0.034	12.253	0.064	0.064	0.000	0.000	0.000	0.000
41	B	62	MET	0	-0.024	-0.029	8.968	-0.015	-0.015	0.000	0.000	0.000	0.000
42	B	63	ASP	-1	-0.962	-0.991	7.566	1.127	1.127	0.000	0.000	0.000	0.000
43	B	64	GLU	-1	-0.897	-0.941	8.017	0.516	0.516	0.000	0.000	0.000	0.000
44	B	65	MET	0	-0.020	0.004	6.397	-0.116	-0.116	0.000	0.000	0.000	0.000
45	B	66	LYS	1	0.870	0.918	3.399	-1.769	-0.780	0.511	-0.275	-1.225	0.001
46	B	67	GLU	-1	-0.953	-0.963	3.854	-0.541	0.533	0.035	-0.536	-0.573	-0.005
47	B	68	LEU	0	0.010	0.010	6.149	-0.453	-0.453	0.000	0.000	0.000	0.000
48	B	69	ALA	0	-0.014	-0.013	2.212	-0.287	-1.664	3.786	-0.882	-1.528	-0.001
49	B	70	LYS	1	0.914	0.949	2.219	-13.385	-10.678	1.879	-1.358	-3.227	0.013
50	B	71	GLN	0	-0.027	-0.012	3.743	0.067	0.149	0.007	0.007	-0.096	0.000
51	B	72	LYS	1	0.922	0.969	5.926	0.900	0.900	0.000	0.000	0.000	0.000
52	B	73	GLY	0	0.003	0.019	6.184	0.045	0.045	0.000	0.000	0.000	0.000
53	B	74	ALA	0	-0.026	-0.006	2.524	-0.298	0.121	0.604	-0.252	-0.772	-0.001
54	B	75	ASN	0	-0.071	-0.037	2.427	-1.951	-0.741	1.744	-0.837	-2.116	-0.011
55	B	76	ALA	0	-0.014	-0.022	2.539	-3.057	-0.510	3.504	-1.961	-4.090	-0.031
56	B	77	ILE	0	0.014	0.014	2.304	-1.738	-0.913	1.931	0.137	-2.892	-0.008
57	B	78	VAL	0	-0.033	-0.016	4.263	0.396	0.489	0.000	-0.031	-0.062	0.000
58	B	79	GLY	0	0.012	0.001	8.039	0.054	0.054	0.000	0.000	0.000	0.000
59	B	80	VAL	0	-0.077	-0.042	7.564	0.043	0.043	0.000	0.000	0.000	0.000
60	B	81	ASP	-1	-0.860	-0.933	10.611	-0.301	-0.301	0.000	0.000	0.000	0.000
61	B	82	VAL	0	-0.109	-0.060	13.562	0.023	0.023	0.000	0.000	0.000	0.000
62	B	83	ASP	-1	-0.855	-0.906	15.590	-0.243	-0.243	0.000	0.000	0.000	0.000
63	B	84	TYR	0	-0.055	-0.049	18.236	0.036	0.036	0.000	0.000	0.000	0.000
64	B	85	GLU	-1	-0.891	-0.946	21.577	-0.107	-0.107	0.000	0.000	0.000	0.000
65	B	86	VAL	0	-0.056	-0.023	24.230	0.013	0.013	0.000	0.000	0.000	0.000
66	B	87	VAL	0	0.044	0.031	24.534	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	88	ARG	1	0.865	0.931	27.555	0.030	0.030	0.000	0.000	0.000	0.000
68	B	89	ASP	-1	-0.825	-0.913	30.853	-0.041	-0.041	0.000	0.000	0.000	0.000
69	B	90	GLY	0	-0.051	-0.025	31.002	0.005	0.005	0.000	0.000	0.000	0.000
70	B	91	MET	0	-0.068	-0.033	25.551	0.005	0.005	0.000	0.000	0.000	0.000
71	B	92	LEU	0	0.002	0.003	22.575	-0.008	-0.008	0.000	0.000	0.000	0.000
72	B	93	MET	0	-0.004	-0.009	19.819	0.015	0.015	0.000	0.000	0.000	0.000
73	B	94	VAL	0	-0.064	-0.028	16.330	-0.011	-0.011	0.000	0.000	0.000	0.000
74	B	95	ALA	0	0.053	0.023	15.788	0.029	0.029	0.000	0.000	0.000	0.000
75	B	96	VAL	0	-0.030	-0.017	10.696	-0.014	-0.014	0.000	0.000	0.000	0.000
76	B	97	SER	0	0.070	0.042	11.066	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	98	GLY	0	0.035	0.000	8.044	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	99	THR	0	-0.030	-0.007	8.056	0.087	0.087	0.000	0.000	0.000	0.000
79	B	100	ALA	0	0.021	0.020	4.235	-0.672	-0.584	-0.001	-0.013	-0.074	0.000
80	B	101	VAL	0	0.006	-0.005	4.451	0.726	0.816	-0.001	-0.004	-0.084	0.000
81	B	102	ARG	1	0.970	0.991	5.030	-0.207	-0.149	-0.001	-0.003	-0.053	0.000
82	B	103	ILE	0	-0.009	-0.014	5.362	0.465	0.465	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)