FMO DATABASE

FMODB ID: 2J5VR

Calculation Name: 5FVL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FVL

Chain ID: A

ChEMBL ID:

UniProt ID: Q04272

Base Structure: X-ray

Registration Date: 2023-06-26

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-546869.203771
FMO2-HF: Nuclear repulsion	513435.93459
FMO2-HF: Total energy	-33433.269181
FMO2-MP2: Total energy	-33531.362402

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-1.446	0.113	-0.018	-0.791	-0.75	0.002

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.002

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	2	SER	0	0.045	0.033	3.876	1.732	3.291	-0.018	-0.791	-0.750	0.002
4	A	3	THR	0	-0.016	0.002	7.171	-0.940	-0.940	0.000	0.000	0.000	0.000
5	A	4	GLY	0	0.045	0.015	10.910	0.128	0.128	0.000	0.000	0.000	0.000
6	A	5	ASP	-1	-0.885	-0.947	9.073	0.027	0.027	0.000	0.000	0.000	0.000
7	A	6	PHE	0	-0.026	-0.016	11.215	-0.207	-0.207	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.046	0.019	12.806	-0.144	-0.144	0.000	0.000	0.000	0.000
9	A	8	THR	0	0.020	0.010	9.452	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.872	0.934	6.991	0.804	0.804	0.000	0.000	0.000	0.000
11	A	10	GLY	0	0.027	0.013	9.359	-0.198	-0.198	0.000	0.000	0.000	0.000
12	A	11	ILE	0	-0.033	-0.020	12.647	0.001	0.001	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.857	-0.919	6.311	-3.429	-3.429	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.078	-0.030	7.823	-0.092	-0.092	0.000	0.000	0.000	0.000
15	A	14	VAL	0	0.048	0.019	10.527	0.103	0.103	0.000	0.000	0.000	0.000
16	A	15	GLN	0	-0.048	-0.027	12.252	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.927	0.949	5.772	3.597	3.597	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.011	0.011	12.280	0.059	0.059	0.000	0.000	0.000	0.000
19	A	18	ILE	0	-0.004	0.001	15.057	0.113	0.113	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.911	-0.940	14.186	-0.862	-0.862	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.037	-0.021	12.947	0.077	0.077	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.778	-0.838	17.248	-0.542	-0.542	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.039	-0.034	20.102	0.087	0.087	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.033	-0.008	19.223	0.056	0.056	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.085	-0.038	21.304	0.036	0.036	0.000	0.000	0.000	0.000
26	A	25	GLN	0	-0.013	0.006	18.013	0.009	0.009	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.043	-0.008	18.507	-0.080	-0.080	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.888	-0.925	18.461	-0.821	-0.821	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.853	-0.936	14.310	-1.060	-1.060	0.000	0.000	0.000	0.000
30	A	29	ALA	0	-0.002	-0.001	14.821	-0.149	-0.149	0.000	0.000	0.000	0.000
31	A	30	TYR	0	-0.015	-0.003	16.722	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.006	-0.011	12.910	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.035	-0.001	12.363	-0.122	-0.122	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.023	-0.051	13.314	-0.039	-0.039	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.013	0.004	16.230	0.067	0.067	0.000	0.000	0.000	0.000
36	A	35	ASN	0	-0.033	-0.018	11.250	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.011	0.001	12.695	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.021	-0.019	13.558	0.132	0.132	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.863	-0.923	15.182	-0.773	-0.773	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.030	-0.027	9.600	0.261	0.261	0.000	0.000	0.000	0.000
41	A	40	LEU	0	0.006	-0.002	14.259	0.150	0.150	0.000	0.000	0.000	0.000
42	A	41	MET	0	-0.013	0.009	16.982	0.130	0.130	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.032	-0.017	14.902	0.104	0.104	0.000	0.000	0.000	0.000
44	A	43	ALA	0	-0.025	-0.012	16.515	0.092	0.092	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.029	-0.021	18.266	0.086	0.086	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.876	0.946	21.272	0.242	0.242	0.000	0.000	0.000	0.000
47	A	46	TYR	0	0.006	0.004	19.191	0.060	0.060	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.761	-0.858	21.355	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.830	0.899	22.050	0.033	0.033	0.000	0.000	0.000	0.000
50	A	49	ASN	0	0.018	0.015	25.009	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.043	0.018	26.496	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	51	LYS	1	1.024	1.008	28.195	0.121	0.121	0.000	0.000	0.000	0.000
53	A	52	SER	0	-0.019	-0.009	22.898	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.913	0.951	24.015	0.135	0.135	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.831	-0.901	25.052	-0.210	-0.210	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.035	-0.015	24.404	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	56	ILE	0	0.023	0.008	19.638	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.862	0.926	22.142	0.195	0.195	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.006	0.007	24.690	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.807	0.883	20.808	0.405	0.405	0.000	0.000	0.000	0.000
61	A	60	PHE	0	0.016	0.009	19.864	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.021	-0.029	21.693	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.840	-0.895	23.132	-0.436	-0.436	0.000	0.000	0.000	0.000
64	A	63	TYR	0	0.044	0.001	18.607	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	64	LEU	0	0.017	0.023	21.357	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	65	ASN	0	-0.014	-0.015	23.081	0.007	0.007	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.795	0.870	22.354	0.540	0.540	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.048	0.011	20.598	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.829	-0.892	22.400	-0.381	-0.381	0.000	0.000	0.000	0.000
70	A	69	GLN	0	0.002	0.001	25.980	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	70	LEU	0	0.003	0.004	20.565	0.011	0.011	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.847	0.917	22.254	0.590	0.590	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.777	0.865	24.843	0.383	0.383	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.002	0.007	26.172	0.031	0.031	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.001	-0.001	21.458	0.011	0.011	0.000	0.000	0.000	0.000
76	A	75	GLU	-1	-0.845	-0.909	25.637	-0.493	-0.493	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.047	-0.017	28.429	0.031	0.031	0.000	0.000	0.000	0.000
78	A	77	GLU	-1	-0.909	-0.947	28.170	-0.342	-0.342	0.000	0.000	0.000	0.000
79	A	78	GLU	-1	-0.919	-0.951	27.633	-0.422	-0.422	0.000	0.000	0.000	0.000
80	A	79	ALA	0	-0.081	-0.049	29.642	0.024	0.024	0.000	0.000	0.000	0.000
81	A	80	ASN	0	-0.095	-0.063	32.916	0.034	0.034	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.029	0.003	31.088	0.016	0.016	0.000	0.000	0.000	0.000
83	A	82	ALA	0	-0.092	-0.031	33.089	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)