FMO DATABASE

FMODB ID: 7GVNK

Calculation Name: 4DHX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DHX

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NPA8

Base Structure: X-ray

Registration Date: 2023-06-19

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-572952.35977
FMO2-HF: Nuclear repulsion	536601.111707
FMO2-HF: Total energy	-36351.248063
FMO2-MP2: Total energy	-36457.469956

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:9:ASP)

Summations of interaction energy for fragment #1(B:9: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.
-223.985	-225.06	28.904	-13.035	-14.795	0.16

Interaction energy analysis for fragmet #1(B:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.759 / q_NPA : -0.888

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	11	GLN	0	0.007	-0.006	1.860	-50.654	-49.151	14.841	-7.681	-8.663	0.090
4	B	12	MET	0	0.020	0.007	1.780	-37.521	-40.795	14.039	-5.045	-5.720	0.067
5	B	13	ARG	1	0.928	0.963	3.758	-52.259	-51.563	0.024	-0.309	-0.412	0.003
6	B	14	ALA	0	-0.015	-0.006	5.746	-7.032	-7.032	0.000	0.000	0.000	0.000
7	B	15	ALA	0	0.036	0.023	6.442	-5.358	-5.358	0.000	0.000	0.000	0.000
8	B	16	ILE	0	0.015	0.004	7.897	-4.472	-4.472	0.000	0.000	0.000	0.000
9	B	17	ASN	0	-0.032	-0.019	9.731	-4.496	-4.496	0.000	0.000	0.000	0.000
10	B	18	GLN	0	-0.020	-0.018	11.158	-1.540	-1.540	0.000	0.000	0.000	0.000
11	B	19	LYS	1	0.951	0.969	12.458	-20.707	-20.707	0.000	0.000	0.000	0.000
12	B	20	LEU	0	-0.037	-0.007	13.166	-1.683	-1.683	0.000	0.000	0.000	0.000
13	B	21	ILE	0	-0.050	-0.025	15.122	-1.406	-1.406	0.000	0.000	0.000	0.000
14	B	22	GLU	-1	-0.801	-0.866	16.751	16.770	16.770	0.000	0.000	0.000	0.000
15	B	23	THR	0	-0.042	-0.041	17.929	-0.930	-0.930	0.000	0.000	0.000	0.000
16	B	24	GLY	0	0.021	0.022	20.241	-0.733	-0.733	0.000	0.000	0.000	0.000
17	B	25	GLU	-1	-0.798	-0.867	18.776	13.763	13.763	0.000	0.000	0.000	0.000
18	B	26	ARG	1	0.883	0.933	14.976	-19.241	-19.241	0.000	0.000	0.000	0.000
19	B	27	GLU	-1	-0.829	-0.909	19.456	12.719	12.719	0.000	0.000	0.000	0.000
20	B	28	ARG	1	0.906	0.927	22.653	-13.408	-13.408	0.000	0.000	0.000	0.000
21	B	29	LEU	0	-0.012	-0.013	18.334	-0.427	-0.427	0.000	0.000	0.000	0.000
22	B	30	LYS	1	0.823	0.903	21.786	-13.440	-13.440	0.000	0.000	0.000	0.000
23	B	31	GLU	-1	-0.955	-0.971	23.051	10.393	10.393	0.000	0.000	0.000	0.000
24	B	32	LEU	0	0.035	0.009	24.973	-0.418	-0.418	0.000	0.000	0.000	0.000
25	B	33	LEU	0	-0.023	-0.011	20.271	-0.272	-0.272	0.000	0.000	0.000	0.000
26	B	34	ARG	1	0.919	0.955	24.980	-11.534	-11.534	0.000	0.000	0.000	0.000
27	B	35	ALA	0	0.026	0.017	27.589	-0.358	-0.358	0.000	0.000	0.000	0.000
28	B	36	LYS	1	0.876	0.921	27.524	-9.998	-9.998	0.000	0.000	0.000	0.000
29	B	37	LEU	0	-0.017	-0.012	25.014	-0.248	-0.248	0.000	0.000	0.000	0.000
30	B	38	ILE	0	-0.044	-0.039	29.342	-0.275	-0.275	0.000	0.000	0.000	0.000
31	B	39	GLU	-1	-0.834	-0.879	32.454	8.999	8.999	0.000	0.000	0.000	0.000
32	B	40	CYS	0	-0.110	-0.044	30.670	-0.148	-0.148	0.000	0.000	0.000	0.000
33	B	41	GLY	0	0.071	0.043	33.450	-0.130	-0.130	0.000	0.000	0.000	0.000
34	B	42	TRP	0	-0.019	-0.022	26.546	-0.067	-0.067	0.000	0.000	0.000	0.000
35	B	43	LYS	1	0.980	0.979	32.028	-9.201	-9.201	0.000	0.000	0.000	0.000
36	B	44	ASP	-1	-0.825	-0.922	33.075	8.108	8.108	0.000	0.000	0.000	0.000
37	B	45	GLN	0	0.018	0.012	33.219	0.007	0.007	0.000	0.000	0.000	0.000
38	B	46	LEU	0	-0.022	0.001	29.564	-0.089	-0.089	0.000	0.000	0.000	0.000
39	B	47	LYS	1	0.849	0.925	33.946	-8.280	-8.280	0.000	0.000	0.000	0.000
40	B	48	ALA	0	0.003	0.006	37.235	-0.160	-0.160	0.000	0.000	0.000	0.000
41	B	49	HIS	0	0.003	-0.001	33.487	-0.304	-0.304	0.000	0.000	0.000	0.000
42	B	50	CYS	0	-0.017	-0.008	35.446	0.015	0.015	0.000	0.000	0.000	0.000
43	B	51	LYS	1	0.946	0.981	37.917	-7.030	-7.030	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.847	-0.931	40.474	6.933	6.933	0.000	0.000	0.000	0.000
45	B	53	VAL	0	0.035	0.020	36.853	-0.096	-0.096	0.000	0.000	0.000	0.000
46	B	54	ILE	0	-0.035	-0.018	40.107	-0.075	-0.075	0.000	0.000	0.000	0.000
47	B	55	LYS	1	0.767	0.885	42.311	-7.047	-7.047	0.000	0.000	0.000	0.000
48	B	56	GLU	-1	-0.908	-0.942	42.343	6.849	6.849	0.000	0.000	0.000	0.000
49	B	57	LYS	1	0.828	0.916	37.968	-8.260	-8.260	0.000	0.000	0.000	0.000
50	B	58	GLY	0	0.070	0.041	43.474	-0.121	-0.121	0.000	0.000	0.000	0.000
51	B	59	LEU	0	-0.025	-0.039	43.613	0.151	0.151	0.000	0.000	0.000	0.000
52	B	60	GLU	-1	-0.990	-0.981	44.983	6.450	6.450	0.000	0.000	0.000	0.000
53	B	61	HIS	0	-0.030	-0.015	43.439	0.094	0.094	0.000	0.000	0.000	0.000
54	B	62	VAL	0	-0.081	-0.021	38.697	0.203	0.203	0.000	0.000	0.000	0.000
55	B	63	THR	0	0.027	-0.016	36.510	0.049	0.049	0.000	0.000	0.000	0.000
56	B	64	VAL	0	-0.006	-0.032	32.914	0.063	0.063	0.000	0.000	0.000	0.000
57	B	65	ASP	-1	-0.892	-0.949	31.195	10.279	10.279	0.000	0.000	0.000	0.000
58	B	66	ASP	-1	-0.818	-0.873	32.180	8.916	8.916	0.000	0.000	0.000	0.000
59	B	67	LEU	0	-0.020	-0.010	34.138	0.098	0.098	0.000	0.000	0.000	0.000
60	B	68	VAL	0	-0.002	-0.004	28.356	0.148	0.148	0.000	0.000	0.000	0.000
61	B	69	ALA	0	-0.001	0.020	29.414	0.326	0.326	0.000	0.000	0.000	0.000
62	B	70	GLU	-1	-0.857	-0.917	30.365	8.880	8.880	0.000	0.000	0.000	0.000
63	B	71	ILE	0	-0.043	-0.038	30.802	0.016	0.016	0.000	0.000	0.000	0.000
64	B	72	THR	0	-0.060	-0.048	25.188	0.296	0.296	0.000	0.000	0.000	0.000
65	B	73	PRO	0	-0.034	-0.017	26.552	0.323	0.323	0.000	0.000	0.000	0.000
66	B	74	LYS	1	1.000	1.004	27.306	-8.814	-8.814	0.000	0.000	0.000	0.000
67	B	75	GLY	0	0.056	0.026	28.379	-0.023	-0.023	0.000	0.000	0.000	0.000
68	B	76	ARG	1	0.924	0.947	21.034	-13.074	-13.074	0.000	0.000	0.000	0.000
69	B	77	ALA	0	-0.029	-0.011	24.449	0.288	0.288	0.000	0.000	0.000	0.000
70	B	78	LEU	0	0.017	0.014	26.507	-0.182	-0.182	0.000	0.000	0.000	0.000
71	B	79	VAL	0	-0.053	-0.006	22.949	-0.147	-0.147	0.000	0.000	0.000	0.000
72	B	80	PRO	0	0.074	0.033	25.366	0.216	0.216	0.000	0.000	0.000	0.000
73	B	81	ASP	-1	-0.807	-0.926	23.321	12.384	12.384	0.000	0.000	0.000	0.000
74	B	82	SER	0	-0.010	0.001	23.490	0.429	0.429	0.000	0.000	0.000	0.000
75	B	83	VAL	0	0.062	0.021	23.679	0.255	0.255	0.000	0.000	0.000	0.000
76	B	84	LYS	1	0.827	0.926	19.766	-12.074	-12.074	0.000	0.000	0.000	0.000
77	B	85	LYS	1	0.953	0.983	19.395	-11.308	-11.308	0.000	0.000	0.000	0.000
78	B	86	GLU	-1	-0.854	-0.919	20.612	11.882	11.882	0.000	0.000	0.000	0.000
79	B	87	LEU	0	0.019	0.011	17.457	0.304	0.304	0.000	0.000	0.000	0.000
80	B	88	LEU	0	-0.010	-0.006	13.807	0.676	0.676	0.000	0.000	0.000	0.000
81	B	89	GLN	0	0.030	0.006	16.384	1.183	1.183	0.000	0.000	0.000	0.000
82	B	90	ARG	1	0.854	0.929	18.876	-12.173	-12.173	0.000	0.000	0.000	0.000
83	B	91	ILE	0	0.012	0.007	12.664	0.328	0.328	0.000	0.000	0.000	0.000
84	B	92	ARG	1	0.956	0.979	14.024	-16.237	-16.237	0.000	0.000	0.000	0.000
85	B	93	THR	0	-0.011	-0.014	15.366	0.012	0.012	0.000	0.000	0.000	0.000
86	B	94	PHE	0	0.018	0.006	14.262	-0.027	-0.027	0.000	0.000	0.000	0.000
87	B	95	LEU	0	-0.015	-0.023	10.652	0.417	0.417	0.000	0.000	0.000	0.000
88	B	96	ALA	0	-0.007	-0.004	14.247	0.275	0.275	0.000	0.000	0.000	0.000
89	B	97	GLN	0	-0.049	-0.021	16.742	-0.349	-0.349	0.000	0.000	0.000	0.000
90	B	98	HIS	0	-0.050	-0.013	15.657	-0.920	-0.920	0.000	0.000	0.000	0.000
91	B	99	ALA	0	-0.033	0.005	12.611	1.264	1.264	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:ASP)