FMO DATABASE

FMODB ID: G5NN1

Calculation Name: 5H07-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H07

Chain ID: D

ChEMBL ID:

UniProt ID: Q8NFZ5

Base Structure: X-ray

Registration Date: 2023-09-20

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-357556.063496
FMO2-HF: Nuclear repulsion	325280.883373
FMO2-HF: Total energy	-32275.180123
FMO2-MP2: Total energy	-32368.143756

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(D:262:SER)

Summations of interaction energy for fragment #1(D:262: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.
-6.122	-2.797	2.32	-2.336	-3.311	-0.016

Interaction energy analysis for fragmet #1(D:262:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.010

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	D	264	LEU	0	0.032	-0.005	3.389	-2.612	-0.786	-0.001	-0.822	-1.004	0.003
4	D	265	ASN	0	0.030	0.020	2.392	-4.517	-3.125	2.322	-1.498	-2.217	-0.019
5	D	266	ARG	1	0.944	0.968	4.414	1.556	1.663	-0.001	-0.016	-0.090	0.000
6	D	267	GLN	0	-0.018	-0.019	6.418	0.776	0.776	0.000	0.000	0.000	0.000
7	D	268	LEU	0	-0.023	0.002	7.718	0.245	0.245	0.000	0.000	0.000	0.000
8	D	269	GLU	-1	-0.901	-0.953	8.503	-1.515	-1.515	0.000	0.000	0.000	0.000
9	D	270	GLU	-1	-0.842	-0.920	10.257	-0.531	-0.531	0.000	0.000	0.000	0.000
10	D	271	LYS	1	0.917	0.962	12.071	0.388	0.388	0.000	0.000	0.000	0.000
11	D	272	ILE	0	-0.057	-0.032	12.602	0.094	0.094	0.000	0.000	0.000	0.000
12	D	273	ASN	0	0.048	0.003	13.653	0.132	0.132	0.000	0.000	0.000	0.000
13	D	274	ASP	-1	-0.952	-0.949	16.315	-0.219	-0.219	0.000	0.000	0.000	0.000
14	D	275	CYS	0	-0.025	-0.025	18.105	0.045	0.045	0.000	0.000	0.000	0.000
15	D	276	ALA	0	0.013	0.018	18.737	0.029	0.029	0.000	0.000	0.000	0.000
16	D	277	GLU	-1	-0.877	-0.939	20.767	-0.307	-0.307	0.000	0.000	0.000	0.000
17	D	278	VAL	0	0.078	0.033	23.944	0.019	0.019	0.000	0.000	0.000	0.000
18	D	279	LYS	1	0.835	0.923	20.919	0.276	0.276	0.000	0.000	0.000	0.000
19	D	280	GLN	0	-0.013	-0.014	21.753	0.001	0.001	0.000	0.000	0.000	0.000
20	D	281	GLU	-1	-0.910	-0.946	25.289	-0.184	-0.184	0.000	0.000	0.000	0.000
21	D	282	LEU	0	-0.040	-0.017	27.878	0.019	0.019	0.000	0.000	0.000	0.000
22	D	283	ALA	0	-0.042	-0.029	26.716	0.016	0.016	0.000	0.000	0.000	0.000
23	D	284	ALA	0	0.043	0.015	28.781	0.013	0.013	0.000	0.000	0.000	0.000
24	D	285	SER	0	-0.001	0.005	30.810	0.015	0.015	0.000	0.000	0.000	0.000
25	D	286	ARG	1	0.916	0.958	27.436	0.157	0.157	0.000	0.000	0.000	0.000
26	D	287	THR	0	0.007	0.012	31.532	0.008	0.008	0.000	0.000	0.000	0.000
27	D	288	ALA	0	0.005	0.005	34.186	0.008	0.008	0.000	0.000	0.000	0.000
28	D	289	ARG	1	0.844	0.902	35.002	0.104	0.104	0.000	0.000	0.000	0.000
29	D	290	ASP	-1	-0.803	-0.900	36.421	-0.090	-0.090	0.000	0.000	0.000	0.000
30	D	291	ALA	0	0.034	0.029	38.303	0.005	0.005	0.000	0.000	0.000	0.000
31	D	292	ALA	0	-0.041	-0.022	39.968	0.005	0.005	0.000	0.000	0.000	0.000
32	D	293	LEU	0	-0.021	-0.018	40.882	0.005	0.005	0.000	0.000	0.000	0.000
33	D	294	GLU	-1	-0.906	-0.942	40.763	-0.081	-0.081	0.000	0.000	0.000	0.000
34	D	295	ARG	1	0.946	0.965	43.900	0.083	0.083	0.000	0.000	0.000	0.000
35	D	296	VAL	0	-0.026	-0.012	45.980	0.003	0.003	0.000	0.000	0.000	0.000
36	D	297	GLN	0	0.038	0.020	46.401	0.005	0.005	0.000	0.000	0.000	0.000
37	D	298	MET	0	-0.008	-0.007	46.835	0.003	0.003	0.000	0.000	0.000	0.000
38	D	299	LEU	0	-0.058	-0.027	49.501	0.002	0.002	0.000	0.000	0.000	0.000
39	D	300	GLU	-1	-0.929	-0.963	51.774	-0.048	-0.048	0.000	0.000	0.000	0.000
40	D	301	GLN	0	-0.007	-0.011	51.415	0.004	0.004	0.000	0.000	0.000	0.000
41	D	302	GLN	0	-0.022	-0.003	53.703	0.004	0.004	0.000	0.000	0.000	0.000
42	D	303	ILE	0	-0.035	-0.011	55.450	0.002	0.002	0.000	0.000	0.000	0.000
43	D	304	LEU	0	-0.032	-0.024	56.761	0.002	0.002	0.000	0.000	0.000	0.000
44	D	305	ALA	0	0.057	0.039	57.475	0.002	0.002	0.000	0.000	0.000	0.000
45	D	306	TYR	0	0.021	0.009	58.383	0.001	0.001	0.000	0.000	0.000	0.000
46	D	307	LYS	1	0.895	0.958	61.541	0.035	0.035	0.000	0.000	0.000	0.000
47	D	308	ASP	-1	-0.898	-0.956	61.430	-0.035	-0.035	0.000	0.000	0.000	0.000
48	D	309	ASP	-1	-0.887	-0.947	62.338	-0.041	-0.041	0.000	0.000	0.000	0.000
49	D	310	PHE	0	-0.067	-0.039	65.305	0.002	0.002	0.000	0.000	0.000	0.000
50	D	311	MET	0	-0.067	-0.037	66.783	0.001	0.001	0.000	0.000	0.000	0.000
51	D	312	SER	0	0.019	0.011	67.274	0.002	0.002	0.000	0.000	0.000	0.000
52	D	313	GLU	-1	-0.895	-0.944	69.400	-0.033	-0.033	0.000	0.000	0.000	0.000
53	D	314	ARG	1	0.830	0.926	71.499	0.030	0.030	0.000	0.000	0.000	0.000
54	D	315	ALA	0	0.078	0.040	72.860	0.001	0.001	0.000	0.000	0.000	0.000
55	D	316	ASP	-1	-0.811	-0.897	72.939	-0.028	-0.028	0.000	0.000	0.000	0.000
56	D	317	ARG	1	0.911	0.964	75.558	0.029	0.029	0.000	0.000	0.000	0.000
57	D	318	GLU	-1	-0.957	-0.992	76.669	-0.024	-0.024	0.000	0.000	0.000	0.000
58	D	319	ARG	1	0.844	0.915	75.493	0.028	0.028	0.000	0.000	0.000	0.000
59	D	320	ALA	0	-0.019	-0.015	79.798	0.001	0.001	0.000	0.000	0.000	0.000
60	D	321	GLN	0	0.027	0.012	81.571	0.000	0.000	0.000	0.000	0.000	0.000
61	D	322	SER	0	0.017	0.009	83.217	0.001	0.001	0.000	0.000	0.000	0.000
62	D	323	ARG	1	0.872	0.947	84.381	0.021	0.021	0.000	0.000	0.000	0.000
63	D	324	ILE	0	0.009	-0.005	84.627	0.000	0.000	0.000	0.000	0.000	0.000
64	D	325	GLN	0	0.025	0.015	87.609	0.000	0.000	0.000	0.000	0.000	0.000
65	D	326	GLU	-1	-0.875	-0.938	87.922	-0.019	-0.019	0.000	0.000	0.000	0.000
66	D	327	LEU	0	-0.103	-0.063	88.494	0.001	0.001	0.000	0.000	0.000	0.000
67	D	328	GLU	-1	-0.910	-0.951	91.079	-0.020	-0.020	0.000	0.000	0.000	0.000
68	D	329	GLU	-1	-0.939	-0.965	93.241	-0.017	-0.017	0.000	0.000	0.000	0.000
69	D	330	LYS	1	0.891	0.936	92.351	0.019	0.019	0.000	0.000	0.000	0.000
70	D	331	VAL	0	0.013	0.014	95.047	0.000	0.000	0.000	0.000	0.000	0.000
71	D	332	ALA	0	0.018	0.007	97.579	0.000	0.000	0.000	0.000	0.000	0.000
72	D	333	SER	0	-0.017	-0.006	99.368	0.001	0.001	0.000	0.000	0.000	0.000
73	D	334	LEU	0	-0.057	-0.044	99.332	0.000	0.000	0.000	0.000	0.000	0.000
74	D	335	LEU	0	-0.027	-0.003	100.652	0.000	0.000	0.000	0.000	0.000	0.000
75	D	336	HIS	0	-0.004	0.008	103.546	0.000	0.000	0.000	0.000	0.000	0.000
76	D	337	GLN	0	-0.068	-0.028	103.599	0.000	0.000	0.000	0.000	0.000	0.000
77	D	338	VAL	0	-0.006	-0.003	106.615	0.000	0.000	0.000	0.000	0.000	0.000
78	D	339	SER	0	-0.074	-0.026	109.194	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:262:SER)