FMO DATABASE

FMODB ID: 8922Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-357602.71178
FMO2-HF: Nuclear repulsion	325327.010212
FMO2-HF: Total energy	-32275.701568
FMO2-MP2: Total energy	-32368.653822

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.
-3.831	-0.622	2.123	-2.118	-3.212	-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 : 0.020 / q_NPA : 0.001

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	D	264	LEU	0	0.036	0.000	3.382	-2.329	-0.579	0.000	-0.763	-0.986	0.002
4	D	265	ASN	0	0.035	0.020	2.407	-2.334	-0.975	2.124	-1.337	-2.146	-0.018
5	D	266	ARG	1	0.911	0.952	4.625	1.399	1.499	-0.001	-0.018	-0.080	0.000
6	D	267	GLN	0	0.011	-0.006	6.632	0.741	0.741	0.000	0.000	0.000	0.000
7	D	268	LEU	0	-0.023	0.002	7.853	0.233	0.233	0.000	0.000	0.000	0.000
8	D	269	GLU	-1	-0.897	-0.952	8.655	-1.414	-1.414	0.000	0.000	0.000	0.000
9	D	270	GLU	-1	-0.819	-0.904	10.445	-0.560	-0.560	0.000	0.000	0.000	0.000
10	D	271	LYS	1	0.824	0.899	12.235	0.334	0.334	0.000	0.000	0.000	0.000
11	D	272	ILE	0	-0.040	-0.020	12.226	0.083	0.083	0.000	0.000	0.000	0.000
12	D	273	ASN	0	0.019	-0.011	13.446	0.127	0.127	0.000	0.000	0.000	0.000
13	D	274	ASP	-1	-0.812	-0.877	16.498	-0.178	-0.178	0.000	0.000	0.000	0.000
14	D	275	CYS	0	-0.050	-0.022	18.290	0.042	0.042	0.000	0.000	0.000	0.000
15	D	276	ALA	0	0.012	0.020	18.904	0.028	0.028	0.000	0.000	0.000	0.000
16	D	277	GLU	-1	-0.877	-0.937	20.924	-0.285	-0.285	0.000	0.000	0.000	0.000
17	D	278	VAL	0	0.068	0.030	24.105	0.018	0.018	0.000	0.000	0.000	0.000
18	D	279	LYS	1	0.813	0.900	20.708	0.248	0.248	0.000	0.000	0.000	0.000
19	D	280	GLN	0	-0.015	-0.015	22.133	0.009	0.009	0.000	0.000	0.000	0.000
20	D	281	GLU	-1	-0.897	-0.942	25.412	-0.168	-0.168	0.000	0.000	0.000	0.000
21	D	282	LEU	0	-0.036	-0.016	28.068	0.017	0.017	0.000	0.000	0.000	0.000
22	D	283	ALA	0	-0.054	-0.037	26.803	0.015	0.015	0.000	0.000	0.000	0.000
23	D	284	ALA	0	0.048	0.028	28.882	0.012	0.012	0.000	0.000	0.000	0.000
24	D	285	SER	0	-0.004	0.004	30.912	0.014	0.014	0.000	0.000	0.000	0.000
25	D	286	ARG	1	0.925	0.959	27.384	0.132	0.132	0.000	0.000	0.000	0.000
26	D	287	THR	0	0.006	0.002	31.625	0.007	0.007	0.000	0.000	0.000	0.000
27	D	288	ALA	0	0.004	0.006	34.266	0.007	0.007	0.000	0.000	0.000	0.000
28	D	289	ARG	1	0.805	0.866	35.654	0.085	0.085	0.000	0.000	0.000	0.000
29	D	290	ASP	-1	-0.780	-0.871	36.365	-0.074	-0.074	0.000	0.000	0.000	0.000
30	D	291	ALA	0	0.042	0.034	38.351	0.005	0.005	0.000	0.000	0.000	0.000
31	D	292	ALA	0	-0.042	-0.023	40.039	0.005	0.005	0.000	0.000	0.000	0.000
32	D	293	LEU	0	-0.017	-0.016	41.040	0.005	0.005	0.000	0.000	0.000	0.000
33	D	294	GLU	-1	-0.917	-0.947	40.992	-0.067	-0.067	0.000	0.000	0.000	0.000
34	D	295	ARG	1	0.949	0.967	43.960	0.073	0.073	0.000	0.000	0.000	0.000
35	D	296	VAL	0	-0.045	-0.018	46.045	0.002	0.002	0.000	0.000	0.000	0.000
36	D	297	GLN	0	-0.006	-0.006	46.583	0.004	0.004	0.000	0.000	0.000	0.000
37	D	298	MET	0	-0.016	-0.013	46.753	0.003	0.003	0.000	0.000	0.000	0.000
38	D	299	LEU	0	-0.049	-0.023	49.550	0.001	0.001	0.000	0.000	0.000	0.000
39	D	300	GLU	-1	-0.864	-0.928	50.900	-0.040	-0.040	0.000	0.000	0.000	0.000
40	D	301	GLN	0	-0.018	-0.013	51.479	0.003	0.003	0.000	0.000	0.000	0.000
41	D	302	GLN	0	-0.007	0.004	53.751	0.003	0.003	0.000	0.000	0.000	0.000
42	D	303	ILE	0	-0.041	-0.017	55.497	0.002	0.002	0.000	0.000	0.000	0.000
43	D	304	LEU	0	-0.038	-0.017	57.299	0.002	0.002	0.000	0.000	0.000	0.000
44	D	305	ALA	0	0.055	0.032	57.484	0.002	0.002	0.000	0.000	0.000	0.000
45	D	306	TYR	0	0.020	0.003	58.002	0.000	0.000	0.000	0.000	0.000	0.000
46	D	307	LYS	1	0.905	0.966	61.590	0.029	0.029	0.000	0.000	0.000	0.000
47	D	308	ASP	-1	-0.890	-0.958	61.770	-0.028	-0.028	0.000	0.000	0.000	0.000
48	D	309	ASP	-1	-0.885	-0.941	62.449	-0.035	-0.035	0.000	0.000	0.000	0.000
49	D	310	PHE	0	-0.063	-0.035	65.337	0.001	0.001	0.000	0.000	0.000	0.000
50	D	311	MET	0	-0.056	-0.031	67.003	0.001	0.001	0.000	0.000	0.000	0.000
51	D	312	SER	0	0.003	0.001	67.154	0.001	0.001	0.000	0.000	0.000	0.000
52	D	313	GLU	-1	-0.918	-0.953	69.273	-0.029	-0.029	0.000	0.000	0.000	0.000
53	D	314	ARG	1	0.787	0.892	71.532	0.024	0.024	0.000	0.000	0.000	0.000
54	D	315	ALA	0	0.036	0.020	72.891	0.001	0.001	0.000	0.000	0.000	0.000
55	D	316	ASP	-1	-0.766	-0.861	73.928	-0.023	-0.023	0.000	0.000	0.000	0.000
56	D	317	ARG	1	0.934	0.977	75.595	0.024	0.024	0.000	0.000	0.000	0.000
57	D	318	GLU	-1	-0.883	-0.948	77.109	-0.021	-0.021	0.000	0.000	0.000	0.000
58	D	319	ARG	1	0.802	0.876	75.549	0.023	0.023	0.000	0.000	0.000	0.000
59	D	320	ALA	0	-0.010	-0.009	79.821	0.001	0.001	0.000	0.000	0.000	0.000
60	D	321	GLN	0	-0.027	-0.015	81.606	0.000	0.000	0.000	0.000	0.000	0.000
61	D	322	SER	0	-0.003	0.001	83.246	0.001	0.001	0.000	0.000	0.000	0.000
62	D	323	ARG	1	0.864	0.927	84.404	0.018	0.018	0.000	0.000	0.000	0.000
63	D	324	ILE	0	0.009	-0.002	84.423	0.000	0.000	0.000	0.000	0.000	0.000
64	D	325	GLN	0	0.016	0.016	87.590	0.000	0.000	0.000	0.000	0.000	0.000
65	D	326	GLU	-1	-0.838	-0.908	87.007	-0.016	-0.016	0.000	0.000	0.000	0.000
66	D	327	LEU	0	-0.031	-0.027	88.312	0.001	0.001	0.000	0.000	0.000	0.000
67	D	328	GLU	-1	-0.878	-0.932	91.104	-0.017	-0.017	0.000	0.000	0.000	0.000
68	D	329	GLU	-1	-0.916	-0.964	93.112	-0.014	-0.014	0.000	0.000	0.000	0.000
69	D	330	LYS	1	0.805	0.896	92.451	0.015	0.015	0.000	0.000	0.000	0.000
70	D	331	VAL	0	0.017	0.015	95.116	0.000	0.000	0.000	0.000	0.000	0.000
71	D	332	ALA	0	0.014	0.007	97.603	0.000	0.000	0.000	0.000	0.000	0.000
72	D	333	SER	0	-0.025	-0.011	99.392	0.000	0.000	0.000	0.000	0.000	0.000
73	D	334	LEU	0	-0.050	-0.040	99.567	0.000	0.000	0.000	0.000	0.000	0.000
74	D	335	LEU	0	-0.033	-0.006	100.356	0.000	0.000	0.000	0.000	0.000	0.000
75	D	336	HIS	0	-0.006	0.004	103.572	0.000	0.000	0.000	0.000	0.000	0.000
76	D	337	GLN	0	-0.047	-0.015	103.410	0.000	0.000	0.000	0.000	0.000	0.000
77	D	338	VAL	0	-0.004	-0.003	106.595	0.000	0.000	0.000	0.000	0.000	0.000
78	D	339	SER	0	-0.073	-0.023	109.216	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)