FMO DATABASE

FMODB ID: NN11Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-357035.374118
FMO2-HF: Nuclear repulsion	324759.414826
FMO2-HF: Total energy	-32275.959292
FMO2-MP2: Total energy	-32368.825846

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.
-3.91	-0.381	2.071	-2.201	-3.398	-0.017

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 : 0.064 / q_NPA : 0.016

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	0.039	0.008	3.470	-2.098	-0.697	0.010	-0.568	-0.842	0.001
4	D	265	ASN	0	0.026	0.013	2.612	-2.702	-0.702	2.062	-1.608	-2.454	-0.018
5	D	266	ARG	1	0.885	0.936	4.472	1.466	1.594	-0.001	-0.025	-0.102	0.000
6	D	267	GLN	0	0.031	0.014	6.446	0.761	0.761	0.000	0.000	0.000	0.000
7	D	268	LEU	0	-0.021	0.000	8.054	0.245	0.245	0.000	0.000	0.000	0.000
8	D	269	GLU	-1	-0.891	-0.943	8.586	-1.483	-1.483	0.000	0.000	0.000	0.000
9	D	270	GLU	-1	-0.820	-0.907	10.280	-0.559	-0.559	0.000	0.000	0.000	0.000
10	D	271	LYS	1	0.813	0.890	12.242	0.330	0.330	0.000	0.000	0.000	0.000
11	D	272	ILE	0	-0.020	-0.006	12.096	0.089	0.089	0.000	0.000	0.000	0.000
12	D	273	ASN	0	0.009	-0.015	13.282	0.124	0.124	0.000	0.000	0.000	0.000
13	D	274	ASP	-1	-0.799	-0.872	16.271	-0.166	-0.166	0.000	0.000	0.000	0.000
14	D	275	CYS	0	-0.038	-0.007	18.268	0.035	0.035	0.000	0.000	0.000	0.000
15	D	276	ALA	0	0.023	0.023	18.863	0.029	0.029	0.000	0.000	0.000	0.000
16	D	277	GLU	-1	-0.872	-0.934	20.921	-0.275	-0.275	0.000	0.000	0.000	0.000
17	D	278	VAL	0	0.065	0.037	24.187	0.019	0.019	0.000	0.000	0.000	0.000
18	D	279	LYS	1	0.765	0.859	20.419	0.255	0.255	0.000	0.000	0.000	0.000
19	D	280	GLN	0	-0.027	-0.016	22.088	0.011	0.011	0.000	0.000	0.000	0.000
20	D	281	GLU	-1	-0.889	-0.945	25.593	-0.160	-0.160	0.000	0.000	0.000	0.000
21	D	282	LEU	0	0.001	0.000	28.078	0.016	0.016	0.000	0.000	0.000	0.000
22	D	283	ALA	0	-0.047	-0.013	26.838	0.015	0.015	0.000	0.000	0.000	0.000
23	D	284	ALA	0	0.052	0.034	28.939	0.012	0.012	0.000	0.000	0.000	0.000
24	D	285	SER	0	-0.008	-0.002	31.206	0.013	0.013	0.000	0.000	0.000	0.000
25	D	286	ARG	1	0.872	0.920	27.392	0.128	0.128	0.000	0.000	0.000	0.000
26	D	287	THR	0	0.022	0.006	31.688	0.007	0.007	0.000	0.000	0.000	0.000
27	D	288	ALA	0	-0.002	-0.001	34.395	0.006	0.006	0.000	0.000	0.000	0.000
28	D	289	ARG	1	0.805	0.869	36.091	0.079	0.079	0.000	0.000	0.000	0.000
29	D	290	ASP	-1	-0.795	-0.872	36.395	-0.069	-0.069	0.000	0.000	0.000	0.000
30	D	291	ALA	0	0.061	0.035	38.366	0.005	0.005	0.000	0.000	0.000	0.000
31	D	292	ALA	0	-0.043	-0.018	40.096	0.004	0.004	0.000	0.000	0.000	0.000
32	D	293	LEU	0	-0.019	-0.018	41.300	0.004	0.004	0.000	0.000	0.000	0.000
33	D	294	GLU	-1	-0.916	-0.949	41.196	-0.063	-0.063	0.000	0.000	0.000	0.000
34	D	295	ARG	1	0.950	0.969	44.079	0.070	0.070	0.000	0.000	0.000	0.000
35	D	296	VAL	0	-0.053	-0.023	46.070	0.002	0.002	0.000	0.000	0.000	0.000
36	D	297	GLN	0	-0.003	-0.012	46.567	0.003	0.003	0.000	0.000	0.000	0.000
37	D	298	MET	0	-0.026	-0.021	46.643	0.003	0.003	0.000	0.000	0.000	0.000
38	D	299	LEU	0	-0.041	-0.023	49.631	0.002	0.002	0.000	0.000	0.000	0.000
39	D	300	GLU	-1	-0.862	-0.923	50.774	-0.038	-0.038	0.000	0.000	0.000	0.000
40	D	301	GLN	0	-0.021	-0.007	51.501	0.004	0.004	0.000	0.000	0.000	0.000
41	D	302	GLN	0	-0.003	0.004	53.889	0.002	0.002	0.000	0.000	0.000	0.000
42	D	303	ILE	0	-0.046	-0.023	55.668	0.001	0.001	0.000	0.000	0.000	0.000
43	D	304	LEU	0	-0.029	-0.009	57.490	0.002	0.002	0.000	0.000	0.000	0.000
44	D	305	ALA	0	0.031	0.014	57.643	0.001	0.001	0.000	0.000	0.000	0.000
45	D	306	TYR	0	0.035	0.013	57.904	0.000	0.000	0.000	0.000	0.000	0.000
46	D	307	LYS	1	0.780	0.894	61.742	0.026	0.026	0.000	0.000	0.000	0.000
47	D	308	ASP	-1	-0.778	-0.897	62.636	-0.024	-0.024	0.000	0.000	0.000	0.000
48	D	309	ASP	-1	-0.875	-0.923	62.343	-0.032	-0.032	0.000	0.000	0.000	0.000
49	D	310	PHE	0	-0.047	-0.025	65.332	0.001	0.001	0.000	0.000	0.000	0.000
50	D	311	MET	0	-0.044	-0.030	67.330	0.001	0.001	0.000	0.000	0.000	0.000
51	D	312	SER	0	-0.021	-0.013	67.057	0.001	0.001	0.000	0.000	0.000	0.000
52	D	313	GLU	-1	-0.917	-0.960	69.189	-0.027	-0.027	0.000	0.000	0.000	0.000
53	D	314	ARG	1	0.777	0.889	71.416	0.022	0.022	0.000	0.000	0.000	0.000
54	D	315	ALA	0	0.052	0.024	72.944	0.001	0.001	0.000	0.000	0.000	0.000
55	D	316	ASP	-1	-0.784	-0.860	73.665	-0.021	-0.021	0.000	0.000	0.000	0.000
56	D	317	ARG	1	0.952	0.983	75.459	0.022	0.022	0.000	0.000	0.000	0.000
57	D	318	GLU	-1	-0.891	-0.946	76.983	-0.019	-0.019	0.000	0.000	0.000	0.000
58	D	319	ARG	1	0.801	0.870	75.808	0.021	0.021	0.000	0.000	0.000	0.000
59	D	320	ALA	0	-0.009	-0.007	79.746	0.001	0.001	0.000	0.000	0.000	0.000
60	D	321	GLN	0	-0.043	-0.028	81.523	0.000	0.000	0.000	0.000	0.000	0.000
61	D	322	SER	0	-0.028	-0.025	83.233	0.001	0.001	0.000	0.000	0.000	0.000
62	D	323	ARG	1	0.880	0.931	84.397	0.016	0.016	0.000	0.000	0.000	0.000
63	D	324	ILE	0	0.013	0.007	84.348	0.000	0.000	0.000	0.000	0.000	0.000
64	D	325	GLN	0	0.009	0.006	87.573	0.000	0.000	0.000	0.000	0.000	0.000
65	D	326	GLU	-1	-0.843	-0.894	86.714	-0.015	-0.015	0.000	0.000	0.000	0.000
66	D	327	LEU	0	-0.009	-0.004	88.497	0.000	0.000	0.000	0.000	0.000	0.000
67	D	328	GLU	-1	-0.877	-0.936	91.121	-0.016	-0.016	0.000	0.000	0.000	0.000
68	D	329	GLU	-1	-0.885	-0.945	93.263	-0.013	-0.013	0.000	0.000	0.000	0.000
69	D	330	LYS	1	0.790	0.888	92.670	0.014	0.014	0.000	0.000	0.000	0.000
70	D	331	VAL	0	0.017	0.008	95.083	0.000	0.000	0.000	0.000	0.000	0.000
71	D	332	ALA	0	0.004	0.007	97.709	0.000	0.000	0.000	0.000	0.000	0.000
72	D	333	SER	0	-0.035	-0.027	99.573	0.000	0.000	0.000	0.000	0.000	0.000
73	D	334	LEU	0	-0.032	-0.032	99.643	0.000	0.000	0.000	0.000	0.000	0.000
74	D	335	LEU	0	-0.022	-0.007	100.281	0.000	0.000	0.000	0.000	0.000	0.000
75	D	336	HIS	0	-0.004	0.011	103.668	0.000	0.000	0.000	0.000	0.000	0.000
76	D	337	GLN	0	-0.019	-0.005	103.194	0.000	0.000	0.000	0.000	0.000	0.000
77	D	338	VAL	0	0.000	0.013	106.547	0.000	0.000	0.000	0.000	0.000	0.000
78	D	339	SER	0	-0.105	-0.047	109.029	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)