FMO DATABASE

FMODB ID: 1NJ7Z

Calculation Name: 3F89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F89

Chain ID: A

ChEMBL ID:

UniProt ID: O88522

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

Total energy (hartree)

FMO2-HF: Electronic energy	-398382.780852
FMO2-HF: Nuclear repulsion	364054.064559
FMO2-HF: Total energy	-34328.716294
FMO2-MP2: Total energy	-34430.316041

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:254:GLU)

Summations of interaction energy for fragment #1(A:254:GLU)

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.
-40.388	-32.706	1.068	-3.563	-5.187	0.032

Interaction energy analysis for fragmet #1(A:254:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.901 / q_NPA : -0.953

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	A	256	LEU	0	-0.003	-0.006	2.427	-22.442	-15.943	1.010	-3.193	-4.316	0.029
4	A	257	ARG	1	0.877	0.941	3.399	-46.472	-45.289	0.058	-0.370	-0.871	0.003
5	A	258	GLN	0	-0.141	-0.061	4.917	-8.818	-8.818	0.000	0.000	0.000	0.000
6	A	259	GLN	0	0.083	0.036	6.449	-2.579	-2.579	0.000	0.000	0.000	0.000
7	A	260	LEU	0	-0.022	-0.010	8.935	-2.050	-2.050	0.000	0.000	0.000	0.000
8	A	261	GLN	0	0.026	0.028	9.173	-1.001	-1.001	0.000	0.000	0.000	0.000
9	A	262	GLN	0	0.052	0.043	11.921	-0.081	-0.081	0.000	0.000	0.000	0.000
10	A	263	ALA	0	-0.019	-0.003	13.695	-1.313	-1.313	0.000	0.000	0.000	0.000
11	A	264	GLU	-1	-0.912	-0.973	13.878	18.168	18.168	0.000	0.000	0.000	0.000
12	A	265	GLU	-1	-0.948	-0.967	16.499	16.088	16.088	0.000	0.000	0.000	0.000
13	A	266	ALA	0	-0.047	-0.028	18.359	-0.858	-0.858	0.000	0.000	0.000	0.000
14	A	267	LEU	0	-0.076	-0.062	18.209	-0.742	-0.742	0.000	0.000	0.000	0.000
15	A	268	VAL	0	0.067	0.057	20.871	-0.613	-0.613	0.000	0.000	0.000	0.000
16	A	269	ALA	0	0.045	0.026	22.796	-0.586	-0.586	0.000	0.000	0.000	0.000
17	A	270	LYS	1	0.869	0.913	23.570	-13.132	-13.132	0.000	0.000	0.000	0.000
18	A	271	GLN	0	-0.047	-0.043	25.817	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	272	GLU	-1	-0.904	-0.932	27.142	10.808	10.808	0.000	0.000	0.000	0.000
20	A	273	LEU	0	-0.072	-0.046	29.012	-0.397	-0.397	0.000	0.000	0.000	0.000
21	A	274	ILE	0	-0.042	-0.020	28.119	-0.344	-0.344	0.000	0.000	0.000	0.000
22	A	275	ASP	-1	-0.747	-0.854	31.395	9.551	9.551	0.000	0.000	0.000	0.000
23	A	276	LYS	1	0.824	0.921	33.326	-8.899	-8.899	0.000	0.000	0.000	0.000
24	A	277	LEU	0	-0.042	-0.031	33.520	-0.218	-0.218	0.000	0.000	0.000	0.000
25	A	278	LYS	1	0.915	0.967	34.303	-9.161	-9.161	0.000	0.000	0.000	0.000
26	A	279	GLU	-1	-0.808	-0.924	36.147	8.441	8.441	0.000	0.000	0.000	0.000
27	A	280	GLU	-1	-0.869	-0.914	38.789	7.750	7.750	0.000	0.000	0.000	0.000
28	A	281	ALA	0	0.003	-0.014	39.906	-0.239	-0.239	0.000	0.000	0.000	0.000
29	A	282	GLU	-1	-0.946	-0.962	41.593	7.089	7.089	0.000	0.000	0.000	0.000
30	A	283	GLN	0	-0.016	-0.023	42.477	-0.308	-0.308	0.000	0.000	0.000	0.000
31	A	284	HIS	0	-0.095	-0.046	41.407	-0.178	-0.178	0.000	0.000	0.000	0.000
32	A	285	ASN	0	-0.076	-0.062	44.386	-0.234	-0.234	0.000	0.000	0.000	0.000
33	A	286	ILE	0	0.041	0.042	47.004	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	287	VAL	0	-0.009	-0.004	49.370	-0.166	-0.166	0.000	0.000	0.000	0.000
35	A	288	MET	0	-0.032	-0.001	49.590	-0.150	-0.150	0.000	0.000	0.000	0.000
36	A	289	GLU	-1	-0.891	-0.950	51.468	5.937	5.937	0.000	0.000	0.000	0.000
37	A	290	THR	0	-0.044	-0.029	53.996	-0.154	-0.154	0.000	0.000	0.000	0.000
38	A	291	VAL	0	-0.010	-0.019	54.510	-0.118	-0.118	0.000	0.000	0.000	0.000
39	A	292	PRO	0	-0.008	0.001	55.570	-0.121	-0.121	0.000	0.000	0.000	0.000
40	A	293	VAL	0	0.027	0.028	58.701	-0.123	-0.123	0.000	0.000	0.000	0.000
41	A	294	LEU	0	0.049	0.030	59.409	-0.110	-0.110	0.000	0.000	0.000	0.000
42	A	295	LYS	1	0.802	0.902	60.718	-5.175	-5.175	0.000	0.000	0.000	0.000
43	A	296	ALA	0	-0.001	-0.004	62.573	-0.088	-0.088	0.000	0.000	0.000	0.000
44	A	297	GLN	0	0.008	-0.008	64.248	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	298	ALA	0	-0.013	0.005	65.663	-0.093	-0.093	0.000	0.000	0.000	0.000
46	A	299	ASP	-1	-0.874	-0.949	66.094	4.843	4.843	0.000	0.000	0.000	0.000
47	A	300	ILE	0	0.005	0.012	68.275	-0.082	-0.082	0.000	0.000	0.000	0.000
48	A	301	TYR	0	0.048	0.022	68.343	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	302	LYS	1	0.901	0.969	71.442	-4.566	-4.566	0.000	0.000	0.000	0.000
50	A	303	ALA	0	-0.037	-0.023	72.946	-0.080	-0.080	0.000	0.000	0.000	0.000
51	A	304	ASP	-1	-0.820	-0.917	73.888	4.291	4.291	0.000	0.000	0.000	0.000
52	A	305	PHE	0	0.015	0.006	75.882	-0.083	-0.083	0.000	0.000	0.000	0.000
53	A	306	GLN	0	-0.083	-0.053	76.029	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	307	ALA	0	0.036	0.024	78.992	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	308	GLU	-1	-0.884	-0.940	80.318	3.890	3.890	0.000	0.000	0.000	0.000
56	A	309	ARG	1	0.824	0.912	79.080	-4.103	-4.103	0.000	0.000	0.000	0.000
57	A	310	HIS	0	-0.065	-0.030	83.366	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	311	ALA	0	0.076	0.046	84.946	-0.054	-0.054	0.000	0.000	0.000	0.000
59	A	312	ARG	1	0.927	0.958	85.026	-3.820	-3.820	0.000	0.000	0.000	0.000
60	A	313	GLU	-1	-0.861	-0.920	87.566	3.580	3.580	0.000	0.000	0.000	0.000
61	A	314	LYS	1	0.853	0.891	89.449	-3.609	-3.609	0.000	0.000	0.000	0.000
62	A	315	LEU	0	-0.034	-0.014	89.263	-0.056	-0.056	0.000	0.000	0.000	0.000
63	A	316	VAL	0	-0.041	-0.022	91.412	-0.044	-0.044	0.000	0.000	0.000	0.000
64	A	317	GLU	-1	-0.781	-0.864	93.758	3.440	3.440	0.000	0.000	0.000	0.000
65	A	318	LYS	1	0.930	0.967	95.563	-3.345	-3.345	0.000	0.000	0.000	0.000
66	A	319	LYS	1	0.887	0.932	96.064	-3.375	-3.375	0.000	0.000	0.000	0.000
67	A	320	GLU	-1	-0.962	-0.988	97.319	3.335	3.335	0.000	0.000	0.000	0.000
68	A	321	TYR	0	0.023	0.007	99.771	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	322	LEU	0	-0.036	-0.009	100.660	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	323	GLN	0	-0.017	-0.014	101.084	0.013	0.013	0.000	0.000	0.000	0.000
71	A	324	GLU	-1	-0.896	-0.942	104.040	3.054	3.054	0.000	0.000	0.000	0.000
72	A	325	GLN	0	-0.098	-0.049	104.468	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	326	LEU	0	-0.007	-0.012	104.957	-0.031	-0.031	0.000	0.000	0.000	0.000
74	A	327	GLU	-1	-0.897	-0.930	105.993	3.049	3.049	0.000	0.000	0.000	0.000
75	A	328	GLN	0	-0.048	-0.048	109.914	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	329	LEU	0	0.074	0.064	111.559	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	330	GLN	0	0.003	-0.019	109.992	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	331	ARG	1	0.904	0.968	111.079	-2.929	-2.929	0.000	0.000	0.000	0.000
79	A	332	GLU	-1	-0.932	-0.964	116.065	2.787	2.787	0.000	0.000	0.000	0.000
80	A	333	PHE	0	-0.006	-0.004	116.583	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	334	ASN	0	-0.033	-0.033	115.788	-0.031	-0.031	0.000	0.000	0.000	0.000
82	A	335	LYS	1	0.861	0.953	119.408	-2.638	-2.638	0.000	0.000	0.000	0.000
83	A	336	LEU	0	-0.028	0.001	121.095	-0.037	-0.037	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:254:GLU)