FMO DATABASE

FMODB ID: 1NKRZ

Calculation Name: 4G7X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G7X

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-23

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-709056.01194
FMO2-HF: Nuclear repulsion	670515.929625
FMO2-HF: Total energy	-38540.082316
FMO2-MP2: Total energy	-38653.658159

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:254:ASN)

Summations of interaction energy for fragment #1(B:254:ASN)

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.
-21.722	-17.389	4.143	-3.327	-5.149	0.032

Interaction energy analysis for fragmet #1(B:254:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.004

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	B	256	ALA	0	0.087	0.042	3.866	2.417	4.364	-0.015	-1.033	-0.899	0.002
4	B	257	ALA	0	0.067	0.043	6.627	0.014	0.014	0.000	0.000	0.000	0.000
5	B	258	ARG	1	0.813	0.877	2.761	-7.165	-5.253	0.991	-0.857	-2.046	0.011
6	B	259	GLN	0	-0.003	-0.010	2.324	-12.182	-11.708	3.167	-1.437	-2.204	0.019
7	B	260	GLN	0	0.018	0.016	5.560	-1.467	-1.467	0.000	0.000	0.000	0.000
8	B	261	PHE	0	-0.001	0.006	7.659	-0.628	-0.628	0.000	0.000	0.000	0.000
9	B	262	VAL	0	-0.002	-0.010	5.990	-0.716	-0.716	0.000	0.000	0.000	0.000
10	B	263	THR	0	-0.027	-0.021	8.784	-0.703	-0.703	0.000	0.000	0.000	0.000
11	B	264	SER	0	0.006	0.007	11.111	-0.424	-0.424	0.000	0.000	0.000	0.000
12	B	265	GLU	-1	-0.786	-0.860	12.117	0.599	0.599	0.000	0.000	0.000	0.000
13	B	266	VAL	0	-0.022	-0.018	11.958	-0.240	-0.240	0.000	0.000	0.000	0.000
14	B	267	GLY	0	0.014	0.017	14.405	-0.170	-0.170	0.000	0.000	0.000	0.000
15	B	268	ARG	1	0.804	0.868	16.600	-0.802	-0.802	0.000	0.000	0.000	0.000
16	B	269	TYR	0	-0.003	-0.019	16.139	-0.106	-0.106	0.000	0.000	0.000	0.000
17	B	270	GLY	0	0.062	0.029	18.302	-0.080	-0.080	0.000	0.000	0.000	0.000
18	B	271	ALA	0	-0.016	0.009	20.065	-0.077	-0.077	0.000	0.000	0.000	0.000
19	B	272	ILE	0	-0.015	-0.007	20.980	-0.061	-0.061	0.000	0.000	0.000	0.000
20	B	273	TYR	0	-0.001	-0.029	19.424	-0.034	-0.034	0.000	0.000	0.000	0.000
21	B	274	THR	0	-0.003	-0.017	23.750	-0.042	-0.042	0.000	0.000	0.000	0.000
22	B	275	GLN	0	-0.022	0.002	26.159	-0.014	-0.014	0.000	0.000	0.000	0.000
23	B	276	LEU	0	0.023	0.010	25.769	-0.024	-0.024	0.000	0.000	0.000	0.000
24	B	277	ILE	0	0.001	0.003	26.504	-0.025	-0.025	0.000	0.000	0.000	0.000
25	B	278	ARG	1	0.884	0.930	27.906	-0.349	-0.349	0.000	0.000	0.000	0.000
26	B	279	GLN	0	-0.019	-0.015	31.082	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	280	ASN	0	-0.022	-0.002	32.481	-0.029	-0.029	0.000	0.000	0.000	0.000
28	B	281	LEU	0	-0.064	-0.023	33.942	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	282	LEU	0	0.004	0.007	36.136	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	283	VAL	0	0.001	-0.003	39.336	0.009	0.009	0.000	0.000	0.000	0.000
31	B	284	GLU	-1	-0.806	-0.880	40.922	0.134	0.134	0.000	0.000	0.000	0.000
32	B	285	ASP	-1	-0.892	-0.950	42.242	0.159	0.159	0.000	0.000	0.000	0.000
33	B	286	SER	0	-0.119	-0.083	43.777	0.009	0.009	0.000	0.000	0.000	0.000
34	B	287	PHE	0	0.025	-0.005	38.476	0.008	0.008	0.000	0.000	0.000	0.000
35	B	288	ARG	1	0.994	0.994	38.742	-0.157	-0.157	0.000	0.000	0.000	0.000
36	B	289	GLY	0	-0.016	-0.007	37.532	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	290	LYS	1	0.832	0.927	36.856	-0.185	-0.185	0.000	0.000	0.000	0.000
38	B	291	GLN	0	0.038	-0.014	30.344	0.019	0.019	0.000	0.000	0.000	0.000
39	B	292	CYS	0	-0.055	-0.013	31.684	-0.010	-0.010	0.000	0.000	0.000	0.000
40	B	293	ARG	1	0.860	0.906	24.641	-0.383	-0.383	0.000	0.000	0.000	0.000
41	B	294	VAL	0	0.012	-0.012	25.385	-0.031	-0.031	0.000	0.000	0.000	0.000
42	B	295	ASN	0	0.007	-0.004	20.180	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	296	LEU	0	0.006	0.009	22.139	-0.048	-0.048	0.000	0.000	0.000	0.000
44	B	297	LYS	1	0.876	0.932	20.849	-0.237	-0.237	0.000	0.000	0.000	0.000
45	B	298	LEU	0	-0.023	-0.004	20.446	-0.029	-0.029	0.000	0.000	0.000	0.000
46	B	299	ILE	0	0.045	0.018	20.730	-0.016	-0.016	0.000	0.000	0.000	0.000
47	B	300	PRO	0	-0.016	-0.013	18.565	0.011	0.011	0.000	0.000	0.000	0.000
48	B	301	THR	0	-0.014	-0.017	21.348	-0.034	-0.034	0.000	0.000	0.000	0.000
49	B	302	GLY	0	0.018	0.010	23.758	0.022	0.022	0.000	0.000	0.000	0.000
50	B	303	THR	0	-0.014	-0.013	21.220	-0.022	-0.022	0.000	0.000	0.000	0.000
51	B	304	GLY	0	0.010	0.013	21.122	0.039	0.039	0.000	0.000	0.000	0.000
52	B	305	ALA	0	0.000	0.007	21.259	-0.033	-0.033	0.000	0.000	0.000	0.000
53	B	306	LEU	0	0.039	0.030	23.379	0.016	0.016	0.000	0.000	0.000	0.000
54	B	307	LEU	0	0.018	0.001	24.712	0.014	0.014	0.000	0.000	0.000	0.000
55	B	308	GLY	0	0.009	0.011	25.175	-0.026	-0.026	0.000	0.000	0.000	0.000
56	B	309	SER	0	-0.033	-0.031	25.510	-0.006	-0.006	0.000	0.000	0.000	0.000
57	B	310	LEU	0	-0.015	-0.001	25.699	0.024	0.024	0.000	0.000	0.000	0.000
58	B	311	THR	0	-0.019	0.002	25.265	-0.028	-0.028	0.000	0.000	0.000	0.000
59	B	312	VAL	0	0.002	-0.019	27.231	0.027	0.027	0.000	0.000	0.000	0.000
60	B	313	LEU	0	-0.064	-0.016	24.167	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	314	ASP	-1	-0.776	-0.856	28.774	0.322	0.322	0.000	0.000	0.000	0.000
62	B	315	GLY	0	0.065	0.018	31.384	0.015	0.015	0.000	0.000	0.000	0.000
63	B	316	ASP	-1	-0.804	-0.861	34.015	0.166	0.166	0.000	0.000	0.000	0.000
64	B	317	SER	0	0.055	0.013	36.944	0.003	0.003	0.000	0.000	0.000	0.000
65	B	318	ARG	1	0.864	0.924	38.335	-0.162	-0.162	0.000	0.000	0.000	0.000
66	B	319	LEU	0	0.044	0.050	34.646	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	321	ALA	0	-0.024	-0.008	34.688	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	322	ALA	0	0.020	0.010	36.917	-0.005	-0.005	0.000	0.000	0.000	0.000
69	B	323	THR	0	-0.002	-0.018	30.816	0.006	0.006	0.000	0.000	0.000	0.000
70	B	324	LYS	1	0.919	0.960	32.448	-0.146	-0.146	0.000	0.000	0.000	0.000
71	B	325	ARG	1	0.912	0.957	33.498	-0.117	-0.117	0.000	0.000	0.000	0.000
72	B	326	ALA	0	0.013	0.006	33.162	-0.006	-0.006	0.000	0.000	0.000	0.000
73	B	327	VAL	0	0.003	-0.018	28.240	0.003	0.003	0.000	0.000	0.000	0.000
74	B	328	ALA	0	-0.068	-0.028	30.702	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	329	GLN	0	0.006	0.018	33.013	-0.022	-0.022	0.000	0.000	0.000	0.000
76	B	330	VAL	0	-0.048	-0.011	27.487	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	331	ASN	0	-0.018	-0.011	30.210	-0.014	-0.014	0.000	0.000	0.000	0.000
78	B	332	SER	0	-0.030	-0.017	26.226	-0.017	-0.017	0.000	0.000	0.000	0.000
79	B	333	PHE	0	0.006	0.005	22.808	0.026	0.026	0.000	0.000	0.000	0.000
80	B	334	PRO	0	0.015	0.001	22.187	-0.013	-0.013	0.000	0.000	0.000	0.000
81	B	335	LEU	0	0.043	0.031	17.221	0.057	0.057	0.000	0.000	0.000	0.000
82	B	336	PRO	0	-0.025	0.012	13.778	-0.035	-0.035	0.000	0.000	0.000	0.000
83	B	337	LYS	1	0.863	0.905	15.092	0.136	0.136	0.000	0.000	0.000	0.000
84	B	338	ASP	-1	-0.817	-0.902	12.418	-0.238	-0.238	0.000	0.000	0.000	0.000
85	B	339	GLN	0	0.014	0.004	9.356	0.098	0.098	0.000	0.000	0.000	0.000
86	B	340	PRO	0	0.065	0.026	8.724	0.268	0.268	0.000	0.000	0.000	0.000
87	B	341	ASP	-1	-0.789	-0.867	5.835	2.367	2.367	0.000	0.000	0.000	0.000
88	B	342	VAL	0	0.021	0.012	8.386	0.436	0.436	0.000	0.000	0.000	0.000
89	B	343	VAL	0	0.021	0.014	10.693	-0.032	-0.032	0.000	0.000	0.000	0.000
90	B	344	GLU	-1	-0.816	-0.897	10.487	-0.063	-0.063	0.000	0.000	0.000	0.000
91	B	345	LYS	1	0.876	0.951	8.435	-1.471	-1.471	0.000	0.000	0.000	0.000
92	B	346	LEU	0	-0.004	-0.005	13.019	-0.054	-0.054	0.000	0.000	0.000	0.000
93	B	347	LYS	1	0.820	0.890	15.444	-0.020	-0.020	0.000	0.000	0.000	0.000
94	B	348	ASN	0	-0.020	0.001	16.254	-0.114	-0.114	0.000	0.000	0.000	0.000
95	B	349	ILE	0	0.040	0.047	17.158	0.083	0.083	0.000	0.000	0.000	0.000
96	B	350	ASN	0	0.007	0.003	18.592	-0.121	-0.121	0.000	0.000	0.000	0.000
97	B	351	LEU	0	-0.015	0.005	20.634	0.056	0.056	0.000	0.000	0.000	0.000
98	B	352	THR	0	-0.041	-0.033	23.432	-0.021	-0.021	0.000	0.000	0.000	0.000
99	B	353	VAL	0	-0.005	0.012	26.823	0.010	0.010	0.000	0.000	0.000	0.000
100	B	354	ALA	0	0.043	0.011	29.883	-0.010	-0.010	0.000	0.000	0.000	0.000
101	B	355	PRO	0	0.008	0.016	33.034	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:254:ASN)