FMO DATABASE

FMODB ID: 6NGVZ

Calculation Name: 4GKW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GKW

Chain ID: A

ChEMBL ID:

UniProt ID: O62479

Base Structure: X-ray

Registration Date: 2023-06-22

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-866523.45967
FMO2-HF: Nuclear repulsion	801236.417784
FMO2-HF: Total energy	-65287.041885
FMO2-MP2: Total energy	-65476.068423

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:250:GLU)

Summations of interaction energy for fragment #1(A:250: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.
79.927	83.441	0.035	-1.625	-1.923	0.001

Interaction energy analysis for fragmet #1(A:250:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -1.019 / q_NPA : -1.022

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	252	LYS	1	0.921	0.949	3.683	-43.558	-40.619	-0.009	-1.482	-1.448	0.001
4	A	253	GLU	-1	-0.990	-0.997	3.331	28.045	28.620	0.044	-0.143	-0.475	0.000
5	A	254	ASP	-1	-0.998	-0.993	4.990	28.890	28.890	0.000	0.000	0.000	0.000
6	A	255	GLU	-1	-0.816	-0.889	6.713	23.934	23.934	0.000	0.000	0.000	0.000
7	A	256	VAL	0	-0.055	-0.037	9.295	-2.084	-2.084	0.000	0.000	0.000	0.000
8	A	257	ALA	0	-0.037	-0.038	10.125	-1.824	-1.824	0.000	0.000	0.000	0.000
9	A	258	ASP	-1	-0.849	-0.927	11.028	23.278	23.278	0.000	0.000	0.000	0.000
10	A	259	LEU	0	-0.013	-0.010	13.433	-1.557	-1.557	0.000	0.000	0.000	0.000
11	A	260	LYS	1	0.903	0.977	13.585	-18.643	-18.643	0.000	0.000	0.000	0.000
12	A	261	GLN	0	0.113	0.083	16.620	-1.276	-1.276	0.000	0.000	0.000	0.000
13	A	262	ASP	-1	-0.926	-0.952	17.270	15.619	15.619	0.000	0.000	0.000	0.000
14	A	263	THR	0	-0.118	-0.107	19.715	-0.772	-0.772	0.000	0.000	0.000	0.000
15	A	264	GLU	-1	-0.982	-0.988	19.820	13.655	13.655	0.000	0.000	0.000	0.000
16	A	265	SER	0	-0.051	-0.043	22.530	-0.780	-0.780	0.000	0.000	0.000	0.000
17	A	266	LEU	0	-0.027	0.001	23.976	-0.580	-0.580	0.000	0.000	0.000	0.000
18	A	267	GLN	0	-0.008	-0.018	23.903	-0.723	-0.723	0.000	0.000	0.000	0.000
19	A	268	LYS	1	0.924	1.002	26.750	-11.292	-11.292	0.000	0.000	0.000	0.000
20	A	269	GLN	0	0.027	0.020	27.935	-0.149	-0.149	0.000	0.000	0.000	0.000
21	A	270	LEU	0	-0.028	-0.025	30.366	-0.379	-0.379	0.000	0.000	0.000	0.000
22	A	271	GLU	-1	-0.937	-0.957	29.826	9.668	9.668	0.000	0.000	0.000	0.000
23	A	272	GLU	-1	-0.876	-0.973	31.803	9.558	9.558	0.000	0.000	0.000	0.000
24	A	273	ASN	0	-0.059	-0.011	34.498	-0.386	-0.386	0.000	0.000	0.000	0.000
25	A	274	GLN	0	-0.020	-0.022	35.330	-0.192	-0.192	0.000	0.000	0.000	0.000
26	A	275	GLU	-1	-0.898	-0.944	36.763	8.142	8.142	0.000	0.000	0.000	0.000
27	A	276	GLU	-1	-0.972	-0.985	38.266	7.946	7.946	0.000	0.000	0.000	0.000
28	A	277	LEU	0	-0.056	-0.048	40.520	-0.280	-0.280	0.000	0.000	0.000	0.000
29	A	278	GLU	-1	-0.920	-0.946	41.969	6.784	6.784	0.000	0.000	0.000	0.000
30	A	279	ILE	0	-0.002	0.006	43.194	-0.271	-0.271	0.000	0.000	0.000	0.000
31	A	280	VAL	0	-0.002	0.007	44.706	-0.229	-0.229	0.000	0.000	0.000	0.000
32	A	281	GLY	0	0.040	0.028	46.334	-0.135	-0.135	0.000	0.000	0.000	0.000
33	A	282	ASN	0	-0.075	-0.071	47.645	-0.320	-0.320	0.000	0.000	0.000	0.000
34	A	283	MET	0	-0.012	-0.002	49.053	-0.142	-0.142	0.000	0.000	0.000	0.000
35	A	284	LEU	0	-0.001	0.016	50.862	-0.150	-0.150	0.000	0.000	0.000	0.000
36	A	285	ARG	1	0.925	0.959	49.272	-6.313	-6.313	0.000	0.000	0.000	0.000
37	A	286	GLU	-1	-0.965	-0.979	54.070	5.600	5.600	0.000	0.000	0.000	0.000
38	A	287	GLU	-1	-0.890	-0.950	55.703	5.351	5.351	0.000	0.000	0.000	0.000
39	A	288	GLN	0	-0.030	-0.021	55.381	-0.100	-0.100	0.000	0.000	0.000	0.000
40	A	289	GLY	0	0.018	0.021	58.484	-0.104	-0.104	0.000	0.000	0.000	0.000
41	A	290	LYS	1	0.907	0.950	58.914	-5.523	-5.523	0.000	0.000	0.000	0.000
42	A	291	VAL	0	0.009	-0.007	61.102	-0.119	-0.119	0.000	0.000	0.000	0.000
43	A	292	ASP	-1	-0.879	-0.931	62.098	4.959	4.959	0.000	0.000	0.000	0.000
44	A	293	GLN	0	-0.037	-0.038	64.631	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	294	LEU	0	-0.027	-0.013	65.271	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	295	GLN	0	-0.010	0.007	65.943	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	296	LYS	1	0.917	0.967	67.405	-4.784	-4.784	0.000	0.000	0.000	0.000
48	A	297	ARG	1	0.971	0.980	67.007	-4.734	-4.734	0.000	0.000	0.000	0.000
49	A	298	ASN	0	0.041	0.031	71.712	-0.076	-0.076	0.000	0.000	0.000	0.000
50	A	299	VAL	0	-0.007	-0.002	73.188	-0.074	-0.074	0.000	0.000	0.000	0.000
51	A	300	ALA	0	-0.064	-0.037	75.189	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	301	HIS	0	0.077	0.023	75.215	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	302	GLN	0	0.028	0.008	76.991	-0.115	-0.115	0.000	0.000	0.000	0.000
54	A	303	LYS	1	0.907	0.957	78.007	-4.150	-4.150	0.000	0.000	0.000	0.000
55	A	304	GLU	-1	-0.973	-0.987	81.079	3.810	3.810	0.000	0.000	0.000	0.000
56	A	305	ILE	0	0.050	0.038	79.985	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	306	GLY	0	-0.028	-0.028	83.931	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	307	LYS	1	0.886	0.949	85.808	-3.783	-3.783	0.000	0.000	0.000	0.000
59	A	308	LEU	0	0.122	0.064	86.090	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	309	ARG	1	0.924	0.967	84.781	-3.794	-3.794	0.000	0.000	0.000	0.000
61	A	310	ALA	0	-0.036	-0.017	89.740	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	311	GLU	-1	-0.957	-0.985	90.463	3.515	3.515	0.000	0.000	0.000	0.000
63	A	312	LEU	0	0.008	0.021	92.143	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	313	GLY	0	0.038	0.005	94.069	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	314	THR	0	-0.028	-0.026	95.943	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	315	ALA	0	0.033	0.028	97.037	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	316	GLN	0	0.020	0.023	96.486	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	317	ARG	1	0.969	0.975	97.305	-3.319	-3.319	0.000	0.000	0.000	0.000
69	A	318	ASN	0	-0.059	-0.032	102.036	-0.045	-0.045	0.000	0.000	0.000	0.000
70	A	319	LEU	0	0.024	0.024	102.360	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	320	GLU	-1	-0.886	-0.945	103.552	3.110	3.110	0.000	0.000	0.000	0.000
72	A	321	LYS	1	0.859	0.926	105.397	-3.104	-3.104	0.000	0.000	0.000	0.000
73	A	322	ALA	0	-0.027	-0.021	107.508	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	323	ASP	-1	-0.811	-0.906	107.840	2.994	2.994	0.000	0.000	0.000	0.000
75	A	324	GLN	0	-0.093	-0.046	110.076	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	325	LEU	0	-0.011	-0.024	112.370	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	326	LEU	0	0.042	0.029	111.483	-0.029	-0.029	0.000	0.000	0.000	0.000
78	A	327	LYS	1	0.925	0.958	111.078	-2.936	-2.936	0.000	0.000	0.000	0.000
79	A	328	ARG	1	0.904	0.958	116.487	-2.785	-2.785	0.000	0.000	0.000	0.000
80	A	329	ASN	0	0.045	0.029	117.823	-0.036	-0.036	0.000	0.000	0.000	0.000
81	A	330	SER	0	0.014	0.016	118.273	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	331	GLN	0	0.023	0.000	120.073	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	332	GLN	0	-0.014	0.010	122.259	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	333	GLN	0	0.026	0.004	121.196	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	334	ASN	0	-0.035	-0.018	124.192	0.000	0.000	0.000	0.000	0.000	0.000
86	A	335	GLN	0	0.000	-0.016	126.846	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	336	GLN	0	0.094	0.062	128.055	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	337	SER	0	-0.060	-0.027	129.003	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	338	LEU	0	-0.057	-0.055	130.844	-0.023	-0.023	0.000	0.000	0.000	0.000
90	A	339	ASP	-1	-0.908	-0.945	132.856	2.403	2.403	0.000	0.000	0.000	0.000
91	A	340	MET	0	0.035	0.008	132.255	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	341	ARG	1	0.867	0.940	131.752	-2.461	-2.461	0.000	0.000	0.000	0.000
93	A	342	LYS	1	0.937	0.963	135.986	-2.406	-2.406	0.000	0.000	0.000	0.000
94	A	343	LEU	0	0.008	0.045	137.581	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	344	GLY	0	0.064	0.004	139.546	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	345	GLU	-1	-0.957	-0.992	141.291	2.297	2.297	0.000	0.000	0.000	0.000
97	A	346	LEU	0	0.001	0.002	142.396	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	347	GLU	-1	-0.951	-0.949	141.625	2.289	2.289	0.000	0.000	0.000	0.000
99	A	348	ALA	0	-0.085	-0.057	145.587	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	349	ASP	-1	-0.918	-0.956	147.271	2.164	2.164	0.000	0.000	0.000	0.000
101	A	350	LEU	0	-0.030	0.002	148.707	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	351	LYS	1	0.988	0.965	147.867	-2.223	-2.223	0.000	0.000	0.000	0.000
103	A	352	GLU	-1	-0.889	-0.936	151.436	2.140	2.140	0.000	0.000	0.000	0.000
104	A	353	LYS	1	0.845	0.913	153.260	-2.144	-2.144	0.000	0.000	0.000	0.000
105	A	354	ASP	-1	-0.938	-0.950	153.776	2.122	2.122	0.000	0.000	0.000	0.000
106	A	355	SER	0	0.049	0.027	155.918	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	356	MET	0	-0.046	-0.027	158.063	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	357	VAL	0	-0.041	-0.025	158.712	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	358	GLU	-1	-0.915	-0.955	158.031	2.057	2.057	0.000	0.000	0.000	0.000
110	A	359	SER	0	0.018	0.018	162.254	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	360	LEU	0	-0.006	-0.014	163.231	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	361	THR	0	0.007	-0.005	164.398	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	362	GLU	-1	-0.956	-0.949	166.336	1.949	1.949	0.000	0.000	0.000	0.000
114	A	363	THR	0	-0.054	-0.039	168.565	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	364	ILE	0	-0.005	-0.003	168.168	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	365	GLY	0	0.008	-0.005	171.031	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	366	ILE	0	-0.012	-0.014	172.647	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	367	LEU	0	0.043	0.035	173.564	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	368	ARG	1	0.906	0.955	172.196	-1.900	-1.900	0.000	0.000	0.000	0.000
120	A	369	LYS	1	0.974	0.996	174.959	-1.880	-1.880	0.000	0.000	0.000	0.000
121	A	370	GLU	-1	-0.947	-0.981	178.636	1.828	1.828	0.000	0.000	0.000	0.000
122	A	371	LEU	0	-0.039	-0.028	178.747	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	372	GLU	-1	-0.950	-0.988	180.435	1.807	1.807	0.000	0.000	0.000	0.000
124	A	373	ASN	0	0.033	0.016	182.416	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	374	GLU	-1	-0.928	-0.958	184.527	1.746	1.746	0.000	0.000	0.000	0.000
126	A	375	LYS	1	0.892	0.947	183.493	-1.784	-1.784	0.000	0.000	0.000	0.000
127	A	376	LEU	0	-0.003	0.006	186.448	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	377	LYS	1	0.966	0.988	188.275	-1.748	-1.748	0.000	0.000	0.000	0.000
129	A	378	ALA	0	-0.045	-0.011	190.651	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	379	ALA	0	0.000	-0.006	191.702	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	380	GLU	-1	-0.910	-0.952	193.544	1.681	1.681	0.000	0.000	0.000	0.000
132	A	381	ASN	0	-0.065	-0.031	195.726	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	382	MET	0	-0.005	-0.010	195.039	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	383	ASP	-1	-0.846	-0.919	197.881	1.634	1.634	0.000	0.000	0.000	0.000
135	A	384	SER	0	-0.096	-0.067	200.001	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	385	PHE	0	0.017	0.013	201.041	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	386	GLU	-1	-0.919	-0.961	200.384	1.627	1.627	0.000	0.000	0.000	0.000
138	A	387	LYS	1	0.921	0.972	202.604	-1.626	-1.626	0.000	0.000	0.000	0.000
139	A	388	LEU	0	0.073	0.034	205.944	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	389	SER	0	-0.058	-0.021	205.623	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	390	MET	0	-0.002	-0.011	207.597	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	391	GLU	-1	-0.952	-0.962	209.837	1.552	1.552	0.000	0.000	0.000	0.000
143	A	392	ASN	0	-0.033	-0.035	210.128	-0.013	-0.013	0.000	0.000	0.000	0.000
144	A	393	GLU	-1	-1.020	-0.994	211.441	1.545	1.545	0.000	0.000	0.000	0.000
145	A	394	ASN	0	0.036	0.022	213.661	-0.012	-0.012	0.000	0.000	0.000	0.000
146	A	395	LEU	0	0.044	0.013	215.345	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	396	LYS	1	0.896	0.950	212.805	-1.547	-1.547	0.000	0.000	0.000	0.000
148	A	397	GLU	-1	-0.908	-0.941	217.518	1.502	1.502	0.000	0.000	0.000	0.000
149	A	398	LYS	1	0.983	0.995	220.215	-1.485	-1.485	0.000	0.000	0.000	0.000
150	A	399	ILE	0	-0.033	-0.031	220.206	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	400	ALA	0	-0.053	-0.043	222.433	-0.009	-0.009	0.000	0.000	0.000	0.000
152	A	401	HIS	0	-0.003	0.006	223.419	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	402	TYR	0	0.033	0.021	225.728	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	403	ARG	1	0.865	0.930	222.139	-1.477	-1.477	0.000	0.000	0.000	0.000
155	A	404	ALA	0	-0.002	0.023	228.579	-0.005	-0.005	0.000	0.000	0.000	0.000
156	A	405	GLN	0	-0.015	-0.024	230.930	0.001	0.001	0.000	0.000	0.000	0.000
157	A	406	ARG	1	0.893	0.951	230.269	-1.424	-1.424	0.000	0.000	0.000	0.000
158	A	407	PHE	0	0.036	0.034	232.663	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:250:GLU)