FMO DATABASE

FMODB ID: R9YG8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-866085.114358
FMO2-HF: Nuclear repulsion	800793.938594
FMO2-HF: Total energy	-65291.175764
FMO2-MP2: Total energy	-65479.831628

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.
71.838	75.014	0.142	-1.35	-1.969	0.004

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 : -0.991 / q_NPA : -1.007

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	0.761	0.861	3.502	-47.609	-45.031	0.015	-1.197	-1.396	0.004
4	A	253	GLU	-1	-0.944	-0.979	2.898	30.750	31.348	0.127	-0.153	-0.573	0.000
5	A	254	ASP	-1	-0.931	-0.962	5.350	29.287	29.287	0.000	0.000	0.000	0.000
6	A	255	GLU	-1	-0.949	-0.968	7.188	20.750	20.750	0.000	0.000	0.000	0.000
7	A	256	VAL	0	-0.037	-0.030	9.252	-2.076	-2.076	0.000	0.000	0.000	0.000
8	A	257	ALA	0	-0.033	-0.012	10.136	-1.694	-1.694	0.000	0.000	0.000	0.000
9	A	258	ASP	-1	-0.891	-0.944	11.192	19.765	19.765	0.000	0.000	0.000	0.000
10	A	259	LEU	0	0.016	0.006	13.109	-1.687	-1.687	0.000	0.000	0.000	0.000
11	A	260	LYS	1	0.783	0.889	14.673	-16.788	-16.788	0.000	0.000	0.000	0.000
12	A	261	GLN	0	0.013	0.012	16.145	-1.749	-1.749	0.000	0.000	0.000	0.000
13	A	262	ASP	-1	-0.874	-0.921	17.944	14.745	14.745	0.000	0.000	0.000	0.000
14	A	263	THR	0	-0.042	-0.034	19.864	-0.690	-0.690	0.000	0.000	0.000	0.000
15	A	264	GLU	-1	-0.823	-0.902	19.466	13.814	13.814	0.000	0.000	0.000	0.000
16	A	265	SER	0	-0.050	-0.030	22.076	-0.692	-0.692	0.000	0.000	0.000	0.000
17	A	266	LEU	0	-0.018	-0.008	23.620	-0.610	-0.610	0.000	0.000	0.000	0.000
18	A	267	GLN	0	-0.067	-0.044	24.592	-0.774	-0.774	0.000	0.000	0.000	0.000
19	A	268	LYS	1	0.891	0.953	27.046	-10.599	-10.599	0.000	0.000	0.000	0.000
20	A	269	GLN	0	0.001	-0.009	28.088	-0.205	-0.205	0.000	0.000	0.000	0.000
21	A	270	LEU	0	-0.033	-0.018	30.299	-0.416	-0.416	0.000	0.000	0.000	0.000
22	A	271	GLU	-1	-0.957	-0.977	29.827	9.666	9.666	0.000	0.000	0.000	0.000
23	A	272	GLU	-1	-0.831	-0.912	32.160	9.405	9.405	0.000	0.000	0.000	0.000
24	A	273	ASN	0	-0.063	-0.040	34.738	-0.285	-0.285	0.000	0.000	0.000	0.000
25	A	274	GLN	0	-0.020	-0.016	35.458	-0.344	-0.344	0.000	0.000	0.000	0.000
26	A	275	GLU	-1	-0.947	-0.962	37.455	7.904	7.904	0.000	0.000	0.000	0.000
27	A	276	GLU	-1	-0.920	-0.950	38.200	7.814	7.814	0.000	0.000	0.000	0.000
28	A	277	LEU	0	-0.035	-0.023	39.889	-0.278	-0.278	0.000	0.000	0.000	0.000
29	A	278	GLU	-1	-0.852	-0.922	42.186	6.535	6.535	0.000	0.000	0.000	0.000
30	A	279	ILE	0	-0.006	0.018	43.232	-0.261	-0.261	0.000	0.000	0.000	0.000
31	A	280	VAL	0	0.007	-0.008	45.031	-0.222	-0.222	0.000	0.000	0.000	0.000
32	A	281	GLY	0	0.029	0.017	46.339	-0.171	-0.171	0.000	0.000	0.000	0.000
33	A	282	ASN	0	-0.113	-0.081	47.393	-0.317	-0.317	0.000	0.000	0.000	0.000
34	A	283	MET	0	0.011	0.004	49.088	-0.146	-0.146	0.000	0.000	0.000	0.000
35	A	284	LEU	0	-0.011	0.007	50.752	-0.160	-0.160	0.000	0.000	0.000	0.000
36	A	285	ARG	1	0.887	0.938	49.230	-6.305	-6.305	0.000	0.000	0.000	0.000
37	A	286	GLU	-1	-0.868	-0.912	54.427	5.515	5.515	0.000	0.000	0.000	0.000
38	A	287	GLU	-1	-0.828	-0.908	55.729	5.344	5.344	0.000	0.000	0.000	0.000
39	A	288	GLN	0	-0.030	-0.014	54.804	-0.106	-0.106	0.000	0.000	0.000	0.000
40	A	289	GLY	0	0.013	0.011	58.724	-0.113	-0.113	0.000	0.000	0.000	0.000
41	A	290	LYS	1	0.781	0.859	57.648	-5.603	-5.603	0.000	0.000	0.000	0.000
42	A	291	VAL	0	0.008	0.001	60.945	-0.124	-0.124	0.000	0.000	0.000	0.000
43	A	292	ASP	-1	-0.824	-0.897	62.881	4.755	4.755	0.000	0.000	0.000	0.000
44	A	293	GLN	0	0.044	0.014	64.561	-0.151	-0.151	0.000	0.000	0.000	0.000
45	A	294	LEU	0	-0.020	-0.005	64.716	-0.111	-0.111	0.000	0.000	0.000	0.000
46	A	295	GLN	0	-0.010	0.001	65.513	-0.096	-0.096	0.000	0.000	0.000	0.000
47	A	296	LYS	1	0.812	0.896	66.514	-4.842	-4.842	0.000	0.000	0.000	0.000
48	A	297	ARG	1	0.914	0.954	66.699	-4.754	-4.754	0.000	0.000	0.000	0.000
49	A	298	ASN	0	0.038	0.018	70.841	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	299	VAL	0	-0.022	-0.015	73.096	-0.079	-0.079	0.000	0.000	0.000	0.000
51	A	300	ALA	0	-0.040	-0.018	75.241	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	301	HIS	0	0.069	0.027	74.506	-0.102	-0.102	0.000	0.000	0.000	0.000
53	A	302	GLN	0	-0.002	0.002	77.782	-0.104	-0.104	0.000	0.000	0.000	0.000
54	A	303	LYS	1	0.916	0.963	77.171	-4.174	-4.174	0.000	0.000	0.000	0.000
55	A	304	GLU	-1	-0.909	-0.938	81.326	3.802	3.802	0.000	0.000	0.000	0.000
56	A	305	ILE	0	0.122	0.056	80.454	-0.064	-0.064	0.000	0.000	0.000	0.000
57	A	306	GLY	0	-0.052	-0.028	83.776	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	307	LYS	1	0.739	0.877	85.308	-3.779	-3.779	0.000	0.000	0.000	0.000
59	A	308	LEU	0	0.152	0.077	85.509	-0.057	-0.057	0.000	0.000	0.000	0.000
60	A	309	ARG	1	0.925	0.958	84.228	-3.801	-3.801	0.000	0.000	0.000	0.000
61	A	310	ALA	0	-0.018	-0.005	89.876	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	311	GLU	-1	-0.871	-0.941	89.993	3.523	3.523	0.000	0.000	0.000	0.000
63	A	312	LEU	0	0.036	0.022	91.965	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	313	GLY	0	0.001	-0.001	93.923	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	314	THR	0	-0.076	-0.043	95.667	-0.044	-0.044	0.000	0.000	0.000	0.000
66	A	315	ALA	0	0.018	0.006	97.237	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	316	GLN	0	-0.004	-0.002	95.626	-0.035	-0.035	0.000	0.000	0.000	0.000
68	A	317	ARG	1	0.973	0.984	96.907	-3.320	-3.320	0.000	0.000	0.000	0.000
69	A	318	ASN	0	-0.016	-0.012	101.591	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	319	LEU	0	0.023	0.030	102.720	-0.035	-0.035	0.000	0.000	0.000	0.000
71	A	320	GLU	-1	-0.886	-0.957	102.766	3.110	3.110	0.000	0.000	0.000	0.000
72	A	321	LYS	1	0.871	0.930	104.897	-3.106	-3.106	0.000	0.000	0.000	0.000
73	A	322	ALA	0	0.016	0.007	107.554	-0.034	-0.034	0.000	0.000	0.000	0.000
74	A	323	ASP	-1	-0.771	-0.869	108.386	2.916	2.916	0.000	0.000	0.000	0.000
75	A	324	GLN	0	-0.017	-0.015	108.937	-0.049	-0.049	0.000	0.000	0.000	0.000
76	A	325	LEU	0	-0.019	-0.006	112.227	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	326	LEU	0	0.014	0.018	110.931	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	327	LYS	1	0.830	0.903	110.770	-2.943	-2.943	0.000	0.000	0.000	0.000
79	A	328	ARG	1	0.911	0.972	116.050	-2.765	-2.765	0.000	0.000	0.000	0.000
80	A	329	ASN	0	0.046	0.021	117.725	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	330	SER	0	-0.011	-0.025	117.565	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	331	GLN	0	-0.031	-0.018	119.119	-0.040	-0.040	0.000	0.000	0.000	0.000
83	A	332	GLN	0	0.007	0.000	121.681	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	333	GLN	0	0.025	0.016	121.125	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	334	ASN	0	-0.017	-0.005	124.203	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	335	GLN	0	0.007	0.000	127.048	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	336	GLN	0	0.010	0.005	127.969	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	337	SER	0	0.005	-0.004	128.794	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	338	LEU	0	-0.053	-0.022	130.729	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	339	ASP	-1	-0.861	-0.923	132.860	2.399	2.399	0.000	0.000	0.000	0.000
91	A	340	MET	0	-0.001	-0.007	132.105	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	341	ARG	1	0.851	0.925	131.273	-2.468	-2.468	0.000	0.000	0.000	0.000
93	A	342	LYS	1	0.806	0.877	136.799	-2.357	-2.357	0.000	0.000	0.000	0.000
94	A	343	LEU	0	0.028	0.023	137.692	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	344	GLY	0	0.029	0.013	139.301	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	345	GLU	-1	-0.813	-0.899	140.701	2.304	2.304	0.000	0.000	0.000	0.000
97	A	346	LEU	0	-0.010	0.001	141.857	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	347	GLU	-1	-0.852	-0.921	142.804	2.235	2.235	0.000	0.000	0.000	0.000
99	A	348	ALA	0	0.000	0.012	145.214	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	349	ASP	-1	-0.825	-0.907	147.088	2.156	2.156	0.000	0.000	0.000	0.000
101	A	350	LEU	0	-0.020	0.006	148.510	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	351	LYS	1	0.834	0.899	146.623	-2.232	-2.232	0.000	0.000	0.000	0.000
103	A	352	GLU	-1	-0.903	-0.952	151.392	2.134	2.134	0.000	0.000	0.000	0.000
104	A	353	LYS	1	0.685	0.829	151.756	-2.164	-2.164	0.000	0.000	0.000	0.000
105	A	354	ASP	-1	-0.879	-0.943	153.235	2.114	2.114	0.000	0.000	0.000	0.000
106	A	355	SER	0	0.020	-0.008	156.129	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	356	MET	0	-0.033	-0.012	158.035	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	357	VAL	0	-0.035	-0.015	158.751	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	358	GLU	-1	-0.867	-0.917	159.219	2.040	2.040	0.000	0.000	0.000	0.000
110	A	359	SER	0	0.034	0.019	162.277	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	360	LEU	0	-0.038	-0.013	162.562	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	361	THR	0	-0.072	-0.049	164.647	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	362	GLU	-1	-0.898	-0.937	166.647	1.925	1.925	0.000	0.000	0.000	0.000
114	A	363	THR	0	-0.058	-0.034	168.542	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	364	ILE	0	-0.010	-0.012	167.614	-0.017	-0.017	0.000	0.000	0.000	0.000
116	A	365	GLY	0	0.002	-0.006	170.913	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	366	ILE	0	-0.051	-0.033	171.805	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	367	LEU	0	0.068	0.033	173.210	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	368	ARG	1	0.868	0.946	172.313	-1.897	-1.897	0.000	0.000	0.000	0.000
120	A	369	LYS	1	1.005	1.014	173.858	-1.885	-1.885	0.000	0.000	0.000	0.000
121	A	370	GLU	-1	-0.898	-0.942	178.043	1.827	1.827	0.000	0.000	0.000	0.000
122	A	371	LEU	0	-0.018	-0.023	178.512	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	372	GLU	-1	-0.967	-0.985	180.286	1.807	1.807	0.000	0.000	0.000	0.000
124	A	373	ASN	0	-0.023	-0.026	182.511	-0.020	-0.020	0.000	0.000	0.000	0.000
125	A	374	GLU	-1	-0.842	-0.903	184.439	1.743	1.743	0.000	0.000	0.000	0.000
126	A	375	LYS	1	0.889	0.946	183.045	-1.788	-1.788	0.000	0.000	0.000	0.000
127	A	376	LEU	0	-0.007	0.003	186.578	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	377	LYS	1	0.892	0.934	187.640	-1.751	-1.751	0.000	0.000	0.000	0.000
129	A	378	ALA	0	-0.006	-0.002	190.622	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	379	ALA	0	-0.014	-0.005	192.019	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	380	GLU	-1	-0.882	-0.942	193.546	1.679	1.679	0.000	0.000	0.000	0.000
132	A	381	ASN	0	-0.058	-0.022	194.780	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	382	MET	0	-0.025	-0.002	195.384	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	383	ASP	-1	-0.781	-0.868	198.019	1.623	1.623	0.000	0.000	0.000	0.000
135	A	384	SER	0	-0.029	-0.042	199.492	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	385	PHE	0	-0.013	-0.003	200.809	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	386	GLU	-1	-0.916	-0.953	200.221	1.626	1.626	0.000	0.000	0.000	0.000
138	A	387	LYS	1	0.790	0.885	202.126	-1.630	-1.630	0.000	0.000	0.000	0.000
139	A	388	LEU	0	0.080	0.042	205.625	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	389	SER	0	-0.041	-0.033	205.362	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	390	MET	0	0.010	-0.001	207.767	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	391	GLU	-1	-0.929	-0.962	208.955	1.556	1.556	0.000	0.000	0.000	0.000
143	A	392	ASN	0	-0.049	-0.032	210.275	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	393	GLU	-1	-0.964	-0.971	211.215	1.544	1.544	0.000	0.000	0.000	0.000
145	A	394	ASN	0	-0.001	-0.007	213.734	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	395	LEU	0	0.001	-0.009	214.684	-0.012	-0.012	0.000	0.000	0.000	0.000
147	A	396	LYS	1	0.842	0.921	213.246	-1.543	-1.543	0.000	0.000	0.000	0.000
148	A	397	GLU	-1	-0.840	-0.902	217.615	1.498	1.498	0.000	0.000	0.000	0.000
149	A	398	LYS	1	0.936	0.975	220.134	-1.480	-1.480	0.000	0.000	0.000	0.000
150	A	399	ILE	0	-0.024	-0.021	219.445	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	400	ALA	0	-0.030	-0.020	222.246	-0.008	-0.008	0.000	0.000	0.000	0.000
152	A	401	HIS	0	-0.034	-0.030	223.163	-0.011	-0.011	0.000	0.000	0.000	0.000
153	A	402	TYR	0	-0.006	-0.003	225.073	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	403	ARG	1	0.916	0.965	221.880	-1.476	-1.476	0.000	0.000	0.000	0.000
155	A	404	ALA	0	-0.018	0.013	228.495	-0.005	-0.005	0.000	0.000	0.000	0.000
156	A	405	GLN	0	-0.031	-0.026	231.056	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	406	ARG	1	0.902	0.949	230.720	-1.419	-1.419	0.000	0.000	0.000	0.000
158	A	407	PHE	0	0.050	0.043	232.913	-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)