FMO DATABASE

FMODB ID: Z6N5N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-866268.767723
FMO2-HF: Nuclear repulsion	800979.331084
FMO2-HF: Total energy	-65289.43664
FMO2-MP2: Total energy	-65478.235775

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.
75.822	79.128	0.07	-1.482	-1.894	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 : -1.006 / q_NPA : -1.014

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	0.767	0.869	3.723	-44.748	-42.073	-0.014	-1.303	-1.358	0.001
4	A	253	GLU	-1	-0.963	-0.980	3.083	29.485	30.116	0.084	-0.179	-0.536	0.000
5	A	254	ASP	-1	-0.985	-0.984	4.937	27.691	27.691	0.000	0.000	0.000	0.000
6	A	255	GLU	-1	-0.885	-0.937	6.714	23.060	23.060	0.000	0.000	0.000	0.000
7	A	256	VAL	0	-0.034	-0.025	9.295	-1.919	-1.919	0.000	0.000	0.000	0.000
8	A	257	ALA	0	-0.037	-0.026	10.082	-1.661	-1.661	0.000	0.000	0.000	0.000
9	A	258	ASP	-1	-0.859	-0.940	11.718	21.114	21.114	0.000	0.000	0.000	0.000
10	A	259	LEU	0	-0.014	-0.006	13.434	-1.451	-1.451	0.000	0.000	0.000	0.000
11	A	260	LYS	1	0.895	0.973	14.148	-17.787	-17.787	0.000	0.000	0.000	0.000
12	A	261	GLN	0	0.113	0.070	16.507	-1.681	-1.681	0.000	0.000	0.000	0.000
13	A	262	ASP	-1	-0.899	-0.942	17.895	15.050	15.050	0.000	0.000	0.000	0.000
14	A	263	THR	0	-0.136	-0.098	19.785	-0.844	-0.844	0.000	0.000	0.000	0.000
15	A	264	GLU	-1	-0.935	-0.967	19.144	13.803	13.803	0.000	0.000	0.000	0.000
16	A	265	SER	0	-0.046	-0.034	22.403	-0.684	-0.684	0.000	0.000	0.000	0.000
17	A	266	LEU	0	-0.026	-0.004	23.815	-0.571	-0.571	0.000	0.000	0.000	0.000
18	A	267	GLN	0	-0.041	-0.038	24.181	-0.759	-0.759	0.000	0.000	0.000	0.000
19	A	268	LYS	1	0.893	0.965	27.059	-10.645	-10.645	0.000	0.000	0.000	0.000
20	A	269	GLN	0	0.016	0.013	28.541	-0.220	-0.220	0.000	0.000	0.000	0.000
21	A	270	LEU	0	-0.023	-0.020	30.364	-0.377	-0.377	0.000	0.000	0.000	0.000
22	A	271	GLU	-1	-0.945	-0.962	30.054	9.543	9.543	0.000	0.000	0.000	0.000
23	A	272	GLU	-1	-0.848	-0.937	31.940	9.452	9.452	0.000	0.000	0.000	0.000
24	A	273	ASN	0	-0.068	-0.034	34.499	-0.274	-0.274	0.000	0.000	0.000	0.000
25	A	274	GLN	0	-0.037	-0.025	35.700	-0.269	-0.269	0.000	0.000	0.000	0.000
26	A	275	GLU	-1	-0.915	-0.948	37.077	7.942	7.942	0.000	0.000	0.000	0.000
27	A	276	GLU	-1	-0.929	-0.955	38.238	7.840	7.840	0.000	0.000	0.000	0.000
28	A	277	LEU	0	-0.054	-0.051	40.065	-0.270	-0.270	0.000	0.000	0.000	0.000
29	A	278	GLU	-1	-0.897	-0.935	41.980	6.634	6.634	0.000	0.000	0.000	0.000
30	A	279	ILE	0	0.022	0.020	43.411	-0.262	-0.262	0.000	0.000	0.000	0.000
31	A	280	VAL	0	0.004	0.008	44.958	-0.221	-0.221	0.000	0.000	0.000	0.000
32	A	281	GLY	0	0.040	0.030	46.344	-0.134	-0.134	0.000	0.000	0.000	0.000
33	A	282	ASN	0	-0.074	-0.072	47.350	-0.327	-0.327	0.000	0.000	0.000	0.000
34	A	283	MET	0	-0.019	-0.003	49.031	-0.139	-0.139	0.000	0.000	0.000	0.000
35	A	284	LEU	0	-0.003	0.015	50.861	-0.153	-0.153	0.000	0.000	0.000	0.000
36	A	285	ARG	1	0.907	0.947	49.444	-6.265	-6.265	0.000	0.000	0.000	0.000
37	A	286	GLU	-1	-0.873	-0.929	54.068	5.500	5.500	0.000	0.000	0.000	0.000
38	A	287	GLU	-1	-0.840	-0.907	55.706	5.325	5.325	0.000	0.000	0.000	0.000
39	A	288	GLN	0	-0.019	-0.011	55.095	-0.098	-0.098	0.000	0.000	0.000	0.000
40	A	289	GLY	0	-0.006	0.006	58.488	-0.106	-0.106	0.000	0.000	0.000	0.000
41	A	290	LYS	1	0.777	0.857	57.742	-5.582	-5.582	0.000	0.000	0.000	0.000
42	A	291	VAL	0	-0.010	-0.016	60.924	-0.117	-0.117	0.000	0.000	0.000	0.000
43	A	292	ASP	-1	-0.832	-0.899	62.695	4.777	4.777	0.000	0.000	0.000	0.000
44	A	293	GLN	0	0.023	-0.006	64.627	-0.143	-0.143	0.000	0.000	0.000	0.000
45	A	294	LEU	0	-0.007	0.004	64.927	-0.113	-0.113	0.000	0.000	0.000	0.000
46	A	295	GLN	0	-0.024	-0.014	65.999	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	296	LYS	1	0.841	0.925	66.477	-4.810	-4.810	0.000	0.000	0.000	0.000
48	A	297	ARG	1	0.940	0.971	66.727	-4.733	-4.733	0.000	0.000	0.000	0.000
49	A	298	ASN	0	0.040	0.032	71.337	-0.082	-0.082	0.000	0.000	0.000	0.000
50	A	299	VAL	0	0.003	-0.002	73.255	-0.074	-0.074	0.000	0.000	0.000	0.000
51	A	300	ALA	0	-0.070	-0.038	75.188	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	301	HIS	0	0.083	0.027	74.826	-0.094	-0.094	0.000	0.000	0.000	0.000
53	A	302	GLN	0	0.033	0.010	77.510	-0.101	-0.101	0.000	0.000	0.000	0.000
54	A	303	LYS	1	0.909	0.961	77.404	-4.151	-4.151	0.000	0.000	0.000	0.000
55	A	304	GLU	-1	-0.965	-0.985	81.075	3.804	3.804	0.000	0.000	0.000	0.000
56	A	305	ILE	0	0.049	0.031	80.258	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	306	GLY	0	-0.028	-0.025	83.929	-0.046	-0.046	0.000	0.000	0.000	0.000
58	A	307	LYS	1	0.838	0.935	85.492	-3.782	-3.782	0.000	0.000	0.000	0.000
59	A	308	LEU	0	0.139	0.071	85.615	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	309	ARG	1	0.925	0.965	84.936	-3.779	-3.779	0.000	0.000	0.000	0.000
61	A	310	ALA	0	-0.041	-0.018	89.781	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	311	GLU	-1	-0.935	-0.978	89.941	3.520	3.520	0.000	0.000	0.000	0.000
63	A	312	LEU	0	0.004	0.015	92.031	-0.037	-0.037	0.000	0.000	0.000	0.000
64	A	313	GLY	0	0.031	0.005	94.104	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	314	THR	0	-0.009	-0.019	96.007	-0.037	-0.037	0.000	0.000	0.000	0.000
66	A	315	ALA	0	0.010	0.019	97.066	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	316	GLN	0	0.028	0.022	96.131	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	317	ARG	1	0.991	0.989	97.120	-3.315	-3.315	0.000	0.000	0.000	0.000
69	A	318	ASN	0	-0.065	-0.036	101.870	-0.054	-0.054	0.000	0.000	0.000	0.000
70	A	319	LEU	0	0.021	0.025	102.433	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	320	GLU	-1	-0.886	-0.948	103.384	3.103	3.103	0.000	0.000	0.000	0.000
72	A	321	LYS	1	0.875	0.931	105.117	-3.096	-3.096	0.000	0.000	0.000	0.000
73	A	322	ALA	0	-0.021	-0.018	107.532	-0.034	-0.034	0.000	0.000	0.000	0.000
74	A	323	ASP	-1	-0.759	-0.878	108.383	2.933	2.933	0.000	0.000	0.000	0.000
75	A	324	GLN	0	-0.004	0.001	109.987	-0.041	-0.041	0.000	0.000	0.000	0.000
76	A	325	LEU	0	-0.021	-0.018	112.207	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	326	LEU	0	0.015	0.023	111.201	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	327	LYS	1	0.824	0.917	111.048	-2.933	-2.933	0.000	0.000	0.000	0.000
79	A	328	ARG	1	0.921	0.964	116.688	-2.771	-2.771	0.000	0.000	0.000	0.000
80	A	329	ASN	0	0.036	0.026	117.774	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	330	SER	0	0.017	-0.010	117.786	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	331	GLN	0	-0.009	-0.007	119.725	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	332	GLN	0	0.000	0.009	122.149	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	333	GLN	0	0.017	0.003	121.267	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	334	ASN	0	-0.038	-0.027	124.535	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	335	GLN	0	-0.003	-0.013	127.396	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	336	GLN	0	0.033	0.029	128.138	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	337	SER	0	-0.017	-0.006	129.171	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	338	LEU	0	-0.066	-0.052	131.021	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	339	ASP	-1	-0.882	-0.933	132.995	2.400	2.400	0.000	0.000	0.000	0.000
91	A	340	MET	0	0.012	0.001	132.182	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	341	ARG	1	0.867	0.935	131.654	-2.461	-2.461	0.000	0.000	0.000	0.000
93	A	342	LYS	1	0.957	0.978	136.947	-2.371	-2.371	0.000	0.000	0.000	0.000
94	A	343	LEU	0	0.013	0.037	137.831	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	344	GLY	0	0.032	-0.002	139.690	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	345	GLU	-1	-0.917	-0.971	141.457	2.298	2.298	0.000	0.000	0.000	0.000
97	A	346	LEU	0	-0.002	0.002	142.184	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	347	GLU	-1	-0.931	-0.949	142.721	2.252	2.252	0.000	0.000	0.000	0.000
99	A	348	ALA	0	-0.011	-0.030	145.697	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	349	ASP	-1	-0.813	-0.893	147.403	2.154	2.154	0.000	0.000	0.000	0.000
101	A	350	LEU	0	-0.028	-0.007	148.763	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	351	LYS	1	0.910	0.949	146.813	-2.231	-2.231	0.000	0.000	0.000	0.000
103	A	352	GLU	-1	-0.891	-0.931	151.731	2.135	2.135	0.000	0.000	0.000	0.000
104	A	353	LYS	1	0.730	0.847	151.971	-2.164	-2.164	0.000	0.000	0.000	0.000
105	A	354	ASP	-1	-0.931	-0.965	153.672	2.112	2.112	0.000	0.000	0.000	0.000
106	A	355	SER	0	0.021	0.021	155.943	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	356	MET	0	-0.041	-0.027	158.147	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	357	VAL	0	-0.049	-0.032	158.810	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	358	GLU	-1	-0.906	-0.940	158.775	2.046	2.046	0.000	0.000	0.000	0.000
110	A	359	SER	0	0.009	0.004	162.305	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	360	LEU	0	-0.030	-0.018	162.926	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	361	THR	0	0.008	-0.001	164.929	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	362	GLU	-1	-0.922	-0.938	166.525	1.934	1.934	0.000	0.000	0.000	0.000
114	A	363	THR	0	-0.059	-0.044	168.788	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	364	ILE	0	-0.020	-0.016	167.782	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	365	GLY	0	0.015	0.002	171.035	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	366	ILE	0	-0.032	-0.021	172.380	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	367	LEU	0	0.062	0.042	173.662	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	368	ARG	1	0.902	0.953	172.151	-1.897	-1.897	0.000	0.000	0.000	0.000
120	A	369	LYS	1	0.959	0.993	174.427	-1.879	-1.879	0.000	0.000	0.000	0.000
121	A	370	GLU	-1	-0.935	-0.973	178.504	1.825	1.825	0.000	0.000	0.000	0.000
122	A	371	LEU	0	-0.029	-0.022	178.541	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	372	GLU	-1	-0.950	-0.991	180.265	1.806	1.806	0.000	0.000	0.000	0.000
124	A	373	ASN	0	0.021	0.012	182.859	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	374	GLU	-1	-0.845	-0.903	184.678	1.741	1.741	0.000	0.000	0.000	0.000
126	A	375	LYS	1	0.894	0.949	183.246	-1.782	-1.782	0.000	0.000	0.000	0.000
127	A	376	LEU	0	0.002	0.009	186.506	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	377	LYS	1	0.890	0.935	188.090	-1.748	-1.748	0.000	0.000	0.000	0.000
129	A	378	ALA	0	-0.050	-0.013	190.655	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	379	ALA	0	-0.002	-0.007	191.727	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	380	GLU	-1	-0.903	-0.954	193.546	1.678	1.678	0.000	0.000	0.000	0.000
132	A	381	ASN	0	-0.065	-0.024	195.261	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	382	MET	0	0.007	-0.001	194.988	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	383	ASP	-1	-0.757	-0.867	197.882	1.626	1.626	0.000	0.000	0.000	0.000
135	A	384	SER	0	-0.035	-0.030	199.768	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	385	PHE	0	-0.022	0.001	201.024	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	386	GLU	-1	-0.924	-0.968	200.463	1.624	1.624	0.000	0.000	0.000	0.000
138	A	387	LYS	1	0.795	0.888	201.961	-1.630	-1.630	0.000	0.000	0.000	0.000
139	A	388	LEU	0	0.105	0.045	205.562	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	389	SER	0	-0.072	-0.020	205.372	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	390	MET	0	0.010	-0.008	207.573	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	391	GLU	-1	-0.939	-0.958	209.421	1.553	1.553	0.000	0.000	0.000	0.000
143	A	392	ASN	0	-0.106	-0.068	210.315	-0.015	-0.015	0.000	0.000	0.000	0.000
144	A	393	GLU	-1	-0.985	-0.979	211.204	1.544	1.544	0.000	0.000	0.000	0.000
145	A	394	ASN	0	0.019	0.016	213.662	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	395	LEU	0	0.025	0.007	215.189	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	396	LYS	1	0.907	0.952	213.224	-1.543	-1.543	0.000	0.000	0.000	0.000
148	A	397	GLU	-1	-0.861	-0.918	217.589	1.498	1.498	0.000	0.000	0.000	0.000
149	A	398	LYS	1	0.980	0.998	220.216	-1.481	-1.481	0.000	0.000	0.000	0.000
150	A	399	ILE	0	-0.029	-0.032	219.820	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	400	ALA	0	-0.051	-0.038	222.376	-0.009	-0.009	0.000	0.000	0.000	0.000
152	A	401	HIS	0	-0.019	-0.011	223.047	-0.009	-0.009	0.000	0.000	0.000	0.000
153	A	402	TYR	0	0.012	0.009	225.479	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	403	ARG	1	0.872	0.935	221.991	-1.475	-1.475	0.000	0.000	0.000	0.000
155	A	404	ALA	0	-0.010	0.020	228.579	-0.005	-0.005	0.000	0.000	0.000	0.000
156	A	405	GLN	0	-0.014	-0.027	230.930	0.000	0.000	0.000	0.000	0.000	0.000
157	A	406	ARG	1	0.900	0.956	230.470	-1.421	-1.421	0.000	0.000	0.000	0.000
158	A	407	PHE	0	0.043	0.037	232.611	-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)