FMO DATABASE

FMODB ID: K3VJ3

Calculation Name: 3LW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LW9

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1I3

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1605502.524778
FMO2-HF: Nuclear repulsion	1537527.974071
FMO2-HF: Total energy	-67974.550707
FMO2-MP2: Total energy	-68173.643404

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:358:GLU)

Summations of interaction energy for fragment #1(A:358: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.
57.98	66.912	3.122	-4.674	-7.38	0.019

Interaction energy analysis for fragmet #1(A:358:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.893 / q_NPA : -0.969

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	360	VAL	0	0.008	0.020	2.629	-22.691	-16.766	0.337	-3.142	-3.121	0.020
4	A	361	PRO	0	-0.009	0.004	4.402	5.066	5.241	-0.001	-0.030	-0.144	0.000
5	A	362	LEU	0	0.012	0.003	5.180	0.009	0.009	0.000	0.000	0.000	0.000
6	A	363	ILE	0	-0.019	-0.011	8.164	-2.562	-2.562	0.000	0.000	0.000	0.000
7	A	364	LEU	0	0.011	0.003	11.885	-0.232	-0.232	0.000	0.000	0.000	0.000
8	A	365	LEU	0	-0.010	-0.002	14.811	-0.826	-0.826	0.000	0.000	0.000	0.000
9	A	366	VAL	0	0.001	-0.007	18.198	-0.182	-0.182	0.000	0.000	0.000	0.000
10	A	367	PRO	0	0.047	0.035	20.731	-0.245	-0.245	0.000	0.000	0.000	0.000
11	A	368	LYS	1	0.812	0.862	24.451	-12.212	-12.212	0.000	0.000	0.000	0.000
12	A	369	SER	0	-0.037	-0.014	26.032	0.038	0.038	0.000	0.000	0.000	0.000
13	A	370	ARG	1	0.742	0.805	24.234	-11.054	-11.054	0.000	0.000	0.000	0.000
14	A	371	ARG	1	0.771	0.867	19.322	-13.965	-13.965	0.000	0.000	0.000	0.000
15	A	372	GLU	-1	-0.769	-0.882	21.743	13.174	13.174	0.000	0.000	0.000	0.000
16	A	373	ASP	-1	-0.874	-0.922	23.896	11.011	11.011	0.000	0.000	0.000	0.000
17	A	374	LEU	0	-0.031	-0.013	19.454	0.196	0.196	0.000	0.000	0.000	0.000
18	A	375	GLU	-1	-0.829	-0.905	17.496	16.761	16.761	0.000	0.000	0.000	0.000
19	A	376	LYS	1	0.825	0.899	20.017	-11.165	-11.165	0.000	0.000	0.000	0.000
20	A	377	ALA	0	-0.047	-0.016	21.503	-0.184	-0.184	0.000	0.000	0.000	0.000
21	A	378	GLN	0	-0.043	-0.026	17.859	0.543	0.543	0.000	0.000	0.000	0.000
22	A	379	LEU	0	0.036	0.014	15.738	0.651	0.651	0.000	0.000	0.000	0.000
23	A	380	ALA	0	0.032	0.019	12.049	0.629	0.629	0.000	0.000	0.000	0.000
24	A	381	GLU	-1	-0.776	-0.874	11.893	22.728	22.728	0.000	0.000	0.000	0.000
25	A	382	ARG	1	0.848	0.935	13.491	-14.051	-14.051	0.000	0.000	0.000	0.000
26	A	383	MET	0	-0.013	-0.002	12.099	0.000	0.000	0.000	0.000	0.000	0.000
27	A	384	ARG	1	0.754	0.855	6.928	-26.203	-26.203	0.000	0.000	0.000	0.000
28	A	385	SER	0	-0.029	-0.022	9.843	0.628	0.628	0.000	0.000	0.000	0.000
29	A	386	GLN	0	-0.065	-0.039	12.473	-0.406	-0.406	0.000	0.000	0.000	0.000
30	A	387	PHE	0	0.034	0.016	7.775	0.008	0.008	0.000	0.000	0.000	0.000
31	A	388	PHE	0	-0.058	-0.027	8.826	0.198	0.198	0.000	0.000	0.000	0.000
32	A	389	ILE	0	-0.038	-0.023	10.535	-0.730	-0.730	0.000	0.000	0.000	0.000
33	A	390	ASP	-1	-0.815	-0.868	13.599	16.836	16.836	0.000	0.000	0.000	0.000
34	A	391	TYR	0	-0.049	-0.030	10.622	-0.772	-0.772	0.000	0.000	0.000	0.000
35	A	392	GLY	0	0.014	0.026	11.421	0.529	0.529	0.000	0.000	0.000	0.000
36	A	393	VAL	0	-0.049	-0.025	5.548	1.605	1.605	0.000	0.000	0.000	0.000
37	A	394	ARG	1	0.932	0.961	3.365	-34.949	-34.510	0.004	-0.073	-0.369	0.000
38	A	395	LEU	0	0.038	0.022	3.202	3.985	5.126	0.075	-0.473	-0.743	-0.004
39	A	396	PRO	0	0.007	0.018	2.200	-6.142	-5.059	2.669	-1.003	-2.749	0.003
40	A	397	GLU	-1	-0.891	-0.948	3.535	22.176	22.345	0.038	0.047	-0.254	0.000
41	A	398	VAL	0	-0.006	-0.024	6.753	2.743	2.743	0.000	0.000	0.000	0.000
42	A	399	LEU	0	-0.044	-0.011	9.444	-2.752	-2.752	0.000	0.000	0.000	0.000
43	A	400	LEU	0	0.031	0.023	12.282	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	401	ARG	1	0.889	0.934	14.822	-19.458	-19.458	0.000	0.000	0.000	0.000
45	A	402	ASP	-1	-0.750	-0.866	18.022	13.054	13.054	0.000	0.000	0.000	0.000
46	A	403	GLY	0	0.001	-0.007	21.224	0.466	0.466	0.000	0.000	0.000	0.000
47	A	404	GLU	-1	-0.870	-0.925	22.396	11.771	11.771	0.000	0.000	0.000	0.000
48	A	405	GLY	0	-0.041	-0.022	25.426	0.108	0.108	0.000	0.000	0.000	0.000
49	A	406	LEU	0	-0.082	-0.019	21.742	-0.044	-0.044	0.000	0.000	0.000	0.000
50	A	407	ASP	-1	-0.895	-0.939	25.886	10.577	10.577	0.000	0.000	0.000	0.000
51	A	408	ASP	-1	-0.761	-0.890	26.355	11.493	11.493	0.000	0.000	0.000	0.000
52	A	409	ASN	0	-0.035	-0.024	25.892	0.078	0.078	0.000	0.000	0.000	0.000
53	A	410	SER	0	0.019	0.027	23.597	0.102	0.102	0.000	0.000	0.000	0.000
54	A	411	ILE	0	-0.022	-0.012	17.237	0.147	0.147	0.000	0.000	0.000	0.000
55	A	412	VAL	0	-0.038	-0.019	16.941	-0.173	-0.173	0.000	0.000	0.000	0.000
56	A	413	LEU	0	0.008	0.024	10.270	0.411	0.411	0.000	0.000	0.000	0.000
57	A	414	LEU	0	-0.016	-0.016	12.362	-0.848	-0.848	0.000	0.000	0.000	0.000
58	A	415	ILE	0	0.041	0.015	5.714	1.921	1.921	0.000	0.000	0.000	0.000
59	A	416	ASN	0	-0.023	-0.014	7.922	1.041	1.041	0.000	0.000	0.000	0.000
60	A	417	GLU	-1	-0.907	-0.958	9.436	22.714	22.714	0.000	0.000	0.000	0.000
61	A	418	ILE	0	-0.029	0.005	11.209	-2.440	-2.440	0.000	0.000	0.000	0.000
62	A	419	ARG	1	0.919	0.950	12.380	-14.749	-14.749	0.000	0.000	0.000	0.000
63	A	420	VAL	0	-0.022	-0.005	9.855	-0.140	-0.140	0.000	0.000	0.000	0.000
64	A	421	GLU	-1	-0.839	-0.911	13.305	17.022	17.022	0.000	0.000	0.000	0.000
65	A	422	GLN	0	-0.012	-0.013	16.000	0.479	0.479	0.000	0.000	0.000	0.000
66	A	423	PHE	0	0.013	0.003	14.605	-0.327	-0.327	0.000	0.000	0.000	0.000
67	A	424	THR	0	0.022	0.016	20.647	-0.095	-0.095	0.000	0.000	0.000	0.000
68	A	425	VAL	0	-0.051	-0.035	20.589	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	426	TYR	0	0.035	0.010	24.012	-0.093	-0.093	0.000	0.000	0.000	0.000
70	A	427	PHE	0	0.021	-0.004	21.990	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	428	ASP	-1	-0.846	-0.874	26.908	10.104	10.104	0.000	0.000	0.000	0.000
72	A	429	LEU	0	-0.067	-0.026	29.188	-0.357	-0.357	0.000	0.000	0.000	0.000
73	A	430	MET	0	-0.040	-0.012	28.458	0.596	0.596	0.000	0.000	0.000	0.000
74	A	431	ARG	1	0.845	0.919	22.935	-12.628	-12.628	0.000	0.000	0.000	0.000
75	A	432	VAL	0	0.028	0.000	28.174	0.012	0.012	0.000	0.000	0.000	0.000
76	A	433	VAL	0	-0.078	-0.041	25.783	0.159	0.159	0.000	0.000	0.000	0.000
77	A	434	ASN	0	-0.005	-0.002	28.298	0.263	0.263	0.000	0.000	0.000	0.000
78	A	435	TYR	0	-0.010	-0.035	31.308	-0.270	-0.270	0.000	0.000	0.000	0.000
79	A	436	SER	0	0.049	0.023	33.469	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	437	ASP	-1	-0.843	-0.906	36.935	8.123	8.123	0.000	0.000	0.000	0.000
81	A	438	GLU	-1	-0.952	-0.962	39.790	7.064	7.064	0.000	0.000	0.000	0.000
82	A	439	VAL	0	0.006	0.015	36.582	-0.122	-0.122	0.000	0.000	0.000	0.000
83	A	440	VAL	0	0.011	0.004	40.054	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	441	SER	0	-0.118	-0.060	42.314	-0.216	-0.216	0.000	0.000	0.000	0.000
85	A	442	PHE	0	0.004	-0.007	40.819	-0.172	-0.172	0.000	0.000	0.000	0.000
86	A	443	GLY	0	-0.026	-0.011	44.584	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	444	ILE	0	-0.047	-0.007	38.101	0.047	0.047	0.000	0.000	0.000	0.000
88	A	445	ASN	0	-0.020	-0.026	39.822	0.020	0.020	0.000	0.000	0.000	0.000
89	A	446	PRO	0	-0.028	0.006	34.269	0.082	0.082	0.000	0.000	0.000	0.000
90	A	447	THR	0	0.010	0.011	31.706	-0.086	-0.086	0.000	0.000	0.000	0.000
91	A	448	ILE	0	-0.022	-0.019	31.782	0.216	0.216	0.000	0.000	0.000	0.000
92	A	449	HIS	0	0.013	0.002	24.481	-0.455	-0.455	0.000	0.000	0.000	0.000
93	A	450	GLN	0	0.002	-0.006	28.573	-0.342	-0.342	0.000	0.000	0.000	0.000
94	A	451	GLN	0	0.007	0.014	20.800	-0.275	-0.275	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.016	0.010	25.618	0.190	0.190	0.000	0.000	0.000	0.000
96	A	453	SER	0	-0.024	-0.018	26.665	-0.244	-0.244	0.000	0.000	0.000	0.000
97	A	454	SER	0	-0.022	0.009	25.643	-0.219	-0.219	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.016	-0.024	27.728	0.012	0.012	0.000	0.000	0.000	0.000
99	A	456	TYR	0	-0.030	-0.013	23.032	0.253	0.253	0.000	0.000	0.000	0.000
100	A	457	PHE	0	0.055	0.030	28.175	-0.090	-0.090	0.000	0.000	0.000	0.000
101	A	458	TRP	0	-0.002	-0.008	24.079	0.352	0.352	0.000	0.000	0.000	0.000
102	A	459	VAL	0	0.027	0.023	31.141	-0.278	-0.278	0.000	0.000	0.000	0.000
103	A	460	THR	0	0.021	-0.031	32.776	0.259	0.259	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.046	0.004	30.103	-0.099	-0.099	0.000	0.000	0.000	0.000
105	A	462	GLU	-1	-0.879	-0.916	34.567	7.354	7.354	0.000	0.000	0.000	0.000
106	A	463	GLU	-1	-0.814	-0.890	36.951	8.078	8.078	0.000	0.000	0.000	0.000
107	A	464	GLY	0	0.025	-0.001	34.144	-0.042	-0.042	0.000	0.000	0.000	0.000
108	A	465	GLU	-1	-0.828	-0.912	33.788	9.095	9.095	0.000	0.000	0.000	0.000
109	A	466	LYS	1	0.835	0.910	36.731	-7.550	-7.550	0.000	0.000	0.000	0.000
110	A	467	LEU	0	0.018	0.013	35.532	-0.094	-0.094	0.000	0.000	0.000	0.000
111	A	468	ARG	1	0.801	0.887	29.603	-9.601	-9.601	0.000	0.000	0.000	0.000
112	A	469	GLU	-1	-0.952	-0.968	36.138	7.821	7.821	0.000	0.000	0.000	0.000
113	A	470	MET	0	-0.096	-0.040	38.945	-0.226	-0.226	0.000	0.000	0.000	0.000
114	A	471	GLY	0	-0.007	0.010	37.223	-0.041	-0.041	0.000	0.000	0.000	0.000
115	A	472	TYR	0	-0.057	-0.037	33.862	0.179	0.179	0.000	0.000	0.000	0.000
116	A	473	VAL	0	-0.016	-0.015	28.006	0.073	0.073	0.000	0.000	0.000	0.000
117	A	474	LEU	0	-0.018	0.001	29.325	0.104	0.104	0.000	0.000	0.000	0.000
118	A	475	ARG	1	0.828	0.926	21.751	-13.071	-13.071	0.000	0.000	0.000	0.000
119	A	476	ASN	0	0.046	-0.004	23.686	0.223	0.223	0.000	0.000	0.000	0.000
120	A	477	ALA	0	0.059	0.021	23.660	0.480	0.480	0.000	0.000	0.000	0.000
121	A	478	LEU	0	0.001	0.008	20.364	0.577	0.577	0.000	0.000	0.000	0.000
122	A	479	ASP	-1	-0.769	-0.866	18.947	14.696	14.696	0.000	0.000	0.000	0.000
123	A	480	GLU	-1	-0.776	-0.869	19.451	13.822	13.822	0.000	0.000	0.000	0.000
124	A	481	LEU	0	0.006	0.014	16.696	0.394	0.394	0.000	0.000	0.000	0.000
125	A	482	TYR	0	-0.052	-0.057	12.131	1.412	1.412	0.000	0.000	0.000	0.000
126	A	483	HIS	0	-0.009	-0.007	14.950	0.463	0.463	0.000	0.000	0.000	0.000
127	A	484	CYS	0	-0.009	-0.003	16.572	0.235	0.235	0.000	0.000	0.000	0.000
128	A	485	LEU	0	0.012	0.022	9.931	0.716	0.716	0.000	0.000	0.000	0.000
129	A	486	ALA	0	0.021	0.003	11.923	1.642	1.642	0.000	0.000	0.000	0.000
130	A	487	VAL	0	0.004	0.000	12.968	0.675	0.675	0.000	0.000	0.000	0.000
131	A	488	THR	0	-0.019	-0.021	12.172	-0.109	-0.109	0.000	0.000	0.000	0.000
132	A	489	LEU	0	-0.022	-0.004	7.019	0.928	0.928	0.000	0.000	0.000	0.000
133	A	490	ALA	0	0.032	0.016	10.460	0.707	0.707	0.000	0.000	0.000	0.000
134	A	491	ARG	1	0.813	0.899	12.972	-19.273	-19.273	0.000	0.000	0.000	0.000
135	A	492	ASN	0	-0.024	-0.026	10.501	-0.390	-0.390	0.000	0.000	0.000	0.000
136	A	493	VAL	0	0.008	0.007	8.928	0.252	0.252	0.000	0.000	0.000	0.000
137	A	494	ASN	0	-0.053	-0.041	11.384	-1.551	-1.551	0.000	0.000	0.000	0.000
138	A	495	GLU	-1	-0.840	-0.907	14.563	17.902	17.902	0.000	0.000	0.000	0.000
139	A	496	TYR	0	-0.008	-0.001	11.166	-0.481	-0.481	0.000	0.000	0.000	0.000
140	A	497	PHE	0	0.011	-0.004	12.669	-0.498	-0.498	0.000	0.000	0.000	0.000
141	A	498	GLY	0	0.073	0.050	15.542	-0.859	-0.859	0.000	0.000	0.000	0.000
142	A	499	ILE	0	-0.032	-0.007	15.063	-0.846	-0.846	0.000	0.000	0.000	0.000
143	A	500	GLN	0	-0.030	-0.020	14.215	-1.124	-1.124	0.000	0.000	0.000	0.000
144	A	501	GLU	-1	-0.904	-0.946	17.814	13.013	13.013	0.000	0.000	0.000	0.000
145	A	502	THR	0	-0.014	-0.023	20.845	-0.894	-0.894	0.000	0.000	0.000	0.000
146	A	503	LYS	1	0.838	0.907	16.096	-19.102	-19.102	0.000	0.000	0.000	0.000
147	A	504	HIS	0	0.014	0.019	22.005	-0.113	-0.113	0.000	0.000	0.000	0.000
148	A	505	MET	0	-0.047	-0.035	23.808	-0.631	-0.631	0.000	0.000	0.000	0.000
149	A	506	LEU	0	-0.058	-0.028	24.389	-0.507	-0.507	0.000	0.000	0.000	0.000
150	A	507	ASP	-1	-0.931	-0.950	25.333	11.518	11.518	0.000	0.000	0.000	0.000
151	A	508	GLN	0	-0.057	-0.036	27.292	-0.552	-0.552	0.000	0.000	0.000	0.000
152	A	509	LEU	0	-0.059	-0.012	29.833	-0.404	-0.404	0.000	0.000	0.000	0.000
153	A	510	GLU	-1	-0.923	-0.962	31.901	8.552	8.552	0.000	0.000	0.000	0.000
154	A	511	ALA	0	-0.075	-0.029	35.231	-0.296	-0.296	0.000	0.000	0.000	0.000
155	A	512	LYS	1	0.975	0.980	35.467	-7.519	-7.519	0.000	0.000	0.000	0.000
156	A	513	PHE	0	0.064	0.021	31.736	-0.164	-0.164	0.000	0.000	0.000	0.000
157	A	514	PRO	0	-0.005	-0.005	36.649	-0.029	-0.029	0.000	0.000	0.000	0.000
158	A	515	ASP	-1	-0.894	-0.952	40.216	7.527	7.527	0.000	0.000	0.000	0.000
159	A	516	LEU	0	0.039	0.027	33.066	-0.086	-0.086	0.000	0.000	0.000	0.000
160	A	517	LEU	0	0.004	-0.005	35.031	0.002	0.002	0.000	0.000	0.000	0.000
161	A	518	LYS	1	0.935	0.971	38.201	-7.146	-7.146	0.000	0.000	0.000	0.000
162	A	519	GLU	-1	-0.864	-0.946	39.417	7.436	7.436	0.000	0.000	0.000	0.000
163	A	520	VAL	0	-0.003	0.000	35.002	-0.034	-0.034	0.000	0.000	0.000	0.000
164	A	521	LEU	0	-0.045	-0.022	38.124	-0.069	-0.069	0.000	0.000	0.000	0.000
165	A	522	ARG	1	0.801	0.925	41.009	-7.142	-7.142	0.000	0.000	0.000	0.000
166	A	523	HIS	0	-0.051	-0.019	39.452	-0.257	-0.257	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:358:GLU)