FMO DATABASE

FMODB ID: 59MLZ

Calculation Name: 3LW9-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1603753.449248
FMO2-HF: Nuclear repulsion	1535761.275958
FMO2-HF: Total energy	-67992.17329
FMO2-MP2: Total energy	-68191.392374

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.
66.805	72.459	3.9	-3.466	-6.088	0.007

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 : -0.957 / q_NPA : -0.985

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	0.012	0.015	3.575	-10.829	-8.089	-0.013	-1.311	-1.416	0.003
4	A	361	PRO	0	-0.001	0.008	3.994	7.025	7.348	0.002	-0.076	-0.249	0.000
5	A	362	LEU	0	-0.009	-0.003	5.769	0.109	0.109	0.000	0.000	0.000	0.000
6	A	363	ILE	0	-0.004	-0.006	7.840	-3.022	-3.022	0.000	0.000	0.000	0.000
7	A	364	LEU	0	0.013	0.001	11.503	-0.190	-0.190	0.000	0.000	0.000	0.000
8	A	365	LEU	0	-0.024	-0.011	14.483	-0.951	-0.951	0.000	0.000	0.000	0.000
9	A	366	VAL	0	0.037	0.004	17.842	-0.096	-0.096	0.000	0.000	0.000	0.000
10	A	367	PRO	0	0.042	0.032	20.421	-0.309	-0.309	0.000	0.000	0.000	0.000
11	A	368	LYS	1	0.877	0.924	24.045	-11.595	-11.595	0.000	0.000	0.000	0.000
12	A	369	SER	0	-0.052	-0.022	25.536	0.064	0.064	0.000	0.000	0.000	0.000
13	A	370	ARG	1	0.806	0.868	23.893	-11.182	-11.182	0.000	0.000	0.000	0.000
14	A	371	ARG	1	0.890	0.956	18.160	-14.496	-14.496	0.000	0.000	0.000	0.000
15	A	372	GLU	-1	-0.902	-0.958	21.915	12.363	12.363	0.000	0.000	0.000	0.000
16	A	373	ASP	-1	-0.912	-0.958	23.972	11.127	11.127	0.000	0.000	0.000	0.000
17	A	374	LEU	0	-0.061	-0.035	19.620	0.276	0.276	0.000	0.000	0.000	0.000
18	A	375	GLU	-1	-0.925	-0.960	18.356	16.472	16.472	0.000	0.000	0.000	0.000
19	A	376	LYS	1	0.898	0.946	20.398	-10.942	-10.942	0.000	0.000	0.000	0.000
20	A	377	ALA	0	-0.049	-0.013	21.623	-0.163	-0.163	0.000	0.000	0.000	0.000
21	A	378	GLN	0	-0.027	-0.017	17.854	0.726	0.726	0.000	0.000	0.000	0.000
22	A	379	LEU	0	0.029	0.014	15.682	0.665	0.665	0.000	0.000	0.000	0.000
23	A	380	ALA	0	0.034	0.015	12.172	0.823	0.823	0.000	0.000	0.000	0.000
24	A	381	GLU	-1	-0.893	-0.958	12.165	21.133	21.133	0.000	0.000	0.000	0.000
25	A	382	ARG	1	0.884	0.956	13.721	-14.264	-14.264	0.000	0.000	0.000	0.000
26	A	383	MET	0	-0.016	-0.007	11.291	-0.090	-0.090	0.000	0.000	0.000	0.000
27	A	384	ARG	1	0.848	0.940	5.754	-27.818	-27.818	0.000	0.000	0.000	0.000
28	A	385	SER	0	0.002	0.001	10.151	0.580	0.580	0.000	0.000	0.000	0.000
29	A	386	GLN	0	-0.060	-0.030	13.016	-0.517	-0.517	0.000	0.000	0.000	0.000
30	A	387	PHE	0	0.024	0.012	6.808	0.283	0.283	0.000	0.000	0.000	0.000
31	A	388	PHE	0	-0.046	-0.020	8.907	0.280	0.280	0.000	0.000	0.000	0.000
32	A	389	ILE	0	-0.036	-0.015	10.674	-0.647	-0.647	0.000	0.000	0.000	0.000
33	A	390	ASP	-1	-0.828	-0.890	13.377	17.473	17.473	0.000	0.000	0.000	0.000
34	A	391	TYR	0	-0.063	-0.037	10.143	-0.533	-0.533	0.000	0.000	0.000	0.000
35	A	392	GLY	0	-0.009	0.017	11.184	0.501	0.501	0.000	0.000	0.000	0.000
36	A	393	VAL	0	-0.020	-0.015	5.052	2.011	2.011	0.000	0.000	0.000	0.000
37	A	394	ARG	1	0.942	0.965	4.559	-33.181	-32.902	0.000	-0.014	-0.265	0.000
38	A	395	LEU	0	0.028	0.019	3.258	5.929	6.972	0.089	-0.415	-0.716	-0.003
39	A	396	PRO	0	0.024	0.020	2.039	-8.240	-7.064	3.769	-1.744	-3.201	0.007
40	A	397	GLU	-1	-0.935	-0.976	3.484	21.392	21.485	0.053	0.094	-0.241	0.000
41	A	398	VAL	0	0.032	0.004	7.038	2.100	2.100	0.000	0.000	0.000	0.000
42	A	399	LEU	0	-0.046	-0.018	9.532	-2.611	-2.611	0.000	0.000	0.000	0.000
43	A	400	LEU	0	0.083	0.053	12.230	0.328	0.328	0.000	0.000	0.000	0.000
44	A	401	ARG	1	0.903	0.939	14.765	-18.883	-18.883	0.000	0.000	0.000	0.000
45	A	402	ASP	-1	-0.830	-0.917	17.880	13.058	13.058	0.000	0.000	0.000	0.000
46	A	403	GLY	0	-0.007	-0.014	21.226	0.331	0.331	0.000	0.000	0.000	0.000
47	A	404	GLU	-1	-0.858	-0.929	22.034	11.524	11.524	0.000	0.000	0.000	0.000
48	A	405	GLY	0	-0.060	-0.032	25.227	0.140	0.140	0.000	0.000	0.000	0.000
49	A	406	LEU	0	-0.058	-0.005	21.327	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	407	ASP	-1	-0.882	-0.937	25.465	10.686	10.686	0.000	0.000	0.000	0.000
51	A	408	ASP	-1	-0.776	-0.892	26.086	11.677	11.677	0.000	0.000	0.000	0.000
52	A	409	ASN	0	-0.044	-0.046	25.566	0.109	0.109	0.000	0.000	0.000	0.000
53	A	410	SER	0	0.024	0.035	23.221	0.232	0.232	0.000	0.000	0.000	0.000
54	A	411	ILE	0	-0.014	-0.013	16.919	0.112	0.112	0.000	0.000	0.000	0.000
55	A	412	VAL	0	-0.043	-0.017	16.182	0.026	0.026	0.000	0.000	0.000	0.000
56	A	413	LEU	0	0.010	0.017	9.771	0.482	0.482	0.000	0.000	0.000	0.000
57	A	414	LEU	0	-0.008	-0.012	11.970	-0.492	-0.492	0.000	0.000	0.000	0.000
58	A	415	ILE	0	0.040	0.009	5.593	2.258	2.258	0.000	0.000	0.000	0.000
59	A	416	ASN	0	-0.004	-0.008	7.707	-0.528	-0.528	0.000	0.000	0.000	0.000
60	A	417	GLU	-1	-0.939	-0.966	9.124	19.988	19.988	0.000	0.000	0.000	0.000
61	A	418	ILE	0	-0.039	-0.001	11.331	-2.341	-2.341	0.000	0.000	0.000	0.000
62	A	419	ARG	1	0.940	0.956	12.364	-14.764	-14.764	0.000	0.000	0.000	0.000
63	A	420	VAL	0	-0.033	-0.008	10.015	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	421	GLU	-1	-0.874	-0.940	13.499	16.454	16.454	0.000	0.000	0.000	0.000
65	A	422	GLN	0	-0.079	-0.044	16.227	-0.072	-0.072	0.000	0.000	0.000	0.000
66	A	423	PHE	0	0.007	0.000	14.466	-0.253	-0.253	0.000	0.000	0.000	0.000
67	A	424	THR	0	0.022	0.010	20.271	-0.261	-0.261	0.000	0.000	0.000	0.000
68	A	425	VAL	0	-0.041	-0.025	20.591	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	426	TYR	0	0.014	0.006	23.777	-0.209	-0.209	0.000	0.000	0.000	0.000
70	A	427	PHE	0	0.001	-0.008	21.651	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	428	ASP	-1	-0.836	-0.892	26.425	10.232	10.232	0.000	0.000	0.000	0.000
72	A	429	LEU	0	-0.078	-0.028	28.815	-0.342	-0.342	0.000	0.000	0.000	0.000
73	A	430	MET	0	-0.033	-0.005	28.223	0.532	0.532	0.000	0.000	0.000	0.000
74	A	431	ARG	1	0.847	0.906	23.021	-12.904	-12.904	0.000	0.000	0.000	0.000
75	A	432	VAL	0	0.014	0.007	27.941	0.001	0.001	0.000	0.000	0.000	0.000
76	A	433	VAL	0	-0.068	-0.038	25.771	0.146	0.146	0.000	0.000	0.000	0.000
77	A	434	ASN	0	-0.007	0.001	28.105	0.255	0.255	0.000	0.000	0.000	0.000
78	A	435	TYR	0	0.042	0.014	31.106	-0.329	-0.329	0.000	0.000	0.000	0.000
79	A	436	SER	0	0.026	0.020	33.224	0.022	0.022	0.000	0.000	0.000	0.000
80	A	437	ASP	-1	-0.845	-0.942	36.658	8.184	8.184	0.000	0.000	0.000	0.000
81	A	438	GLU	-1	-0.999	-0.982	39.630	7.173	7.173	0.000	0.000	0.000	0.000
82	A	439	VAL	0	0.009	0.015	36.220	-0.124	-0.124	0.000	0.000	0.000	0.000
83	A	440	VAL	0	0.027	0.009	39.680	-0.125	-0.125	0.000	0.000	0.000	0.000
84	A	441	SER	0	-0.114	-0.052	41.978	-0.220	-0.220	0.000	0.000	0.000	0.000
85	A	442	PHE	0	-0.002	-0.014	40.812	-0.186	-0.186	0.000	0.000	0.000	0.000
86	A	443	GLY	0	-0.058	-0.022	44.117	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	444	ILE	0	-0.027	0.000	37.821	0.036	0.036	0.000	0.000	0.000	0.000
88	A	445	ASN	0	0.002	-0.011	39.726	0.039	0.039	0.000	0.000	0.000	0.000
89	A	446	PRO	0	-0.004	0.003	34.282	0.090	0.090	0.000	0.000	0.000	0.000
90	A	447	THR	0	-0.013	0.000	31.786	-0.126	-0.126	0.000	0.000	0.000	0.000
91	A	448	ILE	0	-0.016	-0.013	32.026	0.279	0.279	0.000	0.000	0.000	0.000
92	A	449	HIS	0	-0.006	-0.007	24.691	-0.427	-0.427	0.000	0.000	0.000	0.000
93	A	450	GLN	0	0.020	-0.003	29.133	-0.310	-0.310	0.000	0.000	0.000	0.000
94	A	451	GLN	0	0.047	0.026	22.194	-0.041	-0.041	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.011	0.012	26.100	0.216	0.216	0.000	0.000	0.000	0.000
96	A	453	SER	0	-0.012	-0.014	27.190	-0.328	-0.328	0.000	0.000	0.000	0.000
97	A	454	SER	0	-0.035	-0.005	25.763	-0.155	-0.155	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.015	-0.009	27.905	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	456	TYR	0	-0.035	-0.018	23.194	0.173	0.173	0.000	0.000	0.000	0.000
100	A	457	PHE	0	0.038	0.021	28.356	-0.178	-0.178	0.000	0.000	0.000	0.000
101	A	458	TRP	0	0.021	0.006	24.044	0.332	0.332	0.000	0.000	0.000	0.000
102	A	459	VAL	0	0.015	0.018	31.035	-0.316	-0.316	0.000	0.000	0.000	0.000
103	A	460	THR	0	0.051	0.018	32.478	0.281	0.281	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.069	0.017	29.624	-0.081	-0.081	0.000	0.000	0.000	0.000
105	A	462	GLU	-1	-0.944	-0.973	34.171	7.546	7.546	0.000	0.000	0.000	0.000
106	A	463	GLU	-1	-0.888	-0.952	36.587	8.205	8.205	0.000	0.000	0.000	0.000
107	A	464	GLY	0	0.021	-0.059	33.777	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	465	GLU	-1	-0.827	-0.922	33.878	9.061	9.061	0.000	0.000	0.000	0.000
109	A	466	LYS	1	0.955	0.985	36.653	-7.534	-7.534	0.000	0.000	0.000	0.000
110	A	467	LEU	0	0.005	-0.004	35.298	-0.059	-0.059	0.000	0.000	0.000	0.000
111	A	468	ARG	1	0.822	0.898	28.945	-9.820	-9.820	0.000	0.000	0.000	0.000
112	A	469	GLU	-1	-0.944	-0.954	35.749	7.979	7.979	0.000	0.000	0.000	0.000
113	A	470	MET	0	-0.120	-0.056	38.561	-0.233	-0.233	0.000	0.000	0.000	0.000
114	A	471	GLY	0	-0.006	0.012	36.892	0.010	0.010	0.000	0.000	0.000	0.000
115	A	472	TYR	0	-0.038	-0.028	33.647	0.194	0.194	0.000	0.000	0.000	0.000
116	A	473	VAL	0	-0.012	-0.020	27.902	0.057	0.057	0.000	0.000	0.000	0.000
117	A	474	LEU	0	-0.042	0.062	29.241	0.162	0.162	0.000	0.000	0.000	0.000
118	A	475	ARG	1	0.833	0.919	21.433	-13.418	-13.418	0.000	0.000	0.000	0.000
119	A	476	ASN	0	0.054	0.020	23.363	0.261	0.261	0.000	0.000	0.000	0.000
120	A	477	ALA	0	0.106	0.034	23.486	0.501	0.501	0.000	0.000	0.000	0.000
121	A	478	LEU	0	-0.008	-0.002	19.925	0.668	0.668	0.000	0.000	0.000	0.000
122	A	479	ASP	-1	-0.855	-0.929	18.733	14.807	14.807	0.000	0.000	0.000	0.000
123	A	480	GLU	-1	-0.782	-0.865	19.131	14.455	14.455	0.000	0.000	0.000	0.000
124	A	481	LEU	0	-0.006	0.007	16.483	0.593	0.593	0.000	0.000	0.000	0.000
125	A	482	TYR	0	-0.042	-0.045	11.864	1.626	1.626	0.000	0.000	0.000	0.000
126	A	483	HIS	0	-0.019	-0.014	14.582	0.752	0.752	0.000	0.000	0.000	0.000
127	A	484	CYS	0	-0.031	-0.020	16.206	0.362	0.362	0.000	0.000	0.000	0.000
128	A	485	LEU	0	0.018	0.022	9.939	0.922	0.922	0.000	0.000	0.000	0.000
129	A	486	ALA	0	0.057	0.018	11.694	1.878	1.878	0.000	0.000	0.000	0.000
130	A	487	VAL	0	-0.015	0.003	12.757	0.663	0.663	0.000	0.000	0.000	0.000
131	A	488	THR	0	-0.025	-0.015	12.394	-0.141	-0.141	0.000	0.000	0.000	0.000
132	A	489	LEU	0	-0.018	-0.001	7.160	1.129	1.129	0.000	0.000	0.000	0.000
133	A	490	ALA	0	0.061	0.026	10.454	0.857	0.857	0.000	0.000	0.000	0.000
134	A	491	ARG	1	0.899	0.966	12.616	-20.044	-20.044	0.000	0.000	0.000	0.000
135	A	492	ASN	0	-0.030	-0.032	10.427	-0.839	-0.839	0.000	0.000	0.000	0.000
136	A	493	VAL	0	0.008	0.011	8.280	0.206	0.206	0.000	0.000	0.000	0.000
137	A	494	ASN	0	-0.044	-0.047	10.902	-1.842	-1.842	0.000	0.000	0.000	0.000
138	A	495	GLU	-1	-0.871	-0.936	14.541	17.963	17.963	0.000	0.000	0.000	0.000
139	A	496	TYR	0	-0.019	-0.001	10.848	-0.673	-0.673	0.000	0.000	0.000	0.000
140	A	497	PHE	0	0.005	-0.018	11.070	-0.669	-0.669	0.000	0.000	0.000	0.000
141	A	498	GLY	0	0.044	0.037	14.886	-1.148	-1.148	0.000	0.000	0.000	0.000
142	A	499	ILE	0	-0.029	-0.018	14.803	-0.927	-0.927	0.000	0.000	0.000	0.000
143	A	500	GLN	0	-0.044	-0.025	13.677	-1.785	-1.785	0.000	0.000	0.000	0.000
144	A	501	GLU	-1	-0.902	-0.941	17.443	13.355	13.355	0.000	0.000	0.000	0.000
145	A	502	THR	0	0.001	-0.009	20.533	-1.019	-1.019	0.000	0.000	0.000	0.000
146	A	503	LYS	1	0.860	0.925	16.322	-19.256	-19.256	0.000	0.000	0.000	0.000
147	A	504	HIS	0	0.043	0.033	21.550	-0.269	-0.269	0.000	0.000	0.000	0.000
148	A	505	MET	0	-0.046	-0.027	23.212	-0.713	-0.713	0.000	0.000	0.000	0.000
149	A	506	LEU	0	-0.078	-0.049	25.006	-0.554	-0.554	0.000	0.000	0.000	0.000
150	A	507	ASP	-1	-0.949	-0.959	24.900	12.177	12.177	0.000	0.000	0.000	0.000
151	A	508	GLN	0	-0.041	-0.019	26.878	-0.410	-0.410	0.000	0.000	0.000	0.000
152	A	509	LEU	0	-0.076	-0.017	29.362	-0.493	-0.493	0.000	0.000	0.000	0.000
153	A	510	GLU	-1	-0.902	-0.950	31.524	8.929	8.929	0.000	0.000	0.000	0.000
154	A	511	ALA	0	-0.073	-0.022	35.069	-0.318	-0.318	0.000	0.000	0.000	0.000
155	A	512	LYS	1	1.007	0.984	35.349	-7.728	-7.728	0.000	0.000	0.000	0.000
156	A	513	PHE	0	0.054	0.016	31.715	-0.147	-0.147	0.000	0.000	0.000	0.000
157	A	514	PRO	0	-0.004	-0.008	36.876	-0.025	-0.025	0.000	0.000	0.000	0.000
158	A	515	ASP	-1	-0.911	-0.950	39.979	7.600	7.600	0.000	0.000	0.000	0.000
159	A	516	LEU	0	0.021	0.011	32.757	-0.071	-0.071	0.000	0.000	0.000	0.000
160	A	517	LEU	0	-0.021	-0.025	34.831	0.025	0.025	0.000	0.000	0.000	0.000
161	A	518	LYS	1	0.912	0.964	38.190	-7.149	-7.149	0.000	0.000	0.000	0.000
162	A	519	GLU	-1	-0.885	-0.960	38.862	7.767	7.767	0.000	0.000	0.000	0.000
163	A	520	VAL	0	0.012	0.011	35.104	-0.023	-0.023	0.000	0.000	0.000	0.000
164	A	521	LEU	0	-0.013	-0.007	37.978	-0.061	-0.061	0.000	0.000	0.000	0.000
165	A	522	ARG	1	0.862	0.948	40.803	-7.193	-7.193	0.000	0.000	0.000	0.000
166	A	523	HIS	0	-0.068	-0.028	39.108	-0.242	-0.242	0.000	0.000	0.000	0.000
167	A	1	NME	0	-0.022	0.005	37.955	0.033	0.033	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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