FMO DATABASE

FMODB ID: R5L68

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1602225.119896
FMO2-HF: Nuclear repulsion	1534252.062143
FMO2-HF: Total energy	-67973.057754
FMO2-MP2: Total energy	-68172.174809

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.
67.339	72.982	3.871	-3.446	-6.068	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 : -0.959 / q_NPA : -0.986

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	0.011	0.015	3.576	-10.771	-7.991	-0.022	-1.324	-1.435	0.003
4	A	361	PRO	0	0.001	0.009	3.995	7.095	7.407	0.001	-0.074	-0.239	0.000
5	A	362	LEU	0	-0.012	-0.004	5.764	0.145	0.145	0.000	0.000	0.000	0.000
6	A	363	ILE	0	-0.003	-0.006	7.840	-2.875	-2.875	0.000	0.000	0.000	0.000
7	A	364	LEU	0	0.013	0.002	11.503	-0.125	-0.125	0.000	0.000	0.000	0.000
8	A	365	LEU	0	-0.024	-0.012	14.483	-0.897	-0.897	0.000	0.000	0.000	0.000
9	A	366	VAL	0	0.033	0.003	17.842	-0.066	-0.066	0.000	0.000	0.000	0.000
10	A	367	PRO	0	0.042	0.031	20.421	-0.277	-0.277	0.000	0.000	0.000	0.000
11	A	368	LYS	1	0.875	0.924	24.045	-11.588	-11.588	0.000	0.000	0.000	0.000
12	A	369	SER	0	-0.049	-0.022	25.536	0.075	0.075	0.000	0.000	0.000	0.000
13	A	370	ARG	1	0.808	0.869	23.893	-11.195	-11.195	0.000	0.000	0.000	0.000
14	A	371	ARG	1	0.885	0.954	18.160	-14.509	-14.509	0.000	0.000	0.000	0.000
15	A	372	GLU	-1	-0.900	-0.958	21.916	12.370	12.370	0.000	0.000	0.000	0.000
16	A	373	ASP	-1	-0.912	-0.958	23.972	11.132	11.132	0.000	0.000	0.000	0.000
17	A	374	LEU	0	-0.060	-0.035	19.621	0.253	0.253	0.000	0.000	0.000	0.000
18	A	375	GLU	-1	-0.923	-0.960	18.357	16.464	16.464	0.000	0.000	0.000	0.000
19	A	376	LYS	1	0.897	0.945	20.398	-10.928	-10.928	0.000	0.000	0.000	0.000
20	A	377	ALA	0	-0.051	-0.013	21.623	-0.170	-0.170	0.000	0.000	0.000	0.000
21	A	378	GLN	0	-0.027	-0.016	17.854	0.697	0.697	0.000	0.000	0.000	0.000
22	A	379	LEU	0	0.030	0.015	15.682	0.640	0.640	0.000	0.000	0.000	0.000
23	A	380	ALA	0	0.034	0.014	12.172	0.779	0.779	0.000	0.000	0.000	0.000
24	A	381	GLU	-1	-0.895	-0.958	12.165	21.143	21.143	0.000	0.000	0.000	0.000
25	A	382	ARG	1	0.886	0.956	13.721	-14.263	-14.263	0.000	0.000	0.000	0.000
26	A	383	MET	0	-0.016	-0.007	11.287	-0.141	-0.141	0.000	0.000	0.000	0.000
27	A	384	ARG	1	0.849	0.940	5.755	-27.893	-27.893	0.000	0.000	0.000	0.000
28	A	385	SER	0	0.001	0.001	10.151	0.625	0.625	0.000	0.000	0.000	0.000
29	A	386	GLN	0	-0.060	-0.030	13.016	-0.508	-0.508	0.000	0.000	0.000	0.000
30	A	387	PHE	0	0.025	0.012	6.808	0.251	0.251	0.000	0.000	0.000	0.000
31	A	388	PHE	0	-0.048	-0.021	8.908	0.275	0.275	0.000	0.000	0.000	0.000
32	A	389	ILE	0	-0.033	-0.014	10.675	-0.584	-0.584	0.000	0.000	0.000	0.000
33	A	390	ASP	-1	-0.829	-0.890	13.377	17.488	17.488	0.000	0.000	0.000	0.000
34	A	391	TYR	0	-0.063	-0.037	10.143	-0.570	-0.570	0.000	0.000	0.000	0.000
35	A	392	GLY	0	-0.010	0.016	11.184	0.468	0.468	0.000	0.000	0.000	0.000
36	A	393	VAL	0	-0.019	-0.015	5.053	1.913	1.913	0.000	0.000	0.000	0.000
37	A	394	ARG	1	0.940	0.964	4.560	-33.262	-32.986	-0.001	-0.013	-0.261	0.000
38	A	395	LEU	0	0.031	0.021	3.259	5.789	6.803	0.088	-0.405	-0.697	-0.003
39	A	396	PRO	0	0.022	0.020	2.039	-8.315	-7.148	3.752	-1.726	-3.194	0.007
40	A	397	GLU	-1	-0.934	-0.976	3.484	21.631	21.725	0.053	0.096	-0.242	0.000
41	A	398	VAL	0	0.030	0.004	7.039	2.125	2.125	0.000	0.000	0.000	0.000
42	A	399	LEU	0	-0.045	-0.017	9.532	-2.529	-2.529	0.000	0.000	0.000	0.000
43	A	400	LEU	0	0.082	0.053	12.231	0.371	0.371	0.000	0.000	0.000	0.000
44	A	401	ARG	1	0.902	0.939	14.766	-18.852	-18.852	0.000	0.000	0.000	0.000
45	A	402	ASP	-1	-0.828	-0.916	17.881	13.087	13.087	0.000	0.000	0.000	0.000
46	A	403	GLY	0	-0.009	-0.014	21.226	0.332	0.332	0.000	0.000	0.000	0.000
47	A	404	GLU	-1	-0.858	-0.929	22.035	11.548	11.548	0.000	0.000	0.000	0.000
48	A	405	GLY	0	-0.059	-0.032	25.227	0.150	0.150	0.000	0.000	0.000	0.000
49	A	406	LEU	0	-0.057	-0.004	21.330	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	407	ASP	-1	-0.884	-0.937	25.465	10.702	10.702	0.000	0.000	0.000	0.000
51	A	408	ASP	-1	-0.779	-0.893	26.086	11.675	11.675	0.000	0.000	0.000	0.000
52	A	409	ASN	0	-0.042	-0.046	25.565	0.098	0.098	0.000	0.000	0.000	0.000
53	A	410	SER	0	0.026	0.035	23.221	0.212	0.212	0.000	0.000	0.000	0.000
54	A	411	ILE	0	-0.018	-0.013	16.919	0.086	0.086	0.000	0.000	0.000	0.000
55	A	412	VAL	0	-0.044	-0.018	16.182	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	413	LEU	0	0.014	0.019	9.771	0.438	0.438	0.000	0.000	0.000	0.000
57	A	414	LEU	0	-0.009	-0.013	11.970	-0.529	-0.529	0.000	0.000	0.000	0.000
58	A	415	ILE	0	0.041	0.009	5.593	2.147	2.147	0.000	0.000	0.000	0.000
59	A	416	ASN	0	-0.006	-0.008	7.707	-0.514	-0.514	0.000	0.000	0.000	0.000
60	A	417	GLU	-1	-0.938	-0.967	9.124	20.115	20.115	0.000	0.000	0.000	0.000
61	A	418	ILE	0	-0.040	-0.001	11.331	-2.301	-2.301	0.000	0.000	0.000	0.000
62	A	419	ARG	1	0.940	0.956	12.364	-14.760	-14.760	0.000	0.000	0.000	0.000
63	A	420	VAL	0	-0.034	-0.009	10.015	-0.039	-0.039	0.000	0.000	0.000	0.000
64	A	421	GLU	-1	-0.873	-0.940	13.499	16.515	16.515	0.000	0.000	0.000	0.000
65	A	422	GLN	0	-0.079	-0.043	16.227	-0.042	-0.042	0.000	0.000	0.000	0.000
66	A	423	PHE	0	0.005	0.000	14.465	-0.230	-0.230	0.000	0.000	0.000	0.000
67	A	424	THR	0	0.023	0.011	20.271	-0.223	-0.223	0.000	0.000	0.000	0.000
68	A	425	VAL	0	-0.035	-0.024	20.591	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	426	TYR	0	0.012	0.006	23.776	-0.191	-0.191	0.000	0.000	0.000	0.000
70	A	427	PHE	0	0.000	-0.009	21.650	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	428	ASP	-1	-0.837	-0.893	26.424	10.250	10.250	0.000	0.000	0.000	0.000
72	A	429	LEU	0	-0.078	-0.027	28.814	-0.337	-0.337	0.000	0.000	0.000	0.000
73	A	430	MET	0	-0.031	-0.004	28.221	0.522	0.522	0.000	0.000	0.000	0.000
74	A	431	ARG	1	0.847	0.906	23.021	-12.915	-12.915	0.000	0.000	0.000	0.000
75	A	432	VAL	0	0.008	0.005	27.940	0.011	0.011	0.000	0.000	0.000	0.000
76	A	433	VAL	0	-0.061	-0.036	25.770	0.139	0.139	0.000	0.000	0.000	0.000
77	A	434	ASN	0	-0.007	0.001	28.104	0.264	0.264	0.000	0.000	0.000	0.000
78	A	435	TYR	0	0.041	0.014	31.106	-0.319	-0.319	0.000	0.000	0.000	0.000
79	A	436	SER	0	0.026	0.020	33.224	0.032	0.032	0.000	0.000	0.000	0.000
80	A	437	ASP	-1	-0.845	-0.941	36.658	8.194	8.194	0.000	0.000	0.000	0.000
81	A	438	GLU	-1	-1.000	-0.983	39.629	7.181	7.181	0.000	0.000	0.000	0.000
82	A	439	VAL	0	0.010	0.015	36.220	-0.125	-0.125	0.000	0.000	0.000	0.000
83	A	440	VAL	0	0.028	0.009	39.679	-0.119	-0.119	0.000	0.000	0.000	0.000
84	A	441	SER	0	-0.115	-0.053	41.977	-0.212	-0.212	0.000	0.000	0.000	0.000
85	A	442	PHE	0	-0.001	-0.014	40.811	-0.184	-0.184	0.000	0.000	0.000	0.000
86	A	443	GLY	0	-0.059	-0.022	44.117	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	444	ILE	0	-0.026	0.001	37.820	0.029	0.029	0.000	0.000	0.000	0.000
88	A	445	ASN	0	0.002	-0.011	39.726	0.034	0.034	0.000	0.000	0.000	0.000
89	A	446	PRO	0	-0.003	0.004	34.281	0.079	0.079	0.000	0.000	0.000	0.000
90	A	447	THR	0	-0.016	-0.001	31.786	-0.131	-0.131	0.000	0.000	0.000	0.000
91	A	448	ILE	0	-0.013	-0.012	32.025	0.272	0.272	0.000	0.000	0.000	0.000
92	A	449	HIS	0	-0.005	-0.006	24.691	-0.437	-0.437	0.000	0.000	0.000	0.000
93	A	450	GLN	0	0.021	-0.003	29.132	-0.315	-0.315	0.000	0.000	0.000	0.000
94	A	451	GLN	0	0.045	0.026	22.194	-0.054	-0.054	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.010	0.011	26.100	0.220	0.220	0.000	0.000	0.000	0.000
96	A	453	SER	0	-0.012	-0.014	27.191	-0.316	-0.316	0.000	0.000	0.000	0.000
97	A	454	SER	0	-0.033	-0.005	25.763	-0.157	-0.157	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.016	-0.009	27.905	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	456	TYR	0	-0.035	-0.018	23.194	0.171	0.171	0.000	0.000	0.000	0.000
100	A	457	PHE	0	0.038	0.020	28.355	-0.164	-0.164	0.000	0.000	0.000	0.000
101	A	458	TRP	0	0.017	0.005	24.043	0.329	0.329	0.000	0.000	0.000	0.000
102	A	459	VAL	0	0.019	0.020	31.034	-0.303	-0.303	0.000	0.000	0.000	0.000
103	A	460	THR	0	0.050	0.018	32.477	0.282	0.282	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.069	0.017	29.623	-0.080	-0.080	0.000	0.000	0.000	0.000
105	A	462	GLU	-1	-0.945	-0.974	34.170	7.558	7.558	0.000	0.000	0.000	0.000
106	A	463	GLU	-1	-0.887	-0.952	36.587	8.208	8.208	0.000	0.000	0.000	0.000
107	A	464	GLY	0	0.021	-0.057	33.776	-0.027	-0.027	0.000	0.000	0.000	0.000
108	A	465	GLU	-1	-0.826	-0.923	33.877	9.070	9.070	0.000	0.000	0.000	0.000
109	A	466	LYS	1	0.953	0.984	36.652	-7.528	-7.528	0.000	0.000	0.000	0.000
110	A	467	LEU	0	0.006	-0.003	35.297	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	468	ARG	1	0.820	0.897	28.945	-9.827	-9.827	0.000	0.000	0.000	0.000
112	A	469	GLU	-1	-0.944	-0.954	35.748	7.990	7.990	0.000	0.000	0.000	0.000
113	A	470	MET	0	-0.118	-0.056	38.572	-0.228	-0.228	0.000	0.000	0.000	0.000
114	A	471	GLY	0	-0.006	0.012	36.891	0.000	0.000	0.000	0.000	0.000	0.000
115	A	472	TYR	0	-0.040	-0.029	33.646	0.183	0.183	0.000	0.000	0.000	0.000
116	A	473	VAL	0	-0.011	-0.020	27.901	0.047	0.047	0.000	0.000	0.000	0.000
117	A	474	LEU	0	-0.040	0.063	29.240	0.151	0.151	0.000	0.000	0.000	0.000
118	A	475	ARG	1	0.838	0.921	21.433	-13.440	-13.440	0.000	0.000	0.000	0.000
119	A	476	ASN	0	0.051	0.020	23.363	0.260	0.260	0.000	0.000	0.000	0.000
120	A	477	ALA	0	0.108	0.033	23.485	0.483	0.483	0.000	0.000	0.000	0.000
121	A	478	LEU	0	-0.011	-0.003	19.924	0.642	0.642	0.000	0.000	0.000	0.000
122	A	479	ASP	-1	-0.857	-0.930	18.733	14.803	14.803	0.000	0.000	0.000	0.000
123	A	480	GLU	-1	-0.780	-0.864	19.130	14.454	14.454	0.000	0.000	0.000	0.000
124	A	481	LEU	0	-0.004	0.007	16.482	0.567	0.567	0.000	0.000	0.000	0.000
125	A	482	TYR	0	-0.046	-0.046	11.863	1.587	1.587	0.000	0.000	0.000	0.000
126	A	483	HIS	0	-0.019	-0.014	14.581	0.750	0.750	0.000	0.000	0.000	0.000
127	A	484	CYS	0	-0.029	-0.019	16.206	0.339	0.339	0.000	0.000	0.000	0.000
128	A	485	LEU	0	0.017	0.022	9.940	0.864	0.864	0.000	0.000	0.000	0.000
129	A	486	ALA	0	0.058	0.018	11.694	1.851	1.851	0.000	0.000	0.000	0.000
130	A	487	VAL	0	-0.016	0.003	12.756	0.685	0.685	0.000	0.000	0.000	0.000
131	A	488	THR	0	-0.025	-0.015	12.395	-0.178	-0.178	0.000	0.000	0.000	0.000
132	A	489	LEU	0	-0.017	-0.001	7.160	1.043	1.043	0.000	0.000	0.000	0.000
133	A	490	ALA	0	0.061	0.026	10.454	0.898	0.898	0.000	0.000	0.000	0.000
134	A	491	ARG	1	0.897	0.965	12.616	-20.011	-20.011	0.000	0.000	0.000	0.000
135	A	492	ASN	0	-0.029	-0.032	10.427	-0.880	-0.880	0.000	0.000	0.000	0.000
136	A	493	VAL	0	0.009	0.012	8.280	0.172	0.172	0.000	0.000	0.000	0.000
137	A	494	ASN	0	-0.044	-0.047	10.902	-1.748	-1.748	0.000	0.000	0.000	0.000
138	A	495	GLU	-1	-0.870	-0.935	14.541	17.990	17.990	0.000	0.000	0.000	0.000
139	A	496	TYR	0	-0.019	0.000	10.848	-0.705	-0.705	0.000	0.000	0.000	0.000
140	A	497	PHE	0	0.004	-0.018	11.070	-0.627	-0.627	0.000	0.000	0.000	0.000
141	A	498	GLY	0	0.043	0.036	14.886	-1.095	-1.095	0.000	0.000	0.000	0.000
142	A	499	ILE	0	-0.029	-0.018	14.803	-0.919	-0.919	0.000	0.000	0.000	0.000
143	A	500	GLN	0	-0.037	-0.023	13.677	-1.775	-1.775	0.000	0.000	0.000	0.000
144	A	501	GLU	-1	-0.906	-0.942	17.443	13.400	13.400	0.000	0.000	0.000	0.000
145	A	502	THR	0	0.000	-0.010	20.533	-0.995	-0.995	0.000	0.000	0.000	0.000
146	A	503	LYS	1	0.861	0.926	16.322	-19.249	-19.249	0.000	0.000	0.000	0.000
147	A	504	HIS	0	0.043	0.032	21.550	-0.252	-0.252	0.000	0.000	0.000	0.000
148	A	505	MET	0	-0.047	-0.028	23.212	-0.692	-0.692	0.000	0.000	0.000	0.000
149	A	506	LEU	0	-0.078	-0.049	25.006	-0.542	-0.542	0.000	0.000	0.000	0.000
150	A	507	ASP	-1	-0.949	-0.959	24.900	12.181	12.181	0.000	0.000	0.000	0.000
151	A	508	GLN	0	-0.037	-0.018	26.878	-0.393	-0.393	0.000	0.000	0.000	0.000
152	A	509	LEU	0	-0.081	-0.019	29.362	-0.478	-0.478	0.000	0.000	0.000	0.000
153	A	510	GLU	-1	-0.901	-0.949	31.524	8.944	8.944	0.000	0.000	0.000	0.000
154	A	511	ALA	0	-0.071	-0.021	35.069	-0.310	-0.310	0.000	0.000	0.000	0.000
155	A	512	LYS	1	1.007	0.985	35.349	-7.730	-7.730	0.000	0.000	0.000	0.000
156	A	513	PHE	0	0.052	0.016	31.715	-0.144	-0.144	0.000	0.000	0.000	0.000
157	A	514	PRO	0	-0.005	-0.009	36.876	-0.016	-0.016	0.000	0.000	0.000	0.000
158	A	515	ASP	-1	-0.911	-0.950	39.979	7.602	7.602	0.000	0.000	0.000	0.000
159	A	516	LEU	0	0.020	0.011	32.757	-0.075	-0.075	0.000	0.000	0.000	0.000
160	A	517	LEU	0	-0.023	-0.026	34.831	0.027	0.027	0.000	0.000	0.000	0.000
161	A	518	LYS	1	0.913	0.964	38.190	-7.141	-7.141	0.000	0.000	0.000	0.000
162	A	519	GLU	-1	-0.890	-0.963	38.862	7.766	7.766	0.000	0.000	0.000	0.000
163	A	520	VAL	0	-0.002	-0.001	35.106	-0.024	-0.024	0.000	0.000	0.000	0.000
164	A	521	LEU	0	-0.022	-0.010	37.978	-0.054	-0.054	0.000	0.000	0.000	0.000
165	A	522	ARG	1	0.869	0.955	40.803	-7.194	-7.194	0.000	0.000	0.000	0.000
166	A	523	HIS	0	-0.062	-0.009	39.111	-0.215	-0.215	0.000	0.000	0.000	0.000

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