FMO DATABASE

FMODB ID: Q1LZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1602587.831692
FMO2-HF: Nuclear repulsion	1534613.747188
FMO2-HF: Total energy	-67974.084504
FMO2-MP2: Total energy	-68173.180219

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.
71.201	76.472	3.667	-3.077	-5.863	0.006

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 : -0.951 / q_NPA : -0.982

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	-0.002	0.006	3.647	-11.716	-8.868	-0.023	-1.353	-1.472	0.003
4	A	361	PRO	0	-0.005	0.007	4.034	5.915	6.174	0.001	-0.066	-0.194	0.000
5	A	362	LEU	0	0.005	0.002	5.401	0.089	0.089	0.000	0.000	0.000	0.000
6	A	363	ILE	0	-0.011	-0.011	7.852	-2.650	-2.650	0.000	0.000	0.000	0.000
7	A	364	LEU	0	0.013	0.007	11.521	-0.156	-0.156	0.000	0.000	0.000	0.000
8	A	365	LEU	0	-0.014	-0.008	14.491	-0.897	-0.897	0.000	0.000	0.000	0.000
9	A	366	VAL	0	0.017	-0.004	17.855	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	367	PRO	0	0.047	0.035	20.429	-0.267	-0.267	0.000	0.000	0.000	0.000
11	A	368	LYS	1	0.894	0.923	24.055	-11.779	-11.779	0.000	0.000	0.000	0.000
12	A	369	SER	0	-0.053	-0.023	25.551	0.071	0.071	0.000	0.000	0.000	0.000
13	A	370	ARG	1	0.765	0.813	23.968	-11.077	-11.077	0.000	0.000	0.000	0.000
14	A	371	ARG	1	0.790	0.904	18.994	-13.840	-13.840	0.000	0.000	0.000	0.000
15	A	372	GLU	-1	-0.814	-0.920	21.923	12.695	12.695	0.000	0.000	0.000	0.000
16	A	373	ASP	-1	-0.923	-0.965	23.977	11.018	11.018	0.000	0.000	0.000	0.000
17	A	374	LEU	0	-0.049	-0.026	19.612	0.232	0.232	0.000	0.000	0.000	0.000
18	A	375	GLU	-1	-0.837	-0.910	17.896	16.370	16.370	0.000	0.000	0.000	0.000
19	A	376	LYS	1	0.882	0.942	20.459	-10.829	-10.829	0.000	0.000	0.000	0.000
20	A	377	ALA	0	-0.048	-0.016	21.673	-0.163	-0.163	0.000	0.000	0.000	0.000
21	A	378	GLN	0	-0.034	-0.015	17.897	0.571	0.571	0.000	0.000	0.000	0.000
22	A	379	LEU	0	0.035	0.018	15.961	0.629	0.629	0.000	0.000	0.000	0.000
23	A	380	ALA	0	0.045	0.021	12.326	0.746	0.746	0.000	0.000	0.000	0.000
24	A	381	GLU	-1	-0.790	-0.891	11.690	22.237	22.237	0.000	0.000	0.000	0.000
25	A	382	ARG	1	0.868	0.941	13.746	-14.032	-14.032	0.000	0.000	0.000	0.000
26	A	383	MET	0	-0.005	-0.003	11.429	-0.194	-0.194	0.000	0.000	0.000	0.000
27	A	384	ARG	1	0.764	0.881	6.679	-25.531	-25.531	0.000	0.000	0.000	0.000
28	A	385	SER	0	-0.020	-0.015	10.185	0.618	0.618	0.000	0.000	0.000	0.000
29	A	386	GLN	0	-0.069	-0.043	13.034	-0.487	-0.487	0.000	0.000	0.000	0.000
30	A	387	PHE	0	0.038	0.019	7.543	0.151	0.151	0.000	0.000	0.000	0.000
31	A	388	PHE	0	-0.053	-0.022	9.109	0.222	0.222	0.000	0.000	0.000	0.000
32	A	389	ILE	0	-0.031	-0.013	10.808	-0.570	-0.570	0.000	0.000	0.000	0.000
33	A	390	ASP	-1	-0.822	-0.868	13.434	17.350	17.350	0.000	0.000	0.000	0.000
34	A	391	TYR	0	-0.048	-0.031	10.213	-0.574	-0.574	0.000	0.000	0.000	0.000
35	A	392	GLY	0	-0.011	0.019	11.250	0.466	0.466	0.000	0.000	0.000	0.000
36	A	393	VAL	0	-0.038	-0.023	5.064	1.888	1.888	0.000	0.000	0.000	0.000
37	A	394	ARG	1	0.940	0.961	4.142	-34.719	-34.427	-0.001	-0.020	-0.271	0.000
38	A	395	LEU	0	0.030	0.020	3.423	5.859	6.811	0.052	-0.351	-0.654	-0.002
39	A	396	PRO	0	0.018	0.017	2.131	-6.630	-5.853	3.591	-1.343	-3.026	0.005
40	A	397	GLU	-1	-0.927	-0.973	3.568	21.366	21.509	0.047	0.056	-0.246	0.000
41	A	398	VAL	0	0.014	-0.004	7.053	1.851	1.851	0.000	0.000	0.000	0.000
42	A	399	LEU	0	-0.049	-0.014	9.537	-2.467	-2.467	0.000	0.000	0.000	0.000
43	A	400	LEU	0	0.042	0.029	12.250	0.274	0.274	0.000	0.000	0.000	0.000
44	A	401	ARG	1	0.893	0.933	14.718	-18.684	-18.684	0.000	0.000	0.000	0.000
45	A	402	ASP	-1	-0.818	-0.912	17.903	12.847	12.847	0.000	0.000	0.000	0.000
46	A	403	GLY	0	-0.013	-0.016	21.250	0.318	0.318	0.000	0.000	0.000	0.000
47	A	404	GLU	-1	-0.872	-0.926	22.054	11.515	11.515	0.000	0.000	0.000	0.000
48	A	405	GLY	0	-0.043	-0.023	25.260	0.151	0.151	0.000	0.000	0.000	0.000
49	A	406	LEU	0	-0.078	-0.015	21.390	-0.062	-0.062	0.000	0.000	0.000	0.000
50	A	407	ASP	-1	-0.885	-0.933	25.571	10.482	10.482	0.000	0.000	0.000	0.000
51	A	408	ASP	-1	-0.765	-0.886	26.089	11.556	11.556	0.000	0.000	0.000	0.000
52	A	409	ASN	0	-0.040	-0.041	25.603	0.093	0.093	0.000	0.000	0.000	0.000
53	A	410	SER	0	0.017	0.031	23.460	0.216	0.216	0.000	0.000	0.000	0.000
54	A	411	ILE	0	-0.017	-0.008	17.044	0.046	0.046	0.000	0.000	0.000	0.000
55	A	412	VAL	0	-0.041	-0.019	17.049	0.016	0.016	0.000	0.000	0.000	0.000
56	A	413	LEU	0	0.012	0.019	10.246	0.425	0.425	0.000	0.000	0.000	0.000
57	A	414	LEU	0	-0.006	-0.009	12.529	-0.515	-0.515	0.000	0.000	0.000	0.000
58	A	415	ILE	0	0.039	0.011	6.291	1.966	1.966	0.000	0.000	0.000	0.000
59	A	416	ASN	0	-0.021	-0.018	7.689	0.650	0.650	0.000	0.000	0.000	0.000
60	A	417	GLU	-1	-0.911	-0.957	9.343	20.875	20.875	0.000	0.000	0.000	0.000
61	A	418	ILE	0	-0.042	0.000	11.787	-2.331	-2.331	0.000	0.000	0.000	0.000
62	A	419	ARG	1	0.946	0.963	12.825	-14.573	-14.573	0.000	0.000	0.000	0.000
63	A	420	VAL	0	-0.023	-0.006	10.479	-0.051	-0.051	0.000	0.000	0.000	0.000
64	A	421	GLU	-1	-0.871	-0.936	13.868	16.971	16.971	0.000	0.000	0.000	0.000
65	A	422	GLN	0	-0.031	-0.016	16.462	0.525	0.525	0.000	0.000	0.000	0.000
66	A	423	PHE	0	0.011	-0.005	14.312	-0.303	-0.303	0.000	0.000	0.000	0.000
67	A	424	THR	0	0.020	0.012	20.407	-0.189	-0.189	0.000	0.000	0.000	0.000
68	A	425	VAL	0	-0.032	-0.021	20.541	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	426	TYR	0	0.020	0.004	23.844	-0.190	-0.190	0.000	0.000	0.000	0.000
70	A	427	PHE	0	-0.002	-0.004	21.728	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	428	ASP	-1	-0.842	-0.877	26.534	10.164	10.164	0.000	0.000	0.000	0.000
72	A	429	LEU	0	-0.072	-0.029	28.924	-0.334	-0.334	0.000	0.000	0.000	0.000
73	A	430	MET	0	-0.029	-0.001	28.295	0.545	0.545	0.000	0.000	0.000	0.000
74	A	431	ARG	1	0.848	0.912	22.875	-12.940	-12.940	0.000	0.000	0.000	0.000
75	A	432	VAL	0	0.009	0.000	28.014	0.013	0.013	0.000	0.000	0.000	0.000
76	A	433	VAL	0	-0.062	-0.036	25.734	0.143	0.143	0.000	0.000	0.000	0.000
77	A	434	ASN	0	-0.013	-0.005	28.155	0.258	0.258	0.000	0.000	0.000	0.000
78	A	435	TYR	0	0.015	-0.001	31.144	-0.294	-0.294	0.000	0.000	0.000	0.000
79	A	436	SER	0	0.027	0.020	33.260	0.033	0.033	0.000	0.000	0.000	0.000
80	A	437	ASP	-1	-0.827	-0.930	36.684	8.238	8.238	0.000	0.000	0.000	0.000
81	A	438	GLU	-1	-0.987	-0.979	39.654	7.197	7.197	0.000	0.000	0.000	0.000
82	A	439	VAL	0	0.007	0.017	36.251	-0.121	-0.121	0.000	0.000	0.000	0.000
83	A	440	VAL	0	0.023	0.010	39.732	-0.121	-0.121	0.000	0.000	0.000	0.000
84	A	441	SER	0	-0.116	-0.055	42.024	-0.212	-0.212	0.000	0.000	0.000	0.000
85	A	442	PHE	0	0.003	-0.013	40.890	-0.187	-0.187	0.000	0.000	0.000	0.000
86	A	443	GLY	0	-0.050	-0.019	44.183	-0.055	-0.055	0.000	0.000	0.000	0.000
87	A	444	ILE	0	-0.039	-0.004	37.964	0.034	0.034	0.000	0.000	0.000	0.000
88	A	445	ASN	0	-0.008	-0.014	39.780	0.039	0.039	0.000	0.000	0.000	0.000
89	A	446	PRO	0	-0.004	0.003	34.252	0.073	0.073	0.000	0.000	0.000	0.000
90	A	447	THR	0	-0.010	0.003	31.646	-0.124	-0.124	0.000	0.000	0.000	0.000
91	A	448	ILE	0	-0.011	-0.013	32.054	0.272	0.272	0.000	0.000	0.000	0.000
92	A	449	HIS	0	-0.002	-0.014	24.879	-0.456	-0.456	0.000	0.000	0.000	0.000
93	A	450	GLN	0	0.019	0.004	28.936	-0.229	-0.229	0.000	0.000	0.000	0.000
94	A	451	GLN	0	0.025	0.028	21.084	-0.337	-0.337	0.000	0.000	0.000	0.000
95	A	452	GLY	0	0.005	0.001	25.734	0.233	0.233	0.000	0.000	0.000	0.000
96	A	453	SER	0	0.007	-0.001	26.847	-0.329	-0.329	0.000	0.000	0.000	0.000
97	A	454	SER	0	-0.045	-0.009	24.622	-0.433	-0.433	0.000	0.000	0.000	0.000
98	A	455	GLN	0	-0.031	-0.021	27.549	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	456	TYR	0	-0.023	-0.009	23.132	0.205	0.205	0.000	0.000	0.000	0.000
100	A	457	PHE	0	0.039	0.021	28.375	-0.167	-0.167	0.000	0.000	0.000	0.000
101	A	458	TRP	0	0.014	0.005	24.027	0.343	0.343	0.000	0.000	0.000	0.000
102	A	459	VAL	0	0.019	0.019	31.099	-0.310	-0.310	0.000	0.000	0.000	0.000
103	A	460	THR	0	0.025	-0.028	32.570	0.263	0.263	0.000	0.000	0.000	0.000
104	A	461	HIS	0	0.056	0.012	29.717	-0.072	-0.072	0.000	0.000	0.000	0.000
105	A	462	GLU	-1	-0.881	-0.928	34.289	7.438	7.438	0.000	0.000	0.000	0.000
106	A	463	GLU	-1	-0.814	-0.889	36.717	8.182	8.182	0.000	0.000	0.000	0.000
107	A	464	GLY	0	0.023	-0.007	33.867	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	465	GLU	-1	-0.855	-0.921	33.924	9.111	9.111	0.000	0.000	0.000	0.000
109	A	466	LYS	1	0.859	0.926	36.767	-7.610	-7.610	0.000	0.000	0.000	0.000
110	A	467	LEU	0	0.015	0.003	35.299	-0.065	-0.065	0.000	0.000	0.000	0.000
111	A	468	ARG	1	0.840	0.904	29.436	-9.660	-9.660	0.000	0.000	0.000	0.000
112	A	469	GLU	-1	-0.963	-0.964	35.847	7.898	7.898	0.000	0.000	0.000	0.000
113	A	470	MET	0	-0.113	-0.053	38.627	-0.212	-0.212	0.000	0.000	0.000	0.000
114	A	471	GLY	0	-0.008	0.012	36.964	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	472	TYR	0	-0.036	-0.026	33.721	0.181	0.181	0.000	0.000	0.000	0.000
116	A	473	VAL	0	-0.018	-0.018	28.011	0.046	0.046	0.000	0.000	0.000	0.000
117	A	474	LEU	0	-0.007	0.015	29.189	0.129	0.129	0.000	0.000	0.000	0.000
118	A	475	ARG	1	0.813	0.917	21.351	-13.391	-13.391	0.000	0.000	0.000	0.000
119	A	476	ASN	0	0.010	-0.015	23.565	0.178	0.178	0.000	0.000	0.000	0.000
120	A	477	ALA	0	0.089	0.028	23.593	0.487	0.487	0.000	0.000	0.000	0.000
121	A	478	LEU	0	0.003	0.005	20.062	0.624	0.624	0.000	0.000	0.000	0.000
122	A	479	ASP	-1	-0.804	-0.885	18.854	14.758	14.758	0.000	0.000	0.000	0.000
123	A	480	GLU	-1	-0.772	-0.869	19.226	14.344	14.344	0.000	0.000	0.000	0.000
124	A	481	LEU	0	-0.004	0.009	16.588	0.542	0.542	0.000	0.000	0.000	0.000
125	A	482	TYR	0	-0.050	-0.063	11.944	1.522	1.522	0.000	0.000	0.000	0.000
126	A	483	HIS	0	0.001	-0.006	14.652	0.618	0.618	0.000	0.000	0.000	0.000
127	A	484	CYS	0	-0.021	-0.014	16.238	0.342	0.342	0.000	0.000	0.000	0.000
128	A	485	LEU	0	0.017	0.027	9.788	0.798	0.798	0.000	0.000	0.000	0.000
129	A	486	ALA	0	0.045	0.011	11.716	1.799	1.799	0.000	0.000	0.000	0.000
130	A	487	VAL	0	-0.007	0.005	12.779	0.675	0.675	0.000	0.000	0.000	0.000
131	A	488	THR	0	-0.026	-0.021	12.249	-0.138	-0.138	0.000	0.000	0.000	0.000
132	A	489	LEU	0	-0.015	0.005	6.963	1.005	1.005	0.000	0.000	0.000	0.000
133	A	490	ALA	0	0.046	0.017	10.113	0.930	0.930	0.000	0.000	0.000	0.000
134	A	491	ARG	1	0.821	0.907	12.339	-19.764	-19.764	0.000	0.000	0.000	0.000
135	A	492	ASN	0	-0.021	-0.027	10.067	-0.507	-0.507	0.000	0.000	0.000	0.000
136	A	493	VAL	0	0.009	0.006	8.124	0.154	0.154	0.000	0.000	0.000	0.000
137	A	494	ASN	0	-0.048	-0.044	10.703	-1.800	-1.800	0.000	0.000	0.000	0.000
138	A	495	GLU	-1	-0.844	-0.910	14.285	18.298	18.298	0.000	0.000	0.000	0.000
139	A	496	TYR	0	-0.005	0.005	10.882	-0.645	-0.645	0.000	0.000	0.000	0.000
140	A	497	PHE	0	0.007	-0.010	11.405	-0.587	-0.587	0.000	0.000	0.000	0.000
141	A	498	GLY	0	0.048	0.040	14.814	-1.087	-1.087	0.000	0.000	0.000	0.000
142	A	499	ILE	0	-0.021	-0.011	14.751	-0.927	-0.927	0.000	0.000	0.000	0.000
143	A	500	GLN	0	-0.042	-0.024	13.706	-1.669	-1.669	0.000	0.000	0.000	0.000
144	A	501	GLU	-1	-0.901	-0.941	17.436	13.346	13.346	0.000	0.000	0.000	0.000
145	A	502	THR	0	-0.011	-0.017	20.478	-0.976	-0.976	0.000	0.000	0.000	0.000
146	A	503	LYS	1	0.848	0.913	16.061	-19.434	-19.434	0.000	0.000	0.000	0.000
147	A	504	HIS	0	0.007	0.011	21.575	-0.059	-0.059	0.000	0.000	0.000	0.000
148	A	505	MET	0	-0.047	-0.030	23.250	-0.701	-0.701	0.000	0.000	0.000	0.000
149	A	506	LEU	0	-0.077	-0.047	24.426	-0.545	-0.545	0.000	0.000	0.000	0.000
150	A	507	ASP	-1	-0.953	-0.961	24.981	11.976	11.976	0.000	0.000	0.000	0.000
151	A	508	GLN	0	-0.024	-0.009	27.056	-0.214	-0.214	0.000	0.000	0.000	0.000
152	A	509	LEU	0	-0.067	-0.012	29.415	-0.468	-0.468	0.000	0.000	0.000	0.000
153	A	510	GLU	-1	-0.894	-0.943	31.545	8.884	8.884	0.000	0.000	0.000	0.000
154	A	511	ALA	0	-0.084	-0.030	35.105	-0.306	-0.306	0.000	0.000	0.000	0.000
155	A	512	LYS	1	1.003	0.989	35.345	-7.652	-7.652	0.000	0.000	0.000	0.000
156	A	513	PHE	0	0.055	0.013	31.842	-0.145	-0.145	0.000	0.000	0.000	0.000
157	A	514	PRO	0	0.003	-0.001	36.832	-0.019	-0.019	0.000	0.000	0.000	0.000
158	A	515	ASP	-1	-0.905	-0.954	39.906	7.651	7.651	0.000	0.000	0.000	0.000
159	A	516	LEU	0	0.020	0.007	32.748	-0.073	-0.073	0.000	0.000	0.000	0.000
160	A	517	LEU	0	-0.010	-0.014	35.038	0.028	0.028	0.000	0.000	0.000	0.000
161	A	518	LYS	1	0.910	0.959	38.097	-7.160	-7.160	0.000	0.000	0.000	0.000
162	A	519	GLU	-1	-0.853	-0.946	38.805	7.678	7.678	0.000	0.000	0.000	0.000
163	A	520	VAL	0	0.010	0.012	34.791	-0.026	-0.026	0.000	0.000	0.000	0.000
164	A	521	LEU	0	-0.037	-0.008	37.861	-0.052	-0.052	0.000	0.000	0.000	0.000
165	A	522	ARG	1	0.852	0.951	40.665	-7.224	-7.224	0.000	0.000	0.000	0.000
166	A	523	HIS	0	-0.085	-0.036	39.055	-0.258	-0.258	0.000	0.000	0.000	0.000

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