FMO DATABASE

FMODB ID: V5V41

Calculation Name: 1R9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R9W

Chain ID: A

ChEMBL ID:

UniProt ID: P06789

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	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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1294475.849854
FMO2-HF: Nuclear repulsion	1239609.376532
FMO2-HF: Total energy	-54866.473322
FMO2-MP2: Total energy	-55024.279169

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:210:LYS)

Summations of interaction energy for fragment #1(A:210:LYS)

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.
48.811	55.001	0.677	-2.785	-4.083	-0.005

Interaction energy analysis for fragmet #1(A:210:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.028 / q_NPA : 0.996

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	212	GLY	0	0.044	0.020	3.752	-0.906	1.264	-0.011	-1.124	-1.035	0.005
4	A	213	ALA	0	0.025	0.014	3.376	0.393	0.829	0.022	-0.092	-0.365	0.000
5	A	214	MET	0	0.004	0.016	3.352	1.695	2.243	0.012	-0.103	-0.458	0.000
6	A	215	LEU	0	-0.021	-0.007	6.629	3.188	3.188	0.000	0.000	0.000	0.000
7	A	216	ALA	0	-0.016	-0.003	8.147	1.869	1.869	0.000	0.000	0.000	0.000
8	A	217	VAL	0	0.049	0.026	8.788	1.202	1.202	0.000	0.000	0.000	0.000
9	A	218	PHE	0	0.013	0.007	10.493	1.463	1.463	0.000	0.000	0.000	0.000
10	A	219	LYS	1	0.925	0.973	12.495	16.701	16.701	0.000	0.000	0.000	0.000
11	A	220	ASP	-1	-0.948	-0.967	13.454	-18.089	-18.089	0.000	0.000	0.000	0.000
12	A	221	THR	0	-0.063	-0.043	14.199	0.621	0.621	0.000	0.000	0.000	0.000
13	A	222	TYR	0	-0.022	-0.042	15.924	1.179	1.179	0.000	0.000	0.000	0.000
14	A	223	GLY	0	0.009	0.027	17.875	0.819	0.819	0.000	0.000	0.000	0.000
15	A	224	LEU	0	-0.040	-0.020	17.902	0.663	0.663	0.000	0.000	0.000	0.000
16	A	225	SER	0	0.007	-0.011	15.063	-1.459	-1.459	0.000	0.000	0.000	0.000
17	A	226	PHE	0	0.071	0.029	12.255	0.323	0.323	0.000	0.000	0.000	0.000
18	A	227	THR	0	0.004	-0.001	13.196	0.290	0.290	0.000	0.000	0.000	0.000
19	A	228	ASP	-1	-0.934	-0.961	15.478	-13.306	-13.306	0.000	0.000	0.000	0.000
20	A	229	LEU	0	-0.027	-0.017	17.786	0.748	0.748	0.000	0.000	0.000	0.000
21	A	230	VAL	0	-0.065	-0.012	14.316	0.332	0.332	0.000	0.000	0.000	0.000
22	A	231	ARG	1	0.860	0.935	17.113	13.518	13.518	0.000	0.000	0.000	0.000
23	A	239	THR	0	0.027	0.011	21.639	-0.222	-0.222	0.000	0.000	0.000	0.000
24	A	240	CYS	0	-0.066	-0.040	21.154	0.359	0.359	0.000	0.000	0.000	0.000
25	A	241	THR	0	0.051	0.014	22.731	-0.375	-0.375	0.000	0.000	0.000	0.000
26	A	242	ASP	-1	-0.788	-0.844	22.906	-12.138	-12.138	0.000	0.000	0.000	0.000
27	A	243	TRP	0	-0.056	-0.051	15.508	-0.813	-0.813	0.000	0.000	0.000	0.000
28	A	244	VAL	0	0.020	0.034	16.133	0.403	0.403	0.000	0.000	0.000	0.000
29	A	245	THR	0	-0.056	-0.055	14.254	-0.870	-0.870	0.000	0.000	0.000	0.000
30	A	246	ALA	0	0.062	0.037	11.375	1.029	1.029	0.000	0.000	0.000	0.000
31	A	247	ILE	0	-0.028	-0.010	10.178	-2.898	-2.898	0.000	0.000	0.000	0.000
32	A	248	PHE	0	0.029	-0.023	7.071	1.537	1.537	0.000	0.000	0.000	0.000
33	A	249	GLY	0	0.003	0.000	8.247	-2.774	-2.774	0.000	0.000	0.000	0.000
34	A	250	VAL	0	-0.029	0.002	9.892	-0.247	-0.247	0.000	0.000	0.000	0.000
35	A	251	ASN	0	0.047	0.016	12.595	1.521	1.521	0.000	0.000	0.000	0.000
36	A	252	PRO	0	0.091	0.020	15.552	0.195	0.195	0.000	0.000	0.000	0.000
37	A	253	THR	0	0.045	0.029	18.585	0.343	0.343	0.000	0.000	0.000	0.000
38	A	254	ILE	0	-0.045	-0.012	16.397	0.431	0.431	0.000	0.000	0.000	0.000
39	A	255	ALA	0	-0.022	-0.026	16.563	0.226	0.226	0.000	0.000	0.000	0.000
40	A	256	GLU	-1	-0.918	-0.939	18.260	-12.392	-12.392	0.000	0.000	0.000	0.000
41	A	257	GLY	0	-0.008	-0.001	21.403	0.678	0.678	0.000	0.000	0.000	0.000
42	A	258	PHE	0	0.015	-0.008	18.052	0.103	0.103	0.000	0.000	0.000	0.000
43	A	259	LYS	1	0.973	0.996	20.729	11.707	11.707	0.000	0.000	0.000	0.000
44	A	260	THR	0	0.043	-0.004	23.849	0.249	0.249	0.000	0.000	0.000	0.000
45	A	261	LEU	0	-0.040	-0.008	19.969	0.257	0.257	0.000	0.000	0.000	0.000
46	A	262	ILE	0	-0.006	-0.007	19.977	0.090	0.090	0.000	0.000	0.000	0.000
47	A	263	GLN	0	0.041	0.029	22.783	0.062	0.062	0.000	0.000	0.000	0.000
48	A	264	PRO	0	-0.032	-0.015	25.585	0.357	0.357	0.000	0.000	0.000	0.000
49	A	265	PHE	0	-0.033	-0.017	23.677	0.257	0.257	0.000	0.000	0.000	0.000
50	A	266	ILE	0	-0.076	-0.028	23.630	-0.106	-0.106	0.000	0.000	0.000	0.000
51	A	267	LEU	0	-0.021	-0.016	26.685	0.388	0.388	0.000	0.000	0.000	0.000
52	A	268	TYR	0	0.023	0.005	25.946	0.143	0.143	0.000	0.000	0.000	0.000
53	A	269	ALA	0	-0.006	-0.006	23.949	-0.541	-0.541	0.000	0.000	0.000	0.000
54	A	270	HIS	0	-0.038	0.006	23.706	0.085	0.085	0.000	0.000	0.000	0.000
55	A	271	ILE	0	0.033	0.004	19.905	-0.826	-0.826	0.000	0.000	0.000	0.000
56	A	272	GLN	0	0.081	0.042	20.254	0.519	0.519	0.000	0.000	0.000	0.000
57	A	273	CYS	0	0.008	0.001	18.110	-1.194	-1.194	0.000	0.000	0.000	0.000
58	A	274	LEU	0	0.022	0.019	17.376	0.842	0.842	0.000	0.000	0.000	0.000
59	A	275	ASP	-1	-0.875	-0.924	16.255	-17.924	-17.924	0.000	0.000	0.000	0.000
60	A	276	CYS	0	-0.077	-0.036	11.840	-1.117	-1.117	0.000	0.000	0.000	0.000
61	A	277	LYS	1	0.933	0.945	8.694	29.371	29.371	0.000	0.000	0.000	0.000
62	A	278	TRP	0	-0.012	-0.014	6.256	-1.441	-1.441	0.000	0.000	0.000	0.000
63	A	279	GLY	0	0.048	0.037	10.488	-0.586	-0.586	0.000	0.000	0.000	0.000
64	A	280	VAL	0	0.045	0.043	13.198	0.273	0.273	0.000	0.000	0.000	0.000
65	A	281	LEU	0	-0.037	-0.018	11.530	-2.161	-2.161	0.000	0.000	0.000	0.000
66	A	282	ILE	0	0.013	0.017	13.482	1.529	1.529	0.000	0.000	0.000	0.000
67	A	283	LEU	0	-0.032	-0.004	14.502	-1.570	-1.570	0.000	0.000	0.000	0.000
68	A	284	ALA	0	0.032	0.004	16.923	0.986	0.986	0.000	0.000	0.000	0.000
69	A	285	LEU	0	-0.062	-0.001	18.588	-0.682	-0.682	0.000	0.000	0.000	0.000
70	A	286	LEU	0	-0.005	-0.007	19.053	0.512	0.512	0.000	0.000	0.000	0.000
71	A	287	ARG	1	0.910	0.929	22.517	10.831	10.831	0.000	0.000	0.000	0.000
72	A	288	TYR	0	0.004	-0.025	18.808	0.209	0.209	0.000	0.000	0.000	0.000
73	A	289	LYS	1	0.900	0.954	25.392	11.028	11.028	0.000	0.000	0.000	0.000
74	A	290	CYS	0	-0.004	0.001	26.937	0.386	0.386	0.000	0.000	0.000	0.000
75	A	291	GLY	0	0.008	0.004	25.028	-0.477	-0.477	0.000	0.000	0.000	0.000
76	A	292	LYS	1	0.934	0.970	20.501	14.150	14.150	0.000	0.000	0.000	0.000
77	A	293	SER	0	0.079	0.039	18.570	-0.180	-0.180	0.000	0.000	0.000	0.000
78	A	294	ARG	1	0.957	0.945	8.443	27.475	27.475	0.000	0.000	0.000	0.000
79	A	295	LEU	0	0.017	0.015	13.393	-0.580	-0.580	0.000	0.000	0.000	0.000
80	A	296	THR	0	-0.032	-0.027	15.141	-0.403	-0.403	0.000	0.000	0.000	0.000
81	A	297	VAL	0	-0.013	0.001	15.709	0.151	0.151	0.000	0.000	0.000	0.000
82	A	298	ALA	0	0.042	0.013	11.561	-0.163	-0.163	0.000	0.000	0.000	0.000
83	A	299	LYS	1	0.933	0.969	13.280	17.663	17.663	0.000	0.000	0.000	0.000
84	A	300	GLY	0	0.004	0.011	14.986	0.212	0.212	0.000	0.000	0.000	0.000
85	A	301	LEU	0	0.048	0.006	13.806	0.306	0.306	0.000	0.000	0.000	0.000
86	A	302	SER	0	-0.075	-0.046	11.109	0.155	0.155	0.000	0.000	0.000	0.000
87	A	303	THR	0	-0.035	-0.023	13.115	0.285	0.285	0.000	0.000	0.000	0.000
88	A	304	LEU	0	-0.046	-0.021	16.514	0.592	0.592	0.000	0.000	0.000	0.000
89	A	305	LEU	0	-0.009	-0.014	13.378	0.436	0.436	0.000	0.000	0.000	0.000
90	A	306	HIS	0	0.016	0.026	13.544	-1.045	-1.045	0.000	0.000	0.000	0.000
91	A	307	VAL	0	0.027	0.025	7.770	-1.989	-1.989	0.000	0.000	0.000	0.000
92	A	308	PRO	0	0.025	0.028	5.436	1.705	1.705	0.000	0.000	0.000	0.000
93	A	309	GLU	-1	-0.739	-0.890	7.315	-30.155	-30.155	0.000	0.000	0.000	0.000
94	A	310	THR	0	-0.083	-0.056	2.389	-5.004	-3.534	0.567	-0.701	-1.336	-0.004
95	A	311	CYS	0	-0.082	-0.034	3.417	-22.471	-20.964	0.088	-0.763	-0.833	-0.006
96	A	312	MET	0	0.005	0.026	4.995	7.456	7.515	-0.001	-0.002	-0.056	0.000
97	A	313	LEU	0	-0.034	0.005	7.165	-2.087	-2.087	0.000	0.000	0.000	0.000
98	A	314	ILE	0	-0.008	-0.003	9.478	2.004	2.004	0.000	0.000	0.000	0.000
99	A	315	GLN	0	0.011	-0.015	12.388	0.897	0.897	0.000	0.000	0.000	0.000
100	A	316	PRO	0	0.008	0.014	14.646	0.487	0.487	0.000	0.000	0.000	0.000
101	A	317	PRO	0	0.109	0.065	18.296	-0.232	-0.232	0.000	0.000	0.000	0.000
102	A	318	LYS	1	0.865	0.946	19.377	13.998	13.998	0.000	0.000	0.000	0.000
103	A	319	LEU	0	-0.008	-0.011	22.364	0.117	0.117	0.000	0.000	0.000	0.000
104	A	320	ARG	1	0.971	0.981	25.891	10.325	10.325	0.000	0.000	0.000	0.000
105	A	321	SER	0	0.008	0.016	24.169	0.329	0.329	0.000	0.000	0.000	0.000
106	A	322	SER	0	0.091	0.040	26.677	-0.238	-0.238	0.000	0.000	0.000	0.000
107	A	323	VAL	0	0.050	0.028	24.330	0.038	0.038	0.000	0.000	0.000	0.000
108	A	324	ALA	0	-0.003	-0.011	23.066	-0.182	-0.182	0.000	0.000	0.000	0.000
109	A	325	ALA	0	-0.023	-0.009	24.459	-0.173	-0.173	0.000	0.000	0.000	0.000
110	A	326	LEU	0	0.044	0.020	27.626	0.056	0.056	0.000	0.000	0.000	0.000
111	A	327	TYR	0	0.015	0.014	21.063	0.158	0.158	0.000	0.000	0.000	0.000
112	A	328	TRP	0	0.048	0.017	19.550	-0.132	-0.132	0.000	0.000	0.000	0.000
113	A	329	TYR	0	0.012	0.014	26.074	0.152	0.152	0.000	0.000	0.000	0.000
114	A	330	ARG	1	0.949	0.964	29.226	9.469	9.469	0.000	0.000	0.000	0.000
115	A	331	THR	0	-0.023	-0.024	24.266	0.095	0.095	0.000	0.000	0.000	0.000
116	A	332	GLY	0	-0.005	0.016	27.320	-0.104	-0.104	0.000	0.000	0.000	0.000
117	A	333	ILE	0	-0.041	-0.012	28.863	0.199	0.199	0.000	0.000	0.000	0.000
118	A	334	SER	0	-0.033	-0.005	28.868	0.245	0.245	0.000	0.000	0.000	0.000
119	A	335	ASN	0	0.046	0.014	29.702	-0.123	-0.123	0.000	0.000	0.000	0.000
120	A	336	ILE	0	-0.054	-0.028	25.031	-0.201	-0.201	0.000	0.000	0.000	0.000
121	A	337	SER	0	-0.049	-0.037	24.793	-0.562	-0.562	0.000	0.000	0.000	0.000
122	A	338	GLU	-1	-0.904	-0.946	23.846	-12.421	-12.421	0.000	0.000	0.000	0.000
123	A	339	VAL	0	-0.016	-0.018	25.721	-0.422	-0.422	0.000	0.000	0.000	0.000
124	A	340	MET	0	-0.048	-0.009	25.366	0.505	0.505	0.000	0.000	0.000	0.000
125	A	341	GLY	0	0.026	-0.001	29.172	-0.308	-0.308	0.000	0.000	0.000	0.000
126	A	342	ASP	-1	-0.932	-0.965	31.627	-9.021	-9.021	0.000	0.000	0.000	0.000
127	A	343	THR	0	-0.016	-0.008	30.313	-0.417	-0.417	0.000	0.000	0.000	0.000
128	A	344	PRO	0	-0.005	-0.005	27.167	0.282	0.282	0.000	0.000	0.000	0.000
129	A	345	GLU	-1	-0.769	-0.867	30.354	-8.631	-8.631	0.000	0.000	0.000	0.000
130	A	346	TRP	0	-0.042	-0.037	23.993	0.228	0.228	0.000	0.000	0.000	0.000
131	A	347	ILE	0	0.023	0.013	26.573	0.037	0.037	0.000	0.000	0.000	0.000
132	A	348	GLN	0	-0.023	0.004	30.067	0.337	0.337	0.000	0.000	0.000	0.000
133	A	349	ARG	1	0.843	0.900	33.685	8.438	8.438	0.000	0.000	0.000	0.000
134	A	350	LEU	0	-0.056	-0.024	29.654	0.140	0.140	0.000	0.000	0.000	0.000
135	A	351	THR	0	-0.028	-0.027	31.738	-0.167	-0.167	0.000	0.000	0.000	0.000
136	A	352	ILE	0	-0.017	-0.002	32.972	0.268	0.268	0.000	0.000	0.000	0.000
137	A	353	ILE	0	-0.026	-0.018	35.174	-0.134	-0.134	0.000	0.000	0.000	0.000
138	A	354	GLN	0	0.020	0.022	37.887	0.170	0.170	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:210:LYS)