FMO DATABASE

FMODB ID: YZ892

Calculation Name: 4YMR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YMR

Chain ID: A

ChEMBL ID:

UniProt ID: Q3UR97

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1030746.287801
FMO2-HF: Nuclear repulsion	979400.114156
FMO2-HF: Total energy	-51346.173645
FMO2-MP2: Total energy	-51497.474328

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:230:VAL)

Summations of interaction energy for fragment #1(A:230:VAL)

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.
-11.429	-9.647	19.285	-7.41	-13.658	-0.046

Interaction energy analysis for fragmet #1(A:230:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.033

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	232	PRO	0	-0.053	-0.034	2.379	-1.314	1.642	0.524	-1.447	-2.033	0.008
4	A	233	GLU	-1	-0.834	-0.904	3.285	-0.217	0.899	0.051	-0.288	-0.879	0.000
5	A	234	LEU	0	0.016	0.005	2.442	-0.770	0.560	0.874	-0.502	-1.702	0.000
6	A	235	ARG	1	0.876	0.932	5.139	2.188	2.323	-0.001	-0.009	-0.125	0.000
7	A	236	ARG	1	0.855	0.926	8.144	0.667	0.667	0.000	0.000	0.000	0.000
8	A	237	ALA	0	0.069	0.041	7.599	0.168	0.168	0.000	0.000	0.000	0.000
9	A	238	GLN	0	0.027	0.023	9.021	0.046	0.046	0.000	0.000	0.000	0.000
10	A	239	SER	0	-0.061	-0.038	10.895	0.104	0.104	0.000	0.000	0.000	0.000
11	A	240	LEU	0	-0.010	0.000	11.905	0.057	0.057	0.000	0.000	0.000	0.000
12	A	241	THR	0	0.014	-0.015	12.194	0.064	0.064	0.000	0.000	0.000	0.000
13	A	242	CYS	0	-0.106	-0.057	14.428	0.030	0.030	0.000	0.000	0.000	0.000
14	A	243	THR	0	-0.051	-0.037	16.953	0.024	0.024	0.000	0.000	0.000	0.000
15	A	244	GLY	0	0.043	0.042	18.395	0.019	0.019	0.000	0.000	0.000	0.000
16	A	245	LEU	0	-0.021	-0.003	16.911	0.022	0.022	0.000	0.000	0.000	0.000
17	A	246	TYR	0	-0.005	-0.049	15.797	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	247	ARG	1	0.862	0.919	15.230	0.036	0.036	0.000	0.000	0.000	0.000
19	A	248	GLU	-1	-0.824	-0.884	13.480	-0.246	-0.246	0.000	0.000	0.000	0.000
20	A	249	ALA	0	-0.014	-0.017	11.623	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	250	LEU	0	0.002	-0.002	10.411	-0.024	-0.024	0.000	0.000	0.000	0.000
22	A	251	ALA	0	0.015	0.014	10.615	0.032	0.032	0.000	0.000	0.000	0.000
23	A	252	LEU	0	-0.011	0.002	7.358	0.050	0.050	0.000	0.000	0.000	0.000
24	A	253	TRP	0	0.009	-0.002	5.786	-0.042	-0.042	0.000	0.000	0.000	0.000
25	A	254	ALA	0	0.010	0.011	6.714	0.097	0.097	0.000	0.000	0.000	0.000
26	A	255	ASN	0	-0.051	-0.025	5.726	0.138	0.138	0.000	0.000	0.000	0.000
27	A	256	ALA	0	0.051	0.016	2.251	0.154	-0.176	2.904	-1.081	-1.493	0.001
28	A	257	TRP	0	0.006	0.012	2.912	-0.409	-0.371	0.277	0.657	-0.972	-0.011
29	A	258	GLN	0	-0.039	-0.029	5.671	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	259	LEU	0	-0.013	-0.003	2.373	-1.089	-0.018	1.329	-0.494	-1.907	-0.004
31	A	260	GLN	0	-0.024	-0.051	2.370	-1.127	-0.006	0.723	-0.462	-1.382	-0.002
32	A	261	THR	0	-0.037	-0.018	4.759	0.002	0.029	-0.001	-0.010	-0.015	0.000
33	A	262	GLN	0	-0.016	-0.009	7.773	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	263	LEU	0	-0.056	-0.014	6.027	-0.041	-0.041	0.000	0.000	0.000	0.000
35	A	264	GLY	0	0.032	0.005	6.645	0.207	0.207	0.000	0.000	0.000	0.000
36	A	265	THR	0	-0.045	-0.013	8.085	-0.116	-0.116	0.000	0.000	0.000	0.000
37	A	266	PRO	0	-0.031	-0.010	7.182	-0.049	-0.049	0.000	0.000	0.000	0.000
38	A	267	SER	0	0.005	0.012	6.606	0.014	0.014	0.000	0.000	0.000	0.000
39	A	268	GLY	0	-0.002	-0.011	8.816	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	269	PRO	0	0.021	0.002	8.406	0.007	0.007	0.000	0.000	0.000	0.000
41	A	270	ASP	-1	-0.850	-0.930	9.937	-0.092	-0.092	0.000	0.000	0.000	0.000
42	A	271	ARG	1	0.839	0.900	3.713	-0.148	0.072	0.002	-0.031	-0.191	0.000
43	A	272	PRO	0	0.052	0.039	6.455	-0.053	-0.053	0.000	0.000	0.000	0.000
44	A	273	LEU	0	0.001	0.013	8.093	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	274	LEU	0	-0.002	0.005	7.474	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	275	THR	0	-0.009	-0.016	5.586	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	276	LEU	0	-0.033	-0.011	7.722	0.010	0.010	0.000	0.000	0.000	0.000
48	A	277	ALA	0	0.005	0.009	11.168	0.007	0.007	0.000	0.000	0.000	0.000
49	A	278	GLY	0	0.032	0.010	10.358	0.002	0.002	0.000	0.000	0.000	0.000
50	A	279	LEU	0	-0.004	-0.012	9.525	0.011	0.011	0.000	0.000	0.000	0.000
51	A	280	ALA	0	-0.004	-0.001	12.330	0.010	0.010	0.000	0.000	0.000	0.000
52	A	281	VAL	0	0.010	0.002	15.052	0.007	0.007	0.000	0.000	0.000	0.000
53	A	282	CYS	0	-0.046	-0.018	13.387	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	283	HIS	0	-0.031	-0.046	15.393	0.019	0.019	0.000	0.000	0.000	0.000
55	A	284	GLN	0	-0.053	-0.033	17.973	0.010	0.010	0.000	0.000	0.000	0.000
56	A	285	GLU	-1	-0.871	-0.889	19.533	-0.100	-0.100	0.000	0.000	0.000	0.000
57	A	286	LEU	0	-0.058	-0.038	17.232	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	287	GLU	-1	-0.987	-0.968	21.636	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	288	ASP	-1	-0.785	-0.889	19.092	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	289	PRO	0	0.037	0.012	20.708	0.004	0.004	0.000	0.000	0.000	0.000
61	A	290	GLY	0	-0.020	-0.009	22.344	0.001	0.001	0.000	0.000	0.000	0.000
62	A	291	GLU	-1	-0.875	-0.941	17.244	0.047	0.047	0.000	0.000	0.000	0.000
63	A	292	ALA	0	0.043	0.031	17.392	0.000	0.000	0.000	0.000	0.000	0.000
64	A	293	ARG	1	0.840	0.923	18.486	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	294	ALA	0	0.012	0.008	17.750	0.003	0.003	0.000	0.000	0.000	0.000
66	A	295	CYS	0	-0.019	-0.011	14.134	0.012	0.012	0.000	0.000	0.000	0.000
67	A	296	SER	0	-0.008	-0.022	15.395	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	297	GLU	-1	-0.846	-0.895	17.941	0.028	0.028	0.000	0.000	0.000	0.000
69	A	298	LYS	1	0.885	0.944	13.312	-0.091	-0.091	0.000	0.000	0.000	0.000
70	A	299	ALA	0	0.050	0.015	14.550	0.008	0.008	0.000	0.000	0.000	0.000
71	A	300	LEU	0	0.006	-0.005	15.469	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	301	GLN	0	-0.039	-0.029	17.739	0.015	0.015	0.000	0.000	0.000	0.000
73	A	302	LEU	0	-0.064	-0.034	11.710	0.009	0.009	0.000	0.000	0.000	0.000
74	A	303	LEU	0	0.013	0.004	16.113	0.002	0.002	0.000	0.000	0.000	0.000
75	A	304	GLY	0	-0.033	-0.002	18.275	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	305	ASP	-1	-0.816	-0.889	18.830	0.082	0.082	0.000	0.000	0.000	0.000
77	A	306	LYS	1	0.921	0.974	19.383	-0.049	-0.049	0.000	0.000	0.000	0.000
78	A	307	ARG	1	0.841	0.890	14.163	-0.082	-0.082	0.000	0.000	0.000	0.000
79	A	308	PRO	0	-0.016	-0.013	17.695	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	309	HIS	0	0.017	0.012	12.942	0.009	0.009	0.000	0.000	0.000	0.000
81	A	310	PRO	0	-0.010	-0.007	11.662	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	311	PHE	0	0.052	0.011	12.722	0.005	0.005	0.000	0.000	0.000	0.000
83	A	312	LEU	0	-0.001	0.021	17.024	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.061	0.022	20.027	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	314	PRO	0	-0.003	0.002	17.763	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	315	PHE	0	0.023	-0.004	18.911	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	316	LEU	0	-0.036	0.002	22.935	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	317	GLU	-1	-0.786	-0.868	24.198	0.040	0.040	0.000	0.000	0.000	0.000
89	A	318	ALA	0	-0.064	-0.033	24.288	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	319	HIS	0	0.040	0.036	26.273	0.000	0.000	0.000	0.000	0.000	0.000
91	A	320	VAL	0	0.050	0.031	28.768	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	321	ARG	1	0.822	0.891	27.700	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	322	LEU	0	-0.019	-0.020	27.805	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	323	SER	0	-0.007	-0.014	31.781	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	324	TRP	0	0.020	0.009	34.344	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	325	ARG	1	0.865	0.933	34.198	0.000	0.000	0.000	0.000	0.000	0.000
97	A	326	LEU	0	-0.036	-0.017	34.641	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	327	GLY	0	0.000	0.016	37.977	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	328	LEU	0	-0.033	-0.009	35.838	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	329	ASP	-1	-0.798	-0.889	38.020	0.007	0.007	0.000	0.000	0.000	0.000
101	A	330	LYS	1	0.810	0.891	34.310	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	331	ARG	1	0.901	0.925	33.695	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	332	GLN	0	0.011	0.009	33.247	0.003	0.003	0.000	0.000	0.000	0.000
104	A	333	SER	0	-0.014	-0.027	29.353	0.001	0.001	0.000	0.000	0.000	0.000
105	A	334	GLU	-1	-0.800	-0.886	29.542	0.023	0.023	0.000	0.000	0.000	0.000
106	A	335	ALA	0	0.037	0.023	31.105	0.004	0.004	0.000	0.000	0.000	0.000
107	A	336	GLN	0	-0.004	0.000	26.057	0.003	0.003	0.000	0.000	0.000	0.000
108	A	337	LEU	0	0.033	0.009	24.839	0.004	0.004	0.000	0.000	0.000	0.000
109	A	338	GLN	0	-0.039	-0.019	27.286	0.005	0.005	0.000	0.000	0.000	0.000
110	A	339	ALA	0	0.041	0.026	29.200	0.004	0.004	0.000	0.000	0.000	0.000
111	A	340	LEU	0	-0.027	-0.026	22.513	0.003	0.003	0.000	0.000	0.000	0.000
112	A	341	GLN	0	-0.015	0.011	24.836	0.011	0.011	0.000	0.000	0.000	0.000
113	A	342	GLU	-1	-0.938	-0.972	26.537	0.046	0.046	0.000	0.000	0.000	0.000
114	A	343	ALA	0	-0.059	-0.017	26.337	0.000	0.000	0.000	0.000	0.000	0.000
115	A	344	GLY	0	-0.015	-0.009	24.524	0.003	0.003	0.000	0.000	0.000	0.000
116	A	345	LEU	0	-0.075	-0.040	21.028	0.009	0.009	0.000	0.000	0.000	0.000
117	A	346	THR	0	-0.045	-0.034	19.967	0.006	0.006	0.000	0.000	0.000	0.000
118	A	347	SER	0	-0.024	-0.017	21.022	0.000	0.000	0.000	0.000	0.000	0.000
119	A	348	THR	0	0.016	-0.011	22.841	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	349	PRO	0	-0.002	-0.019	25.508	0.002	0.002	0.000	0.000	0.000	0.000
121	A	350	PRO	0	0.007	0.043	21.954	0.011	0.011	0.000	0.000	0.000	0.000
122	A	351	PRO	0	0.023	0.017	17.575	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	352	SER	0	0.002	-0.005	19.898	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	353	LEU	0	0.029	0.002	18.751	0.007	0.007	0.000	0.000	0.000	0.000
125	A	354	LYS	1	0.947	0.965	18.330	-0.036	-0.036	0.000	0.000	0.000	0.000
126	A	355	GLU	-1	-0.800	-0.880	16.650	0.150	0.150	0.000	0.000	0.000	0.000
127	A	356	LEU	0	0.024	0.005	14.058	0.021	0.021	0.000	0.000	0.000	0.000
128	A	357	LEU	0	-0.064	-0.024	13.323	0.000	0.000	0.000	0.000	0.000	0.000
129	A	358	ILE	0	-0.045	-0.021	14.526	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	359	LYS	1	0.845	0.908	11.772	-0.207	-0.207	0.000	0.000	0.000	0.000
131	A	360	GLU	-1	-0.836	-0.873	7.678	0.027	0.027	0.000	0.000	0.000	0.000
132	A	361	VAL	0	0.008	0.003	5.128	-0.079	-0.079	0.000	0.000	0.000	0.000
133	A	362	LEU	0	-0.026	-0.002	6.434	-0.344	-0.344	0.000	0.000	0.000	0.000
134	A	363	ASP	-1	-0.824	-0.900	1.858	-9.018	-14.920	12.603	-3.743	-2.959	-0.038

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Interactive mode: IFIE and PIEDA for fragment #1(A:230:VAL)