FMO DATABASE

FMODB ID: 49Z6N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1025233.029595
FMO2-HF: Nuclear repulsion	973888.233737
FMO2-HF: Total energy	-51344.795858
FMO2-MP2: Total energy	-51496.097636

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.
-14.765	-9.275	16.807	-8.045	-14.252	-0.048

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 : 0.099 / q_NPA : 0.053

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	-0.021	-0.019	2.591	-2.725	0.931	0.210	-1.758	-2.108	0.009
4	A	233	GLU	-1	-0.878	-0.931	3.664	-0.628	0.361	0.019	-0.239	-0.768	0.000
5	A	234	LEU	0	0.004	0.005	2.669	-0.884	0.479	0.565	-0.426	-1.502	0.001
6	A	235	ARG	1	0.893	0.954	5.542	1.488	1.488	0.000	0.000	0.000	0.000
7	A	236	ARG	1	0.966	0.995	8.322	0.475	0.475	0.000	0.000	0.000	0.000
8	A	237	ALA	0	0.055	0.022	7.735	0.113	0.113	0.000	0.000	0.000	0.000
9	A	238	GLN	0	0.011	0.007	9.329	0.054	0.054	0.000	0.000	0.000	0.000
10	A	239	SER	0	-0.064	-0.031	11.162	0.066	0.066	0.000	0.000	0.000	0.000
11	A	240	LEU	0	0.013	-0.005	12.194	0.037	0.037	0.000	0.000	0.000	0.000
12	A	241	THR	0	0.027	0.003	12.333	0.041	0.041	0.000	0.000	0.000	0.000
13	A	242	CYS	0	-0.067	-0.032	14.919	0.023	0.023	0.000	0.000	0.000	0.000
14	A	243	THR	0	-0.086	-0.033	17.256	0.020	0.020	0.000	0.000	0.000	0.000
15	A	244	GLY	0	0.069	0.045	18.175	0.014	0.014	0.000	0.000	0.000	0.000
16	A	245	LEU	0	-0.062	-0.019	17.081	0.015	0.015	0.000	0.000	0.000	0.000
17	A	246	TYR	0	0.074	0.020	16.156	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	247	ARG	1	0.976	0.987	15.437	0.023	0.023	0.000	0.000	0.000	0.000
19	A	248	GLU	-1	-0.944	-0.978	14.794	-0.139	-0.139	0.000	0.000	0.000	0.000
20	A	249	ALA	0	-0.016	-0.011	11.948	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	250	LEU	0	0.002	0.007	10.659	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	251	ALA	0	0.028	0.007	10.690	0.016	0.016	0.000	0.000	0.000	0.000
23	A	252	LEU	0	-0.020	-0.007	7.791	0.029	0.029	0.000	0.000	0.000	0.000
24	A	253	TRP	0	0.025	0.007	6.233	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	254	ALA	0	-0.009	0.007	6.545	0.073	0.073	0.000	0.000	0.000	0.000
26	A	255	ASN	0	0.014	0.003	6.461	0.100	0.100	0.000	0.000	0.000	0.000
27	A	256	ALA	0	0.031	0.020	2.250	-0.127	-0.206	2.040	-0.631	-1.330	0.001
28	A	257	TRP	0	-0.018	-0.011	3.017	-0.827	-0.072	0.221	-0.127	-0.849	-0.007
29	A	258	GLN	0	0.021	0.005	5.700	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	259	LEU	0	-0.029	-0.032	2.105	-0.240	-0.885	3.507	-0.692	-2.171	-0.008
31	A	260	GLN	0	-0.044	-0.056	2.196	-1.000	-0.139	1.260	-0.563	-1.558	-0.003
32	A	261	THR	0	-0.018	0.011	4.559	-0.027	0.014	-0.001	-0.021	-0.019	0.000
33	A	262	GLN	0	-0.019	-0.009	7.799	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	263	LEU	0	-0.073	-0.024	6.461	-0.069	-0.069	0.000	0.000	0.000	0.000
35	A	264	GLY	0	0.041	0.013	6.670	0.192	0.192	0.000	0.000	0.000	0.000
36	A	265	THR	0	-0.060	-0.020	8.802	-0.107	-0.107	0.000	0.000	0.000	0.000
37	A	266	PRO	0	-0.051	0.006	7.032	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	267	SER	0	0.071	0.023	6.731	0.055	0.055	0.000	0.000	0.000	0.000
39	A	268	GLY	0	-0.025	-0.032	8.276	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	269	PRO	0	-0.028	-0.031	8.106	0.015	0.015	0.000	0.000	0.000	0.000
41	A	270	ASP	-1	-0.817	-0.903	9.364	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	271	ARG	1	0.937	0.969	2.838	-0.820	-0.206	0.198	-0.149	-0.663	0.001
43	A	272	PRO	0	0.020	0.050	6.339	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	273	LEU	0	0.034	0.018	7.572	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	274	LEU	0	-0.006	0.005	6.763	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	275	THR	0	-0.016	-0.021	5.603	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	276	LEU	0	-0.024	-0.011	7.649	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	277	ALA	0	0.001	0.009	11.033	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	278	GLY	0	0.022	0.007	10.319	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	279	LEU	0	-0.011	-0.022	9.582	0.004	0.004	0.000	0.000	0.000	0.000
51	A	280	ALA	0	0.008	0.005	12.288	0.004	0.004	0.000	0.000	0.000	0.000
52	A	281	VAL	0	0.027	0.017	15.025	0.002	0.002	0.000	0.000	0.000	0.000
53	A	282	CYS	0	-0.039	-0.008	13.504	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	283	HIS	0	-0.019	-0.026	15.185	0.011	0.011	0.000	0.000	0.000	0.000
55	A	284	GLN	0	-0.032	-0.017	17.765	0.003	0.003	0.000	0.000	0.000	0.000
56	A	285	GLU	-1	-0.935	-0.966	19.330	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	286	LEU	0	-0.128	-0.050	17.441	0.000	0.000	0.000	0.000	0.000	0.000
58	A	287	GLU	-1	-0.962	-0.958	21.385	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	288	ASP	-1	-0.900	-0.960	19.573	0.001	0.001	0.000	0.000	0.000	0.000
60	A	289	PRO	0	0.025	-0.007	20.688	0.001	0.001	0.000	0.000	0.000	0.000
61	A	290	GLY	0	-0.035	-0.022	22.209	0.002	0.002	0.000	0.000	0.000	0.000
62	A	291	GLU	-1	-0.881	-0.951	17.459	0.045	0.045	0.000	0.000	0.000	0.000
63	A	292	ALA	0	0.023	0.019	17.504	0.003	0.003	0.000	0.000	0.000	0.000
64	A	293	ARG	1	0.932	0.965	18.440	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	294	ALA	0	0.007	0.005	17.958	0.003	0.003	0.000	0.000	0.000	0.000
66	A	295	CYS	0	-0.035	-0.013	14.366	0.007	0.007	0.000	0.000	0.000	0.000
67	A	296	SER	0	0.001	-0.006	15.583	0.000	0.000	0.000	0.000	0.000	0.000
68	A	297	GLU	-1	-0.907	-0.947	18.137	0.034	0.034	0.000	0.000	0.000	0.000
69	A	298	LYS	1	0.934	0.975	13.205	-0.097	-0.097	0.000	0.000	0.000	0.000
70	A	299	ALA	0	0.020	-0.001	14.684	0.006	0.006	0.000	0.000	0.000	0.000
71	A	300	LEU	0	0.015	0.001	15.605	0.000	0.000	0.000	0.000	0.000	0.000
72	A	301	GLN	0	-0.028	-0.005	17.550	0.009	0.009	0.000	0.000	0.000	0.000
73	A	302	LEU	0	-0.081	-0.042	11.676	0.005	0.005	0.000	0.000	0.000	0.000
74	A	303	LEU	0	-0.044	-0.028	15.866	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	304	GLY	0	-0.002	0.016	17.703	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	305	ASP	-1	-0.878	-0.920	17.853	0.069	0.069	0.000	0.000	0.000	0.000
77	A	306	LYS	1	0.934	0.960	19.418	-0.044	-0.044	0.000	0.000	0.000	0.000
78	A	307	ARG	1	0.863	0.906	14.170	-0.086	-0.086	0.000	0.000	0.000	0.000
79	A	308	PRO	0	-0.001	0.005	17.044	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	309	HIS	0	0.083	0.052	13.487	0.003	0.003	0.000	0.000	0.000	0.000
81	A	310	PRO	0	0.015	0.008	11.501	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	311	PHE	0	0.040	-0.010	13.282	0.002	0.002	0.000	0.000	0.000	0.000
83	A	312	LEU	0	-0.001	0.016	16.884	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.029	0.009	19.502	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	314	PRO	0	-0.017	0.004	17.802	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	315	PHE	0	0.023	-0.003	18.575	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	316	LEU	0	-0.009	0.018	22.773	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	317	GLU	-1	-0.839	-0.918	24.479	0.027	0.027	0.000	0.000	0.000	0.000
89	A	318	ALA	0	-0.042	-0.025	24.396	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	319	HIS	0	0.022	0.027	26.273	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	320	VAL	0	0.030	0.016	28.505	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	321	ARG	1	0.908	0.950	28.610	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	322	LEU	0	-0.055	-0.050	27.672	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	323	SER	0	0.010	0.015	31.659	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	324	TRP	0	0.001	0.024	34.300	0.000	0.000	0.000	0.000	0.000	0.000
96	A	325	ARG	1	0.898	0.956	34.339	0.002	0.002	0.000	0.000	0.000	0.000
97	A	326	LEU	0	-0.024	-0.025	34.239	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	327	GLY	0	-0.011	0.015	37.657	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	328	LEU	0	-0.045	-0.029	36.099	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	329	ASP	-1	-0.827	-0.913	37.641	0.008	0.008	0.000	0.000	0.000	0.000
101	A	330	LYS	1	0.904	0.942	34.128	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	331	ARG	1	0.876	0.925	33.616	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	332	GLN	0	0.026	0.017	32.761	0.001	0.001	0.000	0.000	0.000	0.000
104	A	333	SER	0	-0.012	-0.041	29.520	0.001	0.001	0.000	0.000	0.000	0.000
105	A	334	GLU	-1	-0.860	-0.923	29.267	0.020	0.020	0.000	0.000	0.000	0.000
106	A	335	ALA	0	-0.006	0.004	30.694	0.003	0.003	0.000	0.000	0.000	0.000
107	A	336	GLN	0	-0.008	0.002	25.684	0.003	0.003	0.000	0.000	0.000	0.000
108	A	337	LEU	0	0.038	0.010	24.701	0.003	0.003	0.000	0.000	0.000	0.000
109	A	338	GLN	0	-0.045	-0.037	27.375	0.004	0.004	0.000	0.000	0.000	0.000
110	A	339	ALA	0	0.038	0.031	28.662	0.001	0.001	0.000	0.000	0.000	0.000
111	A	340	LEU	0	-0.018	-0.025	22.160	0.003	0.003	0.000	0.000	0.000	0.000
112	A	341	GLN	0	-0.011	0.001	24.582	0.007	0.007	0.000	0.000	0.000	0.000
113	A	342	GLU	-1	-0.951	-0.971	26.731	0.038	0.038	0.000	0.000	0.000	0.000
114	A	343	ALA	0	-0.035	-0.006	26.362	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	344	GLY	0	-0.030	-0.016	24.617	0.003	0.003	0.000	0.000	0.000	0.000
116	A	345	LEU	0	-0.076	-0.034	20.472	0.007	0.007	0.000	0.000	0.000	0.000
117	A	346	THR	0	-0.027	-0.019	19.776	0.009	0.009	0.000	0.000	0.000	0.000
118	A	347	SER	0	-0.003	0.006	21.363	0.000	0.000	0.000	0.000	0.000	0.000
119	A	348	THR	0	0.041	-0.005	23.219	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	349	PRO	0	-0.045	-0.032	25.641	0.003	0.003	0.000	0.000	0.000	0.000
121	A	350	PRO	0	0.022	0.058	22.337	0.008	0.008	0.000	0.000	0.000	0.000
122	A	351	PRO	0	0.053	0.031	17.796	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	352	SER	0	-0.010	-0.006	20.163	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	353	LEU	0	0.052	0.000	18.892	0.005	0.005	0.000	0.000	0.000	0.000
125	A	354	LYS	1	0.954	0.976	18.252	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	355	GLU	-1	-0.885	-0.944	16.775	0.109	0.109	0.000	0.000	0.000	0.000
127	A	356	LEU	0	0.041	-0.001	13.927	0.011	0.011	0.000	0.000	0.000	0.000
128	A	357	LEU	0	-0.052	-0.011	13.452	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	358	ILE	0	-0.058	-0.034	13.953	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	359	LYS	1	0.886	0.941	12.189	-0.167	-0.167	0.000	0.000	0.000	0.000
131	A	360	GLU	-1	-0.953	-0.946	7.849	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	361	VAL	0	0.009	0.009	5.014	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	362	LEU	0	-0.043	-0.021	6.672	-0.177	-0.177	0.000	0.000	0.000	0.000
134	A	363	ASP	-1	-0.847	-0.922	1.936	-9.268	-11.333	8.788	-3.439	-3.284	-0.042

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