FMO DATABASE

FMODB ID: V5YM1

Calculation Name: 6EHR-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6EHR

Chain ID: G

ChEMBL ID:

UniProt ID: Q6IAA8

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:

Apendix: None

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1198508.572244
FMO2-HF: Nuclear repulsion	1144244.254012
FMO2-HF: Total energy	-54264.318232
FMO2-MP2: Total energy	-54418.966899

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(G:238:GLY)

Summations of interaction energy for fragment #1(G:238:GLY)

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.
-4.516	0.404	2.754	-3.393	-4.281	-0.015

Interaction energy analysis for fragmet #1(G:238:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.014

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	G	240	LEU	0	0.042	0.036	3.853	1.058	2.237	-0.012	-0.537	-0.630	0.000
4	G	241	PRO	0	0.112	0.055	6.282	0.172	0.172	0.000	0.000	0.000	0.000
5	G	242	THR	0	-0.023	-0.008	5.762	-0.117	-0.117	0.000	0.000	0.000	0.000
6	G	243	LEU	0	0.007	0.012	3.684	-0.844	-0.246	0.027	-0.304	-0.322	0.002
7	G	244	GLU	-1	-0.864	-0.940	7.826	0.195	0.195	0.000	0.000	0.000	0.000
8	G	245	ASN	0	-0.086	-0.039	10.799	-0.166	-0.166	0.000	0.000	0.000	0.000
9	G	246	LEU	0	-0.008	-0.001	8.115	-0.093	-0.093	0.000	0.000	0.000	0.000
10	G	247	LEU	0	0.007	0.014	11.292	-0.095	-0.095	0.000	0.000	0.000	0.000
11	G	248	ASN	0	0.017	0.001	13.723	-0.139	-0.139	0.000	0.000	0.000	0.000
12	G	249	ILE	0	-0.037	-0.014	13.839	-0.058	-0.058	0.000	0.000	0.000	0.000
13	G	250	PHE	0	-0.003	-0.001	15.751	-0.039	-0.039	0.000	0.000	0.000	0.000
14	G	251	ILE	0	0.018	0.009	17.433	-0.038	-0.038	0.000	0.000	0.000	0.000
15	G	252	SER	0	-0.029	-0.016	19.661	-0.039	-0.039	0.000	0.000	0.000	0.000
16	G	253	ASN	0	-0.075	-0.035	20.448	-0.012	-0.012	0.000	0.000	0.000	0.000
17	G	254	SER	0	-0.002	-0.010	20.591	-0.013	-0.013	0.000	0.000	0.000	0.000
18	G	255	GLY	0	-0.023	-0.004	23.399	-0.007	-0.007	0.000	0.000	0.000	0.000
19	G	256	ILE	0	-0.029	-0.015	20.521	-0.012	-0.012	0.000	0.000	0.000	0.000
20	G	257	GLU	-1	-0.875	-0.960	23.094	0.159	0.159	0.000	0.000	0.000	0.000
21	G	258	LYS	1	0.792	0.899	17.996	-0.311	-0.311	0.000	0.000	0.000	0.000
22	G	259	ALA	0	0.012	0.001	16.257	-0.002	-0.002	0.000	0.000	0.000	0.000
23	G	260	PHE	0	0.010	0.013	14.522	0.012	0.012	0.000	0.000	0.000	0.000
24	G	261	LEU	0	0.002	0.000	7.349	0.019	0.019	0.000	0.000	0.000	0.000
25	G	262	PHE	0	0.035	0.001	10.925	0.096	0.096	0.000	0.000	0.000	0.000
26	G	263	ASP	-1	-0.812	-0.880	11.406	0.378	0.378	0.000	0.000	0.000	0.000
27	G	264	VAL	0	-0.023	-0.008	12.693	-0.044	-0.044	0.000	0.000	0.000	0.000
28	G	265	VAL	0	-0.051	-0.019	15.091	-0.042	-0.042	0.000	0.000	0.000	0.000
29	G	266	SER	0	-0.074	-0.068	14.637	-0.031	-0.031	0.000	0.000	0.000	0.000
30	G	267	LYS	1	0.883	0.928	16.939	-0.194	-0.194	0.000	0.000	0.000	0.000
31	G	268	ILE	0	0.006	0.027	11.225	-0.002	-0.002	0.000	0.000	0.000	0.000
32	G	269	TYR	0	0.011	0.001	12.036	0.016	0.016	0.000	0.000	0.000	0.000
33	G	270	ILE	0	-0.038	-0.012	5.495	-0.021	-0.021	0.000	0.000	0.000	0.000
34	G	271	ALA	0	0.022	0.004	8.431	0.059	0.059	0.000	0.000	0.000	0.000
35	G	272	THR	0	-0.023	-0.026	10.334	-0.100	-0.100	0.000	0.000	0.000	0.000
36	G	273	ASP	-1	-0.763	-0.850	13.663	0.361	0.361	0.000	0.000	0.000	0.000
37	G	274	SER	0	-0.026	-0.043	16.132	-0.031	-0.031	0.000	0.000	0.000	0.000
38	G	275	SER	0	-0.049	-0.025	18.312	-0.039	-0.039	0.000	0.000	0.000	0.000
39	G	276	PRO	0	0.002	-0.002	19.810	0.022	0.022	0.000	0.000	0.000	0.000
40	G	277	VAL	0	0.010	-0.002	18.442	0.015	0.015	0.000	0.000	0.000	0.000
41	G	278	ASP	-1	-0.811	-0.880	21.810	0.143	0.143	0.000	0.000	0.000	0.000
42	G	279	MET	0	-0.021	-0.001	23.616	-0.010	-0.010	0.000	0.000	0.000	0.000
43	G	280	GLN	0	0.029	0.006	24.466	0.006	0.006	0.000	0.000	0.000	0.000
44	G	281	SER	0	0.000	-0.032	23.739	0.003	0.003	0.000	0.000	0.000	0.000
45	G	282	TYR	0	-0.055	-0.044	17.601	0.007	0.007	0.000	0.000	0.000	0.000
46	G	283	GLU	-1	-0.916	-0.956	21.659	0.128	0.128	0.000	0.000	0.000	0.000
47	G	284	LEU	0	0.021	0.012	24.217	0.002	0.002	0.000	0.000	0.000	0.000
48	G	285	CYS	0	-0.072	-0.040	20.013	0.010	0.010	0.000	0.000	0.000	0.000
49	G	286	CYS	0	-0.047	-0.025	20.845	0.018	0.018	0.000	0.000	0.000	0.000
50	G	287	ASP	-1	-0.867	-0.924	22.009	0.130	0.130	0.000	0.000	0.000	0.000
51	G	288	MET	0	-0.103	-0.040	22.709	0.001	0.001	0.000	0.000	0.000	0.000
52	G	289	ILE	0	-0.013	-0.014	17.649	0.002	0.002	0.000	0.000	0.000	0.000
53	G	290	ASP	-1	-0.796	-0.893	21.423	0.161	0.161	0.000	0.000	0.000	0.000
54	G	291	VAL	0	0.003	0.008	23.937	-0.010	-0.010	0.000	0.000	0.000	0.000
55	G	292	VAL	0	-0.009	-0.006	22.579	-0.008	-0.008	0.000	0.000	0.000	0.000
56	G	293	ILE	0	-0.001	0.015	19.656	-0.004	-0.004	0.000	0.000	0.000	0.000
57	G	294	ASP	-1	-0.856	-0.923	23.751	0.099	0.099	0.000	0.000	0.000	0.000
58	G	295	VAL	0	-0.053	-0.031	27.459	-0.009	-0.009	0.000	0.000	0.000	0.000
59	G	296	SER	0	-0.049	-0.045	24.478	-0.004	-0.004	0.000	0.000	0.000	0.000
60	G	297	CYS	0	-0.101	-0.064	25.435	-0.006	-0.006	0.000	0.000	0.000	0.000
61	G	298	ILE	0	-0.057	-0.010	27.832	-0.009	-0.009	0.000	0.000	0.000	0.000
62	G	299	TYR	0	-0.035	-0.031	30.234	-0.008	-0.008	0.000	0.000	0.000	0.000
63	G	300	GLY	0	-0.004	0.015	26.907	0.001	0.001	0.000	0.000	0.000	0.000
64	G	301	LEU	0	-0.065	-0.019	26.429	0.001	0.001	0.000	0.000	0.000	0.000
65	G	302	LYS	1	0.940	0.965	26.084	-0.098	-0.098	0.000	0.000	0.000	0.000
66	G	303	GLU	-1	-0.892	-0.950	30.851	0.057	0.057	0.000	0.000	0.000	0.000
67	G	304	ASP	-1	-0.891	-0.931	33.457	0.048	0.048	0.000	0.000	0.000	0.000
68	G	305	GLY	0	-0.083	-0.040	33.410	-0.003	-0.003	0.000	0.000	0.000	0.000
69	G	306	SER	0	-0.102	-0.069	27.775	0.002	0.002	0.000	0.000	0.000	0.000
70	G	307	GLY	0	0.043	0.011	26.968	-0.003	-0.003	0.000	0.000	0.000	0.000
71	G	308	SER	0	-0.113	-0.053	21.480	0.002	0.002	0.000	0.000	0.000	0.000
72	G	309	ALA	0	0.090	0.051	22.580	0.008	0.008	0.000	0.000	0.000	0.000
73	G	310	TYR	0	-0.028	-0.016	14.253	-0.004	-0.004	0.000	0.000	0.000	0.000
74	G	311	ASP	-1	-0.861	-0.927	18.332	0.188	0.188	0.000	0.000	0.000	0.000
75	G	312	LYS	1	0.946	0.950	14.801	-0.201	-0.201	0.000	0.000	0.000	0.000
76	G	313	GLU	-1	-0.878	-0.926	17.801	0.273	0.273	0.000	0.000	0.000	0.000
77	G	314	SER	0	-0.038	0.009	19.107	-0.010	-0.010	0.000	0.000	0.000	0.000
78	G	315	MET	0	-0.034	-0.026	19.356	0.034	0.034	0.000	0.000	0.000	0.000
79	G	316	ALA	0	0.011	0.011	21.762	-0.024	-0.024	0.000	0.000	0.000	0.000
80	G	317	ILE	0	-0.015	-0.019	23.513	0.016	0.016	0.000	0.000	0.000	0.000
81	G	318	ILE	0	0.015	0.018	26.249	-0.014	-0.014	0.000	0.000	0.000	0.000
82	G	319	LYS	1	0.805	0.891	28.382	-0.119	-0.119	0.000	0.000	0.000	0.000
83	G	320	LEU	0	0.035	0.010	29.087	-0.008	-0.008	0.000	0.000	0.000	0.000
84	G	321	ASN	0	0.039	0.006	32.865	-0.004	-0.004	0.000	0.000	0.000	0.000
85	G	322	ASN	0	-0.049	-0.022	35.148	0.000	0.000	0.000	0.000	0.000	0.000
86	G	323	THR	0	-0.005	0.001	34.495	-0.001	-0.001	0.000	0.000	0.000	0.000
87	G	324	THR	0	-0.032	0.002	28.620	0.004	0.004	0.000	0.000	0.000	0.000
88	G	325	VAL	0	-0.008	-0.004	26.600	-0.006	-0.006	0.000	0.000	0.000	0.000
89	G	326	LEU	0	0.043	0.024	24.269	0.010	0.010	0.000	0.000	0.000	0.000
90	G	327	TYR	0	-0.054	-0.057	19.255	-0.008	-0.008	0.000	0.000	0.000	0.000
91	G	328	LEU	0	0.042	0.018	18.661	0.033	0.033	0.000	0.000	0.000	0.000
92	G	329	LYS	1	0.877	0.934	17.460	-0.321	-0.321	0.000	0.000	0.000	0.000
93	G	330	GLU	-1	-0.783	-0.871	14.117	0.503	0.503	0.000	0.000	0.000	0.000
94	G	331	VAL	0	-0.032	-0.022	9.206	0.028	0.028	0.000	0.000	0.000	0.000
95	G	332	THR	0	0.012	0.000	7.926	-0.002	-0.002	0.000	0.000	0.000	0.000
96	G	333	LYS	1	0.962	0.983	11.222	-0.142	-0.142	0.000	0.000	0.000	0.000
97	G	334	PHE	0	0.005	-0.006	9.921	-0.078	-0.078	0.000	0.000	0.000	0.000
98	G	335	LEU	0	0.016	0.019	6.545	0.050	0.050	0.000	0.000	0.000	0.000
99	G	336	ALA	0	0.056	0.033	11.199	-0.037	-0.037	0.000	0.000	0.000	0.000
100	G	337	LEU	0	-0.054	-0.013	13.580	0.067	0.067	0.000	0.000	0.000	0.000
101	G	338	VAL	0	0.004	-0.006	14.728	-0.074	-0.074	0.000	0.000	0.000	0.000
102	G	339	CYS	0	-0.062	-0.020	17.803	0.033	0.033	0.000	0.000	0.000	0.000
103	G	340	ILE	0	0.049	0.022	20.195	-0.025	-0.025	0.000	0.000	0.000	0.000
104	G	341	LEU	0	-0.039	-0.012	23.623	0.008	0.008	0.000	0.000	0.000	0.000
105	G	342	ARG	1	0.893	0.930	26.178	-0.127	-0.127	0.000	0.000	0.000	0.000
106	G	343	GLU	-1	-0.763	-0.882	29.671	0.129	0.129	0.000	0.000	0.000	0.000
107	G	344	GLU	-1	-0.844	-0.898	31.979	0.103	0.103	0.000	0.000	0.000	0.000
108	G	345	SER	0	-0.055	-0.029	27.589	-0.007	-0.007	0.000	0.000	0.000	0.000
109	G	346	PHE	0	0.004	-0.001	25.326	0.007	0.007	0.000	0.000	0.000	0.000
110	G	347	GLU	-1	-0.899	-0.945	29.099	0.102	0.102	0.000	0.000	0.000	0.000
111	G	348	ARG	1	0.888	0.942	28.092	-0.127	-0.127	0.000	0.000	0.000	0.000
112	G	349	LYS	1	0.901	0.949	26.239	-0.168	-0.168	0.000	0.000	0.000	0.000
113	G	350	GLY	0	0.000	0.001	25.867	0.013	0.013	0.000	0.000	0.000	0.000
114	G	351	LEU	0	-0.012	-0.014	25.513	0.005	0.005	0.000	0.000	0.000	0.000
115	G	352	ILE	0	0.042	0.039	22.056	0.016	0.016	0.000	0.000	0.000	0.000
116	G	353	ASP	-1	-0.770	-0.867	21.297	0.255	0.255	0.000	0.000	0.000	0.000
117	G	354	TYR	0	-0.033	-0.004	21.086	0.016	0.016	0.000	0.000	0.000	0.000
118	G	355	ASN	0	0.007	-0.015	19.539	0.006	0.006	0.000	0.000	0.000	0.000
119	G	356	PHE	0	0.030	0.013	15.331	0.032	0.032	0.000	0.000	0.000	0.000
120	G	357	HIS	0	-0.024	-0.006	16.210	0.070	0.070	0.000	0.000	0.000	0.000
121	G	358	CYS	0	-0.064	-0.036	16.010	0.011	0.011	0.000	0.000	0.000	0.000
122	G	359	PHE	0	0.011	0.005	11.900	0.054	0.054	0.000	0.000	0.000	0.000
123	G	360	ARG	1	0.755	0.860	11.597	-0.242	-0.242	0.000	0.000	0.000	0.000
124	G	361	LYS	1	0.802	0.883	11.271	-0.178	-0.178	0.000	0.000	0.000	0.000
125	G	362	ALA	0	0.018	0.010	10.492	0.016	0.016	0.000	0.000	0.000	0.000
126	G	363	ILE	0	0.017	0.002	6.310	0.097	0.097	0.000	0.000	0.000	0.000
127	G	364	HIS	0	-0.082	-0.038	6.321	0.216	0.216	0.000	0.000	0.000	0.000
128	G	365	GLU	-1	-0.794	-0.878	7.373	0.225	0.225	0.000	0.000	0.000	0.000
129	G	366	VAL	0	-0.049	-0.034	3.103	-0.588	-0.295	0.058	-0.128	-0.222	0.000
130	G	367	PHE	0	-0.062	-0.047	2.124	-4.683	-1.905	2.683	-2.404	-3.057	-0.017
131	G	368	GLU	-1	-0.936	-0.950	4.114	-0.326	-0.282	-0.001	-0.011	-0.032	0.000
132	G	369	VAL	0	-0.039	-0.012	4.363	-0.211	-0.183	-0.001	-0.009	-0.018	0.000
133	G	370	GLY	0	0.013	0.010	5.319	-0.146	-0.146	0.000	0.000	0.000	0.000
134	G	371	VAL	0	0.007	0.027	6.449	0.079	0.079	0.000	0.000	0.000	0.000
135	G	372	THR	0	-0.113	-0.073	8.053	-0.064	-0.064	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:238:GLY)