FMO DATABASE

FMODB ID: JL449

Calculation Name: 5J8Y-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J8Y

Chain ID: C

ChEMBL ID:

UniProt ID: Q9VHA0

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-424778.491939
FMO2-HF: Nuclear repulsion	396393.584549
FMO2-HF: Total energy	-28384.90739
FMO2-MP2: Total energy	-28463.85299

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(C:1136:MET)

Summations of interaction energy for fragment #1(C:1136:MET)

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.
-11.037	-2.154	2.617	-4.402	-7.097	-0.028

Interaction energy analysis for fragmet #1(C:1136:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.011

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

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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	C	1138	ASP	-1	-0.922	-0.963	2.465	-9.916	-5.540	1.364	-2.374	-3.366	-0.022
4	C	1139	THR	0	-0.052	-0.048	2.471	-1.116	2.123	1.214	-1.631	-2.822	-0.008
5	C	1140	TRP	0	-0.017	0.013	3.425	-1.024	-0.021	0.036	-0.346	-0.692	0.002
6	C	1141	ASN	0	0.075	0.016	6.003	0.352	0.352	0.000	0.000	0.000	0.000
7	C	1142	VAL	0	0.025	-0.009	9.702	0.107	0.107	0.000	0.000	0.000	0.000
8	C	1143	TYR	0	-0.019	-0.015	11.219	0.115	0.115	0.000	0.000	0.000	0.000
9	C	1144	ASP	-1	-0.790	-0.874	7.004	-0.840	-0.840	0.000	0.000	0.000	0.000
10	C	1145	VAL	0	-0.016	-0.001	8.995	0.258	0.258	0.000	0.000	0.000	0.000
11	C	1146	SER	0	-0.033	-0.016	10.811	0.122	0.122	0.000	0.000	0.000	0.000
12	C	1147	GLN	0	0.006	-0.008	10.821	0.013	0.013	0.000	0.000	0.000	0.000
13	C	1148	PHE	0	0.026	0.018	9.314	0.069	0.069	0.000	0.000	0.000	0.000
14	C	1149	LEU	0	0.030	0.007	11.271	0.014	0.014	0.000	0.000	0.000	0.000
15	C	1150	ARG	1	0.911	0.957	14.664	-0.055	-0.055	0.000	0.000	0.000	0.000
16	C	1151	VAL	0	-0.033	-0.016	12.266	-0.016	-0.016	0.000	0.000	0.000	0.000
17	C	1152	ASN	0	-0.043	-0.013	11.981	0.025	0.025	0.000	0.000	0.000	0.000
18	C	1153	ASP	-1	-0.906	-0.940	16.204	0.161	0.161	0.000	0.000	0.000	0.000
19	C	1154	CYS	0	-0.056	-0.034	17.281	-0.036	-0.036	0.000	0.000	0.000	0.000
20	C	1155	THR	0	0.029	-0.011	19.067	-0.023	-0.023	0.000	0.000	0.000	0.000
21	C	1156	ALA	0	-0.041	-0.018	20.002	-0.021	-0.021	0.000	0.000	0.000	0.000
22	C	1157	HIS	0	0.022	0.006	19.390	-0.007	-0.007	0.000	0.000	0.000	0.000
23	C	1158	CYS	0	-0.017	0.023	16.363	-0.020	-0.020	0.000	0.000	0.000	0.000
24	C	1159	ASP	-1	-0.835	-0.920	18.431	-0.106	-0.106	0.000	0.000	0.000	0.000
25	C	1160	THR	0	-0.044	-0.064	21.065	-0.019	-0.019	0.000	0.000	0.000	0.000
26	C	1161	PHE	0	0.070	0.040	14.951	-0.020	-0.020	0.000	0.000	0.000	0.000
27	C	1162	SER	0	0.028	0.004	17.165	-0.056	-0.056	0.000	0.000	0.000	0.000
28	C	1163	ARG	1	0.852	0.973	18.121	0.084	0.084	0.000	0.000	0.000	0.000
29	C	1164	ASN	0	-0.082	-0.058	19.936	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	1165	LYS	1	0.909	0.960	16.911	0.352	0.352	0.000	0.000	0.000	0.000
31	C	1166	ILE	0	-0.002	0.009	13.486	-0.040	-0.040	0.000	0.000	0.000	0.000
32	C	1167	ASP	-1	-0.888	-0.943	10.583	-0.902	-0.902	0.000	0.000	0.000	0.000
33	C	1168	GLY	0	0.067	0.017	7.597	0.150	0.150	0.000	0.000	0.000	0.000
34	C	1169	LYS	1	0.968	0.985	8.476	0.964	0.964	0.000	0.000	0.000	0.000
35	C	1170	ARG	1	0.966	0.982	9.383	0.505	0.505	0.000	0.000	0.000	0.000
36	C	1171	LEU	0	0.014	0.008	8.918	0.132	0.132	0.000	0.000	0.000	0.000
37	C	1172	LEU	0	-0.042	-0.030	6.182	0.212	0.212	0.000	0.000	0.000	0.000
38	C	1173	GLN	0	-0.057	-0.029	10.847	0.043	0.043	0.000	0.000	0.000	0.000
39	C	1174	LEU	0	-0.070	-0.018	13.811	0.070	0.070	0.000	0.000	0.000	0.000
40	C	1175	THR	0	0.018	0.014	16.317	0.033	0.033	0.000	0.000	0.000	0.000
41	C	1176	LYS	1	0.948	0.936	19.180	0.022	0.022	0.000	0.000	0.000	0.000
42	C	1177	ASP	-1	-0.876	-0.933	21.471	-0.081	-0.081	0.000	0.000	0.000	0.000
43	C	1178	ASP	-1	-0.876	-0.927	19.807	-0.200	-0.200	0.000	0.000	0.000	0.000
44	C	1179	ILE	0	-0.046	-0.027	16.942	0.004	0.004	0.000	0.000	0.000	0.000
45	C	1180	MET	0	-0.044	-0.003	20.925	0.016	0.016	0.000	0.000	0.000	0.000
46	C	1181	PRO	0	0.042	0.018	24.246	0.011	0.011	0.000	0.000	0.000	0.000
47	C	1182	LEU	0	-0.045	-0.018	18.945	0.002	0.002	0.000	0.000	0.000	0.000
48	C	1183	LEU	0	-0.028	-0.005	20.659	0.009	0.009	0.000	0.000	0.000	0.000
49	C	1184	GLY	0	-0.032	-0.014	24.377	0.013	0.013	0.000	0.000	0.000	0.000
50	C	1185	MET	0	-0.007	-0.009	27.177	0.004	0.004	0.000	0.000	0.000	0.000
51	C	1186	LYS	1	0.956	0.989	27.045	0.027	0.027	0.000	0.000	0.000	0.000
52	C	1187	VAL	0	0.088	0.024	26.011	0.000	0.000	0.000	0.000	0.000	0.000
53	C	1188	GLY	0	0.003	0.012	25.360	0.004	0.004	0.000	0.000	0.000	0.000
54	C	1189	PRO	0	-0.011	-0.028	23.280	0.010	0.010	0.000	0.000	0.000	0.000
55	C	1190	ALA	0	0.068	0.041	21.474	0.006	0.006	0.000	0.000	0.000	0.000
56	C	1191	LEU	0	-0.027	-0.037	20.677	-0.005	-0.005	0.000	0.000	0.000	0.000
57	C	1192	LYS	1	0.978	0.999	20.307	-0.061	-0.061	0.000	0.000	0.000	0.000
58	C	1193	ILE	0	0.065	0.044	16.068	0.022	0.022	0.000	0.000	0.000	0.000
59	C	1194	SER	0	-0.043	-0.020	15.833	-0.001	-0.001	0.000	0.000	0.000	0.000
60	C	1195	ASP	-1	-0.944	-0.970	15.937	0.140	0.140	0.000	0.000	0.000	0.000
61	C	1196	LEU	0	0.037	0.032	12.969	0.022	0.022	0.000	0.000	0.000	0.000
62	C	1197	ILE	0	-0.012	-0.020	11.026	0.072	0.072	0.000	0.000	0.000	0.000
63	C	1198	ALA	0	-0.034	-0.010	11.044	-0.003	-0.003	0.000	0.000	0.000	0.000
64	C	1199	GLN	0	0.068	0.024	12.350	-0.021	-0.021	0.000	0.000	0.000	0.000
65	C	1200	LEU	0	-0.094	-0.041	5.896	0.101	0.101	0.000	0.000	0.000	0.000
66	C	1201	LYS	1	0.870	0.914	7.764	0.387	0.387	0.000	0.000	0.000	0.000
67	C	1202	CYS	0	-0.027	0.025	9.022	-0.045	-0.045	0.000	0.000	0.000	0.000
68	C	1203	LYS	1	0.918	0.974	8.190	-0.995	-0.995	0.000	0.000	0.000	0.000
69	C	1204	VAL	0	0.017	0.008	3.760	-0.057	0.208	0.003	-0.051	-0.217	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1136:MET)