FMO DATABASE

FMODB ID: 39KKL

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	OptHSide
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	-424475.02932
FMO2-HF: Nuclear repulsion	396089.670406
FMO2-HF: Total energy	-28385.358913
FMO2-MP2: Total energy	-28464.332229

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.
-11.021	-2.619	2.772	-4.224	-6.951	-0.023

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 : -0.016 / 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

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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	-0.914	-0.956	2.429	-8.861	-5.136	1.729	-2.184	-3.270	-0.017
4	C	1139	THR	0	-0.051	-0.052	2.506	-1.641	1.607	0.977	-1.558	-2.668	-0.009
5	C	1140	TRP	0	-0.037	0.004	3.347	-1.181	-0.053	0.060	-0.416	-0.772	0.003
6	C	1141	ASN	0	0.046	-0.010	6.080	0.327	0.327	0.000	0.000	0.000	0.000
7	C	1142	VAL	0	0.011	0.002	9.775	0.130	0.130	0.000	0.000	0.000	0.000
8	C	1143	TYR	0	-0.011	-0.008	11.084	0.129	0.129	0.000	0.000	0.000	0.000
9	C	1144	ASP	-1	-0.788	-0.877	6.974	-0.717	-0.717	0.000	0.000	0.000	0.000
10	C	1145	VAL	0	0.003	0.009	9.093	0.254	0.254	0.000	0.000	0.000	0.000
11	C	1146	SER	0	-0.044	-0.024	10.920	0.104	0.104	0.000	0.000	0.000	0.000
12	C	1147	GLN	0	0.044	0.011	11.029	0.020	0.020	0.000	0.000	0.000	0.000
13	C	1148	PHE	0	0.026	0.019	9.272	0.068	0.068	0.000	0.000	0.000	0.000
14	C	1149	LEU	0	0.037	0.013	11.271	0.004	0.004	0.000	0.000	0.000	0.000
15	C	1150	ARG	1	0.884	0.945	14.720	-0.104	-0.104	0.000	0.000	0.000	0.000
16	C	1151	VAL	0	-0.031	-0.014	12.251	-0.019	-0.019	0.000	0.000	0.000	0.000
17	C	1152	ASN	0	-0.050	-0.026	11.978	0.019	0.019	0.000	0.000	0.000	0.000
18	C	1153	ASP	-1	-0.899	-0.929	16.156	0.188	0.188	0.000	0.000	0.000	0.000
19	C	1154	CYS	0	-0.073	-0.048	17.231	-0.037	-0.037	0.000	0.000	0.000	0.000
20	C	1155	THR	0	0.037	-0.006	19.146	-0.024	-0.024	0.000	0.000	0.000	0.000
21	C	1156	ALA	0	-0.040	-0.018	20.079	-0.022	-0.022	0.000	0.000	0.000	0.000
22	C	1157	HIS	0	0.021	0.002	19.351	-0.010	-0.010	0.000	0.000	0.000	0.000
23	C	1158	CYS	0	-0.017	0.027	16.326	-0.019	-0.019	0.000	0.000	0.000	0.000
24	C	1159	ASP	-1	-0.848	-0.922	18.541	-0.075	-0.075	0.000	0.000	0.000	0.000
25	C	1160	THR	0	-0.046	-0.036	21.171	-0.024	-0.024	0.000	0.000	0.000	0.000
26	C	1161	PHE	0	0.079	0.045	15.188	-0.019	-0.019	0.000	0.000	0.000	0.000
27	C	1162	SER	0	0.019	-0.001	17.264	-0.053	-0.053	0.000	0.000	0.000	0.000
28	C	1163	ARG	1	0.881	0.949	18.219	0.051	0.051	0.000	0.000	0.000	0.000
29	C	1164	ASN	0	-0.078	-0.053	20.095	-0.009	-0.009	0.000	0.000	0.000	0.000
30	C	1165	LYS	1	0.902	0.957	16.996	0.335	0.335	0.000	0.000	0.000	0.000
31	C	1166	ILE	0	-0.004	0.006	13.509	-0.039	-0.039	0.000	0.000	0.000	0.000
32	C	1167	ASP	-1	-0.831	-0.922	10.849	-0.897	-0.897	0.000	0.000	0.000	0.000
33	C	1168	GLY	0	0.059	0.016	7.598	0.163	0.163	0.000	0.000	0.000	0.000
34	C	1169	LYS	1	0.909	0.955	8.476	0.890	0.890	0.000	0.000	0.000	0.000
35	C	1170	ARG	1	0.840	0.905	9.778	0.440	0.440	0.000	0.000	0.000	0.000
36	C	1171	LEU	0	0.029	0.007	9.170	0.124	0.124	0.000	0.000	0.000	0.000
37	C	1172	LEU	0	-0.019	-0.014	6.242	0.192	0.192	0.000	0.000	0.000	0.000
38	C	1173	GLN	0	-0.019	-0.001	10.884	-0.013	-0.013	0.000	0.000	0.000	0.000
39	C	1174	LEU	0	-0.093	-0.024	13.980	0.055	0.055	0.000	0.000	0.000	0.000
40	C	1175	THR	0	0.036	0.003	16.325	0.034	0.034	0.000	0.000	0.000	0.000
41	C	1176	LYS	1	0.953	0.938	19.178	-0.036	-0.036	0.000	0.000	0.000	0.000
42	C	1177	ASP	-1	-0.880	-0.941	21.460	-0.046	-0.046	0.000	0.000	0.000	0.000
43	C	1178	ASP	-1	-0.800	-0.850	19.764	-0.170	-0.170	0.000	0.000	0.000	0.000
44	C	1179	ILE	0	-0.026	-0.023	16.826	0.001	0.001	0.000	0.000	0.000	0.000
45	C	1180	MET	0	-0.031	0.001	20.905	0.014	0.014	0.000	0.000	0.000	0.000
46	C	1181	PRO	0	0.038	0.015	24.283	0.009	0.009	0.000	0.000	0.000	0.000
47	C	1182	LEU	0	-0.056	-0.013	18.936	0.000	0.000	0.000	0.000	0.000	0.000
48	C	1183	LEU	0	-0.009	-0.004	20.334	0.009	0.009	0.000	0.000	0.000	0.000
49	C	1184	GLY	0	-0.035	-0.015	24.343	0.011	0.011	0.000	0.000	0.000	0.000
50	C	1185	MET	0	-0.016	-0.009	27.144	0.003	0.003	0.000	0.000	0.000	0.000
51	C	1186	LYS	1	0.954	0.991	27.021	0.002	0.002	0.000	0.000	0.000	0.000
52	C	1187	VAL	0	0.092	0.022	25.979	0.002	0.002	0.000	0.000	0.000	0.000
53	C	1188	GLY	0	0.008	0.016	25.329	0.006	0.006	0.000	0.000	0.000	0.000
54	C	1189	PRO	0	-0.004	-0.025	23.236	0.012	0.012	0.000	0.000	0.000	0.000
55	C	1190	ALA	0	0.068	0.039	21.438	0.010	0.010	0.000	0.000	0.000	0.000
56	C	1191	LEU	0	-0.040	-0.035	20.649	0.001	0.001	0.000	0.000	0.000	0.000
57	C	1192	LYS	1	0.978	0.998	20.277	-0.099	-0.099	0.000	0.000	0.000	0.000
58	C	1193	ILE	0	0.058	0.035	16.067	0.026	0.026	0.000	0.000	0.000	0.000
59	C	1194	SER	0	-0.044	-0.015	15.802	0.006	0.006	0.000	0.000	0.000	0.000
60	C	1195	ASP	-1	-0.945	-0.969	15.916	0.201	0.201	0.000	0.000	0.000	0.000
61	C	1196	LEU	0	0.036	0.029	13.000	0.029	0.029	0.000	0.000	0.000	0.000
62	C	1197	ILE	0	-0.008	-0.020	11.038	0.080	0.080	0.000	0.000	0.000	0.000
63	C	1198	ALA	0	-0.030	-0.005	11.027	0.016	0.016	0.000	0.000	0.000	0.000
64	C	1199	GLN	0	0.081	0.033	12.339	0.004	0.004	0.000	0.000	0.000	0.000
65	C	1200	LEU	0	-0.107	-0.043	5.700	0.104	0.104	0.000	0.000	0.000	0.000
66	C	1201	LYS	1	0.849	0.900	7.747	0.254	0.254	0.000	0.000	0.000	0.000
67	C	1202	CYS	0	-0.049	0.007	9.021	-0.035	-0.035	0.000	0.000	0.000	0.000
68	C	1203	LYS	1	0.927	0.976	8.144	-1.087	-1.087	0.000	0.000	0.000	0.000
69	C	1204	VAL	0	0.024	0.011	3.682	-0.111	0.190	0.006	-0.066	-0.241	0.000

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