FMO DATABASE

FMODB ID: YZ8R2

Calculation Name: 5F67-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F67

Chain ID: A

ChEMBL ID:

UniProt ID: Q24008

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-692668.186575
FMO2-HF: Nuclear repulsion	655226.696189
FMO2-HF: Total energy	-37441.490386
FMO2-MP2: Total energy	-37550.718957

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:351:SER)

Summations of interaction energy for fragment #1(A:351:SER)

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.
-15.77	-10.711	2.154	-3.23	-3.983	-0.021

Interaction energy analysis for fragmet #1(A:351:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.015

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	353	GLU	-1	-0.857	-0.930	2.249	-16.945	-12.068	2.154	-3.198	-3.833	-0.021
4	A	354	THR	0	-0.055	-0.040	4.119	0.418	0.600	0.000	-0.032	-0.150	0.000
5	A	355	LYS	1	0.917	0.960	5.911	1.287	1.287	0.000	0.000	0.000	0.000
6	A	356	PHE	0	0.036	0.015	6.717	0.458	0.458	0.000	0.000	0.000	0.000
7	A	357	ILE	0	0.044	0.029	8.869	0.320	0.320	0.000	0.000	0.000	0.000
8	A	358	PHE	0	-0.081	-0.044	10.958	0.186	0.186	0.000	0.000	0.000	0.000
9	A	359	ASP	-1	-0.893	-0.938	12.081	-0.575	-0.575	0.000	0.000	0.000	0.000
10	A	360	GLN	0	-0.063	-0.021	13.497	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	361	PHE	0	-0.027	-0.036	15.077	0.108	0.108	0.000	0.000	0.000	0.000
12	A	362	PRO	0	0.037	0.023	16.698	0.000	0.000	0.000	0.000	0.000	0.000
13	A	363	LYS	1	0.873	0.938	17.711	0.318	0.318	0.000	0.000	0.000	0.000
14	A	364	ALA	0	-0.014	0.009	16.292	0.033	0.033	0.000	0.000	0.000	0.000
15	A	365	ARG	1	0.802	0.878	17.771	0.315	0.315	0.000	0.000	0.000	0.000
16	A	366	THR	0	0.038	0.011	14.510	-0.070	-0.070	0.000	0.000	0.000	0.000
17	A	367	VAL	0	-0.044	-0.011	16.997	0.058	0.058	0.000	0.000	0.000	0.000
18	A	368	GLN	0	0.040	0.016	14.703	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	369	VAL	0	0.010	0.003	19.447	0.037	0.037	0.000	0.000	0.000	0.000
20	A	370	ARG	1	0.930	0.980	21.531	0.108	0.108	0.000	0.000	0.000	0.000
21	A	371	LYS	1	0.810	0.907	22.920	0.232	0.232	0.000	0.000	0.000	0.000
22	A	372	GLU	-1	-0.856	-0.922	24.707	-0.099	-0.099	0.000	0.000	0.000	0.000
23	A	373	GLY	0	-0.006	0.011	28.160	0.004	0.004	0.000	0.000	0.000	0.000
24	A	374	PHE	0	-0.034	-0.045	27.668	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	375	LEU	0	0.045	0.016	22.073	0.007	0.007	0.000	0.000	0.000	0.000
26	A	376	GLY	0	-0.006	-0.013	26.193	0.008	0.008	0.000	0.000	0.000	0.000
27	A	377	ILE	0	0.016	0.024	23.337	0.002	0.002	0.000	0.000	0.000	0.000
28	A	378	MET	0	-0.038	-0.009	27.884	0.006	0.006	0.000	0.000	0.000	0.000
29	A	379	VAL	0	0.029	0.021	23.177	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	380	ILE	0	0.018	0.008	26.318	0.018	0.018	0.000	0.000	0.000	0.000
31	A	381	TYR	0	0.024	0.014	22.055	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	382	GLY	0	-0.007	-0.007	25.484	0.025	0.025	0.000	0.000	0.000	0.000
33	A	383	LYS	1	0.913	0.946	25.887	0.224	0.224	0.000	0.000	0.000	0.000
34	A	384	HIS	0	0.039	0.028	25.918	0.008	0.008	0.000	0.000	0.000	0.000
35	A	385	ALA	0	-0.015	-0.017	26.999	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	386	GLU	-1	-0.954	-0.982	26.022	-0.247	-0.247	0.000	0.000	0.000	0.000
37	A	387	VAL	0	-0.014	-0.006	21.348	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	388	GLY	0	0.000	0.023	22.283	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	389	SER	0	-0.030	-0.046	23.855	0.019	0.019	0.000	0.000	0.000	0.000
40	A	390	GLY	0	0.086	0.050	21.161	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	391	ILE	0	0.004	0.013	20.143	0.044	0.044	0.000	0.000	0.000	0.000
42	A	392	PHE	0	-0.021	-0.006	21.793	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	393	ILE	0	-0.008	-0.005	23.025	0.014	0.014	0.000	0.000	0.000	0.000
44	A	394	SER	0	-0.014	-0.022	25.993	0.005	0.005	0.000	0.000	0.000	0.000
45	A	395	ASP	-1	-0.884	-0.941	29.365	-0.141	-0.141	0.000	0.000	0.000	0.000
46	A	396	LEU	0	-0.056	-0.037	28.423	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	397	ARG	1	0.905	0.970	31.144	0.131	0.131	0.000	0.000	0.000	0.000
48	A	398	GLU	-1	-0.878	-0.936	33.023	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	399	GLY	0	-0.025	-0.021	34.799	0.005	0.005	0.000	0.000	0.000	0.000
50	A	400	SER	0	-0.103	-0.047	30.168	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	401	ASN	0	0.015	-0.037	26.379	0.005	0.005	0.000	0.000	0.000	0.000
52	A	402	ALA	0	-0.012	-0.006	25.855	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	403	GLU	-1	-0.865	-0.928	26.859	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	404	LEU	0	-0.017	-0.011	29.045	0.000	0.000	0.000	0.000	0.000	0.000
55	A	405	ALA	0	-0.045	-0.004	23.903	0.003	0.003	0.000	0.000	0.000	0.000
56	A	406	GLY	0	-0.045	-0.021	25.028	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	407	VAL	0	-0.018	-0.006	23.588	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	408	LYS	1	0.892	0.950	25.824	0.206	0.206	0.000	0.000	0.000	0.000
59	A	409	VAL	0	0.046	0.020	26.979	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	410	GLY	0	-0.014	-0.010	28.075	0.007	0.007	0.000	0.000	0.000	0.000
61	A	411	ASP	-1	-0.745	-0.833	23.041	-0.290	-0.290	0.000	0.000	0.000	0.000
62	A	412	MET	0	-0.014	0.007	19.183	0.004	0.004	0.000	0.000	0.000	0.000
63	A	413	LEU	0	-0.012	-0.020	18.006	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	414	LEU	0	-0.022	-0.020	14.661	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	415	ALA	0	0.063	0.031	11.874	-0.115	-0.115	0.000	0.000	0.000	0.000
66	A	416	VAL	0	-0.005	-0.001	13.702	0.115	0.115	0.000	0.000	0.000	0.000
67	A	417	ASN	0	-0.005	-0.020	12.323	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	418	GLN	0	-0.022	-0.033	6.080	-0.493	-0.493	0.000	0.000	0.000	0.000
69	A	419	ASP	-1	-0.896	-0.929	8.705	-0.913	-0.913	0.000	0.000	0.000	0.000
70	A	420	VAL	0	0.011	-0.002	8.602	0.104	0.104	0.000	0.000	0.000	0.000
71	A	421	THR	0	-0.033	-0.047	11.369	0.072	0.072	0.000	0.000	0.000	0.000
72	A	422	LEU	0	-0.061	-0.029	12.703	0.080	0.080	0.000	0.000	0.000	0.000
73	A	423	GLU	-1	-0.922	-0.953	14.857	-0.541	-0.541	0.000	0.000	0.000	0.000
74	A	424	SER	0	-0.038	0.005	16.334	0.023	0.023	0.000	0.000	0.000	0.000
75	A	425	ASN	0	0.049	0.029	18.144	0.026	0.026	0.000	0.000	0.000	0.000
76	A	426	TYR	0	-0.002	-0.022	21.499	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	427	ASP	-1	-0.878	-0.931	23.779	-0.230	-0.230	0.000	0.000	0.000	0.000
78	A	428	ASP	-1	-0.910	-0.959	18.622	-0.359	-0.359	0.000	0.000	0.000	0.000
79	A	429	ALA	0	-0.004	-0.002	19.042	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	430	THR	0	-0.042	-0.038	20.083	0.008	0.008	0.000	0.000	0.000	0.000
81	A	431	GLY	0	-0.003	-0.004	21.927	0.018	0.018	0.000	0.000	0.000	0.000
82	A	432	LEU	0	-0.013	-0.006	15.474	0.032	0.032	0.000	0.000	0.000	0.000
83	A	433	LEU	0	0.004	0.008	19.012	0.016	0.016	0.000	0.000	0.000	0.000
84	A	434	LYS	1	0.896	0.946	21.241	0.215	0.215	0.000	0.000	0.000	0.000
85	A	435	ARG	1	0.955	0.973	18.000	0.332	0.332	0.000	0.000	0.000	0.000
86	A	436	ALA	0	0.011	0.044	18.330	0.014	0.014	0.000	0.000	0.000	0.000
87	A	437	GLU	-1	-0.917	-0.957	19.027	-0.119	-0.119	0.000	0.000	0.000	0.000
88	A	438	GLY	0	0.007	0.002	19.216	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	439	VAL	0	-0.049	-0.039	17.991	0.001	0.001	0.000	0.000	0.000	0.000
90	A	440	VAL	0	0.018	0.019	17.360	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	441	THR	0	0.005	-0.005	13.259	0.018	0.018	0.000	0.000	0.000	0.000
92	A	442	MET	0	-0.024	-0.001	15.857	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	443	ILE	0	0.018	0.029	11.615	0.047	0.047	0.000	0.000	0.000	0.000
94	A	444	LEU	0	-0.006	-0.003	16.057	0.009	0.009	0.000	0.000	0.000	0.000
95	A	445	LEU	0	0.028	0.015	19.315	0.003	0.003	0.000	0.000	0.000	0.000
96	A	446	THR	0	-0.059	-0.049	20.958	0.019	0.019	0.000	0.000	0.000	0.000
97	A	447	LEU	0	-0.020	-0.006	23.497	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	448	LYS	1	0.954	0.988	26.435	0.239	0.239	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:351:SER)