FMO DATABASE

FMODB ID: JQQR9

Calculation Name: 5FM5-O-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FM5

Chain ID: O

ChEMBL ID:

UniProt ID: P52179

Base Structure: X-ray

Registration Date: 2023-09-21

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-707542.452916
FMO2-HF: Nuclear repulsion	667949.565662
FMO2-HF: Total energy	-39592.887254
FMO2-MP2: Total energy	-39705.95696

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(O:243:PRO)

Summations of interaction energy for fragment #1(O:243:PRO)

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.
-4.921	-0.369	0.275	-2.205	-2.621	-0.004

Interaction energy analysis for fragmet #1(O:243:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.012

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	O	245	GLY	0	0.016	0.024	3.661	-2.168	0.594	-0.025	-1.405	-1.332	0.004
4	O	246	SER	0	-0.036	-0.020	5.423	0.012	0.012	0.000	0.000	0.000	0.000
5	O	247	GLY	0	0.019	-0.007	8.653	-0.100	-0.100	0.000	0.000	0.000	0.000
6	O	248	ILE	0	0.005	0.023	9.005	0.010	0.010	0.000	0.000	0.000	0.000
7	O	249	LEU	0	0.034	0.010	7.500	0.018	0.018	0.000	0.000	0.000	0.000
8	O	250	MET	0	-0.023	-0.011	11.055	0.096	0.096	0.000	0.000	0.000	0.000
9	O	251	ALA	0	0.048	0.027	13.040	-0.040	-0.040	0.000	0.000	0.000	0.000
10	O	252	PRO	0	-0.012	0.000	14.581	0.051	0.051	0.000	0.000	0.000	0.000
11	O	253	LYS	1	0.944	0.977	15.057	-0.127	-0.127	0.000	0.000	0.000	0.000
12	O	254	THR	0	0.045	0.022	17.657	-0.022	-0.022	0.000	0.000	0.000	0.000
13	O	255	PHE	0	-0.055	-0.032	17.380	0.020	0.020	0.000	0.000	0.000	0.000
14	O	256	TRP	0	0.054	0.018	22.518	-0.012	-0.012	0.000	0.000	0.000	0.000
15	O	257	VAL	0	-0.014	-0.007	26.209	0.012	0.012	0.000	0.000	0.000	0.000
16	O	258	ASN	0	-0.029	-0.016	28.020	-0.009	-0.009	0.000	0.000	0.000	0.000
17	O	259	GLU	-1	-0.804	-0.913	31.616	-0.016	-0.016	0.000	0.000	0.000	0.000
18	O	260	GLY	0	0.001	0.004	33.279	0.004	0.004	0.000	0.000	0.000	0.000
19	O	261	LYS	1	0.897	0.948	31.038	-0.020	-0.020	0.000	0.000	0.000	0.000
20	O	262	HIS	0	0.031	0.019	28.237	-0.008	-0.008	0.000	0.000	0.000	0.000
21	O	263	ALA	0	0.042	0.021	24.346	0.008	0.008	0.000	0.000	0.000	0.000
22	O	264	LYS	1	0.880	0.949	21.124	-0.129	-0.129	0.000	0.000	0.000	0.000
23	O	265	PHE	0	0.021	0.026	17.701	0.012	0.012	0.000	0.000	0.000	0.000
24	O	266	ARG	1	0.930	0.958	15.346	-0.308	-0.308	0.000	0.000	0.000	0.000
25	O	267	CYS	0	-0.009	-0.004	11.074	0.051	0.051	0.000	0.000	0.000	0.000
26	O	268	TYR	0	-0.006	-0.003	10.424	-0.044	-0.044	0.000	0.000	0.000	0.000
27	O	269	VAL	0	0.026	0.014	7.404	0.107	0.107	0.000	0.000	0.000	0.000
28	O	270	MET	0	-0.032	-0.016	6.350	0.043	0.043	0.000	0.000	0.000	0.000
29	O	271	GLY	0	0.076	0.026	6.084	-0.047	-0.047	0.000	0.000	0.000	0.000
30	O	272	LYS	1	0.875	0.970	7.808	-0.360	-0.360	0.000	0.000	0.000	0.000
31	O	273	PRO	0	0.067	0.007	9.670	-0.054	-0.054	0.000	0.000	0.000	0.000
32	O	274	GLU	-1	-0.846	-0.936	11.124	0.099	0.099	0.000	0.000	0.000	0.000
33	O	275	PRO	0	-0.056	-0.018	8.445	-0.058	-0.058	0.000	0.000	0.000	0.000
34	O	276	GLU	-1	-0.917	-0.938	11.147	-0.122	-0.122	0.000	0.000	0.000	0.000
35	O	277	ILE	0	-0.068	-0.048	11.267	-0.073	-0.073	0.000	0.000	0.000	0.000
36	O	278	GLU	-1	-0.909	-0.956	13.231	-0.267	-0.267	0.000	0.000	0.000	0.000
37	O	279	TRP	0	-0.004	-0.019	14.272	-0.030	-0.030	0.000	0.000	0.000	0.000
38	O	280	HIS	0	0.036	0.020	14.566	0.015	0.015	0.000	0.000	0.000	0.000
39	O	281	TRP	0	-0.072	-0.054	17.992	0.010	0.010	0.000	0.000	0.000	0.000
40	O	282	GLU	-1	-0.931	-0.977	20.528	-0.141	-0.141	0.000	0.000	0.000	0.000
41	O	283	GLY	0	-0.005	0.009	19.097	-0.001	-0.001	0.000	0.000	0.000	0.000
42	O	284	ARG	1	0.917	0.969	20.159	0.142	0.142	0.000	0.000	0.000	0.000
43	O	285	PRO	0	0.083	0.055	19.804	-0.002	-0.002	0.000	0.000	0.000	0.000
44	O	286	LEU	0	-0.044	-0.038	19.870	0.026	0.026	0.000	0.000	0.000	0.000
45	O	287	LEU	0	0.001	-0.006	21.351	-0.004	-0.004	0.000	0.000	0.000	0.000
46	O	288	PRO	0	-0.067	-0.039	23.303	0.009	0.009	0.000	0.000	0.000	0.000
47	O	289	ASP	-1	-0.878	-0.921	25.723	-0.062	-0.062	0.000	0.000	0.000	0.000
48	O	290	ARG	1	0.926	0.944	29.042	0.024	0.024	0.000	0.000	0.000	0.000
49	O	291	ARG	1	0.818	0.883	29.759	0.033	0.033	0.000	0.000	0.000	0.000
50	O	292	ARG	1	0.972	1.000	24.847	0.075	0.075	0.000	0.000	0.000	0.000
51	O	293	LEU	0	0.050	0.030	25.296	-0.002	-0.002	0.000	0.000	0.000	0.000
52	O	294	MET	0	0.008	0.004	20.246	0.000	0.000	0.000	0.000	0.000	0.000
53	O	295	TYR	0	-0.003	0.011	21.062	-0.005	-0.005	0.000	0.000	0.000	0.000
54	O	296	ARG	1	0.899	0.951	13.880	-0.168	-0.168	0.000	0.000	0.000	0.000
55	O	297	ASP	-1	-0.869	-0.942	18.977	0.149	0.149	0.000	0.000	0.000	0.000
56	O	298	ARG	1	0.960	0.972	19.989	-0.093	-0.093	0.000	0.000	0.000	0.000
57	O	299	ASP	-1	-0.946	-0.947	19.673	0.215	0.215	0.000	0.000	0.000	0.000
58	O	300	GLY	0	0.002	0.003	16.464	0.049	0.049	0.000	0.000	0.000	0.000
59	O	301	GLY	0	-0.052	-0.037	13.995	0.005	0.005	0.000	0.000	0.000	0.000
60	O	302	PHE	0	0.041	0.008	12.150	-0.035	-0.035	0.000	0.000	0.000	0.000
61	O	303	VAL	0	-0.042	-0.025	16.205	0.017	0.017	0.000	0.000	0.000	0.000
62	O	304	LEU	0	0.030	0.027	19.019	-0.020	-0.020	0.000	0.000	0.000	0.000
63	O	305	LYS	1	0.929	0.949	20.469	-0.036	-0.036	0.000	0.000	0.000	0.000
64	O	306	VAL	0	0.039	0.026	23.610	-0.009	-0.009	0.000	0.000	0.000	0.000
65	O	307	LEU	0	-0.023	-0.024	26.110	0.010	0.010	0.000	0.000	0.000	0.000
66	O	308	TYR	0	-0.034	-0.010	29.673	-0.007	-0.007	0.000	0.000	0.000	0.000
67	O	309	CYS	0	-0.039	-0.009	28.125	-0.006	-0.006	0.000	0.000	0.000	0.000
68	O	310	GLN	0	0.048	0.021	30.498	0.005	0.005	0.000	0.000	0.000	0.000
69	O	311	ALA	0	0.112	0.062	30.578	-0.004	-0.004	0.000	0.000	0.000	0.000
70	O	312	LYS	1	0.933	0.950	30.385	0.043	0.043	0.000	0.000	0.000	0.000
71	O	313	ASP	-1	-0.822	-0.903	27.051	-0.050	-0.050	0.000	0.000	0.000	0.000
72	O	314	ARG	1	0.944	0.994	25.685	0.085	0.085	0.000	0.000	0.000	0.000
73	O	315	GLY	0	0.025	0.018	23.520	-0.008	-0.008	0.000	0.000	0.000	0.000
74	O	316	LEU	0	-0.024	-0.002	16.636	0.018	0.018	0.000	0.000	0.000	0.000
75	O	317	TYR	0	-0.043	-0.044	18.102	-0.011	-0.011	0.000	0.000	0.000	0.000
76	O	318	VAL	0	0.004	-0.010	12.264	0.006	0.006	0.000	0.000	0.000	0.000
77	O	319	CYS	0	-0.039	-0.012	11.749	0.036	0.036	0.000	0.000	0.000	0.000
78	O	320	ALA	0	0.023	0.006	10.025	-0.083	-0.083	0.000	0.000	0.000	0.000
79	O	321	ALA	0	0.034	0.019	7.602	0.138	0.138	0.000	0.000	0.000	0.000
80	O	322	ARG	1	0.957	0.970	7.714	0.422	0.422	0.000	0.000	0.000	0.000
81	O	323	ASN	0	0.000	0.005	8.189	-0.001	-0.001	0.000	0.000	0.000	0.000
82	O	324	SER	0	0.017	-0.008	10.594	-0.073	-0.073	0.000	0.000	0.000	0.000
83	O	325	ALA	0	-0.031	0.000	7.741	0.002	0.002	0.000	0.000	0.000	0.000
84	O	326	GLY	0	0.027	0.013	6.270	-0.169	-0.169	0.000	0.000	0.000	0.000
85	O	327	GLN	0	-0.004	-0.007	6.662	0.462	0.462	0.000	0.000	0.000	0.000
86	O	328	THR	0	-0.018	0.002	2.926	-2.865	-1.151	0.301	-0.797	-1.218	-0.008
87	O	329	LEU	0	-0.005	-0.002	5.182	0.470	0.546	-0.001	-0.003	-0.071	0.000
88	O	330	SER	0	0.030	0.012	7.697	-0.086	-0.086	0.000	0.000	0.000	0.000
89	O	331	ALA	0	-0.032	-0.005	9.820	0.010	0.010	0.000	0.000	0.000	0.000
90	O	332	VAL	0	-0.026	-0.018	13.284	0.065	0.065	0.000	0.000	0.000	0.000
91	O	333	GLN	0	0.022	0.018	16.295	-0.018	-0.018	0.000	0.000	0.000	0.000
92	O	334	LEU	0	-0.035	0.005	19.999	0.025	0.025	0.000	0.000	0.000	0.000
93	O	335	HIS	0	-0.004	-0.010	23.001	-0.020	-0.020	0.000	0.000	0.000	0.000
94	O	336	VAL	0	0.011	-0.010	26.445	0.010	0.010	0.000	0.000	0.000	0.000
95	O	337	LYS	1	0.930	0.965	29.626	-0.027	-0.027	0.000	0.000	0.000	0.000
96	O	338	GLU	-1	-0.916	-0.958	32.435	-0.022	-0.022	0.000	0.000	0.000	0.000
97	O	339	PRO	0	-0.026	0.002	35.733	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(O:243:PRO)