FMO DATABASE

FMODB ID: 3JJ4L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-707831.392131
FMO2-HF: Nuclear repulsion	668237.949428
FMO2-HF: Total energy	-39593.442703
FMO2-MP2: Total energy	-39706.530391

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.
-4.459	0.082	0.305	-2.201	-2.644	-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 : 0.025 / q_NPA : 0.013

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	0.017	0.023	3.651	-2.082	0.705	-0.025	-1.412	-1.350	0.004
4	O	246	SER	0	-0.025	-0.017	5.424	0.005	0.005	0.000	0.000	0.000	0.000
5	O	247	GLY	0	0.013	-0.009	8.641	-0.084	-0.084	0.000	0.000	0.000	0.000
6	O	248	ILE	0	0.000	0.020	8.889	0.021	0.021	0.000	0.000	0.000	0.000
7	O	249	LEU	0	0.030	0.012	7.371	0.028	0.028	0.000	0.000	0.000	0.000
8	O	250	MET	0	-0.015	-0.009	11.005	0.105	0.105	0.000	0.000	0.000	0.000
9	O	251	ALA	0	0.044	0.024	13.000	-0.037	-0.037	0.000	0.000	0.000	0.000
10	O	252	PRO	0	-0.005	-0.002	14.577	0.047	0.047	0.000	0.000	0.000	0.000
11	O	253	LYS	1	0.938	0.981	15.082	-0.059	-0.059	0.000	0.000	0.000	0.000
12	O	254	THR	0	0.041	0.017	17.642	-0.021	-0.021	0.000	0.000	0.000	0.000
13	O	255	PHE	0	-0.047	-0.028	17.193	0.019	0.019	0.000	0.000	0.000	0.000
14	O	256	TRP	0	0.050	0.017	22.517	-0.011	-0.011	0.000	0.000	0.000	0.000
15	O	257	VAL	0	-0.010	-0.004	26.260	0.012	0.012	0.000	0.000	0.000	0.000
16	O	258	ASN	0	-0.003	0.007	28.030	-0.007	-0.007	0.000	0.000	0.000	0.000
17	O	259	GLU	-1	-0.777	-0.892	31.633	-0.026	-0.026	0.000	0.000	0.000	0.000
18	O	260	GLY	0	-0.017	-0.003	33.274	0.004	0.004	0.000	0.000	0.000	0.000
19	O	261	LYS	1	0.895	0.947	31.073	-0.008	-0.008	0.000	0.000	0.000	0.000
20	O	262	HIS	0	0.031	0.024	28.369	-0.008	-0.008	0.000	0.000	0.000	0.000
21	O	263	ALA	0	0.042	0.025	24.229	0.007	0.007	0.000	0.000	0.000	0.000
22	O	264	LYS	1	0.761	0.876	20.918	-0.111	-0.111	0.000	0.000	0.000	0.000
23	O	265	PHE	0	0.020	0.020	17.745	0.010	0.010	0.000	0.000	0.000	0.000
24	O	266	ARG	1	0.882	0.930	16.160	-0.258	-0.258	0.000	0.000	0.000	0.000
25	O	267	CYS	0	-0.012	-0.002	11.151	0.040	0.040	0.000	0.000	0.000	0.000
26	O	268	TYR	0	-0.006	-0.001	10.527	-0.040	-0.040	0.000	0.000	0.000	0.000
27	O	269	VAL	0	0.017	0.007	7.256	0.087	0.087	0.000	0.000	0.000	0.000
28	O	270	MET	0	-0.029	-0.012	6.378	0.060	0.060	0.000	0.000	0.000	0.000
29	O	271	GLY	0	0.079	0.028	6.116	-0.050	-0.050	0.000	0.000	0.000	0.000
30	O	272	LYS	1	0.876	0.972	7.838	-0.375	-0.375	0.000	0.000	0.000	0.000
31	O	273	PRO	0	0.070	0.008	9.725	-0.043	-0.043	0.000	0.000	0.000	0.000
32	O	274	GLU	-1	-0.780	-0.885	11.193	0.117	0.117	0.000	0.000	0.000	0.000
33	O	275	PRO	0	-0.057	-0.015	8.644	-0.055	-0.055	0.000	0.000	0.000	0.000
34	O	276	GLU	-1	-0.916	-0.941	11.049	-0.128	-0.128	0.000	0.000	0.000	0.000
35	O	277	ILE	0	-0.066	-0.047	10.944	-0.075	-0.075	0.000	0.000	0.000	0.000
36	O	278	GLU	-1	-0.863	-0.917	13.114	-0.286	-0.286	0.000	0.000	0.000	0.000
37	O	279	TRP	0	0.010	-0.020	14.176	-0.035	-0.035	0.000	0.000	0.000	0.000
38	O	280	HIS	0	-0.013	-0.017	14.903	0.016	0.016	0.000	0.000	0.000	0.000
39	O	281	TRP	0	-0.058	-0.044	17.925	0.008	0.008	0.000	0.000	0.000	0.000
40	O	282	GLU	-1	-0.850	-0.925	20.466	-0.147	-0.147	0.000	0.000	0.000	0.000
41	O	283	GLY	0	-0.003	0.006	19.099	0.001	0.001	0.000	0.000	0.000	0.000
42	O	284	ARG	1	0.915	0.971	20.158	0.152	0.152	0.000	0.000	0.000	0.000
43	O	285	PRO	0	0.076	0.050	19.765	-0.003	-0.003	0.000	0.000	0.000	0.000
44	O	286	LEU	0	-0.051	-0.034	19.361	0.025	0.025	0.000	0.000	0.000	0.000
45	O	287	LEU	0	0.020	0.002	21.261	-0.004	-0.004	0.000	0.000	0.000	0.000
46	O	288	PRO	0	-0.059	-0.030	23.322	0.008	0.008	0.000	0.000	0.000	0.000
47	O	289	ASP	-1	-0.877	-0.921	25.596	-0.070	-0.070	0.000	0.000	0.000	0.000
48	O	290	ARG	1	0.945	0.950	28.911	0.027	0.027	0.000	0.000	0.000	0.000
49	O	291	ARG	1	0.789	0.869	29.645	0.044	0.044	0.000	0.000	0.000	0.000
50	O	292	ARG	1	0.902	0.951	24.670	0.082	0.082	0.000	0.000	0.000	0.000
51	O	293	LEU	0	0.034	0.022	25.125	-0.001	-0.001	0.000	0.000	0.000	0.000
52	O	294	MET	0	0.008	0.000	20.053	-0.002	-0.002	0.000	0.000	0.000	0.000
53	O	295	TYR	0	-0.054	-0.023	20.864	-0.005	-0.005	0.000	0.000	0.000	0.000
54	O	296	ARG	1	0.846	0.913	13.580	-0.142	-0.142	0.000	0.000	0.000	0.000
55	O	297	ASP	-1	-0.719	-0.850	19.023	0.119	0.119	0.000	0.000	0.000	0.000
56	O	298	ARG	1	0.971	0.977	19.999	-0.082	-0.082	0.000	0.000	0.000	0.000
57	O	299	ASP	-1	-0.930	-0.945	19.755	0.191	0.191	0.000	0.000	0.000	0.000
58	O	300	GLY	0	0.032	0.020	16.443	0.048	0.048	0.000	0.000	0.000	0.000
59	O	301	GLY	0	-0.030	-0.020	14.012	0.003	0.003	0.000	0.000	0.000	0.000
60	O	302	PHE	0	0.035	0.004	12.271	-0.029	-0.029	0.000	0.000	0.000	0.000
61	O	303	VAL	0	-0.039	-0.024	16.100	0.012	0.012	0.000	0.000	0.000	0.000
62	O	304	LEU	0	0.022	0.023	18.766	-0.017	-0.017	0.000	0.000	0.000	0.000
63	O	305	LYS	1	0.937	0.956	20.282	-0.022	-0.022	0.000	0.000	0.000	0.000
64	O	306	VAL	0	0.042	0.031	23.290	-0.008	-0.008	0.000	0.000	0.000	0.000
65	O	307	LEU	0	0.008	-0.008	25.941	0.009	0.009	0.000	0.000	0.000	0.000
66	O	308	TYR	0	-0.013	-0.005	29.526	-0.007	-0.007	0.000	0.000	0.000	0.000
67	O	309	CYS	0	-0.055	-0.015	28.207	-0.007	-0.007	0.000	0.000	0.000	0.000
68	O	310	GLN	0	-0.005	-0.014	30.525	0.003	0.003	0.000	0.000	0.000	0.000
69	O	311	ALA	0	0.110	0.051	30.591	-0.005	-0.005	0.000	0.000	0.000	0.000
70	O	312	LYS	1	0.945	0.958	30.401	0.047	0.047	0.000	0.000	0.000	0.000
71	O	313	ASP	-1	-0.777	-0.868	26.887	-0.062	-0.062	0.000	0.000	0.000	0.000
72	O	314	ARG	1	0.868	0.951	25.573	0.103	0.103	0.000	0.000	0.000	0.000
73	O	315	GLY	0	0.029	0.020	23.465	-0.007	-0.007	0.000	0.000	0.000	0.000
74	O	316	LEU	0	-0.039	-0.010	16.629	0.015	0.015	0.000	0.000	0.000	0.000
75	O	317	TYR	0	-0.035	-0.042	17.997	-0.009	-0.009	0.000	0.000	0.000	0.000
76	O	318	VAL	0	-0.007	-0.018	12.368	-0.001	-0.001	0.000	0.000	0.000	0.000
77	O	319	CYS	0	-0.049	-0.015	11.498	0.040	0.040	0.000	0.000	0.000	0.000
78	O	320	ALA	0	0.029	0.006	9.968	-0.095	-0.095	0.000	0.000	0.000	0.000
79	O	321	ALA	0	0.032	0.016	7.474	0.139	0.139	0.000	0.000	0.000	0.000
80	O	322	ARG	1	0.945	0.954	7.677	0.410	0.410	0.000	0.000	0.000	0.000
81	O	323	ASN	0	-0.015	-0.011	8.418	0.010	0.010	0.000	0.000	0.000	0.000
82	O	324	SER	0	0.017	-0.004	10.491	-0.071	-0.071	0.000	0.000	0.000	0.000
83	O	325	ALA	0	-0.032	-0.004	7.771	0.001	0.001	0.000	0.000	0.000	0.000
84	O	326	GLY	0	0.031	0.016	6.130	-0.162	-0.162	0.000	0.000	0.000	0.000
85	O	327	GLN	0	0.020	0.019	6.509	0.396	0.396	0.000	0.000	0.000	0.000
86	O	328	THR	0	-0.011	0.001	2.846	-2.643	-0.971	0.331	-0.786	-1.217	-0.008
87	O	329	LEU	0	-0.007	0.008	5.188	0.455	0.537	-0.001	-0.003	-0.077	0.000
88	O	330	SER	0	0.006	-0.002	7.622	-0.014	-0.014	0.000	0.000	0.000	0.000
89	O	331	ALA	0	-0.025	-0.003	9.843	0.021	0.021	0.000	0.000	0.000	0.000
90	O	332	VAL	0	-0.021	-0.015	13.296	0.059	0.059	0.000	0.000	0.000	0.000
91	O	333	GLN	0	0.018	0.019	16.302	-0.025	-0.025	0.000	0.000	0.000	0.000
92	O	334	LEU	0	-0.035	0.005	20.003	0.024	0.024	0.000	0.000	0.000	0.000
93	O	335	HIS	0	-0.004	-0.008	23.011	-0.019	-0.019	0.000	0.000	0.000	0.000
94	O	336	VAL	0	0.016	-0.007	26.450	0.010	0.010	0.000	0.000	0.000	0.000
95	O	337	LYS	1	0.897	0.940	29.635	-0.012	-0.012	0.000	0.000	0.000	0.000
96	O	338	GLU	-1	-0.904	-0.955	32.440	-0.031	-0.031	0.000	0.000	0.000	0.000
97	O	339	PRO	0	-0.024	0.004	35.741	0.002	0.002	0.000	0.000	0.000	0.000

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