FMO DATABASE

FMODB ID: 85LRY

Calculation Name: 5IP4-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IP4

Chain ID: D

ChEMBL ID:

UniProt ID: O43602

Base Structure: X-ray

Registration Date: 2023-09-20

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-518775.074085
FMO2-HF: Nuclear repulsion	487707.75251
FMO2-HF: Total energy	-31067.321574
FMO2-MP2: Total energy	-31158.90629

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(D:255:LYS)

Summations of interaction energy for fragment #1(D:255:LYS)

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.
87.288	93.476	1.468	-2.642	-5.014	0.008

Interaction energy analysis for fragmet #1(D:255:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.986 / q_NPA : 0.975

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	D	257	PHE	0	0.030	0.007	2.598	1.786	5.174	0.584	-1.703	-2.270	0.010
4	D	258	VAL	0	-0.044	-0.011	2.319	2.654	4.225	0.847	-0.663	-1.755	-0.001
5	D	259	ARG	1	0.932	0.973	3.924	48.618	49.124	0.001	-0.097	-0.410	0.000
6	D	260	PRO	0	-0.006	0.003	5.160	-6.365	-6.425	-0.001	-0.010	0.071	0.000
7	D	261	LYS	1	0.853	0.926	3.003	53.101	53.774	0.039	-0.157	-0.555	-0.001
8	D	262	LEU	0	-0.043	-0.018	5.250	7.661	7.717	-0.001	-0.002	-0.053	0.000
9	D	263	VAL	0	0.046	0.036	6.670	-2.744	-2.744	0.000	0.000	0.000	0.000
10	D	264	THR	0	-0.038	-0.032	8.726	3.464	3.464	0.000	0.000	0.000	0.000
11	D	265	ILE	0	0.000	0.003	12.051	-0.140	-0.140	0.000	0.000	0.000	0.000
12	D	266	ILE	0	-0.003	-0.010	14.922	1.041	1.041	0.000	0.000	0.000	0.000
13	D	267	ARG	1	0.952	1.000	18.163	12.688	12.688	0.000	0.000	0.000	0.000
14	D	268	SER	0	0.013	-0.028	21.371	0.364	0.364	0.000	0.000	0.000	0.000
15	D	269	GLY	0	0.007	0.015	23.793	0.171	0.171	0.000	0.000	0.000	0.000
16	D	270	VAL	0	-0.039	-0.021	25.701	0.381	0.381	0.000	0.000	0.000	0.000
17	D	271	LYS	1	1.010	0.988	27.365	9.600	9.600	0.000	0.000	0.000	0.000
18	D	272	PRO	0	-0.005	0.012	28.564	-0.082	-0.082	0.000	0.000	0.000	0.000
19	D	273	ARG	1	0.946	0.976	22.229	12.975	12.975	0.000	0.000	0.000	0.000
20	D	274	LYS	1	0.879	0.949	21.096	13.917	13.917	0.000	0.000	0.000	0.000
21	D	275	ALA	0	0.044	0.030	17.233	-0.292	-0.292	0.000	0.000	0.000	0.000
22	D	276	VAL	0	-0.033	-0.015	15.760	0.629	0.629	0.000	0.000	0.000	0.000
23	D	277	ARG	1	0.958	0.979	12.350	20.696	20.696	0.000	0.000	0.000	0.000
24	D	278	VAL	0	0.025	0.016	11.789	1.389	1.389	0.000	0.000	0.000	0.000
25	D	279	LEU	0	-0.003	-0.004	8.963	-2.595	-2.595	0.000	0.000	0.000	0.000
26	D	280	LEU	0	0.027	0.026	8.496	2.549	2.549	0.000	0.000	0.000	0.000
27	D	281	ASN	0	0.036	-0.003	7.965	-6.558	-6.558	0.000	0.000	0.000	0.000
28	D	282	LYS	1	0.913	0.954	5.439	45.673	45.673	0.000	0.000	0.000	0.000
29	D	283	LYS	1	0.870	0.927	6.935	30.504	30.504	0.000	0.000	0.000	0.000
30	D	284	THR	0	0.015	0.011	10.571	1.831	1.831	0.000	0.000	0.000	0.000
31	D	285	ALA	0	-0.034	0.007	11.700	1.491	1.491	0.000	0.000	0.000	0.000
32	D	286	HIS	0	0.029	0.007	13.436	-0.112	-0.112	0.000	0.000	0.000	0.000
33	D	287	SER	0	0.045	0.020	16.018	0.340	0.340	0.000	0.000	0.000	0.000
34	D	288	PHE	0	0.012	-0.003	14.856	-0.480	-0.480	0.000	0.000	0.000	0.000
35	D	289	GLU	-1	-0.787	-0.867	17.085	-13.314	-13.314	0.000	0.000	0.000	0.000
36	D	290	GLN	0	-0.018	-0.029	18.913	0.697	0.697	0.000	0.000	0.000	0.000
37	D	291	VAL	0	0.046	0.034	13.296	-0.171	-0.171	0.000	0.000	0.000	0.000
38	D	292	LEU	0	-0.019	0.001	16.630	-0.100	-0.100	0.000	0.000	0.000	0.000
39	D	293	THR	0	0.005	0.014	18.682	0.582	0.582	0.000	0.000	0.000	0.000
40	D	294	ASP	-1	-0.827	-0.898	17.423	-16.533	-16.533	0.000	0.000	0.000	0.000
41	D	295	ILE	0	-0.072	-0.050	13.999	0.024	0.024	0.000	0.000	0.000	0.000
42	D	296	THR	0	-0.035	-0.039	17.860	0.472	0.472	0.000	0.000	0.000	0.000
43	D	297	GLU	-1	-0.849	-0.910	21.438	-12.565	-12.565	0.000	0.000	0.000	0.000
44	D	298	ALA	0	-0.053	-0.017	18.609	0.505	0.505	0.000	0.000	0.000	0.000
45	D	299	ILE	0	-0.087	-0.056	18.850	0.311	0.311	0.000	0.000	0.000	0.000
46	D	300	LYS	1	0.836	0.911	21.536	13.500	13.500	0.000	0.000	0.000	0.000
47	D	301	LEU	0	-0.039	-0.016	23.388	0.447	0.447	0.000	0.000	0.000	0.000
48	D	302	GLU	-1	-0.869	-0.924	25.969	-10.442	-10.442	0.000	0.000	0.000	0.000
49	D	303	THR	0	0.050	-0.003	25.461	-0.290	-0.290	0.000	0.000	0.000	0.000
50	D	304	GLY	0	0.004	0.009	25.527	0.399	0.399	0.000	0.000	0.000	0.000
51	D	305	VAL	0	-0.024	-0.005	26.643	0.139	0.139	0.000	0.000	0.000	0.000
52	D	306	VAL	0	-0.051	-0.013	21.392	-0.009	-0.009	0.000	0.000	0.000	0.000
53	D	307	LYS	1	0.844	0.894	22.660	12.322	12.322	0.000	0.000	0.000	0.000
54	D	308	LYS	1	0.893	0.942	19.565	12.855	12.855	0.000	0.000	0.000	0.000
55	D	309	LEU	0	-0.029	0.002	14.698	0.412	0.412	0.000	0.000	0.000	0.000
56	D	310	TYR	0	0.000	0.004	17.665	0.595	0.595	0.000	0.000	0.000	0.000
57	D	311	THR	0	0.065	0.045	13.130	0.066	0.066	0.000	0.000	0.000	0.000
58	D	312	LEU	0	-0.007	-0.015	14.295	1.359	1.359	0.000	0.000	0.000	0.000
59	D	313	ASP	-1	-0.895	-0.934	15.889	-17.950	-17.950	0.000	0.000	0.000	0.000
60	D	314	GLY	0	-0.039	-0.018	18.005	0.878	0.878	0.000	0.000	0.000	0.000
61	D	315	LYS	1	0.945	0.983	16.120	18.673	18.673	0.000	0.000	0.000	0.000
62	D	316	GLN	0	0.012	-0.010	17.563	-0.128	-0.128	0.000	0.000	0.000	0.000
63	D	317	VAL	0	-0.036	-0.003	13.624	-0.438	-0.438	0.000	0.000	0.000	0.000
64	D	318	THR	0	-0.052	-0.053	16.449	1.136	1.136	0.000	0.000	0.000	0.000
65	D	319	CYS	0	-0.027	-0.006	15.377	0.425	0.425	0.000	0.000	0.000	0.000
66	D	320	LEU	0	0.054	0.014	11.759	-1.244	-1.244	0.000	0.000	0.000	0.000
67	D	321	HIS	0	0.004	0.002	10.449	-3.070	-3.070	0.000	0.000	0.000	0.000
68	D	322	ASP	-1	-0.770	-0.892	9.821	-23.388	-23.388	0.000	0.000	0.000	0.000
69	D	323	PHE	0	-0.050	-0.017	8.891	-0.478	-0.478	0.000	0.000	0.000	0.000
70	D	324	PHE	0	-0.106	-0.061	4.893	-4.460	-4.460	0.000	0.000	0.000	0.000
71	D	325	GLY	0	0.051	0.022	5.878	-1.808	-1.808	0.000	0.000	0.000	0.000
72	D	326	ASP	-1	-0.895	-0.955	5.392	-43.268	-43.268	0.000	0.000	0.000	0.000
73	D	327	ASP	-1	-0.910	-0.935	6.984	-25.750	-25.750	0.000	0.000	0.000	0.000
74	D	328	ASP	-1	-0.879	-0.956	4.622	-61.643	-61.589	-0.001	-0.010	-0.042	0.000
75	D	329	VAL	0	-0.055	-0.031	7.665	2.104	2.104	0.000	0.000	0.000	0.000
76	D	330	PHE	0	0.042	0.018	9.104	0.872	0.872	0.000	0.000	0.000	0.000
77	D	331	ILE	0	-0.036	-0.014	14.141	0.817	0.817	0.000	0.000	0.000	0.000
78	D	332	ALA	0	0.049	0.017	17.879	-0.041	-0.041	0.000	0.000	0.000	0.000
79	D	333	CYS	0	-0.058	-0.044	20.008	0.400	0.400	0.000	0.000	0.000	0.000
80	D	334	GLY	0	0.063	0.045	23.571	0.233	0.233	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:255:LYS)