FMO DATABASE

FMODB ID: N94KQ

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	OptAll
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	-519869.972055
FMO2-HF: Nuclear repulsion	488802.35028
FMO2-HF: Total energy	-31067.621774
FMO2-MP2: Total energy	-31159.210745

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.
74.576	81.081	1.353	-2.9	-4.958	-0.004

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 : 0.977 / q_NPA : 0.963

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	0.048	0.020	3.259	3.191	5.686	0.061	-1.077	-1.479	0.005
4	D	258	VAL	0	-0.016	0.011	2.150	2.811	3.945	0.907	-0.653	-1.388	0.000
5	D	259	ARG	1	0.938	0.962	4.239	45.223	45.617	-0.001	-0.082	-0.312	0.000
6	D	260	PRO	0	0.008	0.000	5.309	-5.647	-5.647	0.000	0.000	0.000	0.000
7	D	261	LYS	1	0.800	0.908	2.514	59.976	61.100	0.386	-0.388	-1.122	-0.004
8	D	262	LEU	0	-0.052	-0.022	4.909	7.785	7.854	-0.001	-0.004	-0.064	0.000
9	D	263	VAL	0	0.044	0.035	5.894	-4.362	-4.362	0.000	0.000	0.000	0.000
10	D	264	THR	0	-0.031	-0.024	8.094	4.108	4.108	0.000	0.000	0.000	0.000
11	D	265	ILE	0	0.006	0.007	11.453	-0.220	-0.220	0.000	0.000	0.000	0.000
12	D	266	ILE	0	-0.007	-0.009	14.384	1.155	1.155	0.000	0.000	0.000	0.000
13	D	267	ARG	1	0.912	0.980	17.617	12.975	12.975	0.000	0.000	0.000	0.000
14	D	268	SER	0	0.034	-0.007	20.900	0.296	0.296	0.000	0.000	0.000	0.000
15	D	269	GLY	0	0.025	0.027	23.290	0.239	0.239	0.000	0.000	0.000	0.000
16	D	270	VAL	0	-0.028	-0.021	25.255	0.432	0.432	0.000	0.000	0.000	0.000
17	D	271	LYS	1	0.989	0.990	26.835	9.884	9.884	0.000	0.000	0.000	0.000
18	D	272	PRO	0	0.044	0.026	27.803	-0.195	-0.195	0.000	0.000	0.000	0.000
19	D	273	ARG	1	0.935	0.969	21.518	13.397	13.397	0.000	0.000	0.000	0.000
20	D	274	LYS	1	0.832	0.925	20.657	14.293	14.293	0.000	0.000	0.000	0.000
21	D	275	ALA	0	0.042	0.025	16.878	-0.315	-0.315	0.000	0.000	0.000	0.000
22	D	276	VAL	0	-0.041	-0.027	15.149	0.824	0.824	0.000	0.000	0.000	0.000
23	D	277	ARG	1	0.956	0.979	12.109	21.595	21.595	0.000	0.000	0.000	0.000
24	D	278	VAL	0	0.021	0.015	11.232	1.458	1.458	0.000	0.000	0.000	0.000
25	D	279	LEU	0	0.004	-0.003	9.034	-3.115	-3.115	0.000	0.000	0.000	0.000
26	D	280	LEU	0	0.052	0.037	7.762	2.645	2.645	0.000	0.000	0.000	0.000
27	D	281	ASN	0	0.054	0.003	7.497	-6.838	-6.838	0.000	0.000	0.000	0.000
28	D	282	LYS	1	0.894	0.951	4.977	49.104	49.104	0.000	0.000	0.000	0.000
29	D	283	LYS	1	0.836	0.919	7.104	30.173	30.173	0.000	0.000	0.000	0.000
30	D	284	THR	0	0.001	0.000	10.846	2.027	2.027	0.000	0.000	0.000	0.000
31	D	285	ALA	0	-0.038	-0.005	11.147	1.496	1.496	0.000	0.000	0.000	0.000
32	D	286	HIS	0	0.006	0.001	13.044	-0.317	-0.317	0.000	0.000	0.000	0.000
33	D	287	SER	0	0.050	0.020	15.832	0.628	0.628	0.000	0.000	0.000	0.000
34	D	288	PHE	0	0.014	0.002	14.594	-0.499	-0.499	0.000	0.000	0.000	0.000
35	D	289	GLU	-1	-0.751	-0.850	16.901	-13.738	-13.738	0.000	0.000	0.000	0.000
36	D	290	GLN	0	-0.058	-0.026	18.376	0.793	0.793	0.000	0.000	0.000	0.000
37	D	291	VAL	0	0.040	0.021	12.822	-0.144	-0.144	0.000	0.000	0.000	0.000
38	D	292	LEU	0	-0.017	-0.004	16.165	-0.330	-0.330	0.000	0.000	0.000	0.000
39	D	293	THR	0	-0.016	0.012	18.340	0.629	0.629	0.000	0.000	0.000	0.000
40	D	294	ASP	-1	-0.817	-0.908	16.953	-17.102	-17.102	0.000	0.000	0.000	0.000
41	D	295	ILE	0	-0.054	-0.037	13.671	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	296	THR	0	-0.027	-0.027	17.489	0.444	0.444	0.000	0.000	0.000	0.000
43	D	297	GLU	-1	-0.807	-0.895	21.061	-12.477	-12.477	0.000	0.000	0.000	0.000
44	D	298	ALA	0	-0.050	-0.013	18.145	0.482	0.482	0.000	0.000	0.000	0.000
45	D	299	ILE	0	-0.077	-0.049	18.405	0.337	0.337	0.000	0.000	0.000	0.000
46	D	300	LYS	1	0.855	0.924	20.974	13.693	13.693	0.000	0.000	0.000	0.000
47	D	301	LEU	0	-0.019	-0.014	23.222	0.310	0.310	0.000	0.000	0.000	0.000
48	D	302	GLU	-1	-0.855	-0.923	25.792	-10.722	-10.722	0.000	0.000	0.000	0.000
49	D	303	THR	0	-0.012	-0.032	24.904	-0.284	-0.284	0.000	0.000	0.000	0.000
50	D	304	GLY	0	0.035	0.027	25.273	0.390	0.390	0.000	0.000	0.000	0.000
51	D	305	VAL	0	-0.046	-0.023	26.128	-0.003	-0.003	0.000	0.000	0.000	0.000
52	D	306	VAL	0	-0.042	-0.015	20.488	0.011	0.011	0.000	0.000	0.000	0.000
53	D	307	LYS	1	0.836	0.891	21.414	12.377	12.377	0.000	0.000	0.000	0.000
54	D	308	LYS	1	0.903	0.955	19.162	13.300	13.300	0.000	0.000	0.000	0.000
55	D	309	LEU	0	-0.025	-0.001	14.462	0.369	0.369	0.000	0.000	0.000	0.000
56	D	310	TYR	0	-0.004	-0.002	16.926	0.754	0.754	0.000	0.000	0.000	0.000
57	D	311	THR	0	0.003	0.002	12.337	0.102	0.102	0.000	0.000	0.000	0.000
58	D	312	LEU	0	-0.010	-0.017	13.155	1.506	1.506	0.000	0.000	0.000	0.000
59	D	313	ASP	-1	-0.898	-0.927	15.094	-18.779	-18.779	0.000	0.000	0.000	0.000
60	D	314	GLY	0	-0.045	-0.024	17.031	0.941	0.941	0.000	0.000	0.000	0.000
61	D	315	LYS	1	0.955	0.979	14.828	20.789	20.789	0.000	0.000	0.000	0.000
62	D	316	GLN	0	0.031	0.013	16.428	-0.335	-0.335	0.000	0.000	0.000	0.000
63	D	317	VAL	0	-0.042	-0.006	13.198	-0.355	-0.355	0.000	0.000	0.000	0.000
64	D	318	THR	0	-0.072	-0.059	15.872	1.337	1.337	0.000	0.000	0.000	0.000
65	D	319	CYS	0	-0.031	-0.005	14.885	0.407	0.407	0.000	0.000	0.000	0.000
66	D	320	LEU	0	0.037	-0.001	11.727	-1.298	-1.298	0.000	0.000	0.000	0.000
67	D	321	HIS	0	0.017	0.003	10.131	-3.208	-3.208	0.000	0.000	0.000	0.000
68	D	322	ASP	-1	-0.742	-0.869	9.429	-24.528	-24.528	0.000	0.000	0.000	0.000
69	D	323	PHE	0	-0.017	-0.009	8.709	-0.760	-0.760	0.000	0.000	0.000	0.000
70	D	324	PHE	0	-0.087	-0.058	4.833	-5.719	-5.719	0.000	0.000	0.000	0.000
71	D	325	GLY	0	0.052	0.035	5.787	-1.959	-1.959	0.000	0.000	0.000	0.000
72	D	326	ASP	-1	-0.901	-0.960	4.930	-48.813	-48.707	-0.001	-0.004	-0.100	0.000
73	D	327	ASP	-1	-0.871	-0.918	5.966	-27.437	-27.437	0.000	0.000	0.000	0.000
74	D	328	ASP	-1	-0.851	-0.943	3.562	-76.009	-74.826	0.002	-0.692	-0.493	-0.005
75	D	329	VAL	0	-0.061	-0.042	6.685	2.590	2.590	0.000	0.000	0.000	0.000
76	D	330	PHE	0	0.025	0.016	8.271	1.149	1.149	0.000	0.000	0.000	0.000
77	D	331	ILE	0	-0.026	-0.014	13.291	0.956	0.956	0.000	0.000	0.000	0.000
78	D	332	ALA	0	0.042	0.012	17.115	-0.045	-0.045	0.000	0.000	0.000	0.000
79	D	333	CYS	0	-0.057	-0.044	19.408	0.526	0.526	0.000	0.000	0.000	0.000
80	D	334	GLY	0	0.044	0.043	22.828	0.228	0.228	0.000	0.000	0.000	0.000

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