FMO DATABASE

FMODB ID: QYKKY

Calculation Name: 5I41-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I41

Chain ID: B

ChEMBL ID:

UniProt ID: P45870

Base Structure: X-ray

Registration Date: 2023-06-22

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-382474.231169
FMO2-HF: Nuclear repulsion	356266.854755
FMO2-HF: Total energy	-26207.376414
FMO2-MP2: Total energy	-26283.864112

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(B:-1:SER)

Summations of interaction energy for fragment #1(B:-1: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.
-12.467	-7.093	0.263	-2.951	-2.686	-0.017

Interaction energy analysis for fragmet #1(B:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004

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	B	1	MET	0	-0.016	0.015	3.804	1.202	2.847	-0.024	-0.892	-0.728	0.003
4	B	2	ASN	0	0.073	0.040	7.103	-0.303	-0.303	0.000	0.000	0.000	0.000
5	B	3	THR	0	0.037	-0.007	8.928	-0.087	-0.087	0.000	0.000	0.000	0.000
6	B	4	ASN	0	-0.006	-0.009	12.645	-0.060	-0.060	0.000	0.000	0.000	0.000
7	B	5	MET	0	0.040	0.029	9.160	-0.013	-0.013	0.000	0.000	0.000	0.000
8	B	6	VAL	0	0.019	0.013	11.074	-0.049	-0.049	0.000	0.000	0.000	0.000
9	B	7	ALA	0	-0.017	-0.018	13.557	-0.011	-0.011	0.000	0.000	0.000	0.000
10	B	8	SER	0	0.006	0.001	15.216	-0.001	-0.001	0.000	0.000	0.000	0.000
11	B	9	GLU	-1	-0.874	-0.921	13.609	-0.068	-0.068	0.000	0.000	0.000	0.000
12	B	10	LEU	0	-0.052	-0.009	16.530	-0.013	-0.013	0.000	0.000	0.000	0.000
13	B	11	GLY	0	0.020	0.023	19.162	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	12	VAL	0	-0.059	-0.019	20.065	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	13	SER	0	0.036	0.020	20.348	0.008	0.008	0.000	0.000	0.000	0.000
16	B	14	ALA	0	0.093	0.025	17.040	-0.014	-0.014	0.000	0.000	0.000	0.000
17	B	15	LYS	1	0.959	0.967	18.416	0.004	0.004	0.000	0.000	0.000	0.000
18	B	16	THR	0	-0.030	-0.013	20.979	-0.010	-0.010	0.000	0.000	0.000	0.000
19	B	17	VAL	0	0.055	0.033	15.153	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	18	GLN	0	-0.006	-0.003	14.848	-0.022	-0.022	0.000	0.000	0.000	0.000
21	B	19	ARG	1	0.926	0.971	18.647	0.061	0.061	0.000	0.000	0.000	0.000
22	B	20	TRP	0	0.071	0.019	20.274	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	21	VAL	0	0.028	0.017	15.596	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	22	LYS	1	0.892	0.951	18.329	0.155	0.155	0.000	0.000	0.000	0.000
25	B	23	GLN	0	-0.014	-0.012	21.051	0.002	0.002	0.000	0.000	0.000	0.000
26	B	24	LEU	0	-0.002	-0.002	21.801	0.006	0.006	0.000	0.000	0.000	0.000
27	B	25	ASN	0	-0.068	-0.020	21.298	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	26	LEU	0	-0.010	0.000	17.140	-0.010	-0.010	0.000	0.000	0.000	0.000
29	B	27	PRO	0	0.000	0.010	14.055	0.011	0.011	0.000	0.000	0.000	0.000
30	B	28	ALA	0	0.011	-0.009	11.930	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	29	GLU	-1	-0.889	-0.929	8.079	-0.851	-0.851	0.000	0.000	0.000	0.000
32	B	30	ARG	1	0.811	0.880	8.477	0.618	0.618	0.000	0.000	0.000	0.000
33	B	31	ASN	0	0.049	0.024	4.307	-0.752	-0.668	-0.001	-0.008	-0.076	0.000
34	B	32	GLU	-1	-0.843	-0.934	2.897	-12.970	-9.325	0.288	-2.051	-1.882	-0.020
35	B	33	LEU	0	-0.058	-0.017	6.505	0.326	0.326	0.000	0.000	0.000	0.000
36	B	34	GLY	0	0.019	0.018	8.718	0.105	0.105	0.000	0.000	0.000	0.000
37	B	35	HIS	0	-0.049	-0.020	9.243	0.128	0.128	0.000	0.000	0.000	0.000
38	B	36	TYR	0	-0.009	-0.016	8.824	-0.104	-0.104	0.000	0.000	0.000	0.000
39	B	37	SER	0	-0.030	-0.016	5.212	0.319	0.319	0.000	0.000	0.000	0.000
40	B	38	PHE	0	-0.008	-0.005	7.568	-0.073	-0.073	0.000	0.000	0.000	0.000
41	B	39	THR	0	0.043	-0.012	6.437	-0.153	-0.153	0.000	0.000	0.000	0.000
42	B	40	ALA	0	0.044	0.000	8.278	0.244	0.244	0.000	0.000	0.000	0.000
43	B	41	GLU	-1	-0.797	-0.878	10.816	-0.190	-0.190	0.000	0.000	0.000	0.000
44	B	42	ASP	-1	-0.766	-0.864	10.707	-0.617	-0.617	0.000	0.000	0.000	0.000
45	B	43	VAL	0	-0.021	-0.012	11.701	0.097	0.097	0.000	0.000	0.000	0.000
46	B	44	LYS	1	0.824	0.903	14.356	0.334	0.334	0.000	0.000	0.000	0.000
47	B	45	VAL	0	0.002	0.003	16.339	0.046	0.046	0.000	0.000	0.000	0.000
48	B	46	LEU	0	0.017	-0.004	14.947	0.039	0.039	0.000	0.000	0.000	0.000
49	B	47	LYS	1	0.855	0.915	16.891	0.148	0.148	0.000	0.000	0.000	0.000
50	B	48	SER	0	-0.034	0.001	20.345	0.027	0.027	0.000	0.000	0.000	0.000
51	B	49	VAL	0	0.039	0.024	21.509	0.013	0.013	0.000	0.000	0.000	0.000
52	B	50	LYS	1	0.887	0.942	22.613	0.066	0.066	0.000	0.000	0.000	0.000
53	B	51	LYS	1	0.938	0.977	24.373	0.103	0.103	0.000	0.000	0.000	0.000
54	B	52	GLN	0	0.039	0.015	25.232	0.012	0.012	0.000	0.000	0.000	0.000
55	B	53	ILE	0	0.018	0.013	25.720	0.006	0.006	0.000	0.000	0.000	0.000
56	B	54	SER	0	-0.104	-0.065	27.686	0.008	0.008	0.000	0.000	0.000	0.000
57	B	55	GLU	-1	-0.974	-0.982	30.275	-0.048	-0.048	0.000	0.000	0.000	0.000
58	B	56	GLY	0	-0.026	0.001	32.434	0.003	0.003	0.000	0.000	0.000	0.000
59	B	57	THR	0	-0.074	-0.029	30.487	0.001	0.001	0.000	0.000	0.000	0.000
60	B	58	ALA	0	-0.005	0.002	31.246	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	59	ILE	0	-0.009	-0.020	25.459	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	60	GLN	0	-0.056	-0.049	28.565	-0.010	-0.010	0.000	0.000	0.000	0.000
63	B	61	ASP	-1	-0.857	-0.920	30.933	-0.073	-0.073	0.000	0.000	0.000	0.000
64	B	62	ILE	0	-0.061	-0.020	25.114	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	63	HIS	0	-0.012	0.007	26.353	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	64	LEU	0	-0.023	-0.021	21.186	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	65	PRO	0	0.007	0.009	20.048	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:-1:SER)