FMO DATABASE

FMODB ID: 49YGN

Calculation Name: 5EKQ-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EKQ

Chain ID: E

ChEMBL ID:

UniProt ID: P0A940

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-562642.439671
FMO2-HF: Nuclear repulsion	527618.17268
FMO2-HF: Total energy	-35024.266991
FMO2-MP2: Total energy	-35126.961498

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(E:22:THR)

Summations of interaction energy for fragment #1(E:22:THR)

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.
-1.443	0.83	-0.012	-0.9	-1.36	0

Interaction energy analysis for fragmet #1(E:22:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.022

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].
3	E	24	GLU	-1	-0.889	-0.927	3.493	-2.835	-0.562	-0.012	-0.900	-1.360
4	E	25	ARG	1	0.907	0.939	5.545	1.844	1.844	0.000	0.000	0.000
5	E	26	VAL	0	-0.011	-0.003	6.565	-0.495	-0.495	0.000	0.000	0.000
6	E	27	VAL	0	-0.010	0.006	8.899	0.247	0.247	0.000	0.000	0.000
7	E	28	TYR	0	0.023	0.008	11.641	-0.053	-0.053	0.000	0.000	0.000
8	E	29	ARG	1	0.889	0.912	14.881	0.304	0.304	0.000	0.000	0.000
9	E	30	PRO	0	-0.016	0.021	17.319	-0.009	-0.009	0.000	0.000	0.000
10	E	31	ASP	-1	-0.824	-0.923	20.575	-0.213	-0.213	0.000	0.000	0.000
11	E	32	ILE	0	-0.067	-0.020	19.940	0.020	0.020	0.000	0.000	0.000
12	E	33	ASN	0	0.002	0.002	23.602	-0.008	-0.008	0.000	0.000	0.000
13	E	34	GLN	0	-0.034	-0.028	25.117	0.016	0.016	0.000	0.000	0.000
14	E	35	GLY	0	0.055	0.017	27.854	-0.002	-0.002	0.000	0.000	0.000
15	E	36	ASN	0	-0.035	-0.003	30.993	0.003	0.003	0.000	0.000	0.000
16	E	37	TYR	0	0.043	0.011	32.633	-0.006	-0.006	0.000	0.000	0.000
17	E	38	LEU	0	-0.018	-0.005	33.896	0.005	0.005	0.000	0.000	0.000
18	E	39	THR	0	-0.012	-0.047	35.126	-0.005	-0.005	0.000	0.000	0.000
19	E	40	ALA	0	0.047	0.028	36.393	-0.002	-0.002	0.000	0.000	0.000
20	E	41	ASN	0	0.027	0.007	37.896	0.006	0.006	0.000	0.000	0.000
21	E	42	ASP	-1	-0.808	-0.881	40.566	-0.047	-0.047	0.000	0.000	0.000
22	E	43	VAL	0	0.038	0.011	37.383	0.003	0.003	0.000	0.000	0.000
23	E	44	SER	0	-0.055	-0.023	40.831	0.002	0.002	0.000	0.000	0.000
24	E	45	LYS	1	0.837	0.935	43.474	0.044	0.044	0.000	0.000	0.000
25	E	46	ILE	0	-0.025	0.003	42.563	0.003	0.003	0.000	0.000	0.000
26	E	47	ARG	1	0.936	0.952	45.788	0.032	0.032	0.000	0.000	0.000
27	E	48	VAL	0	0.032	0.006	47.612	0.001	0.001	0.000	0.000	0.000
28	E	49	GLY	0	0.025	0.019	49.602	0.000	0.000	0.000	0.000	0.000
29	E	50	MET	0	-0.044	-0.013	48.067	0.001	0.001	0.000	0.000	0.000
30	E	51	THR	0	0.051	0.019	50.797	0.001	0.001	0.000	0.000	0.000
31	E	52	GLN	0	0.058	0.049	46.509	0.001	0.001	0.000	0.000	0.000
32	E	53	GLN	0	0.008	-0.013	47.907	-0.001	-0.001	0.000	0.000	0.000
33	E	54	GLN	0	0.007	-0.013	49.495	0.000	0.000	0.000	0.000	0.000
34	E	55	VAL	0	-0.008	0.006	43.825	-0.001	-0.001	0.000	0.000	0.000
35	E	56	ALA	0	-0.019	-0.008	44.560	-0.002	-0.002	0.000	0.000	0.000
36	E	57	TYR	0	-0.065	-0.006	45.647	-0.001	-0.001	0.000	0.000	0.000
37	E	58	ALA	0	-0.019	-0.021	45.114	-0.001	-0.001	0.000	0.000	0.000
38	E	59	LEU	0	-0.009	-0.004	40.339	-0.001	-0.001	0.000	0.000	0.000
39	E	60	GLY	0	0.039	0.019	40.639	-0.003	-0.003	0.000	0.000	0.000
40	E	61	THR	0	0.017	0.019	40.772	0.002	0.002	0.000	0.000	0.000
41	E	62	PRO	0	-0.035	0.001	38.326	-0.002	-0.002	0.000	0.000	0.000
42	E	63	LEU	0	-0.007	-0.021	33.786	0.002	0.002	0.000	0.000	0.000
43	E	64	MET	0	-0.039	-0.009	30.717	0.001	0.001	0.000	0.000	0.000
44	E	65	SER	0	0.031	0.005	35.672	-0.002	-0.002	0.000	0.000	0.000
45	E	66	ASP	-1	-0.812	-0.880	37.533	-0.008	-0.008	0.000	0.000	0.000
46	E	67	PRO	0	-0.078	0.020	37.471	0.001	0.001	0.000	0.000	0.000
47	E	68	PHE	0	0.038	-0.010	35.524	0.000	0.000	0.000	0.000	0.000
48	E	69	GLY	0	-0.006	-0.007	40.608	0.000	0.000	0.000	0.000	0.000
49	E	70	THR	0	-0.056	-0.042	41.329	0.000	0.000	0.000	0.000	0.000
50	E	71	ASN	0	-0.040	-0.031	43.501	-0.001	-0.001	0.000	0.000	0.000
51	E	72	THR	0	-0.002	-0.033	39.422	-0.002	-0.002	0.000	0.000	0.000
52	E	73	TRP	0	-0.051	-0.029	39.800	0.000	0.000	0.000	0.000	0.000
53	E	74	PHE	0	0.031	0.010	34.244	-0.003	-0.003	0.000	0.000	0.000
54	E	75	TYR	0	-0.005	-0.017	35.609	0.000	0.000	0.000	0.000	0.000
55	E	76	VAL	0	0.002	-0.004	28.984	-0.003	-0.003	0.000	0.000	0.000
56	E	77	PHE	0	0.002	0.025	29.240	0.002	0.002	0.000	0.000	0.000
57	E	78	ARG	1	0.941	0.967	20.619	0.081	0.081	0.000	0.000	0.000
58	E	79	GLN	0	-0.012	-0.004	24.958	0.004	0.004	0.000	0.000	0.000
59	E	80	GLN	0	-0.001	-0.005	17.542	-0.009	-0.009	0.000	0.000	0.000
60	E	81	PRO	0	0.082	0.048	21.016	-0.001	-0.001	0.000	0.000	0.000
61	E	82	GLY	0	0.070	0.032	18.770	-0.025	-0.025	0.000	0.000	0.000
62	E	83	HIS	0	-0.101	-0.055	12.473	-0.028	-0.028	0.000	0.000	0.000
63	E	84	GLU	-1	-0.947	-0.951	15.290	-0.315	-0.315	0.000	0.000	0.000
64	E	85	GLY	0	0.027	0.002	16.995	-0.024	-0.024	0.000	0.000	0.000
65	E	86	VAL	0	-0.080	-0.037	18.509	0.022	0.022	0.000	0.000	0.000
66	E	87	THR	0	0.018	0.011	20.830	0.002	0.002	0.000	0.000	0.000
67	E	88	GLN	0	0.062	-0.006	24.403	0.007	0.007	0.000	0.000	0.000
68	E	89	GLN	0	-0.007	0.026	26.821	0.004	0.004	0.000	0.000	0.000
69	E	90	THR	0	-0.056	-0.038	29.427	0.004	0.004	0.000	0.000	0.000
70	E	91	LEU	0	0.008	0.019	32.020	0.001	0.001	0.000	0.000	0.000
71	E	92	THR	0	-0.016	0.007	34.777	0.002	0.002	0.000	0.000	0.000
72	E	93	LEU	0	-0.010	-0.009	37.405	0.000	0.000	0.000	0.000	0.000
73	E	94	THR	0	0.056	0.036	41.204	0.002	0.002	0.000	0.000	0.000
74	E	95	PHE	0	-0.014	0.005	43.184	-0.001	-0.001	0.000	0.000	0.000
75	E	96	ASN	0	0.018	0.010	46.763	0.001	0.001	0.000	0.000	0.000
76	E	97	SER	0	0.022	-0.004	49.772	0.000	0.000	0.000	0.000	0.000
77	E	98	SER	0	-0.044	-0.024	51.928	0.001	0.001	0.000	0.000	0.000
78	E	99	GLY	0	0.028	0.030	50.399	0.000	0.000	0.000	0.000	0.000
79	E	100	VAL	0	-0.022	-0.013	50.820	-0.001	-0.001	0.000	0.000	0.000
80	E	101	LEU	0	-0.028	-0.002	45.336	0.001	0.001	0.000	0.000	0.000
81	E	102	THR	0	-0.003	-0.022	47.022	-0.001	-0.001	0.000	0.000	0.000
82	E	103	ASN	0	-0.024	-0.027	41.665	-0.001	-0.001	0.000	0.000	0.000
83	E	104	ILE	0	-0.006	0.000	40.882	0.000	0.000	0.000	0.000	0.000
84	E	105	ASP	-1	-0.863	-0.923	35.863	-0.036	-0.036	0.000	0.000	0.000
85	E	106	ASN	0	-0.046	-0.035	35.290	-0.003	-0.003	0.000	0.000	0.000
86	E	107	LYS	1	0.945	0.970	30.819	0.040	0.040	0.000	0.000	0.000
87	E	108	PRO	0	-0.004	-0.012	30.834	-0.003	-0.003	0.000	0.000	0.000
88	E	109	ALA	0	-0.002	0.009	25.995	-0.002	-0.002	0.000	0.000	0.000
89	E	110	LEU	0	0.008	-0.013	22.636	0.008	0.008	0.000	0.000	0.000
90	E	111	SER	0	-0.008	0.016	22.865	-0.008	-0.008	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(E:22:THR)