FMO DATABASE

FMODB ID: 6YL5Z

Calculation Name: 2FYZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FYZ

Chain ID: A

ChEMBL ID:

UniProt ID: P11236

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	OptH
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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-210367.119016
FMO2-HF: Nuclear repulsion	188676.16807
FMO2-HF: Total energy	-21690.950946
FMO2-MP2: Total energy	-21753.706786

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(A:123:SER)

Summations of interaction energy for fragment #1(A:123: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.
-9.782	-5.048	4.738	-3.681	-5.791	0.015

Interaction energy analysis for fragmet #1(A:123:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.021

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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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	A	125	VAL	0	0.062	0.021	2.870	-5.606	-1.532	0.435	-1.506	-3.003	0.016
4	A	126	SER	0	0.002	0.000	1.990	-3.857	-3.528	4.288	-2.177	-2.440	-0.001
5	A	127	LEU	0	0.043	0.015	3.415	-0.233	0.098	0.015	0.002	-0.348	0.000
6	A	128	VAL	0	0.065	0.026	5.707	0.198	0.198	0.000	0.000	0.000	0.000
7	A	129	GLN	0	-0.027	0.000	6.539	-0.171	-0.171	0.000	0.000	0.000	0.000
8	A	130	ALA	0	0.017	0.002	7.498	-0.061	-0.061	0.000	0.000	0.000	0.000
9	A	131	GLN	0	0.011	0.011	9.454	0.132	0.132	0.000	0.000	0.000	0.000
10	A	132	THR	0	-0.027	-0.045	10.968	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	133	ASN	0	0.022	0.008	10.802	0.039	0.039	0.000	0.000	0.000	0.000
12	A	134	ALA	0	-0.002	0.010	13.420	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	135	ARG	1	0.949	0.984	13.176	-0.246	-0.246	0.000	0.000	0.000	0.000
14	A	136	ALA	0	0.028	0.023	16.762	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	137	ILE	0	0.016	0.004	16.205	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	138	ALA	0	-0.037	-0.010	19.515	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	139	ALA	0	0.038	0.010	21.303	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	140	MET	0	0.002	-0.005	20.066	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	141	LYS	1	0.952	0.997	23.767	0.049	0.049	0.000	0.000	0.000	0.000
20	A	142	ASN	0	-0.027	-0.027	25.679	0.007	0.007	0.000	0.000	0.000	0.000
21	A	143	SER	0	-0.007	0.010	26.915	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	144	ILE	0	0.054	0.013	26.302	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	145	GLN	0	-0.012	-0.003	29.577	0.004	0.004	0.000	0.000	0.000	0.000
24	A	146	ALA	0	0.014	0.007	31.594	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	147	THR	0	-0.001	-0.001	31.752	0.001	0.001	0.000	0.000	0.000	0.000
26	A	148	ASN	0	-0.001	-0.015	32.873	0.000	0.000	0.000	0.000	0.000	0.000
27	A	149	ARG	1	0.931	0.968	35.769	0.001	0.001	0.000	0.000	0.000	0.000
28	A	150	ALA	0	0.059	0.040	37.295	0.000	0.000	0.000	0.000	0.000	0.000
29	A	151	VAL	0	0.004	0.006	37.071	0.000	0.000	0.000	0.000	0.000	0.000
30	A	152	PHE	0	-0.036	-0.016	39.890	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	153	GLU	-1	-0.851	-0.932	41.780	0.004	0.004	0.000	0.000	0.000	0.000
32	A	154	VAL	0	-0.006	0.009	42.321	0.001	0.001	0.000	0.000	0.000	0.000
33	A	155	LYS	1	0.880	0.955	44.032	0.011	0.011	0.000	0.000	0.000	0.000
34	A	156	GLU	-1	-0.967	-0.997	45.775	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	157	GLY	0	0.023	0.009	47.358	0.000	0.000	0.000	0.000	0.000	0.000
36	A	158	THR	0	-0.014	-0.023	47.857	0.000	0.000	0.000	0.000	0.000	0.000
37	A	159	GLN	0	0.000	0.008	49.947	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	160	ARG	1	0.945	0.959	50.756	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	161	LEU	0	0.012	0.019	53.148	0.000	0.000	0.000	0.000	0.000	0.000
40	A	162	ALA	0	0.017	0.001	54.380	0.000	0.000	0.000	0.000	0.000	0.000
41	A	163	ILE	0	-0.017	-0.005	55.431	0.000	0.000	0.000	0.000	0.000	0.000
42	A	164	ALA	0	0.009	0.009	57.782	0.000	0.000	0.000	0.000	0.000	0.000
43	A	165	VAL	0	-0.006	-0.004	58.024	0.000	0.000	0.000	0.000	0.000	0.000
44	A	166	GLN	0	-0.023	-0.009	60.279	0.000	0.000	0.000	0.000	0.000	0.000
45	A	167	ALA	0	0.034	0.020	62.091	0.000	0.000	0.000	0.000	0.000	0.000
46	A	168	ILE	0	-0.029	-0.017	62.384	0.000	0.000	0.000	0.000	0.000	0.000
47	A	169	GLN	0	0.010	0.009	64.687	0.001	0.001	0.000	0.000	0.000	0.000
48	A	170	ASP	-1	-0.893	-0.955	66.160	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	171	HIS	0	-0.059	-0.012	68.072	0.000	0.000	0.000	0.000	0.000	0.000
50	A	172	ILE	0	0.020	0.001	68.056	0.000	0.000	0.000	0.000	0.000	0.000
51	A	173	ASN	0	-0.001	-0.012	69.582	0.000	0.000	0.000	0.000	0.000	0.000
52	A	174	THR	0	-0.015	-0.035	71.788	0.000	0.000	0.000	0.000	0.000	0.000
53	A	175	ILE	0	-0.044	0.006	74.345	0.000	0.000	0.000	0.000	0.000	0.000
54	A	176	MET	0	-0.061	-0.043	71.905	0.001	0.001	0.000	0.000	0.000	0.000
55	A	177	ASN	0	-0.054	-0.008	75.004	0.000	0.000	0.000	0.000	0.000	0.000
56	A	178	THR	0	-0.023	-0.001	76.989	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	179	GLN	0	-0.043	-0.015	79.796	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:123:SER)