FMO DATABASE

FMODB ID: R8N48

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

Total energy (hartree)

FMO2-HF: Electronic energy	-210136.785953
FMO2-HF: Nuclear repulsion	188445.258161
FMO2-HF: Total energy	-21691.527792
FMO2-MP2: Total energy	-21754.14065

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.
-19.371	-15.682	4.404	-3.321	-4.773	0.017

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 : 0.051 / q_NPA : 0.018

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	A	125	VAL	0	0.038	0.014	2.706	-3.146	-0.415	0.304	-1.231	-1.805	0.005
4	A	126	SER	0	0.016	0.008	2.342	-8.780	-8.343	4.072	-1.856	-2.654	0.010
5	A	127	LEU	0	0.027	0.014	4.055	-3.056	-2.535	0.028	-0.234	-0.314	0.002
6	A	128	VAL	0	0.018	0.006	6.076	-0.546	-0.546	0.000	0.000	0.000	0.000
7	A	129	GLN	0	0.041	0.018	7.033	-0.665	-0.665	0.000	0.000	0.000	0.000
8	A	130	ALA	0	-0.015	-0.005	8.189	-0.538	-0.538	0.000	0.000	0.000	0.000
9	A	131	GLN	0	0.019	0.012	10.087	-0.262	-0.262	0.000	0.000	0.000	0.000
10	A	132	THR	0	-0.008	-0.010	11.569	-0.256	-0.256	0.000	0.000	0.000	0.000
11	A	133	ASN	0	0.043	0.023	11.752	-0.194	-0.194	0.000	0.000	0.000	0.000
12	A	134	ALA	0	-0.001	0.008	14.364	-0.127	-0.127	0.000	0.000	0.000	0.000
13	A	135	ARG	1	0.886	0.934	12.482	-1.023	-1.023	0.000	0.000	0.000	0.000
14	A	136	ALA	0	0.035	0.020	17.251	-0.071	-0.071	0.000	0.000	0.000	0.000
15	A	137	ILE	0	0.006	-0.004	17.220	-0.066	-0.066	0.000	0.000	0.000	0.000
16	A	138	ALA	0	-0.026	-0.006	20.428	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	139	ALA	0	0.043	0.022	22.029	-0.037	-0.037	0.000	0.000	0.000	0.000
18	A	140	MET	0	0.004	-0.002	20.385	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	141	LYS	1	0.965	0.990	24.492	-0.259	-0.259	0.000	0.000	0.000	0.000
20	A	142	ASN	0	-0.025	-0.023	26.447	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	143	SER	0	0.051	0.025	27.664	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	144	ILE	0	-0.004	0.016	27.197	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	145	GLN	0	-0.024	-0.014	30.464	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	146	ALA	0	-0.009	0.001	32.346	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	147	THR	0	0.000	-0.013	32.295	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	148	ASN	0	-0.003	-0.016	33.896	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	149	ARG	1	0.945	0.980	36.455	-0.148	-0.148	0.000	0.000	0.000	0.000
28	A	150	ALA	0	0.041	0.027	37.989	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	151	VAL	0	0.006	0.000	38.031	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	152	PHE	0	-0.029	-0.007	40.586	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	153	GLU	-1	-0.861	-0.945	42.671	0.099	0.099	0.000	0.000	0.000	0.000
32	A	154	VAL	0	-0.017	0.002	42.883	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	155	LYS	1	0.844	0.943	44.731	-0.092	-0.092	0.000	0.000	0.000	0.000
34	A	156	GLU	-1	-0.819	-0.915	46.563	0.080	0.080	0.000	0.000	0.000	0.000
35	A	157	GLY	0	-0.010	0.000	48.254	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	158	THR	0	-0.015	-0.020	48.389	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	159	GLN	0	0.005	0.005	50.713	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	160	ARG	1	0.880	0.922	49.573	-0.085	-0.085	0.000	0.000	0.000	0.000
39	A	161	LEU	0	0.014	0.016	53.943	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	162	ALA	0	0.010	0.002	55.057	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	163	ILE	0	0.004	0.001	56.068	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	164	ALA	0	-0.003	0.002	58.537	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	165	VAL	0	-0.006	-0.009	58.884	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	166	GLN	0	-0.054	-0.020	61.060	0.000	0.000	0.000	0.000	0.000	0.000
45	A	167	ALA	0	0.018	0.006	62.932	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	168	ILE	0	-0.018	-0.007	62.677	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	169	GLN	0	-0.030	-0.013	65.467	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	170	ASP	-1	-0.802	-0.914	66.932	0.043	0.043	0.000	0.000	0.000	0.000
49	A	171	HIS	0	-0.051	-0.013	68.763	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	172	ILE	0	-0.007	-0.011	68.500	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	173	ASN	0	-0.015	-0.013	69.533	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	174	THR	0	-0.012	-0.007	72.629	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	175	ILE	0	-0.062	-0.029	75.112	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	176	MET	0	-0.008	0.002	72.241	0.000	0.000	0.000	0.000	0.000	0.000
55	A	177	ASN	0	-0.039	-0.013	75.576	0.000	0.000	0.000	0.000	0.000	0.000
56	A	178	THR	0	-0.024	-0.006	77.574	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	179	GLN	0	-0.062	-0.023	80.210	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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