FMO DATABASE

FMODB ID: ZVR9N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-210031.169893
FMO2-HF: Nuclear repulsion	188339.841058
FMO2-HF: Total energy	-21691.328835
FMO2-MP2: Total energy	-21754.002565

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.
-16.97	-12.423	2.624	-2.35	-4.822	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 : 0.070 / 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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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	0.059	0.017	2.653	-2.971	-0.227	0.178	-0.643	-2.278	0.005
4	A	126	SER	0	0.024	0.013	2.584	-6.480	-5.145	2.431	-1.534	-2.233	0.010
5	A	127	LEU	0	0.024	0.010	4.133	-3.066	-2.598	0.015	-0.173	-0.311	0.002
6	A	128	VAL	0	0.026	0.011	6.157	-0.630	-0.630	0.000	0.000	0.000	0.000
7	A	129	GLN	0	0.035	0.025	7.016	-0.638	-0.638	0.000	0.000	0.000	0.000
8	A	130	ALA	0	0.010	0.000	8.268	-0.527	-0.527	0.000	0.000	0.000	0.000
9	A	131	GLN	0	0.016	0.004	10.150	-0.315	-0.315	0.000	0.000	0.000	0.000
10	A	132	THR	0	-0.034	-0.039	11.545	-0.256	-0.256	0.000	0.000	0.000	0.000
11	A	133	ASN	0	0.026	0.010	11.908	-0.219	-0.219	0.000	0.000	0.000	0.000
12	A	134	ALA	0	-0.003	0.009	14.186	-0.130	-0.130	0.000	0.000	0.000	0.000
13	A	135	ARG	1	0.932	0.973	13.096	-0.933	-0.933	0.000	0.000	0.000	0.000
14	A	136	ALA	0	0.034	0.024	17.415	-0.070	-0.070	0.000	0.000	0.000	0.000
15	A	137	ILE	0	0.019	0.000	17.050	-0.064	-0.064	0.000	0.000	0.000	0.000
16	A	138	ALA	0	-0.034	-0.007	20.306	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	139	ALA	0	0.031	0.009	21.991	-0.039	-0.039	0.000	0.000	0.000	0.000
18	A	140	MET	0	0.005	-0.001	20.615	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	141	LYS	1	0.953	0.996	24.552	-0.282	-0.282	0.000	0.000	0.000	0.000
20	A	142	ASN	0	-0.018	-0.021	26.485	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	143	SER	0	0.048	0.030	27.658	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	144	ILE	0	0.012	0.006	27.063	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	145	GLN	0	-0.032	-0.013	30.347	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	146	ALA	0	0.005	0.004	32.338	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	147	THR	0	-0.014	-0.019	32.445	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	148	ASN	0	0.001	-0.010	33.877	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	149	ARG	1	0.948	0.975	36.577	-0.150	-0.150	0.000	0.000	0.000	0.000
28	A	150	ALA	0	0.052	0.036	38.046	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	151	VAL	0	0.008	0.007	38.104	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	152	PHE	0	-0.028	-0.010	40.673	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	153	GLU	-1	-0.875	-0.941	42.544	0.100	0.100	0.000	0.000	0.000	0.000
32	A	154	VAL	0	0.002	0.011	43.324	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	155	LYS	1	0.879	0.951	44.815	-0.095	-0.095	0.000	0.000	0.000	0.000
34	A	156	GLU	-1	-0.875	-0.940	46.578	0.083	0.083	0.000	0.000	0.000	0.000
35	A	157	GLY	0	0.016	0.010	48.117	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	158	THR	0	-0.012	-0.023	48.598	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	159	GLN	0	0.000	0.010	50.745	0.000	0.000	0.000	0.000	0.000	0.000
38	A	160	ARG	1	0.873	0.910	50.111	-0.085	-0.085	0.000	0.000	0.000	0.000
39	A	161	LEU	0	-0.002	0.011	53.919	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	162	ALA	0	0.015	0.001	55.168	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	163	ILE	0	-0.004	0.000	56.026	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	164	ALA	0	0.005	0.007	58.559	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	165	VAL	0	-0.003	-0.005	59.090	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	166	GLN	0	-0.007	0.004	61.076	0.000	0.000	0.000	0.000	0.000	0.000
45	A	167	ALA	0	0.012	0.005	62.885	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	168	ILE	0	-0.017	-0.010	62.893	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	169	GLN	0	-0.041	-0.016	65.471	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	170	ASP	-1	-0.873	-0.948	67.158	0.045	0.045	0.000	0.000	0.000	0.000
49	A	171	HIS	0	-0.060	-0.014	68.859	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	172	ILE	0	0.012	-0.006	68.567	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	173	ASN	0	0.007	-0.002	70.106	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	174	THR	0	-0.009	-0.028	72.600	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	175	ILE	0	-0.029	0.010	75.146	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	176	MET	0	-0.056	-0.046	72.688	0.000	0.000	0.000	0.000	0.000	0.000
55	A	177	ASN	0	-0.058	0.001	75.751	0.000	0.000	0.000	0.000	0.000	0.000
56	A	178	THR	0	-0.018	-0.006	77.773	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	179	GLN	0	-0.044	-0.011	80.564	-0.001	-0.001	0.000	0.000	0.000	0.000

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