FMO DATABASE

FMODB ID: ZVR5N

Calculation Name: 2P58-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: A

ChEMBL ID:

UniProt ID: O68690

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-263580.692351
FMO2-HF: Nuclear repulsion	241454.269409
FMO2-HF: Total energy	-22126.422942
FMO2-MP2: Total energy	-22188.659603

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:10:ASN)

Summations of interaction energy for fragment #1(A:10:ASN)

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.
-16.241	-10.26	5.148	-4.449	-6.68	0.02

Interaction energy analysis for fragmet #1(A:10:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.020

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	12	GLU	-1	-0.805	-0.891	2.101	-7.915	-4.756	4.015	-3.074	-4.101	0.032
4	A	13	THR	0	0.000	-0.004	2.377	-6.740	-4.221	1.132	-1.295	-2.355	-0.012
5	A	14	VAL	0	0.050	0.038	3.967	0.302	0.605	0.001	-0.080	-0.224	0.000
6	A	15	ARG	1	0.894	0.952	6.311	-1.711	-1.711	0.000	0.000	0.000	0.000
7	A	16	SER	0	-0.011	-0.009	6.933	-0.253	-0.253	0.000	0.000	0.000	0.000
8	A	17	ILE	0	0.019	-0.005	7.516	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	18	THR	0	-0.004	-0.015	9.891	0.038	0.038	0.000	0.000	0.000	0.000
10	A	19	MET	0	-0.018	-0.013	11.512	0.106	0.106	0.000	0.000	0.000	0.000
11	A	20	GLN	0	-0.028	-0.004	12.488	-0.076	-0.076	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.005	-0.003	13.425	0.013	0.013	0.000	0.000	0.000	0.000
13	A	22	GLU	-1	-0.844	-0.931	15.813	0.079	0.079	0.000	0.000	0.000	0.000
14	A	23	MET	0	-0.065	-0.026	15.193	0.018	0.018	0.000	0.000	0.000	0.000
15	A	24	ALA	0	-0.016	-0.003	18.450	0.000	0.000	0.000	0.000	0.000	0.000
16	A	25	LEU	0	0.013	0.011	20.126	0.004	0.004	0.000	0.000	0.000	0.000
17	A	26	THR	0	-0.021	-0.018	21.541	0.013	0.013	0.000	0.000	0.000	0.000
18	A	27	LYS	1	0.844	0.903	23.049	0.069	0.069	0.000	0.000	0.000	0.000
19	A	28	LEU	0	0.023	0.038	24.459	0.003	0.003	0.000	0.000	0.000	0.000
20	A	29	LYS	1	0.885	0.920	24.800	0.011	0.011	0.000	0.000	0.000	0.000
21	A	30	LYS	1	0.941	0.972	25.828	-0.054	-0.054	0.000	0.000	0.000	0.000
22	A	31	ASP	-1	-0.802	-0.878	27.849	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	32	MET	0	-0.017	0.000	29.923	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	33	MET	0	-0.026	0.005	32.362	0.001	0.001	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.805	0.899	30.274	0.027	0.027	0.000	0.000	0.000	0.000
26	A	35	GLY	0	0.027	0.039	36.225	0.001	0.001	0.000	0.000	0.000	0.000
27	A	36	GLY	0	0.015	-0.011	37.220	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.834	-0.923	38.953	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	38	ALA	0	0.044	0.008	38.498	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	39	LYS	1	0.951	0.962	37.544	0.052	0.052	0.000	0.000	0.000	0.000
31	A	40	GLN	0	0.009	0.021	32.501	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	41	TYR	0	-0.015	-0.027	33.538	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	42	GLN	0	-0.066	-0.018	33.154	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	43	VAL	0	-0.004	-0.003	30.073	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	44	TRP	0	0.066	0.014	29.085	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	45	GLN	0	0.033	0.024	28.305	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.894	0.940	27.823	0.081	0.081	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.920	-0.951	23.940	-0.132	-0.132	0.000	0.000	0.000	0.000
39	A	48	SER	0	0.048	0.006	23.598	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.883	0.954	23.701	0.085	0.085	0.000	0.000	0.000	0.000
41	A	50	ALA	0	0.011	0.027	21.609	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.018	0.007	18.819	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.818	-0.910	18.779	-0.051	-0.051	0.000	0.000	0.000	0.000
44	A	53	SER	0	-0.077	-0.069	19.643	0.010	0.010	0.000	0.000	0.000	0.000
45	A	54	ALA	0	0.010	0.013	15.454	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	55	ILE	0	-0.013	-0.002	14.876	-0.055	-0.055	0.000	0.000	0.000	0.000
47	A	56	ALA	0	0.001	0.010	15.233	0.002	0.002	0.000	0.000	0.000	0.000
48	A	57	ILE	0	0.005	0.002	13.544	0.003	0.003	0.000	0.000	0.000	0.000
49	A	58	ILE	0	-0.005	0.000	9.398	-0.062	-0.062	0.000	0.000	0.000	0.000
50	A	59	HIS	0	0.010	0.000	11.593	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	60	TYR	0	-0.050	-0.044	13.637	0.032	0.032	0.000	0.000	0.000	0.000
52	A	61	VAL	0	-0.049	-0.013	10.211	0.021	0.021	0.000	0.000	0.000	0.000
53	A	62	ALA	0	-0.046	-0.013	7.291	-0.073	-0.073	0.000	0.000	0.000	0.000
54	A	63	GLY	0	-0.050	-0.009	9.016	0.131	0.131	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ASN)