FMO DATABASE

FMODB ID: QVV8Y

Calculation Name: 3PH0-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH0

Chain ID: C

ChEMBL ID:

UniProt ID: Q1EHA4

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-258719.090669
FMO2-HF: Nuclear repulsion	236947.263794
FMO2-HF: Total energy	-21771.826876
FMO2-MP2: Total energy	-21830.706439

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(C:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

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.
-6.019	-1.417	3.666	-2.76	-5.509	0.013

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.004

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	C	3	VAL	0	0.078	0.023	3.616	-0.221	1.071	-0.001	-0.653	-0.639	0.003
4	C	4	GLN	0	0.027	0.006	6.198	0.271	0.271	0.000	0.000	0.000	0.000
5	C	5	LEU	0	0.028	0.030	2.058	-1.068	-0.650	3.163	-1.037	-2.543	0.001
6	C	6	LYS	1	0.829	0.897	3.181	-2.889	-1.551	0.212	-0.505	-1.045	0.005
7	C	7	LYS	1	0.919	0.951	4.617	-1.063	-0.971	-0.001	-0.017	-0.074	0.000
8	C	8	GLN	0	-0.017	0.002	6.802	-0.136	-0.136	0.000	0.000	0.000	0.000
9	C	9	LEU	0	0.010	0.006	3.983	-0.331	-0.119	0.002	-0.036	-0.178	0.000
10	C	10	ALA	0	0.017	0.015	7.770	-0.134	-0.134	0.000	0.000	0.000	0.000
11	C	11	GLU	-1	-0.926	-0.958	10.346	0.066	0.066	0.000	0.000	0.000	0.000
12	C	12	LEU	0	-0.003	-0.001	10.371	-0.053	-0.053	0.000	0.000	0.000	0.000
13	C	13	ALA	0	0.000	-0.007	11.704	-0.048	-0.048	0.000	0.000	0.000	0.000
14	C	14	LEU	0	-0.023	-0.017	13.378	-0.030	-0.030	0.000	0.000	0.000	0.000
15	C	15	ALA	0	0.000	0.002	15.428	-0.019	-0.019	0.000	0.000	0.000	0.000
16	C	16	GLY	0	0.026	0.012	15.960	-0.018	-0.018	0.000	0.000	0.000	0.000
17	C	17	THR	0	-0.049	-0.037	17.368	-0.011	-0.011	0.000	0.000	0.000	0.000
18	C	18	GLY	0	-0.018	0.005	19.673	-0.004	-0.004	0.000	0.000	0.000	0.000
19	C	19	HIS	0	-0.088	-0.054	20.201	-0.005	-0.005	0.000	0.000	0.000	0.000
20	C	20	HIS	0	0.020	0.020	22.176	-0.015	-0.015	0.000	0.000	0.000	0.000
21	C	21	CYS	0	-0.048	-0.012	17.511	-0.018	-0.018	0.000	0.000	0.000	0.000
22	C	22	HIS	0	0.029	-0.015	17.634	-0.006	-0.006	0.000	0.000	0.000	0.000
23	C	23	GLN	0	-0.040	-0.008	17.576	0.020	0.020	0.000	0.000	0.000	0.000
24	C	24	GLU	-1	-0.820	-0.918	14.084	-0.182	-0.182	0.000	0.000	0.000	0.000
25	C	25	ALA	0	0.021	0.006	13.230	0.009	0.009	0.000	0.000	0.000	0.000
26	C	26	ALA	0	-0.013	0.003	13.893	0.053	0.053	0.000	0.000	0.000	0.000
27	C	27	SER	0	-0.013	-0.007	12.289	0.004	0.004	0.000	0.000	0.000	0.000
28	C	28	ILE	0	-0.053	-0.026	8.434	0.025	0.025	0.000	0.000	0.000	0.000
29	C	29	ALA	0	-0.013	-0.016	10.187	0.150	0.150	0.000	0.000	0.000	0.000
30	C	30	ASP	-1	-0.832	-0.912	12.765	0.067	0.067	0.000	0.000	0.000	0.000
31	C	31	TRP	0	-0.040	-0.008	3.123	-1.194	0.056	0.291	-0.512	-1.030	0.004
32	C	32	LEU	0	-0.029	-0.027	7.048	0.159	0.159	0.000	0.000	0.000	0.000
33	C	33	ALA	0	-0.006	0.005	9.653	-0.031	-0.031	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.077	-0.032	9.557	-0.071	-0.071	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.871	-0.922	7.659	0.662	0.662	0.000	0.000	0.000	0.000
36	C	36	GLU	-1	-0.888	-0.945	11.283	0.120	0.120	0.000	0.000	0.000	0.000
37	C	37	CYS	0	-0.082	-0.040	11.453	0.010	0.010	0.000	0.000	0.000	0.000
38	C	38	MET	0	-0.012	-0.013	9.663	0.096	0.096	0.000	0.000	0.000	0.000
39	C	39	ALA	0	0.041	0.031	13.021	-0.012	-0.012	0.000	0.000	0.000	0.000
40	C	40	GLU	-1	-0.844	-0.942	16.375	0.118	0.118	0.000	0.000	0.000	0.000
41	C	41	CYS	0	-0.049	-0.016	12.917	0.004	0.004	0.000	0.000	0.000	0.000
42	C	42	VAL	0	0.016	0.008	13.639	-0.021	-0.021	0.000	0.000	0.000	0.000
43	C	43	THR	0	-0.007	0.004	15.157	-0.038	-0.038	0.000	0.000	0.000	0.000
44	C	44	LEU	0	0.023	0.018	17.871	-0.024	-0.024	0.000	0.000	0.000	0.000
45	C	45	ILE	0	0.009	0.019	12.910	-0.021	-0.021	0.000	0.000	0.000	0.000
46	C	46	ARG	1	0.921	0.932	16.504	-0.108	-0.108	0.000	0.000	0.000	0.000
47	C	47	LEU	0	-0.006	0.003	19.438	-0.018	-0.018	0.000	0.000	0.000	0.000
48	C	48	SER	0	0.025	0.013	19.933	-0.017	-0.017	0.000	0.000	0.000	0.000
49	C	49	SER	0	-0.013	-0.008	19.532	-0.017	-0.017	0.000	0.000	0.000	0.000
50	C	50	LEU	0	-0.063	-0.044	21.587	-0.011	-0.011	0.000	0.000	0.000	0.000
51	C	51	MET	0	-0.072	-0.030	24.689	-0.004	-0.004	0.000	0.000	0.000	0.000
52	C	52	ASN	0	-0.054	-0.023	23.620	-0.006	-0.006	0.000	0.000	0.000	0.000
53	C	53	GLN	0	-0.049	0.005	23.605	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)