FMO DATABASE

FMODB ID: R8818

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

Total energy (hartree)

FMO2-HF: Electronic energy	-258552.305083
FMO2-HF: Nuclear repulsion	236780.836677
FMO2-HF: Total energy	-21771.468405
FMO2-MP2: Total energy	-21830.378618

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.
-5.277	-2.04	5.777	-3.06	-5.955	0.011

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 : 0.057 / 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	C	3	VAL	0	0.089	0.027	3.587	-0.381	0.898	0.004	-0.642	-0.641	0.002
4	C	4	GLN	0	-0.007	-0.012	6.166	0.239	0.239	0.000	0.000	0.000	0.000
5	C	5	LEU	0	0.021	0.023	1.914	-0.457	-1.272	5.244	-1.400	-3.031	0.002
6	C	6	LYS	1	0.937	0.965	3.440	-3.059	-1.751	0.113	-0.461	-0.961	0.002
7	C	7	LYS	1	0.953	0.969	4.592	-1.078	-0.987	-0.001	-0.016	-0.074	0.000
8	C	8	GLN	0	0.028	0.026	6.632	-0.123	-0.123	0.000	0.000	0.000	0.000
9	C	9	LEU	0	0.012	0.008	4.120	-0.308	-0.103	0.001	-0.029	-0.176	0.000
10	C	10	ALA	0	0.017	0.015	7.763	-0.123	-0.123	0.000	0.000	0.000	0.000
11	C	11	GLU	-1	-0.943	-0.964	10.330	0.061	0.061	0.000	0.000	0.000	0.000
12	C	12	LEU	0	-0.004	-0.011	9.779	-0.058	-0.058	0.000	0.000	0.000	0.000
13	C	13	ALA	0	0.003	-0.001	11.710	-0.048	-0.048	0.000	0.000	0.000	0.000
14	C	14	LEU	0	-0.014	-0.007	13.396	-0.032	-0.032	0.000	0.000	0.000	0.000
15	C	15	ALA	0	0.007	0.013	15.425	-0.023	-0.023	0.000	0.000	0.000	0.000
16	C	16	GLY	0	0.024	0.010	15.944	-0.019	-0.019	0.000	0.000	0.000	0.000
17	C	17	THR	0	-0.080	-0.034	17.379	-0.011	-0.011	0.000	0.000	0.000	0.000
18	C	18	GLY	0	0.013	0.014	19.692	-0.004	-0.004	0.000	0.000	0.000	0.000
19	C	19	HIS	0	-0.090	-0.053	20.223	-0.010	-0.010	0.000	0.000	0.000	0.000
20	C	20	HIS	0	0.023	0.014	22.184	-0.014	-0.014	0.000	0.000	0.000	0.000
21	C	21	CYS	0	-0.022	0.006	17.353	-0.020	-0.020	0.000	0.000	0.000	0.000
22	C	22	HIS	0	0.023	-0.014	17.653	-0.003	-0.003	0.000	0.000	0.000	0.000
23	C	23	GLN	0	0.016	0.027	17.815	0.035	0.035	0.000	0.000	0.000	0.000
24	C	24	GLU	-1	-0.881	-0.956	14.076	-0.166	-0.166	0.000	0.000	0.000	0.000
25	C	25	ALA	0	0.009	-0.001	13.255	0.022	0.022	0.000	0.000	0.000	0.000
26	C	26	ALA	0	-0.012	0.002	13.925	0.063	0.063	0.000	0.000	0.000	0.000
27	C	27	SER	0	-0.003	0.004	12.115	0.009	0.009	0.000	0.000	0.000	0.000
28	C	28	ILE	0	-0.058	-0.024	8.665	0.047	0.047	0.000	0.000	0.000	0.000
29	C	29	ALA	0	-0.012	-0.021	10.228	0.174	0.174	0.000	0.000	0.000	0.000
30	C	30	ASP	-1	-0.837	-0.916	12.811	0.137	0.137	0.000	0.000	0.000	0.000
31	C	31	TRP	0	-0.031	-0.006	2.952	-0.985	0.184	0.416	-0.512	-1.072	0.005
32	C	32	LEU	0	-0.028	-0.029	6.978	0.195	0.195	0.000	0.000	0.000	0.000
33	C	33	ALA	0	-0.003	0.008	9.653	-0.036	-0.036	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.084	-0.039	9.467	-0.050	-0.050	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.983	-0.998	8.331	0.721	0.721	0.000	0.000	0.000	0.000
36	C	36	GLU	-1	-0.895	-0.953	11.338	0.166	0.166	0.000	0.000	0.000	0.000
37	C	37	CYS	0	-0.089	-0.029	11.453	0.004	0.004	0.000	0.000	0.000	0.000
38	C	38	MET	0	-0.020	-0.024	9.609	0.108	0.108	0.000	0.000	0.000	0.000
39	C	39	ALA	0	0.058	0.040	13.021	-0.016	-0.016	0.000	0.000	0.000	0.000
40	C	40	GLU	-1	-0.854	-0.936	16.375	0.156	0.156	0.000	0.000	0.000	0.000
41	C	41	CYS	0	-0.061	-0.023	12.730	0.006	0.006	0.000	0.000	0.000	0.000
42	C	42	VAL	0	0.043	0.018	13.839	-0.026	-0.026	0.000	0.000	0.000	0.000
43	C	43	THR	0	-0.026	-0.011	15.157	-0.053	-0.053	0.000	0.000	0.000	0.000
44	C	44	LEU	0	0.010	0.014	17.807	-0.028	-0.028	0.000	0.000	0.000	0.000
45	C	45	ILE	0	0.009	0.024	12.818	-0.025	-0.025	0.000	0.000	0.000	0.000
46	C	46	ARG	1	0.909	0.925	16.584	-0.165	-0.165	0.000	0.000	0.000	0.000
47	C	47	LEU	0	-0.008	0.003	19.474	-0.022	-0.022	0.000	0.000	0.000	0.000
48	C	48	SER	0	0.006	-0.025	19.897	-0.016	-0.016	0.000	0.000	0.000	0.000
49	C	49	SER	0	-0.036	-0.026	19.546	-0.021	-0.021	0.000	0.000	0.000	0.000
50	C	50	LEU	0	-0.065	-0.047	21.616	-0.013	-0.013	0.000	0.000	0.000	0.000
51	C	51	MET	0	-0.077	-0.030	24.721	-0.005	-0.005	0.000	0.000	0.000	0.000
52	C	52	ASN	0	-0.030	-0.005	23.398	-0.010	-0.010	0.000	0.000	0.000	0.000
53	C	53	GLN	0	-0.060	0.000	23.700	-0.012	-0.012	0.000	0.000	0.000	0.000

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