FMO DATABASE

FMODB ID: ZYQ8N

Calculation Name: 5D60-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D60

Chain ID: A

ChEMBL ID:

UniProt ID: G0SB31

Base Structure: X-ray

Registration Date: 2023-06-20

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-217937.644615
FMO2-HF: Nuclear repulsion	195580.220788
FMO2-HF: Total energy	-22357.423827
FMO2-MP2: Total energy	-22420.650921

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:160:SER)

Summations of interaction energy for fragment #1(A:160: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.
-16.969	-10.43	4.74	-4.402	-6.877	0.022

Interaction energy analysis for fragmet #1(A:160:SER)

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 : 0.007

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	162	GLN	0	0.072	0.035	2.631	-5.043	-2.068	1.255	-1.628	-2.602	0.012
4	A	163	GLN	0	-0.016	-0.009	2.330	-10.777	-7.909	3.473	-2.602	-3.740	0.010
5	A	164	ILE	0	0.029	0.009	3.673	-0.961	-0.265	0.012	-0.172	-0.535	0.000
6	A	165	ALA	0	0.025	0.022	6.068	-0.054	-0.054	0.000	0.000	0.000	0.000
7	A	166	ALA	0	0.020	0.010	7.153	-0.194	-0.194	0.000	0.000	0.000	0.000
8	A	167	LEU	0	0.005	-0.005	7.039	-0.097	-0.097	0.000	0.000	0.000	0.000
9	A	168	SER	0	-0.036	-0.015	9.793	0.031	0.031	0.000	0.000	0.000	0.000
10	A	169	GLU	-1	-0.888	-0.945	11.673	0.148	0.148	0.000	0.000	0.000	0.000
11	A	170	SER	0	-0.026	-0.007	12.543	-0.037	-0.037	0.000	0.000	0.000	0.000
12	A	171	LEU	0	-0.020	-0.013	13.006	0.001	0.001	0.000	0.000	0.000	0.000
13	A	172	GLN	0	-0.036	-0.014	15.849	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	173	ALA	0	0.056	0.032	17.432	0.001	0.001	0.000	0.000	0.000	0.000
15	A	174	THR	0	-0.021	-0.011	17.657	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	175	GLN	0	-0.009	-0.011	20.032	0.016	0.016	0.000	0.000	0.000	0.000
17	A	176	GLN	0	-0.026	-0.009	21.788	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	177	GLN	0	0.004	-0.011	21.390	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	178	LEU	0	0.005	0.002	23.281	0.000	0.000	0.000	0.000	0.000	0.000
20	A	179	GLN	0	0.019	0.021	26.147	0.002	0.002	0.000	0.000	0.000	0.000
21	A	180	ALA	0	-0.012	0.001	27.598	0.003	0.003	0.000	0.000	0.000	0.000
22	A	181	LEU	0	0.013	0.008	27.055	0.001	0.001	0.000	0.000	0.000	0.000
23	A	182	GLN	0	-0.019	-0.014	28.763	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	183	GLN	0	0.006	0.004	32.152	0.002	0.002	0.000	0.000	0.000	0.000
25	A	184	GLN	0	0.017	0.005	31.603	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	185	CYS	0	-0.023	-0.019	33.569	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	186	TYR	0	-0.013	-0.003	35.150	0.002	0.002	0.000	0.000	0.000	0.000
28	A	187	GLU	-1	-0.889	-0.934	37.807	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	188	LEU	0	-0.012	-0.005	37.305	0.000	0.000	0.000	0.000	0.000	0.000
30	A	189	GLU	-1	-0.843	-0.889	40.520	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	190	LYS	1	0.922	0.954	41.606	0.012	0.012	0.000	0.000	0.000	0.000
32	A	191	THR	0	-0.029	-0.022	43.483	0.001	0.001	0.000	0.000	0.000	0.000
33	A	192	ASN	0	0.016	0.003	43.046	0.000	0.000	0.000	0.000	0.000	0.000
34	A	193	ARG	1	0.799	0.875	44.449	0.014	0.014	0.000	0.000	0.000	0.000
35	A	194	LEU	0	0.001	0.006	48.508	0.001	0.001	0.000	0.000	0.000	0.000
36	A	195	LEU	0	0.032	0.018	47.797	0.000	0.000	0.000	0.000	0.000	0.000
37	A	196	VAL	0	-0.022	-0.009	50.096	0.000	0.000	0.000	0.000	0.000	0.000
38	A	197	SER	0	-0.022	-0.008	52.556	0.001	0.001	0.000	0.000	0.000	0.000
39	A	198	GLU	-1	-0.864	-0.935	53.948	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	199	VAL	0	-0.005	-0.005	54.255	0.000	0.000	0.000	0.000	0.000	0.000
41	A	200	MET	0	-0.061	-0.036	55.267	0.001	0.001	0.000	0.000	0.000	0.000
42	A	201	THR	0	0.008	0.007	58.702	0.001	0.001	0.000	0.000	0.000	0.000
43	A	202	LEU	0	0.020	0.002	58.052	0.000	0.000	0.000	0.000	0.000	0.000
44	A	203	GLN	0	0.001	0.003	58.306	0.001	0.001	0.000	0.000	0.000	0.000
45	A	204	LYS	1	0.930	0.961	61.956	0.010	0.010	0.000	0.000	0.000	0.000
46	A	205	MET	0	-0.006	0.005	64.054	0.000	0.000	0.000	0.000	0.000	0.000
47	A	206	VAL	0	0.032	0.023	64.326	0.000	0.000	0.000	0.000	0.000	0.000
48	A	207	LYS	1	0.932	0.953	65.637	0.013	0.013	0.000	0.000	0.000	0.000
49	A	208	ALA	0	0.029	0.020	68.849	0.000	0.000	0.000	0.000	0.000	0.000
50	A	209	GLN	0	0.010	0.009	68.336	0.000	0.000	0.000	0.000	0.000	0.000
51	A	210	ASN	0	-0.014	-0.002	70.871	0.000	0.000	0.000	0.000	0.000	0.000
52	A	211	GLN	0	-0.009	-0.009	72.816	0.000	0.000	0.000	0.000	0.000	0.000
53	A	212	ALA	0	-0.017	-0.001	74.722	0.000	0.000	0.000	0.000	0.000	0.000
54	A	213	SER	0	-0.071	-0.036	74.362	0.000	0.000	0.000	0.000	0.000	0.000
55	A	214	ASN	0	-0.083	-0.028	76.166	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:160:SER)