FMO DATABASE

FMODB ID: 43RQN

Calculation Name: 3RD4-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD4

Chain ID: A

ChEMBL ID:

UniProt ID: C0AZM8

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-508354.811994
FMO2-HF: Nuclear repulsion	476451.578727
FMO2-HF: Total energy	-31903.233268
FMO2-MP2: Total energy	-31995.887192

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:1:ACE )

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

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.
2.025	2.729	-0.006	-0.346	-0.352	0

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.003

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].
3	A	3	PRO	0	-0.013	-0.001	3.846	1.132	1.836	-0.006	-0.346	-0.352
4	A	4	VAL	0	0.027	0.001	7.148	-0.055	-0.055	0.000	0.000	0.000
5	A	5	LYS	1	0.907	0.956	9.775	0.811	0.811	0.000	0.000	0.000
6	A	6	LEU	0	0.019	0.013	12.597	0.040	0.040	0.000	0.000	0.000
7	A	7	TYR	0	-0.038	-0.019	12.682	-0.023	-0.023	0.000	0.000	0.000
8	A	8	MET	0	0.029	0.024	18.607	0.016	0.016	0.000	0.000	0.000
9	A	9	VAL	0	0.003	-0.012	21.251	-0.003	-0.003	0.000	0.000	0.000
10	A	10	GLU	-1	-0.870	-0.938	23.663	-0.074	-0.074	0.000	0.000	0.000
11	A	11	VAL	0	-0.036	-0.004	25.070	-0.008	-0.008	0.000	0.000	0.000
12	A	12	ILE	0	-0.018	0.006	26.673	0.007	0.007	0.000	0.000	0.000
13	A	13	ASP	-1	-0.834	-0.943	27.095	-0.056	-0.056	0.000	0.000	0.000
14	A	14	LYS	1	0.856	0.922	26.843	0.036	0.036	0.000	0.000	0.000
15	A	15	LYS	1	0.868	0.954	27.013	0.060	0.060	0.000	0.000	0.000
16	A	16	GLU	-1	-0.860	-0.932	26.896	-0.019	-0.019	0.000	0.000	0.000
17	A	17	ILE	0	-0.070	-0.025	24.619	0.000	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.020	0.006	27.007	0.002	0.002	0.000	0.000	0.000
19	A	19	ALA	0	0.000	-0.002	25.958	0.001	0.001	0.000	0.000	0.000
20	A	20	ASN	0	0.094	0.039	27.829	0.007	0.007	0.000	0.000	0.000
21	A	21	NME	0	-0.030	-0.009	28.633	0.001	0.001	0.000	0.000	0.000
22	A	32	ACE	0	-0.045	-0.037	34.950	0.000	0.000	0.000	0.000	0.000
23	A	33	GLU	-1	-0.882	-0.931	30.965	0.004	0.004	0.000	0.000	0.000
24	A	34	ILE	0	-0.111	-0.054	26.103	0.005	0.005	0.000	0.000	0.000
25	A	35	THR	0	-0.043	-0.020	22.641	0.006	0.006	0.000	0.000	0.000
26	A	36	HIS	0	-0.006	0.005	25.137	-0.002	-0.002	0.000	0.000	0.000
27	A	37	TYR	0	-0.038	-0.024	19.492	0.001	0.001	0.000	0.000	0.000
28	A	38	TYR	0	0.006	0.004	22.612	0.002	0.002	0.000	0.000	0.000
29	A	39	GLN	0	0.039	0.016	22.061	-0.004	-0.004	0.000	0.000	0.000
30	A	40	VAL	0	0.025	0.012	21.644	0.007	0.007	0.000	0.000	0.000
31	A	41	THR	0	-0.039	-0.013	22.150	-0.013	-0.013	0.000	0.000	0.000
32	A	42	PHE	0	0.032	0.020	20.232	0.005	0.005	0.000	0.000	0.000
33	A	43	ARG	1	0.916	0.958	22.213	0.083	0.083	0.000	0.000	0.000
34	A	44	LEU	0	-0.067	-0.049	19.472	-0.004	-0.004	0.000	0.000	0.000
35	A	45	THR	0	-0.011	-0.007	23.396	0.014	0.014	0.000	0.000	0.000
36	A	46	THR	0	-0.126	-0.121	23.419	0.006	0.006	0.000	0.000	0.000
37	A	47	ASP	-1	-0.915	-0.956	25.950	-0.145	-0.145	0.000	0.000	0.000
38	A	48	ASP	-1	-0.854	-0.860	21.477	-0.198	-0.198	0.000	0.000	0.000
39	A	49	ARG	1	0.941	0.954	24.157	0.110	0.110	0.000	0.000	0.000
40	A	50	LYS	1	0.940	0.987	16.693	0.301	0.301	0.000	0.000	0.000
41	A	51	ASP	-1	-0.794	-0.884	22.807	-0.118	-0.118	0.000	0.000	0.000
42	A	52	LEU	0	-0.066	-0.049	16.767	-0.020	-0.020	0.000	0.000	0.000
43	A	53	VAL	0	0.010	0.013	19.854	0.013	0.013	0.000	0.000	0.000
44	A	54	LEU	0	-0.034	-0.017	15.393	-0.012	-0.012	0.000	0.000	0.000
45	A	55	ASN	0	-0.005	0.003	16.903	0.022	0.022	0.000	0.000	0.000
46	A	56	ILE	0	-0.028	-0.019	17.146	-0.009	-0.009	0.000	0.000	0.000
47	A	57	ASP	-1	-0.812	-0.906	19.191	-0.020	-0.020	0.000	0.000	0.000
48	A	58	LYS	1	0.958	0.979	20.808	-0.001	-0.001	0.000	0.000	0.000
49	A	59	SER	0	-0.023	-0.027	23.550	-0.005	-0.005	0.000	0.000	0.000
50	A	60	SER	0	0.038	0.006	20.724	-0.004	-0.004	0.000	0.000	0.000
51	A	61	TYR	0	-0.024	-0.013	23.388	-0.006	-0.006	0.000	0.000	0.000
52	A	62	GLN	0	-0.044	-0.036	25.151	0.002	0.002	0.000	0.000	0.000
53	A	63	ASN	0	-0.035	0.004	26.304	0.002	0.002	0.000	0.000	0.000
54	A	64	ILE	0	-0.036	-0.008	22.710	-0.005	-0.005	0.000	0.000	0.000
55	A	65	GLU	-1	-0.901	-0.998	27.351	-0.035	-0.035	0.000	0.000	0.000
56	A	66	PRO	0	-0.029	-0.031	29.747	-0.006	-0.006	0.000	0.000	0.000
57	A	67	GLU	-1	-0.915	-0.963	30.367	-0.049	-0.049	0.000	0.000	0.000
58	A	68	MET	0	-0.032	0.038	27.182	0.000	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.923	0.964	27.323	0.065	0.065	0.000	0.000	0.000
60	A	70	GLY	0	0.058	0.031	25.150	0.007	0.007	0.000	0.000	0.000
61	A	71	ARG	1	0.817	0.927	20.536	0.093	0.093	0.000	0.000	0.000
62	A	72	LEU	0	0.006	0.010	16.935	0.009	0.009	0.000	0.000	0.000
63	A	73	PHE	0	0.011	-0.004	14.552	-0.041	-0.041	0.000	0.000	0.000
64	A	74	MET	0	0.028	0.027	12.043	0.028	0.028	0.000	0.000	0.000
65	A	75	GLN	0	0.043	0.038	5.034	0.090	0.090	0.000	0.000	0.000
66	A	76	GLY	0	-0.035	-0.027	7.650	-0.078	-0.078	0.000	0.000	0.000
67	A	77	SER	0	0.011	-0.007	8.527	0.108	0.108	0.000	0.000	0.000
68	A	78	ARG	1	0.896	0.951	8.602	0.171	0.171	0.000	0.000	0.000
69	A	79	PHE	0	0.040	0.027	11.372	-0.054	-0.054	0.000	0.000	0.000
70	A	80	VAL	0	-0.097	-0.052	11.279	0.034	0.034	0.000	0.000	0.000
71	A	81	GLN	0	0.092	0.047	14.186	0.030	0.030	0.000	0.000	0.000
72	A	82	PHE	0	-0.021	-0.026	17.731	-0.027	-0.027	0.000	0.000	0.000
73	A	83	GLU	-1	-0.925	-0.962	20.859	-0.080	-0.080	0.000	0.000	0.000
74	A	84	THR	0	0.016	0.002	23.501	-0.008	-0.008	0.000	0.000	0.000
75	A	85	ASP	-1	-0.867	-0.934	26.767	-0.087	-0.087	0.000	0.000	0.000
76	A	86	VAL	0	-0.048	-0.028	29.361	0.003	0.003	0.000	0.000	0.000
77	A	87	PRO	0	-0.014	-0.014	32.135	-0.001	-0.001	0.000	0.000	0.000
78	A	88	ILE	0	-0.037	-0.019	34.364	0.004	0.004	0.000	0.000	0.000
79	A	89	ASP	-1	-0.895	-0.933	35.080	-0.043	-0.043	0.000	0.000	0.000
80	A	90	NME	0	-0.046	-0.018	38.322	0.000	0.000	0.000	0.000	0.000

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