FMO DATABASE

FMODB ID: V2141

Calculation Name: 3D3R-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3R

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EF93

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-458869.451662
FMO2-HF: Nuclear repulsion	425401.190723
FMO2-HF: Total energy	-33468.26094
FMO2-MP2: Total energy	-33564.133207

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:-7:ACE )

Summations of interaction energy for fragment #1(A:-7: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.
1.214	2.511	0.128	-0.498	-0.927	0

Interaction energy analysis for fragmet #1(A:-7: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 : -0.024

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	-5	ASN	0	0.025	0.008	3.840	0.955	1.752	-0.005	-0.330	-0.462
4	A	-4	LEU	0	-0.016	0.008	2.855	0.119	0.507	0.133	-0.152	-0.369
5	A	-3	TYR	0	-0.057	-0.014	4.469	0.145	0.257	0.000	-0.016	-0.096
6	A	-2	PHE	0	0.014	0.014	7.799	-0.043	-0.043	0.000	0.000	0.000
7	A	-1	GLN	0	0.081	0.021	11.350	0.004	0.004	0.000	0.000	0.000
8	A	0	GLY	0	0.009	0.006	10.378	-0.027	-0.027	0.000	0.000	0.000
9	A	1	MET	0	-0.058	-0.034	10.802	-0.009	-0.009	0.000	0.000	0.000
10	A	2	CYS	0	-0.029	-0.011	11.783	0.094	0.094	0.000	0.000	0.000
11	A	3	LEU	0	0.038	0.019	7.725	-0.079	-0.079	0.000	0.000	0.000
12	A	4	SER	0	0.016	0.004	9.386	0.040	0.040	0.000	0.000	0.000
13	A	5	ILE	0	-0.042	-0.012	11.016	0.069	0.069	0.000	0.000	0.000
14	A	6	PRO	0	-0.014	-0.008	12.032	-0.022	-0.022	0.000	0.000	0.000
15	A	7	SER	0	-0.012	0.020	14.123	-0.012	-0.012	0.000	0.000	0.000
16	A	8	GLN	0	0.008	0.015	17.342	0.009	0.009	0.000	0.000	0.000
17	A	9	VAL	0	0.046	0.028	19.425	-0.017	-0.017	0.000	0.000	0.000
18	A	10	VAL	0	-0.058	-0.047	21.912	0.008	0.008	0.000	0.000	0.000
19	A	11	ALA	0	0.003	-0.005	25.408	0.001	0.001	0.000	0.000	0.000
20	A	12	VAL	0	0.006	0.008	24.235	-0.005	-0.005	0.000	0.000	0.000
21	A	13	ASP	-1	-0.878	-0.936	26.783	-0.022	-0.022	0.000	0.000	0.000
22	A	14	ASN	0	0.032	-0.010	26.005	-0.010	-0.010	0.000	0.000	0.000
23	A	15	GLU	-1	-0.970	-0.971	28.519	-0.024	-0.024	0.000	0.000	0.000
24	A	16	ARG	1	0.872	0.933	30.945	0.027	0.027	0.000	0.000	0.000
25	A	17	GLN	0	-0.032	0.004	25.959	-0.009	-0.009	0.000	0.000	0.000
26	A	18	SER	0	-0.016	0.003	25.250	-0.008	-0.008	0.000	0.000	0.000
27	A	19	VAL	0	0.028	0.012	21.007	0.007	0.007	0.000	0.000	0.000
28	A	20	THR	0	-0.028	-0.045	24.346	-0.007	-0.007	0.000	0.000	0.000
29	A	21	VAL	0	-0.013	-0.002	19.231	0.009	0.009	0.000	0.000	0.000
30	A	22	ASP	-1	-0.863	-0.937	21.665	0.008	0.008	0.000	0.000	0.000
31	A	23	THR	0	-0.019	-0.048	17.611	0.005	0.005	0.000	0.000	0.000
32	A	24	LEU	0	-0.037	-0.028	18.421	-0.005	-0.005	0.000	0.000	0.000
33	A	25	GLY	0	0.021	0.018	21.516	-0.003	-0.003	0.000	0.000	0.000
34	A	26	VAL	0	-0.065	-0.024	23.409	-0.005	-0.005	0.000	0.000	0.000
35	A	27	ARG	1	0.900	0.951	23.440	-0.005	-0.005	0.000	0.000	0.000
36	A	28	ARG	1	0.934	0.963	21.345	0.052	0.052	0.000	0.000	0.000
37	A	29	ASP	-1	-0.805	-0.847	24.140	-0.030	-0.030	0.000	0.000	0.000
38	A	30	VAL	0	-0.071	-0.053	20.447	-0.009	-0.009	0.000	0.000	0.000
39	A	31	SER	0	0.033	0.019	23.693	0.009	0.009	0.000	0.000	0.000
40	A	32	SER	0	0.041	-0.001	21.294	-0.009	-0.009	0.000	0.000	0.000
41	A	33	HIS	0	-0.041	-0.031	21.459	0.002	0.002	0.000	0.000	0.000
42	A	34	LEU	0	-0.032	-0.006	17.042	-0.004	-0.004	0.000	0.000	0.000
43	A	35	MET	0	-0.029	0.006	16.440	-0.016	-0.016	0.000	0.000	0.000
44	A	36	THR	0	-0.001	-0.013	12.547	0.000	0.000	0.000	0.000	0.000
45	A	37	GLU	-1	-0.970	-0.975	15.073	0.068	0.068	0.000	0.000	0.000
46	A	38	PRO	0	-0.064	-0.038	18.106	-0.004	-0.004	0.000	0.000	0.000
47	A	39	LEU	0	0.043	0.033	17.193	0.008	0.008	0.000	0.000	0.000
48	A	40	ALA	0	-0.032	-0.024	21.243	-0.006	-0.006	0.000	0.000	0.000
49	A	41	ILE	0	-0.042	-0.039	22.639	0.004	0.004	0.000	0.000	0.000
50	A	42	GLY	0	-0.032	-0.012	23.275	0.005	0.005	0.000	0.000	0.000
51	A	43	ASP	-1	-0.826	-0.886	18.454	0.068	0.068	0.000	0.000	0.000
52	A	44	TYR	0	-0.049	-0.037	15.568	-0.011	-0.011	0.000	0.000	0.000
53	A	45	VAL	0	0.006	0.006	14.012	0.015	0.015	0.000	0.000	0.000
54	A	46	LEU	0	-0.035	-0.028	7.811	0.029	0.029	0.000	0.000	0.000
55	A	47	ILE	0	0.018	0.005	11.718	-0.026	-0.026	0.000	0.000	0.000
56	A	48	HIS	0	0.020	0.008	9.903	-0.008	-0.008	0.000	0.000	0.000
57	A	49	ILE	0	-0.043	0.000	12.571	0.050	0.050	0.000	0.000	0.000
58	A	50	GLY	0	0.029	0.002	13.955	-0.081	-0.081	0.000	0.000	0.000
59	A	51	PHE	0	-0.063	-0.029	15.207	0.051	0.051	0.000	0.000	0.000
60	A	52	VAL	0	0.057	0.033	16.329	-0.026	-0.026	0.000	0.000	0.000
61	A	53	MET	0	-0.033	-0.024	18.315	0.010	0.010	0.000	0.000	0.000
62	A	54	ASN	0	0.037	0.030	21.559	0.008	0.008	0.000	0.000	0.000
63	A	55	LYS	1	0.928	0.960	24.924	0.077	0.077	0.000	0.000	0.000
64	A	56	ILE	0	0.054	0.023	27.791	0.004	0.004	0.000	0.000	0.000
65	A	57	ASP	-1	-0.889	-0.945	31.037	-0.061	-0.061	0.000	0.000	0.000
66	A	58	ARG	1	0.984	0.982	34.251	0.065	0.065	0.000	0.000	0.000
67	A	59	ASN	0	-0.022	-0.020	35.132	-0.002	-0.002	0.000	0.000	0.000
68	A	60	ASP	-1	-0.835	-0.903	36.019	-0.059	-0.059	0.000	0.000	0.000
69	A	61	ALA	0	-0.045	-0.030	33.135	-0.002	-0.002	0.000	0.000	0.000
70	A	62	LEU	0	-0.057	-0.046	34.857	-0.001	-0.001	0.000	0.000	0.000
71	A	63	GLN	0	0.004	0.012	37.524	0.001	0.001	0.000	0.000	0.000
72	A	64	SER	0	-0.032	-0.004	35.598	-0.001	-0.001	0.000	0.000	0.000
73	A	65	LEU	0	0.000	-0.018	32.480	-0.002	-0.002	0.000	0.000	0.000
74	A	66	GLU	-1	-0.928	-0.957	36.495	-0.058	-0.058	0.000	0.000	0.000
75	A	67	LEU	0	0.033	0.020	38.777	0.000	0.000	0.000	0.000	0.000
76	A	68	TYR	0	-0.039	-0.025	31.765	-0.003	-0.003	0.000	0.000	0.000
77	A	69	GLN	0	0.018	-0.003	36.049	-0.004	-0.004	0.000	0.000	0.000
78	A	70	GLU	-1	-0.914	-0.944	37.410	-0.055	-0.055	0.000	0.000	0.000
79	A	71	ILE	0	-0.041	-0.017	35.816	0.002	0.002	0.000	0.000	0.000
80	A	72	VAL	0	-0.017	-0.012	33.632	0.000	0.000	0.000	0.000	0.000
81	A	73	SER	0	-0.028	-0.020	36.378	0.001	0.001	0.000	0.000	0.000
82	A	74	LYS	1	0.860	0.938	39.819	0.057	0.057	0.000	0.000	0.000
83	A	75	LEU	0	-0.080	-0.062	36.553	0.003	0.003	0.000	0.000	0.000
84	A	76	GLU	-1	-0.963	-0.941	35.706	-0.087	-0.087	0.000	0.000	0.000
85	A	77	NME	0	-0.025	-0.008	37.442	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:ACE )