FMO DATABASE

FMODB ID: R5LM8

Calculation Name: 3DSP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DSP

Chain ID: A

ChEMBL ID:

UniProt ID: Q58AD3

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptAll
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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-379699.089316
FMO2-HF: Nuclear repulsion	352062.451766
FMO2-HF: Total energy	-27636.63755
FMO2-MP2: Total energy	-27711.969391

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:VAL)

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

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.
-13.74	-4.559	8.626	-5.069	-12.734	-0.036

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.021

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	MET	0	-0.007	-0.028	2.351	-2.419	0.167	2.959	-1.582	-3.963	-0.005
4	A	4	SER	0	-0.040	-0.023	3.456	0.559	0.750	0.033	0.079	-0.302	0.000
5	A	5	ASN	0	-0.040	-0.020	5.661	0.382	0.382	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.080	-0.030	2.911	-0.521	0.197	0.340	-0.190	-0.867	0.000
7	A	7	VAL	0	0.009	0.015	5.934	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.917	0.962	8.044	0.314	0.314	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.023	0.010	5.131	-0.175	-0.114	-0.001	0.000	-0.059	0.000
10	A	10	TYR	0	0.038	0.030	7.038	0.076	0.076	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.745	-0.857	8.154	-0.894	-0.894	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.000	0.005	10.045	0.082	0.082	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.013	-0.006	12.774	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.878	-0.903	13.714	-0.201	-0.201	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.005	-0.011	13.084	0.035	0.035	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.102	-0.071	9.554	-0.096	-0.096	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.855	0.915	5.092	1.085	1.085	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.031	0.016	6.791	0.035	0.035	0.000	0.000	0.000	0.000
19	A	19	HIS	1	0.786	0.863	2.690	-0.421	0.932	2.854	-0.879	-3.327	-0.002
20	A	20	VAL	0	0.063	0.025	5.011	0.150	0.215	-0.001	-0.002	-0.062	0.000
21	A	21	PHE	0	0.014	0.004	2.424	-0.708	-0.376	1.482	-0.384	-1.430	-0.002
22	A	22	LYS	1	0.965	0.974	7.531	0.195	0.195	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.876	-0.944	9.944	0.042	0.042	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.020	0.023	11.264	0.027	0.027	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.879	0.942	8.438	-0.096	-0.096	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.003	-0.008	6.937	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.003	0.013	4.921	0.166	0.166	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.038	-0.007	5.603	-0.202	-0.202	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.811	-0.889	2.488	-10.952	-7.154	0.961	-2.110	-2.649	-0.027
30	A	30	ASN	0	0.082	0.020	6.254	-0.111	-0.111	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.900	0.947	7.863	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.007	0.010	9.247	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.027	0.041	4.870	0.232	0.232	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.849	0.904	5.065	-0.053	0.024	-0.001	-0.001	-0.075	0.000
35	A	35	SER	0	0.034	0.023	6.061	-0.244	-0.244	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.038	-0.022	7.103	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.031	0.010	9.448	0.038	0.038	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.003	0.003	8.311	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.024	-0.009	11.750	0.013	0.013	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.765	-0.870	15.447	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.001	-0.003	17.167	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.880	0.955	15.480	0.102	0.102	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.026	0.010	17.635	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.066	-0.040	12.638	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.785	-0.863	16.810	-0.141	-0.141	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.066	-0.080	13.723	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.834	0.897	11.396	0.453	0.453	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.865	-0.902	15.209	-0.262	-0.262	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.015	0.015	17.285	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.023	0.027	16.977	0.021	0.021	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.869	0.905	18.040	0.104	0.104	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.001	0.001	12.562	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.004	-0.003	16.883	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.031	0.011	12.655	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.864	0.904	15.482	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.038	0.013	17.896	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.060	-0.032	12.923	0.026	0.026	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.892	-0.932	14.897	-0.052	-0.052	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.066	-0.055	11.414	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.036	0.036	14.980	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.772	0.832	16.527	0.146	0.146	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.023	-0.008	19.213	0.011	0.011	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.828	-0.907	22.041	-0.092	-0.092	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.795	-0.863	21.513	-0.138	-0.138	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.059	-0.017	25.538	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.119	-0.067	27.313	0.007	0.007	0.000	0.000	0.000	0.000

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