FMO DATABASE

FMODB ID: 6647Z

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	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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-379858.548979
FMO2-HF: Nuclear repulsion	352222.75572
FMO2-HF: Total energy	-27635.793259
FMO2-MP2: Total energy	-27711.112072

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.
-15.323	-9.557	15.324	-6.551	-14.537	-0.051

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 : -0.053 / q_NPA : -0.033

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	-0.017	-0.038	2.357	-1.116	-0.491	6.436	-2.234	-4.827	-0.012
4	A	4	SER	0	-0.035	-0.036	3.649	0.478	0.732	0.018	-0.007	-0.265	0.000
5	A	5	ASN	0	0.014	-0.001	5.748	0.184	0.184	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.085	-0.028	2.971	-0.524	0.189	0.296	-0.198	-0.811	0.000
7	A	7	VAL	0	-0.001	0.007	5.866	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.916	0.960	7.791	0.146	0.146	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.036	0.010	5.327	0.028	0.028	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.013	0.002	7.220	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.800	-0.890	8.768	-0.754	-0.754	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.021	0.016	10.356	0.074	0.074	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.027	0.001	12.828	-0.057	-0.057	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.918	-0.913	13.491	-0.173	-0.173	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.019	-0.027	12.672	0.017	0.017	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.101	-0.063	9.302	-0.133	-0.133	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.825	0.891	5.360	0.965	0.965	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.041	0.023	6.544	0.052	0.052	0.000	0.000	0.000	0.000
19	A	19	HIS	1	0.799	0.894	2.916	-1.343	0.723	1.741	-0.764	-3.043	-0.002
20	A	20	VAL	0	0.057	0.033	4.884	0.142	0.221	-0.001	-0.003	-0.075	0.000
21	A	21	PHE	0	0.006	-0.008	2.179	-0.006	-0.853	3.448	-0.583	-2.017	-0.001
22	A	22	LYS	1	1.016	1.002	7.216	0.033	0.033	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.930	-0.969	9.950	0.269	0.269	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.010	0.003	10.872	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.906	0.974	8.025	-0.336	-0.336	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.020	0.017	7.116	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.014	-0.010	4.394	0.127	0.187	-0.001	-0.007	-0.051	0.000
28	A	28	MET	0	-0.029	0.008	5.365	-0.299	-0.266	-0.001	-0.002	-0.030	0.000
29	A	29	GLU	-1	-0.821	-0.912	2.123	-12.731	-10.111	3.390	-2.746	-3.265	-0.036
30	A	30	ASN	0	0.057	0.010	5.948	-0.122	-0.122	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.971	0.985	7.644	-0.091	-0.091	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.054	-0.030	9.107	-0.063	-0.063	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.039	0.031	4.753	0.118	0.156	-0.001	-0.002	-0.034	0.000
34	A	34	LYS	1	0.892	0.951	4.567	0.040	0.165	-0.001	-0.005	-0.119	0.000
35	A	35	SER	0	0.038	0.016	6.077	-0.336	-0.336	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.029	-0.013	6.826	-0.172	-0.172	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.021	0.010	9.194	0.102	0.102	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.003	-0.003	8.940	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.034	-0.012	12.071	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.854	-0.933	15.651	0.109	0.109	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.070	-0.053	17.626	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.951	0.983	17.295	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.017	0.006	18.010	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.066	-0.037	13.041	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.901	-0.943	17.086	-0.098	-0.098	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.070	-0.072	14.362	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.959	0.945	11.009	0.465	0.465	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.921	-0.931	15.672	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.032	0.029	17.333	0.014	0.014	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.026	0.035	17.119	0.023	0.023	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.942	0.956	18.332	0.052	0.052	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.009	-0.004	12.621	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.018	0.002	17.022	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	MET	0	0.012	0.027	13.178	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.938	0.941	15.919	-0.052	-0.052	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.071	0.052	18.465	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.028	-0.030	12.688	0.017	0.017	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.881	-0.917	14.635	0.054	0.054	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.055	-0.044	11.182	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.002	0.019	15.171	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.941	0.939	16.384	0.096	0.096	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.025	-0.012	19.076	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.879	-0.940	22.358	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.920	-0.974	22.772	-0.083	-0.083	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.060	-0.007	25.577	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.071	-0.024	27.843	0.002	0.002	0.000	0.000	0.000	0.000

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