FMO DATABASE

FMODB ID: ZYZLN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-380819.216869
FMO2-HF: Nuclear repulsion	353182.803071
FMO2-HF: Total energy	-27636.413798
FMO2-MP2: Total energy	-27711.759419

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.
-16.093	-9.12	13.919	-6.262	-14.629	-0.046

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 : -0.050 / q_NPA : -0.035

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	-0.018	-0.035	2.320	-2.191	0.330	3.204	-1.740	-3.984	-0.006
4	A	4	SER	0	-0.040	-0.029	3.571	0.478	0.691	0.023	0.023	-0.259	0.000
5	A	5	ASN	0	-0.010	-0.010	5.990	0.258	0.258	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.074	-0.026	2.830	-0.520	0.173	0.281	-0.180	-0.794	0.000
7	A	7	VAL	0	-0.002	0.006	6.082	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.911	0.956	7.784	0.223	0.223	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.032	0.015	5.233	-0.061	-0.061	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.016	0.018	7.136	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.736	-0.849	8.530	-0.893	-0.893	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.015	0.021	10.411	0.089	0.089	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.024	-0.005	12.886	-0.059	-0.059	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.911	-0.909	13.483	-0.194	-0.194	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.009	-0.018	12.669	0.034	0.034	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.097	-0.066	9.274	-0.127	-0.127	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.872	0.919	5.226	1.144	1.144	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.032	0.018	6.523	0.025	0.025	0.000	0.000	0.000	0.000
19	A	19	HIS	1	0.780	0.863	2.693	-0.426	0.939	3.671	-1.020	-4.016	-0.002
20	A	20	VAL	0	0.053	0.028	4.778	0.179	0.263	-0.001	-0.005	-0.078	0.000
21	A	21	PHE	0	0.016	0.001	2.335	-0.506	-0.504	2.274	-0.501	-1.776	-0.002
22	A	22	LYS	1	1.005	1.001	7.294	0.088	0.088	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.896	-0.953	9.594	0.194	0.194	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.011	0.009	10.930	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.875	0.950	8.042	-0.247	-0.247	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.017	0.012	6.991	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.012	-0.006	4.237	0.123	0.197	-0.001	-0.013	-0.060	0.000
28	A	28	MET	0	-0.031	0.003	5.201	-0.334	-0.294	-0.001	-0.002	-0.036	0.000
29	A	29	GLU	-1	-0.800	-0.876	2.071	-13.057	-11.234	4.471	-2.817	-3.477	-0.036
30	A	30	ASN	0	0.070	0.011	5.897	-0.104	-0.104	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.904	0.944	7.658	-0.056	-0.056	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.001	0.004	9.144	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.051	0.041	4.788	0.180	0.216	-0.001	-0.002	-0.033	0.000
34	A	34	LYS	1	0.812	0.897	4.619	-0.041	0.081	-0.001	-0.005	-0.116	0.000
35	A	35	SER	0	0.060	0.032	6.048	-0.329	-0.329	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.036	-0.013	6.843	-0.152	-0.152	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.019	0.007	8.993	0.084	0.084	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.001	0.001	8.564	-0.074	-0.074	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.018	-0.006	11.867	0.010	0.010	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.792	-0.886	15.453	0.057	0.057	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.047	-0.039	17.438	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.941	0.987	16.185	0.040	0.040	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.024	0.006	17.813	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.072	-0.042	12.833	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.792	-0.868	17.050	-0.123	-0.123	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.059	-0.074	14.193	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.840	0.884	11.335	0.502	0.502	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.892	-0.917	15.698	-0.238	-0.238	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.023	0.021	17.365	0.017	0.017	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.004	0.023	17.147	0.024	0.024	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.875	0.907	18.244	0.085	0.085	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.004	0.003	12.436	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.021	0.001	16.865	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.007	0.021	12.841	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.871	0.901	15.757	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.063	0.035	18.338	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.048	-0.042	12.616	0.026	0.026	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.871	-0.916	14.549	0.010	0.010	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.061	-0.047	11.445	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.001	0.015	15.051	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.830	0.869	16.339	0.124	0.124	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.026	-0.010	18.953	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.852	-0.921	22.255	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.815	-0.890	21.456	-0.120	-0.120	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.058	-0.012	25.481	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.095	-0.052	27.340	0.003	0.003	0.000	0.000	0.000	0.000

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