FMO DATABASE

FMODB ID: 53M5Z

Calculation Name: 3W0D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q4WZ11

Base Structure: X-ray

Registration Date: 2023-06-20

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-387851.218004
FMO2-HF: Nuclear repulsion	360764.154616
FMO2-HF: Total energy	-27087.063388
FMO2-MP2: Total energy	-27163.747483

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:ASP)

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

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.
18.091	23.042	2.273	-2.865	-4.359	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.879 / q_NPA : -0.942

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

Sort

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	ALA	0	0.044	0.024	3.828	-6.814	-5.186	0.002	-0.695	-0.935	0.003
4	A	4	THR	0	-0.067	-0.044	2.473	-6.995	-5.937	0.547	-0.554	-1.051	0.002
5	A	5	CYS	0	0.071	0.095	4.281	-6.163	-5.882	-0.002	-0.120	-0.159	0.000
6	A	6	GLU	-1	-0.913	-0.983	5.951	23.865	23.865	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.923	0.970	7.997	-26.472	-26.472	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.733	-0.819	6.655	32.809	32.809	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.010	-0.004	9.996	-2.010	-2.010	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.072	-0.046	11.921	-1.352	-1.352	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.015	0.006	13.272	-1.269	-1.269	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.015	0.001	13.644	-1.156	-1.156	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.834	0.908	14.398	-19.459	-19.459	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.078	-0.017	17.963	-0.396	-0.396	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.881	-0.939	18.533	13.520	13.520	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.050	-0.030	17.012	-0.405	-0.405	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.011	0.013	19.349	-0.115	-0.115	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.011	-0.003	22.111	-0.432	-0.432	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.050	-0.020	22.195	-0.484	-0.484	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.010	0.008	22.756	0.360	0.360	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.022	0.002	15.241	0.720	0.720	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.003	-0.005	19.851	-0.419	-0.419	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.852	-0.937	19.051	14.630	14.630	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.031	-0.001	18.589	0.739	0.739	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.011	0.009	15.713	0.598	0.598	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.010	-0.007	14.622	1.137	1.137	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.058	-0.051	13.665	1.620	1.620	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.052	-0.005	14.306	0.723	0.723	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.073	-0.029	10.489	0.848	0.848	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.012	-0.022	8.013	-0.691	-0.691	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.033	-0.051	4.829	4.908	4.908	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.066	-0.015	4.308	-7.185	-7.049	-0.001	-0.004	-0.131	0.000
33	A	33	PRO	0	-0.026	-0.016	4.662	6.355	6.470	-0.001	-0.002	-0.111	0.000
34	A	34	ILE	0	0.043	0.007	7.660	0.938	0.938	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.851	0.914	10.128	-20.692	-20.692	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.019	0.015	13.142	0.072	0.072	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.085	-0.029	15.934	0.047	0.047	0.000	0.000	0.000	0.000
38	A	38	HIS	0	0.040	-0.004	18.601	-0.229	-0.229	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.024	-0.013	22.375	0.008	0.008	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.004	-0.007	25.001	-0.462	-0.462	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.859	-0.897	20.664	13.796	13.796	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.033	-0.016	23.213	-0.070	-0.070	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.014	-0.015	17.757	0.580	0.580	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.022	0.007	18.756	-0.582	-0.582	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.055	-0.024	17.355	1.066	1.066	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.885	-0.934	14.129	17.260	17.260	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.040	-0.025	10.351	1.096	1.096	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.017	-0.024	6.691	0.801	0.801	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.025	0.013	6.467	0.597	0.597	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.035	0.001	2.348	-7.089	-5.528	1.729	-1.509	-1.782	-0.003
51	A	51	ARG	1	0.850	0.933	3.831	-23.789	-23.617	-0.001	0.019	-0.190	0.000
52	A	52	LEU	0	0.063	0.028	6.971	-2.806	-2.806	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.073	-0.040	8.554	-1.495	-1.495	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.027	0.001	12.336	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.009	0.003	15.074	-0.659	-0.659	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.011	0.013	18.493	-0.154	-0.154	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.013	-0.028	21.361	-0.155	-0.155	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.921	-0.977	25.178	9.748	9.748	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.098	-0.044	28.039	-0.297	-0.297	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.035	-0.028	22.942	0.372	0.372	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.819	-0.879	23.498	10.962	10.962	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.003	-0.006	17.901	0.246	0.246	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.019	-0.012	20.642	-0.426	-0.426	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.032	-0.022	18.599	0.116	0.116	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.062	0.037	13.179	0.331	0.331	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.005	-0.003	12.538	0.063	0.063	0.000	0.000	0.000	0.000
67	A	68	ALA	0	0.012	0.035	9.429	-2.096	-2.096	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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