FMO DATABASE

FMODB ID: K3NV3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-386619.876628
FMO2-HF: Nuclear repulsion	359533.568327
FMO2-HF: Total energy	-27086.3083
FMO2-MP2: Total energy	-27163.07393

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.
19.476	23.773	1.89	-2.178	-4.007	0.007

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 : -0.895 / q_NPA : -0.954

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	ALA	0	0.014	0.014	3.448	-7.382	-5.490	0.023	-0.767	-1.148	0.004
4	A	4	THR	0	-0.017	-0.011	2.370	-7.047	-6.333	1.435	-0.725	-1.424	0.001
5	A	5	CYS	0	0.046	0.070	4.167	-4.898	-4.597	-0.002	-0.094	-0.204	0.000
6	A	6	GLU	-1	-0.921	-0.988	5.559	22.658	22.658	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.915	0.963	7.805	-25.302	-25.302	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.730	-0.858	6.851	31.088	31.088	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.028	0.005	9.938	-2.062	-2.062	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.077	-0.032	11.959	-2.349	-2.349	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.073	0.035	13.115	-1.144	-1.144	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.011	0.016	13.329	-1.018	-1.018	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.855	0.917	15.254	-18.443	-18.443	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.088	-0.039	17.589	-0.342	-0.342	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.914	-0.960	18.650	13.029	13.029	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.051	-0.027	16.731	-0.346	-0.346	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.045	-0.005	19.829	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.016	-0.014	22.140	-0.413	-0.413	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.026	-0.005	22.320	-0.197	-0.197	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.013	0.008	22.630	0.381	0.381	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.030	0.017	15.210	0.750	0.750	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.015	-0.018	20.290	-0.128	-0.128	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.822	-0.925	18.914	14.771	14.771	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.065	-0.028	18.308	0.712	0.712	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.004	-0.003	15.640	0.640	0.640	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.011	0.005	14.381	1.103	1.103	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.026	-0.019	13.433	1.840	1.840	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.090	-0.034	13.768	0.966	0.966	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.058	-0.015	10.030	0.816	0.816	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.028	-0.021	7.596	-1.606	-1.606	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.072	-0.045	4.523	5.948	6.007	-0.001	-0.007	-0.051	0.000
32	A	32	ASN	0	-0.002	0.018	4.659	-8.079	-7.964	-0.001	-0.002	-0.111	0.000
33	A	33	PRO	0	-0.058	-0.029	4.865	7.073	7.209	-0.001	-0.001	-0.133	0.000
34	A	34	ILE	0	0.058	0.013	7.919	0.688	0.688	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.855	0.908	10.344	-20.860	-20.860	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.022	0.016	13.389	0.151	0.151	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.083	-0.038	16.157	-0.287	-0.287	0.000	0.000	0.000	0.000
38	A	38	HIS	0	0.027	0.019	18.820	-0.316	-0.316	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.000	-0.011	22.533	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.017	-0.001	25.707	-0.206	-0.206	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.844	-0.916	21.285	13.523	13.523	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.044	-0.023	23.553	-0.094	-0.094	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.037	-0.026	17.660	0.658	0.658	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.005	0.012	19.328	-0.749	-0.749	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.072	-0.052	17.547	0.931	0.931	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.830	-0.910	14.362	17.038	17.038	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.075	-0.042	11.172	1.168	1.168	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.003	-0.012	6.901	0.727	0.727	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.037	-0.001	7.184	0.427	0.427	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.018	0.002	2.487	-5.241	-4.303	0.438	-0.569	-0.808	0.002
51	A	51	ARG	1	0.899	0.977	4.331	-22.797	-22.655	-0.001	-0.013	-0.128	0.000
52	A	52	LEU	0	0.070	0.037	7.119	-2.551	-2.551	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.083	-0.039	8.961	-1.441	-1.441	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.052	0.022	12.754	-0.240	-0.240	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.031	-0.014	15.304	-0.757	-0.757	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.059	0.040	18.768	-0.156	-0.156	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.036	-0.028	21.518	-0.141	-0.141	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.921	-0.990	25.257	9.717	9.717	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.069	-0.009	27.743	-0.416	-0.416	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.040	-0.032	23.081	0.369	0.369	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.851	-0.917	23.903	10.870	10.870	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.011	0.013	18.140	0.299	0.299	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.020	-0.017	20.996	-0.402	-0.402	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.032	-0.031	18.774	0.150	0.150	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.049	0.029	13.410	0.364	0.364	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.049	-0.022	12.962	-0.337	-0.337	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.009	0.030	9.723	-1.486	-1.486	0.000	0.000	0.000	0.000

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