FMO DATABASE

FMODB ID: 43RMN

Calculation Name: 3W0D-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	67
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-386423.090938
FMO2-HF: Nuclear repulsion	359337.322439
FMO2-HF: Total energy	-27085.768499
FMO2-MP2: Total energy	-27162.53689

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.
43.465	47.703	1.868	-2.112	-3.994	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 : -0.903 / q_NPA : -0.958

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	0.006	0.011	3.448	-7.591	-5.759	0.027	-0.746	-1.113	0.004
4	A	4	THR	0	-0.025	-0.017	2.371	-7.128	-6.406	1.409	-0.709	-1.423	0.001
5	A	67	CYS	0	0.051	0.067	4.168	-4.814	-4.509	0.000	-0.092	-0.213	0.000
6	A	6	GLU	-1	-0.916	-0.984	5.559	22.498	22.498	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.904	0.957	7.805	-25.443	-25.443	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.735	-0.861	6.851	30.955	30.955	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.038	0.010	9.938	-2.141	-2.141	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.080	-0.032	11.958	-2.428	-2.428	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.068	0.032	13.114	-1.206	-1.206	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.015	0.018	13.328	-1.070	-1.070	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.861	0.921	15.254	-18.493	-18.493	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.100	-0.043	17.588	-0.378	-0.378	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.919	-0.964	18.649	13.004	13.004	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.055	-0.029	16.730	-0.369	-0.369	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.038	-0.001	19.827	-0.121	-0.121	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.016	-0.015	22.140	-0.438	-0.438	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.029	-0.007	22.320	-0.205	-0.205	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.009	0.007	22.630	0.380	0.380	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.035	0.021	15.210	0.743	0.743	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.018	-0.020	20.291	-0.134	-0.134	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.822	-0.926	18.914	14.769	14.769	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.069	-0.029	18.308	0.715	0.715	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.004	-0.002	15.640	0.654	0.654	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.014	0.007	14.382	1.127	1.127	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.026	-0.020	13.433	1.840	1.840	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.094	-0.036	13.768	0.985	0.985	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.055	-0.013	10.030	0.843	0.843	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.035	-0.025	7.596	-1.543	-1.543	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.069	-0.044	4.523	6.024	6.090	0.000	-0.007	-0.059	0.000
32	A	32	ASN	0	-0.009	0.013	4.660	-8.045	-7.946	0.000	-0.003	-0.095	0.000
33	A	33	PRO	0	-0.051	-0.025	4.865	7.148	7.300	0.000	-0.002	-0.150	0.000
34	A	34	ILE	0	0.052	0.012	7.920	0.531	0.531	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.847	0.906	10.345	-21.270	-21.270	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.014	0.012	13.389	0.053	0.053	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.073	-0.033	16.154	-0.388	-0.388	0.000	0.000	0.000	0.000
38	A	38	HIS	0	0.022	0.015	18.820	-0.380	-0.380	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.002	-0.012	22.534	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.023	-0.004	25.706	-0.214	-0.214	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.844	-0.916	21.284	13.496	13.496	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.051	-0.027	23.552	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.028	-0.021	17.659	0.619	0.619	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.007	0.005	19.328	-0.768	-0.768	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.067	-0.048	17.546	0.891	0.891	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.847	-0.920	14.361	16.952	16.952	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.078	-0.038	11.171	1.107	1.107	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.029	-0.023	6.904	0.939	0.939	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.036	0.004	7.183	0.671	0.671	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.004	-0.011	2.487	-4.328	-3.408	0.432	-0.540	-0.812	0.002
51	A	51	ARG	1	0.825	0.926	4.330	-22.177	-22.035	0.000	-0.013	-0.129	0.000
52	A	52	LEU	0	0.055	0.032	7.118	-2.578	-2.578	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.089	-0.042	8.962	-1.661	-1.661	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.038	0.013	12.754	-0.350	-0.350	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.028	-0.013	15.305	-0.828	-0.828	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.057	0.039	18.768	-0.194	-0.194	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.040	-0.030	21.518	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.920	-0.989	25.258	9.689	9.689	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.076	-0.013	27.743	-0.422	-0.422	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.040	-0.031	23.082	0.375	0.375	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.853	-0.919	23.903	10.864	10.864	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.011	0.015	18.140	0.300	0.300	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.020	-0.018	20.996	-0.425	-0.425	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.038	-0.033	18.774	0.159	0.159	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.046	0.027	13.410	0.370	0.370	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.064	-0.029	12.961	-0.426	-0.426	0.000	0.000	0.000	0.000
67	A	68	ALA	-1	-0.741	-0.828	9.794	23.091	23.091	0.000	0.000	0.000	0.000

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