FMO DATABASE

FMODB ID: 437YN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-386700.03058
FMO2-HF: Nuclear repulsion	359613.159788
FMO2-HF: Total energy	-27086.870792
FMO2-MP2: Total energy	-27163.54339

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.
21.482	25.845	1.514	-2.003	-3.87	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 : -0.891 / q_NPA : -0.955

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	0.009	0.013	3.396	-7.916	-5.918	0.020	-0.827	-1.191	0.004
4	A	4	THR	0	-0.004	-0.012	2.397	-7.121	-6.267	1.077	-0.576	-1.354	0.001
5	A	5	CYS	0	0.030	0.072	4.207	-5.646	-5.360	-0.002	-0.101	-0.184	0.000
6	A	6	GLU	-1	-0.921	-0.985	5.601	22.780	22.780	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.919	0.969	7.806	-26.413	-26.413	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.738	-0.846	6.392	32.558	32.558	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.028	0.010	9.991	-2.113	-2.113	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.074	-0.036	12.001	-1.389	-1.389	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.028	0.014	13.132	-1.260	-1.260	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.016	0.003	13.497	-1.082	-1.082	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.821	0.904	14.838	-19.046	-19.046	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.054	-0.012	17.634	-0.382	-0.382	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.921	-0.965	18.594	13.427	13.427	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.050	-0.030	16.833	-0.399	-0.399	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.032	0.001	19.567	-0.122	-0.122	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.008	-0.008	22.181	-0.408	-0.408	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.038	-0.005	22.265	-0.375	-0.375	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.025	0.008	22.666	0.383	0.383	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.023	0.016	15.153	0.779	0.779	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.002	-0.017	20.330	-0.111	-0.111	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.830	-0.924	18.941	14.527	14.527	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.035	-0.009	18.334	0.778	0.778	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.007	0.006	15.792	0.671	0.671	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.002	0.001	14.409	1.114	1.114	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.068	-0.051	13.459	1.679	1.679	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.071	-0.022	13.797	0.991	0.991	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.054	-0.014	10.102	0.873	0.873	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.024	-0.019	7.657	-1.009	-1.009	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.050	-0.059	4.697	5.234	5.295	-0.001	-0.004	-0.055	0.000
32	A	32	ASN	0	-0.061	0.000	4.661	-7.572	-7.439	-0.001	-0.002	-0.129	0.000
33	A	33	PRO	0	-0.025	-0.019	4.894	5.960	6.054	-0.001	-0.001	-0.091	0.000
34	A	34	ILE	0	0.042	0.001	7.921	0.799	0.799	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.853	0.909	10.352	-20.441	-20.441	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.024	0.018	13.396	0.222	0.222	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.091	-0.038	16.310	-0.258	-0.258	0.000	0.000	0.000	0.000
38	A	38	HIS	0	0.028	-0.001	18.846	-0.254	-0.254	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.002	-0.001	22.546	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.014	-0.010	25.785	-0.201	-0.201	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.830	-0.895	21.233	13.441	13.441	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.054	-0.026	23.634	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.032	-0.026	17.854	0.649	0.649	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.021	0.016	19.404	-0.704	-0.704	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.073	-0.048	17.604	0.924	0.924	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.844	-0.917	14.341	16.781	16.781	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.061	-0.033	10.831	1.106	1.106	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.004	-0.011	6.958	0.756	0.756	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.030	0.000	6.763	0.393	0.393	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.015	0.001	2.497	-3.537	-2.739	0.423	-0.481	-0.740	0.002
51	A	51	ARG	1	0.880	0.942	4.418	-21.628	-21.489	-0.001	-0.011	-0.126	0.000
52	A	52	LEU	0	0.063	0.038	7.211	-2.346	-2.346	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.059	-0.024	8.981	-1.013	-1.013	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.037	0.013	12.594	-0.180	-0.180	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.029	-0.012	15.329	-0.668	-0.668	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.031	0.023	18.792	-0.153	-0.153	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.016	-0.029	21.542	-0.133	-0.133	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.920	-0.982	25.281	9.641	9.641	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.108	-0.048	27.770	-0.345	-0.345	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.030	-0.019	23.031	0.363	0.363	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.809	-0.877	23.931	10.828	10.828	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.004	0.005	18.210	0.303	0.303	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.018	-0.012	21.021	-0.393	-0.393	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.018	-0.021	18.900	0.178	0.178	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.054	0.034	13.423	0.362	0.362	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.011	-0.007	12.988	-0.047	-0.047	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.016	0.034	9.708	-2.219	-2.219	0.000	0.000	0.000	0.000

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