FMO DATABASE

FMODB ID: VR3G1

Calculation Name: 3W1S-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1S

Chain ID: C

ChEMBL ID:

UniProt ID: P38316

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-540383.28657
FMO2-HF: Nuclear repulsion	507441.288003
FMO2-HF: Total energy	-32941.998567
FMO2-MP2: Total energy	-33034.14376

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(C:101:ILE)

Summations of interaction energy for fragment #1(C:101:ILE)

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.
-4.995	-0.487	2.159	-2.094	-4.572	0.002

Interaction energy analysis for fragmet #1(C:101:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.022

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	C	103	LYS	1	0.910	0.943	2.527	-1.679	0.504	0.317	-0.754	-1.746	0.006
4	C	104	ILE	0	0.049	0.027	5.277	-0.036	0.041	-0.001	-0.005	-0.071	0.000
5	C	105	GLN	0	0.005	-0.012	8.877	0.056	0.056	0.000	0.000	0.000	0.000
6	C	106	ILE	0	0.026	0.034	11.403	0.033	0.033	0.000	0.000	0.000	0.000
7	C	107	LYS	1	0.963	0.983	13.933	-0.004	-0.004	0.000	0.000	0.000	0.000
8	C	108	PHE	0	-0.019	-0.027	14.344	0.010	0.010	0.000	0.000	0.000	0.000
9	C	109	GLN	0	-0.043	-0.022	19.328	-0.012	-0.012	0.000	0.000	0.000	0.000
10	C	110	PRO	0	0.010	0.011	22.967	0.006	0.006	0.000	0.000	0.000	0.000
11	C	111	ILE	0	0.025	0.001	25.424	-0.002	-0.002	0.000	0.000	0.000	0.000
12	C	112	GLY	0	0.034	0.019	28.531	0.001	0.001	0.000	0.000	0.000	0.000
13	C	120	SER	0	0.007	-0.003	17.986	-0.003	-0.003	0.000	0.000	0.000	0.000
14	C	121	VAL	0	0.062	0.043	14.951	0.013	0.013	0.000	0.000	0.000	0.000
15	C	122	CYS	0	-0.085	-0.041	12.006	-0.014	-0.014	0.000	0.000	0.000	0.000
16	C	123	LYS	1	0.988	1.001	7.815	0.403	0.403	0.000	0.000	0.000	0.000
17	C	124	ILE	0	0.010	0.012	7.111	0.073	0.073	0.000	0.000	0.000	0.000
18	C	125	SER	0	-0.009	-0.005	2.361	-2.645	-1.292	1.809	-1.107	-2.055	-0.004
19	C	126	MET	0	0.063	0.026	4.313	-0.117	0.122	-0.001	-0.021	-0.218	0.000
20	C	127	SER	0	-0.013	0.001	3.137	-0.657	-0.032	0.036	-0.205	-0.455	0.000
21	C	128	GLN	0	-0.002	0.000	5.218	-0.141	-0.110	-0.001	-0.002	-0.027	0.000
22	C	129	SER	0	0.098	0.036	7.883	-0.024	-0.024	0.000	0.000	0.000	0.000
23	C	130	PHE	0	0.075	0.024	11.573	-0.011	-0.011	0.000	0.000	0.000	0.000
24	C	131	ALA	0	0.025	0.006	14.432	-0.021	-0.021	0.000	0.000	0.000	0.000
25	C	132	MET	0	-0.055	-0.016	10.194	0.005	0.005	0.000	0.000	0.000	0.000
26	C	133	VAL	0	0.031	0.023	11.914	-0.016	-0.016	0.000	0.000	0.000	0.000
27	C	134	ILE	0	0.020	0.011	13.997	-0.025	-0.025	0.000	0.000	0.000	0.000
28	C	135	LEU	0	-0.012	-0.002	15.161	-0.017	-0.017	0.000	0.000	0.000	0.000
29	C	136	PHE	0	-0.048	-0.024	11.658	-0.020	-0.020	0.000	0.000	0.000	0.000
30	C	137	LEU	0	0.031	0.007	14.936	-0.019	-0.019	0.000	0.000	0.000	0.000
31	C	138	LYS	1	0.901	0.972	17.919	-0.070	-0.070	0.000	0.000	0.000	0.000
32	C	139	ARG	1	0.973	0.993	14.446	-0.077	-0.077	0.000	0.000	0.000	0.000
33	C	140	ARG	1	0.937	0.973	14.554	-0.001	-0.001	0.000	0.000	0.000	0.000
34	C	141	LEU	0	-0.010	-0.008	19.704	-0.008	-0.008	0.000	0.000	0.000	0.000
35	C	142	LYS	1	0.817	0.911	21.002	-0.004	-0.004	0.000	0.000	0.000	0.000
36	C	143	MET	0	-0.008	0.001	23.808	-0.001	-0.001	0.000	0.000	0.000	0.000
37	C	144	ASP	-1	-0.841	-0.940	24.399	0.044	0.044	0.000	0.000	0.000	0.000
38	C	145	HIS	0	-0.068	-0.016	25.927	0.005	0.005	0.000	0.000	0.000	0.000
39	C	146	VAL	0	-0.022	-0.029	22.649	-0.003	-0.003	0.000	0.000	0.000	0.000
40	C	147	TYR	0	-0.019	0.006	24.379	0.008	0.008	0.000	0.000	0.000	0.000
41	C	148	CYS	0	-0.040	-0.029	20.095	-0.004	-0.004	0.000	0.000	0.000	0.000
42	C	149	TYR	0	0.028	0.005	22.174	0.005	0.005	0.000	0.000	0.000	0.000
43	C	150	ILE	0	0.013	0.016	17.641	-0.004	-0.004	0.000	0.000	0.000	0.000
44	C	151	ASN	0	0.027	0.002	21.235	-0.006	-0.006	0.000	0.000	0.000	0.000
45	C	152	ASN	0	-0.030	-0.002	23.505	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	153	SER	0	-0.037	-0.025	25.176	-0.003	-0.003	0.000	0.000	0.000	0.000
47	C	154	PHE	0	0.023	0.011	21.050	0.000	0.000	0.000	0.000	0.000	0.000
48	C	155	ALA	0	0.006	0.016	22.922	0.002	0.002	0.000	0.000	0.000	0.000
49	C	156	PRO	0	-0.018	0.001	18.422	0.001	0.001	0.000	0.000	0.000	0.000
50	C	157	SER	0	0.037	0.022	19.882	-0.004	-0.004	0.000	0.000	0.000	0.000
51	C	158	PRO	0	0.005	-0.016	17.886	0.015	0.015	0.000	0.000	0.000	0.000
52	C	159	GLN	0	0.034	0.001	15.841	0.027	0.027	0.000	0.000	0.000	0.000
53	C	160	GLN	0	0.025	0.034	14.710	0.009	0.009	0.000	0.000	0.000	0.000
54	C	161	ASN	0	0.025	0.004	8.134	0.002	0.002	0.000	0.000	0.000	0.000
55	C	162	ILE	0	0.013	0.010	8.773	-0.032	-0.032	0.000	0.000	0.000	0.000
56	C	163	GLY	0	0.028	0.002	8.715	-0.054	-0.054	0.000	0.000	0.000	0.000
57	C	164	GLU	-1	-0.912	-0.962	9.532	0.303	0.303	0.000	0.000	0.000	0.000
58	C	165	LEU	0	-0.031	-0.019	12.684	-0.037	-0.037	0.000	0.000	0.000	0.000
59	C	166	TRP	0	-0.086	-0.059	11.146	-0.025	-0.025	0.000	0.000	0.000	0.000
60	C	167	MET	0	-0.028	-0.035	10.650	-0.020	-0.020	0.000	0.000	0.000	0.000
61	C	168	GLN	0	-0.047	0.003	14.371	-0.021	-0.021	0.000	0.000	0.000	0.000
62	C	169	PHE	0	-0.003	-0.013	17.280	-0.012	-0.012	0.000	0.000	0.000	0.000
63	C	170	LYS	1	0.893	0.969	14.561	-0.092	-0.092	0.000	0.000	0.000	0.000
64	C	171	THR	0	0.015	0.004	17.593	0.002	0.002	0.000	0.000	0.000	0.000
65	C	172	ASN	0	-0.010	-0.014	19.490	-0.005	-0.005	0.000	0.000	0.000	0.000
66	C	173	ASP	-1	-0.893	-0.946	14.969	-0.048	-0.048	0.000	0.000	0.000	0.000
67	C	174	GLU	-1	-0.931	-0.954	14.296	-0.052	-0.052	0.000	0.000	0.000	0.000
68	C	175	LEU	0	-0.022	-0.005	13.586	0.017	0.017	0.000	0.000	0.000	0.000
69	C	176	ILE	0	0.008	-0.002	16.073	-0.004	-0.004	0.000	0.000	0.000	0.000
70	C	177	VAL	0	-0.031	-0.009	16.217	0.012	0.012	0.000	0.000	0.000	0.000
71	C	178	SER	0	0.019	0.004	19.384	-0.007	-0.007	0.000	0.000	0.000	0.000
72	C	179	TYR	0	0.008	-0.007	21.896	0.007	0.007	0.000	0.000	0.000	0.000
73	C	180	CYS	0	-0.030	-0.005	24.235	-0.006	-0.006	0.000	0.000	0.000	0.000
74	C	181	ALA	0	0.090	0.046	26.993	0.004	0.004	0.000	0.000	0.000	0.000
75	C	182	SER	0	-0.019	-0.019	29.522	0.001	0.001	0.000	0.000	0.000	0.000
76	C	183	VAL	0	0.026	-0.007	31.413	0.002	0.002	0.000	0.000	0.000	0.000
77	C	184	ALA	0	-0.047	-0.004	29.978	0.002	0.002	0.000	0.000	0.000	0.000
78	C	185	PHE	0	0.024	0.010	31.160	0.003	0.003	0.000	0.000	0.000	0.000
79	C	186	GLY	0	0.017	0.025	31.032	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:101:ILE)