FMO DATABASE

FMODB ID: 52ZGZ

Calculation Name: 3W6V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W6V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S166

Base Structure: X-ray

Registration Date: 2023-06-21

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-868615.505024
FMO2-HF: Nuclear repulsion	824634.211129
FMO2-HF: Total energy	-43981.293894
FMO2-MP2: Total energy	-44111.672018

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:230:SER)

Summations of interaction energy for fragment #1(A:230:SER)

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.
3.48	5.459	-0.022	-0.991	-0.967	0.002

Interaction energy analysis for fragmet #1(A:230:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.014

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	232	PRO	0	0.070	0.036	3.846	0.059	2.038	-0.022	-0.991	-0.967	0.002
4	A	233	LEU	0	-0.042	-0.021	6.604	0.183	0.183	0.000	0.000	0.000	0.000
5	A	234	ALA	0	0.007	0.005	6.040	0.229	0.229	0.000	0.000	0.000	0.000
6	A	235	GLU	-1	-0.947	-0.972	5.643	1.981	1.981	0.000	0.000	0.000	0.000
7	A	236	VAL	0	-0.005	-0.006	7.505	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	237	VAL	0	-0.041	-0.018	10.581	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	238	ALA	0	0.023	-0.002	9.928	0.002	0.002	0.000	0.000	0.000	0.000
10	A	239	TRP	0	0.018	0.011	11.399	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	240	ALA	0	-0.005	-0.014	13.203	-0.037	-0.037	0.000	0.000	0.000	0.000
12	A	241	LEU	0	-0.078	-0.041	14.257	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	242	GLU	-1	-0.919	-0.955	14.815	0.315	0.315	0.000	0.000	0.000	0.000
14	A	243	HIS	0	-0.062	-0.014	15.905	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	244	LEU	0	-0.014	-0.007	19.123	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	245	HIS	0	-0.016	-0.008	21.293	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	246	GLU	-1	-0.899	-0.933	21.575	0.150	0.150	0.000	0.000	0.000	0.000
18	A	247	GLN	0	-0.065	-0.057	23.612	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	248	PHE	0	0.003	0.003	19.449	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	249	ASP	-1	-0.839	-0.920	22.750	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	250	VAL	0	-0.014	-0.023	20.213	0.006	0.006	0.000	0.000	0.000	0.000
22	A	251	GLU	-1	-0.973	-0.994	19.595	-0.068	-0.068	0.000	0.000	0.000	0.000
23	A	252	THR	0	0.014	0.009	18.370	0.000	0.000	0.000	0.000	0.000	0.000
24	A	253	LEU	0	0.008	0.004	16.040	0.008	0.008	0.000	0.000	0.000	0.000
25	A	254	ALA	0	-0.034	-0.019	14.836	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	255	ALA	0	0.043	0.023	14.735	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	256	ARG	1	0.900	0.961	13.071	-0.300	-0.300	0.000	0.000	0.000	0.000
28	A	257	ALA	0	0.018	0.019	10.398	0.099	0.099	0.000	0.000	0.000	0.000
29	A	258	TYR	0	-0.008	-0.002	7.529	-0.250	-0.250	0.000	0.000	0.000	0.000
30	A	259	MET	0	-0.059	-0.017	10.785	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	260	SER	0	0.062	0.062	14.821	0.045	0.045	0.000	0.000	0.000	0.000
32	A	261	ARG	1	1.054	0.987	18.052	0.089	0.089	0.000	0.000	0.000	0.000
33	A	262	ARG	1	0.927	0.973	19.662	0.183	0.183	0.000	0.000	0.000	0.000
34	A	263	THR	0	-0.049	-0.051	15.575	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	264	PHE	0	0.081	0.053	14.050	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	265	ASP	-1	-0.844	-0.916	16.643	-0.158	-0.158	0.000	0.000	0.000	0.000
37	A	266	ARG	1	0.904	0.943	18.895	0.318	0.318	0.000	0.000	0.000	0.000
38	A	267	ARG	1	0.970	0.962	10.212	0.973	0.973	0.000	0.000	0.000	0.000
39	A	268	PHE	0	0.070	0.051	14.756	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	269	ARG	1	0.907	0.978	15.967	0.146	0.146	0.000	0.000	0.000	0.000
41	A	270	SER	0	-0.093	-0.049	16.061	0.022	0.022	0.000	0.000	0.000	0.000
42	A	271	LEU	0	0.017	0.023	10.443	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	272	THR	0	-0.067	-0.013	14.520	0.032	0.032	0.000	0.000	0.000	0.000
44	A	273	GLY	0	0.055	0.037	16.714	0.037	0.037	0.000	0.000	0.000	0.000
45	A	274	SER	0	-0.036	-0.062	19.678	0.017	0.017	0.000	0.000	0.000	0.000
46	A	275	ALA	0	0.057	0.022	19.993	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	276	PRO	0	0.066	0.033	18.824	0.021	0.021	0.000	0.000	0.000	0.000
48	A	277	LEU	0	0.067	0.013	20.400	0.017	0.017	0.000	0.000	0.000	0.000
49	A	278	GLN	0	-0.013	0.001	23.528	0.013	0.013	0.000	0.000	0.000	0.000
50	A	279	TRP	0	0.052	0.022	16.285	0.005	0.005	0.000	0.000	0.000	0.000
51	A	280	LEU	0	0.023	0.027	19.519	0.015	0.015	0.000	0.000	0.000	0.000
52	A	281	ILE	0	-0.040	-0.001	22.068	0.014	0.014	0.000	0.000	0.000	0.000
53	A	282	THR	0	-0.034	-0.011	23.321	0.006	0.006	0.000	0.000	0.000	0.000
54	A	283	GLN	0	0.033	-0.007	19.262	0.013	0.013	0.000	0.000	0.000	0.000
55	A	284	ARG	1	0.848	0.927	22.702	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	285	VAL	0	-0.028	-0.022	25.018	0.006	0.006	0.000	0.000	0.000	0.000
57	A	286	LEU	0	0.019	0.017	23.174	0.004	0.004	0.000	0.000	0.000	0.000
58	A	287	GLN	0	0.007	0.005	23.311	0.017	0.017	0.000	0.000	0.000	0.000
59	A	288	ALA	0	0.007	-0.039	26.025	0.004	0.004	0.000	0.000	0.000	0.000
60	A	289	GLN	0	-0.045	-0.039	29.044	0.001	0.001	0.000	0.000	0.000	0.000
61	A	290	ARG	1	1.025	1.020	22.899	-0.116	-0.116	0.000	0.000	0.000	0.000
62	A	291	LEU	0	-0.004	0.013	28.178	0.001	0.001	0.000	0.000	0.000	0.000
63	A	292	LEU	0	-0.065	-0.017	30.983	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	293	GLU	-1	-0.874	-0.916	31.623	0.058	0.058	0.000	0.000	0.000	0.000
65	A	294	THR	0	-0.022	-0.022	30.554	0.001	0.001	0.000	0.000	0.000	0.000
66	A	295	SER	0	-0.032	-0.021	32.626	0.001	0.001	0.000	0.000	0.000	0.000
67	A	296	ASP	-1	-0.843	-0.925	34.584	0.058	0.058	0.000	0.000	0.000	0.000
68	A	297	TYR	0	-0.021	0.005	31.970	0.000	0.000	0.000	0.000	0.000	0.000
69	A	298	SER	0	0.064	0.049	36.742	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	299	VAL	0	0.005	-0.022	36.765	0.002	0.002	0.000	0.000	0.000	0.000
71	A	300	ASP	-1	-0.857	-0.948	35.893	0.034	0.034	0.000	0.000	0.000	0.000
72	A	301	GLU	-1	-0.874	-0.936	35.341	0.063	0.063	0.000	0.000	0.000	0.000
73	A	302	VAL	0	-0.033	-0.013	31.253	0.006	0.006	0.000	0.000	0.000	0.000
74	A	303	ALA	0	-0.007	-0.020	30.995	0.003	0.003	0.000	0.000	0.000	0.000
75	A	304	GLY	0	0.033	0.029	30.600	0.000	0.000	0.000	0.000	0.000	0.000
76	A	305	ARG	1	0.967	0.991	28.762	-0.092	-0.092	0.000	0.000	0.000	0.000
77	A	306	CYS	0	-0.093	-0.012	26.630	0.012	0.012	0.000	0.000	0.000	0.000
78	A	307	GLY	0	0.079	0.059	26.108	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	308	PHE	0	-0.121	-0.060	27.135	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	309	ARG	1	0.995	0.991	29.101	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	310	SER	0	0.029	0.014	31.991	0.000	0.000	0.000	0.000	0.000	0.000
82	A	311	PRO	0	0.083	0.030	34.714	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	312	VAL	0	-0.026	-0.014	36.599	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.004	0.008	32.968	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	314	LEU	0	-0.006	0.015	32.007	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	315	ARG	1	0.903	0.941	33.663	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	316	GLY	0	0.015	0.021	36.013	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	317	HIS	0	0.061	0.012	30.564	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	318	PHE	0	0.014	0.010	32.229	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	319	ARG	1	0.938	0.958	33.343	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	320	ARG	1	0.856	0.939	31.095	0.016	0.016	0.000	0.000	0.000	0.000
92	A	321	GLN	0	0.020	0.011	27.408	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	322	LEU	0	0.001	0.008	30.319	0.001	0.001	0.000	0.000	0.000	0.000
94	A	323	GLY	0	0.027	0.036	33.944	0.001	0.001	0.000	0.000	0.000	0.000
95	A	324	SER	0	-0.052	-0.043	37.327	0.001	0.001	0.000	0.000	0.000	0.000
96	A	325	SER	0	-0.003	-0.004	37.475	0.001	0.001	0.000	0.000	0.000	0.000
97	A	326	PRO	0	0.069	0.032	35.710	0.001	0.001	0.000	0.000	0.000	0.000
98	A	327	ALA	0	0.053	0.023	37.209	0.002	0.002	0.000	0.000	0.000	0.000
99	A	328	ALA	0	0.025	0.008	40.440	0.001	0.001	0.000	0.000	0.000	0.000
100	A	329	TYR	0	-0.060	-0.020	33.330	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	330	ARG	1	0.850	0.883	36.369	-0.054	-0.054	0.000	0.000	0.000	0.000
102	A	331	ALA	0	-0.027	-0.013	38.898	0.002	0.002	0.000	0.000	0.000	0.000
103	A	332	ALA	0	0.022	0.001	40.899	0.000	0.000	0.000	0.000	0.000	0.000
104	A	333	TYR	0	-0.021	-0.011	34.670	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	334	ARG	1	0.874	0.932	36.896	-0.058	-0.058	0.000	0.000	0.000	0.000
106	A	335	ALA	0	0.012	0.029	41.606	0.000	0.000	0.000	0.000	0.000	0.000
107	A	336	ARG	1	0.966	0.977	37.385	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	337	ARG	1	0.847	0.913	33.725	-0.056	-0.056	0.000	0.000	0.000	0.000
109	A	338	PRO	0	0.036	0.032	40.085	0.004	0.004	0.000	0.000	0.000	0.000
110	A	339	GLN	0	-0.014	-0.010	40.497	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	340	GLY	0	-0.017	0.013	35.128	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:230:SER)