FMO DATABASE

FMODB ID: V58Y1

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	OptAll
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	-872982.826978
FMO2-HF: Nuclear repulsion	829000.366745
FMO2-HF: Total energy	-43982.460233
FMO2-MP2: Total energy	-44112.770469

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.
6.158	8.223	-0.017	-1.042	-1.007	0.003

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 : 0.046 / q_NPA : 0.026

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	0.045	0.021	3.571	0.761	2.826	-0.017	-1.042	-1.007	0.003
4	A	233	LEU	0	-0.066	-0.021	6.121	0.759	0.759	0.000	0.000	0.000	0.000
5	A	234	ALA	0	0.021	-0.001	5.656	0.475	0.475	0.000	0.000	0.000	0.000
6	A	235	GLU	-1	-0.890	-0.924	5.715	0.977	0.977	0.000	0.000	0.000	0.000
7	A	236	VAL	0	0.007	-0.001	7.374	0.165	0.165	0.000	0.000	0.000	0.000
8	A	237	VAL	0	-0.028	-0.014	10.504	0.096	0.096	0.000	0.000	0.000	0.000
9	A	238	ALA	0	0.027	0.004	9.515	0.067	0.067	0.000	0.000	0.000	0.000
10	A	239	TRP	0	-0.022	-0.012	11.169	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	240	ALA	0	0.004	-0.015	13.019	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	241	LEU	0	-0.078	-0.042	13.979	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	242	GLU	-1	-0.910	-0.947	14.632	0.318	0.318	0.000	0.000	0.000	0.000
14	A	243	HIS	0	-0.028	-0.015	15.846	0.026	0.026	0.000	0.000	0.000	0.000
15	A	244	LEU	0	-0.039	-0.014	19.117	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	245	HIS	0	-0.059	-0.025	20.960	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	246	GLU	-1	-0.853	-0.918	20.901	0.130	0.130	0.000	0.000	0.000	0.000
18	A	247	GLN	0	-0.009	-0.013	23.714	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	248	PHE	0	0.014	0.004	19.397	0.002	0.002	0.000	0.000	0.000	0.000
20	A	249	ASP	-1	-0.815	-0.892	22.246	-0.175	-0.175	0.000	0.000	0.000	0.000
21	A	250	VAL	0	-0.025	-0.031	19.470	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	251	GLU	-1	-0.931	-0.984	18.648	-0.265	-0.265	0.000	0.000	0.000	0.000
23	A	252	THR	0	0.005	0.003	18.018	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	253	LEU	0	-0.007	0.005	15.451	0.006	0.006	0.000	0.000	0.000	0.000
25	A	254	ALA	0	-0.020	-0.015	13.993	-0.067	-0.067	0.000	0.000	0.000	0.000
26	A	255	ALA	0	0.022	0.006	13.839	-0.086	-0.086	0.000	0.000	0.000	0.000
27	A	256	ARG	1	0.889	0.939	11.341	-0.270	-0.270	0.000	0.000	0.000	0.000
28	A	257	ALA	0	-0.030	0.000	9.666	0.011	0.011	0.000	0.000	0.000	0.000
29	A	258	TYR	0	-0.002	0.005	6.979	-0.347	-0.347	0.000	0.000	0.000	0.000
30	A	259	MET	0	-0.065	-0.022	9.696	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	260	SER	0	0.068	0.037	13.572	0.093	0.093	0.000	0.000	0.000	0.000
32	A	261	ARG	1	0.968	0.952	17.193	0.229	0.229	0.000	0.000	0.000	0.000
33	A	262	ARG	1	0.924	0.971	18.948	0.373	0.373	0.000	0.000	0.000	0.000
34	A	263	THR	0	-0.020	-0.021	14.584	0.002	0.002	0.000	0.000	0.000	0.000
35	A	264	PHE	0	0.079	0.047	13.092	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	265	ASP	-1	-0.821	-0.910	15.844	-0.380	-0.380	0.000	0.000	0.000	0.000
37	A	266	ARG	1	0.874	0.944	18.345	0.627	0.627	0.000	0.000	0.000	0.000
38	A	267	ARG	1	0.969	0.969	8.966	2.129	2.129	0.000	0.000	0.000	0.000
39	A	268	PHE	0	0.062	0.042	14.448	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	269	ARG	1	0.890	0.944	15.469	0.346	0.346	0.000	0.000	0.000	0.000
41	A	270	SER	0	-0.077	-0.044	15.500	0.051	0.051	0.000	0.000	0.000	0.000
42	A	271	LEU	0	0.002	0.022	9.648	-0.047	-0.047	0.000	0.000	0.000	0.000
43	A	272	THR	0	0.016	0.005	14.115	0.048	0.048	0.000	0.000	0.000	0.000
44	A	273	GLY	0	0.051	0.045	16.443	0.071	0.071	0.000	0.000	0.000	0.000
45	A	274	SER	0	-0.051	-0.035	19.598	0.039	0.039	0.000	0.000	0.000	0.000
46	A	275	ALA	0	0.036	0.010	19.987	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	276	PRO	0	0.040	0.022	18.257	0.038	0.038	0.000	0.000	0.000	0.000
48	A	277	LEU	0	0.063	0.028	20.066	0.029	0.029	0.000	0.000	0.000	0.000
49	A	278	GLN	0	0.038	0.016	23.329	0.036	0.036	0.000	0.000	0.000	0.000
50	A	279	TRP	0	0.031	0.034	15.870	0.005	0.005	0.000	0.000	0.000	0.000
51	A	280	LEU	0	0.035	0.024	19.028	0.029	0.029	0.000	0.000	0.000	0.000
52	A	281	ILE	0	-0.046	-0.019	21.860	0.026	0.026	0.000	0.000	0.000	0.000
53	A	282	THR	0	-0.031	-0.027	23.159	0.017	0.017	0.000	0.000	0.000	0.000
54	A	283	GLN	0	0.052	0.009	19.160	0.028	0.028	0.000	0.000	0.000	0.000
55	A	284	ARG	1	0.827	0.931	22.385	0.050	0.050	0.000	0.000	0.000	0.000
56	A	285	VAL	0	-0.037	-0.017	25.049	0.016	0.016	0.000	0.000	0.000	0.000
57	A	286	LEU	0	0.020	0.014	23.444	0.011	0.011	0.000	0.000	0.000	0.000
58	A	287	GLN	0	-0.005	-0.002	22.872	0.018	0.018	0.000	0.000	0.000	0.000
59	A	288	ALA	0	0.042	-0.006	25.868	0.011	0.011	0.000	0.000	0.000	0.000
60	A	289	GLN	0	-0.039	-0.033	28.843	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	290	ARG	1	0.953	0.978	22.607	-0.066	-0.066	0.000	0.000	0.000	0.000
62	A	291	LEU	0	0.026	0.025	28.460	0.008	0.008	0.000	0.000	0.000	0.000
63	A	292	LEU	0	-0.075	-0.019	30.887	0.001	0.001	0.000	0.000	0.000	0.000
64	A	293	GLU	-1	-0.770	-0.829	31.832	0.022	0.022	0.000	0.000	0.000	0.000
65	A	294	THR	0	-0.025	-0.015	30.006	0.003	0.003	0.000	0.000	0.000	0.000
66	A	295	SER	0	-0.052	-0.036	32.679	0.007	0.007	0.000	0.000	0.000	0.000
67	A	296	ASP	-1	-0.803	-0.903	34.588	0.042	0.042	0.000	0.000	0.000	0.000
68	A	297	TYR	0	0.013	0.025	31.464	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	298	SER	0	0.059	0.040	36.433	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	299	VAL	0	0.028	-0.007	36.218	0.001	0.001	0.000	0.000	0.000	0.000
71	A	300	ASP	-1	-0.772	-0.873	35.357	0.004	0.004	0.000	0.000	0.000	0.000
72	A	301	GLU	-1	-0.781	-0.875	34.304	0.056	0.056	0.000	0.000	0.000	0.000
73	A	302	VAL	0	-0.019	-0.012	31.101	0.005	0.005	0.000	0.000	0.000	0.000
74	A	303	ALA	0	0.003	0.001	30.725	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	304	GLY	0	0.031	0.028	30.157	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	305	ARG	1	0.859	0.925	28.604	-0.074	-0.074	0.000	0.000	0.000	0.000
77	A	306	CYS	0	-0.061	-0.014	26.049	0.011	0.011	0.000	0.000	0.000	0.000
78	A	307	GLY	0	0.083	0.054	26.122	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	308	PHE	0	-0.104	-0.054	27.145	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	309	ARG	1	0.907	0.935	28.992	0.044	0.044	0.000	0.000	0.000	0.000
81	A	310	SER	0	0.044	0.025	31.692	0.002	0.002	0.000	0.000	0.000	0.000
82	A	311	PRO	0	0.073	0.025	34.120	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	312	VAL	0	-0.022	0.001	36.089	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.008	0.010	32.374	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	314	LEU	0	-0.011	0.014	31.648	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	315	ARG	1	0.808	0.850	33.046	0.001	0.001	0.000	0.000	0.000	0.000
87	A	316	GLY	0	0.019	0.015	36.058	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	317	HIS	0	0.048	0.019	30.354	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	318	PHE	0	0.033	0.010	31.759	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	319	ARG	1	0.882	0.931	33.038	0.038	0.038	0.000	0.000	0.000	0.000
91	A	320	ARG	1	0.791	0.897	30.181	0.095	0.095	0.000	0.000	0.000	0.000
92	A	321	GLN	0	0.004	0.004	26.935	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	322	LEU	0	0.044	0.031	30.268	0.000	0.000	0.000	0.000	0.000	0.000
94	A	323	GLY	0	0.015	0.026	33.866	0.006	0.006	0.000	0.000	0.000	0.000
95	A	324	SER	0	-0.011	-0.007	37.068	0.004	0.004	0.000	0.000	0.000	0.000
96	A	325	SER	0	0.042	0.008	37.415	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	326	PRO	0	0.032	0.011	34.907	0.002	0.002	0.000	0.000	0.000	0.000
98	A	327	ALA	0	0.042	0.021	36.912	0.004	0.004	0.000	0.000	0.000	0.000
99	A	328	ALA	0	0.016	0.013	40.285	0.003	0.003	0.000	0.000	0.000	0.000
100	A	329	TYR	0	-0.046	-0.040	33.423	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	330	ARG	1	0.831	0.901	35.488	-0.034	-0.034	0.000	0.000	0.000	0.000
102	A	331	ALA	0	-0.011	0.002	38.670	0.003	0.003	0.000	0.000	0.000	0.000
103	A	332	ALA	0	0.037	0.004	40.691	0.002	0.002	0.000	0.000	0.000	0.000
104	A	333	TYR	0	-0.102	-0.077	33.018	0.000	0.000	0.000	0.000	0.000	0.000
105	A	334	ARG	1	0.821	0.874	36.565	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	335	ALA	0	0.017	0.018	41.323	0.002	0.002	0.000	0.000	0.000	0.000
107	A	336	ARG	1	0.904	0.963	36.633	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	337	ARG	1	0.854	0.914	33.079	-0.035	-0.035	0.000	0.000	0.000	0.000
109	A	338	PRO	0	0.038	0.033	39.776	0.004	0.004	0.000	0.000	0.000	0.000
110	A	339	GLN	0	-0.009	-0.004	40.385	0.001	0.001	0.000	0.000	0.000	0.000
111	A	340	GLY	0	0.011	0.030	35.208	0.004	0.004	0.000	0.000	0.000	0.000

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