FMO DATABASE

FMODB ID: 2JV9R

Calculation Name: 3FDW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FDW

Chain ID: A

ChEMBL ID:

UniProt ID: Q96C24

Base Structure: X-ray

Registration Date: 2023-09-20

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	130
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219606.888514
FMO2-HF: Nuclear repulsion	1166662.551262
FMO2-HF: Total energy	-52944.337252
FMO2-MP2: Total energy	-53100.927744

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:354:ILE)

Summations of interaction energy for fragment #1(A:354: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.
-5.822	-2.887	10.925	-3.256	-10.603	-0.017

Interaction energy analysis for fragmet #1(A:354:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.029

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	356	VAL	0	-0.026	-0.005	3.078	-1.730	0.374	0.300	-0.715	-1.689	-0.003
4	A	357	THR	0	-0.013	-0.011	3.906	0.432	0.577	0.001	-0.004	-0.142	0.000
5	A	358	GLY	0	0.044	0.028	6.624	-0.077	-0.077	0.000	0.000	0.000	0.000
6	A	359	ARG	1	0.734	0.785	9.639	0.391	0.391	0.000	0.000	0.000	0.000
7	A	360	ILE	0	-0.012	-0.008	12.456	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	361	ALA	0	0.071	0.047	14.272	0.028	0.028	0.000	0.000	0.000	0.000
9	A	362	PHE	0	-0.013	-0.022	17.642	0.008	0.008	0.000	0.000	0.000	0.000
10	A	363	SER	0	0.003	-0.006	20.452	0.007	0.007	0.000	0.000	0.000	0.000
11	A	364	LEU	0	-0.045	0.001	22.465	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	365	LYS	1	0.898	0.935	25.923	0.150	0.150	0.000	0.000	0.000	0.000
13	A	366	TYR	0	-0.016	-0.031	29.323	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	367	GLU	-1	-0.767	-0.814	31.848	-0.104	-0.104	0.000	0.000	0.000	0.000
15	A	368	GLN	0	0.078	0.024	34.549	0.000	0.000	0.000	0.000	0.000	0.000
16	A	369	GLN	0	-0.035	-0.014	36.182	0.002	0.002	0.000	0.000	0.000	0.000
17	A	370	THR	0	-0.010	-0.043	34.372	0.001	0.001	0.000	0.000	0.000	0.000
18	A	371	GLN	0	-0.012	0.006	35.187	0.002	0.002	0.000	0.000	0.000	0.000
19	A	372	SER	0	0.020	0.022	30.416	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	373	LEU	0	-0.002	0.008	24.960	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	374	VAL	0	-0.047	-0.033	27.266	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	375	VAL	0	0.003	-0.014	20.879	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	376	HIS	0	-0.030	-0.015	23.095	0.003	0.003	0.000	0.000	0.000	0.000
24	A	377	VAL	0	-0.004	-0.015	16.536	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	378	LYS	1	0.935	0.965	19.271	0.223	0.223	0.000	0.000	0.000	0.000
26	A	379	GLU	-1	-0.883	-0.948	16.253	-0.267	-0.267	0.000	0.000	0.000	0.000
27	A	380	CYS	0	-0.112	-0.043	11.015	-0.045	-0.045	0.000	0.000	0.000	0.000
28	A	381	HIS	0	0.051	0.034	12.418	0.037	0.037	0.000	0.000	0.000	0.000
29	A	382	GLN	0	0.014	-0.006	10.415	-0.094	-0.094	0.000	0.000	0.000	0.000
30	A	383	LEU	0	-0.010	0.003	6.275	-0.134	-0.134	0.000	0.000	0.000	0.000
31	A	384	ALA	0	0.043	0.031	2.420	0.066	-0.314	2.250	-0.603	-1.267	-0.001
32	A	385	TYR	0	0.014	0.001	4.398	-0.072	0.144	-0.001	-0.018	-0.197	0.000
33	A	386	ALA	0	-0.006	-0.019	2.128	-1.568	-1.054	3.287	-1.895	-1.906	-0.001
34	A	387	ASP	-1	-0.924	-0.951	3.080	1.910	0.490	0.007	1.834	-0.422	-0.002
35	A	388	GLU	-1	-0.711	-0.853	5.751	-0.284	-0.284	0.000	0.000	0.000	0.000
36	A	389	ALA	0	-0.049	-0.017	7.318	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	390	LYS	1	0.899	0.925	10.358	-0.174	-0.174	0.000	0.000	0.000	0.000
38	A	391	LYS	1	0.808	0.926	9.280	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	392	ARG	1	0.891	0.941	8.312	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	393	SER	0	-0.026	-0.018	5.380	0.059	0.059	0.000	0.000	0.000	0.000
41	A	394	ASN	0	-0.049	-0.024	7.286	0.009	0.009	0.000	0.000	0.000	0.000
42	A	395	PRO	0	0.061	0.047	8.452	0.029	0.029	0.000	0.000	0.000	0.000
43	A	396	TYR	0	-0.086	-0.037	9.720	0.049	0.049	0.000	0.000	0.000	0.000
44	A	397	VAL	0	0.079	0.038	10.788	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	398	LYS	1	0.851	0.929	11.347	0.468	0.468	0.000	0.000	0.000	0.000
46	A	399	THR	0	0.036	0.009	14.531	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	400	TYR	0	-0.046	-0.023	14.863	0.016	0.016	0.000	0.000	0.000	0.000
48	A	401	LEU	0	0.059	0.052	19.304	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	402	LEU	0	-0.020	0.020	17.962	0.024	0.024	0.000	0.000	0.000	0.000
50	A	403	PRO	0	0.049	-0.001	22.027	0.005	0.005	0.000	0.000	0.000	0.000
51	A	404	ASP	-1	-0.799	-0.882	23.254	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	405	LYS	1	0.859	0.927	15.524	0.285	0.285	0.000	0.000	0.000	0.000
53	A	406	SER	0	-0.015	-0.023	19.858	0.004	0.004	0.000	0.000	0.000	0.000
54	A	407	ARG	1	1.009	0.984	20.462	0.082	0.082	0.000	0.000	0.000	0.000
55	A	408	GLN	0	-0.020	-0.009	21.537	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	409	GLY	0	0.121	0.086	23.020	0.004	0.004	0.000	0.000	0.000	0.000
57	A	410	LYS	1	0.854	0.937	15.995	0.162	0.162	0.000	0.000	0.000	0.000
58	A	411	ARG	1	0.823	0.916	18.968	0.173	0.173	0.000	0.000	0.000	0.000
59	A	412	LYS	1	0.904	0.944	15.657	0.137	0.137	0.000	0.000	0.000	0.000
60	A	413	THR	0	0.059	0.057	15.515	0.009	0.009	0.000	0.000	0.000	0.000
61	A	414	SER	0	-0.119	-0.081	16.563	0.004	0.004	0.000	0.000	0.000	0.000
62	A	415	ILE	0	-0.012	-0.021	12.173	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	416	LYS	1	0.853	0.951	13.311	0.238	0.238	0.000	0.000	0.000	0.000
64	A	417	ARG	1	0.911	0.945	12.488	0.064	0.064	0.000	0.000	0.000	0.000
65	A	418	ASP	-1	-0.869	-0.959	11.419	-0.133	-0.133	0.000	0.000	0.000	0.000
66	A	419	THR	0	0.030	0.014	10.973	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	420	VAL	0	-0.005	-0.004	7.625	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	421	ASN	0	0.005	0.009	10.044	-0.120	-0.120	0.000	0.000	0.000	0.000
69	A	422	PRO	0	-0.032	0.002	11.449	0.052	0.052	0.000	0.000	0.000	0.000
70	A	423	LEU	0	0.117	0.067	14.365	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	424	TYR	0	-0.139	-0.119	12.553	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	425	ASP	-1	-0.798	-0.889	18.964	-0.175	-0.175	0.000	0.000	0.000	0.000
73	A	426	GLU	-1	-0.789	-0.861	19.511	-0.188	-0.188	0.000	0.000	0.000	0.000
74	A	427	THR	0	-0.026	-0.022	21.888	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	428	LEU	0	-0.059	-0.020	18.526	0.008	0.008	0.000	0.000	0.000	0.000
76	A	429	ARG	1	0.823	0.872	23.239	0.116	0.116	0.000	0.000	0.000	0.000
77	A	430	TYR	0	-0.054	-0.041	21.157	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	431	GLU	-1	-0.922	-0.962	27.174	-0.090	-0.090	0.000	0.000	0.000	0.000
79	A	432	ILE	0	-0.039	-0.028	28.793	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	433	PRO	0	0.073	0.061	31.869	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	434	GLU	-1	-0.804	-0.899	33.274	-0.107	-0.107	0.000	0.000	0.000	0.000
82	A	435	SER	0	-0.006	-0.005	33.866	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	436	LEU	0	0.018	0.003	31.881	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	437	LEU	0	-0.005	-0.002	27.390	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	438	ALA	0	-0.004	-0.007	28.950	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	439	GLN	0	0.005	0.005	29.656	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	440	ARG	1	0.848	0.940	25.193	0.132	0.132	0.000	0.000	0.000	0.000
88	A	441	THR	0	0.033	0.016	20.187	0.008	0.008	0.000	0.000	0.000	0.000
89	A	442	LEU	0	-0.033	-0.001	20.064	0.000	0.000	0.000	0.000	0.000	0.000
90	A	443	GLN	0	-0.007	-0.027	14.876	0.003	0.003	0.000	0.000	0.000	0.000
91	A	444	PHE	0	0.017	-0.004	14.366	0.025	0.025	0.000	0.000	0.000	0.000
92	A	445	SER	0	0.003	0.002	10.140	-0.044	-0.044	0.000	0.000	0.000	0.000
93	A	446	VAL	0	0.056	0.031	7.872	0.143	0.143	0.000	0.000	0.000	0.000
94	A	447	TRP	0	-0.024	-0.024	6.324	-0.241	-0.241	0.000	0.000	0.000	0.000
95	A	448	HIS	0	0.079	0.047	4.605	-0.172	-0.029	-0.001	-0.008	-0.134	0.000
96	A	449	HIS	0	-0.038	-0.023	6.594	0.117	0.117	0.000	0.000	0.000	0.000
97	A	450	GLY	0	0.060	0.017	7.990	0.011	0.011	0.000	0.000	0.000	0.000
98	A	451	ARG	1	0.974	0.976	8.912	-0.352	-0.352	0.000	0.000	0.000	0.000
99	A	452	PHE	0	-0.017	-0.015	11.293	0.016	0.016	0.000	0.000	0.000	0.000
100	A	453	GLY	0	0.067	0.048	12.578	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	454	ARG	1	0.917	0.960	7.762	-0.305	-0.305	0.000	0.000	0.000	0.000
102	A	455	ASN	0	0.021	0.025	8.164	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	456	THR	0	-0.026	-0.019	2.273	0.113	-0.659	2.840	-0.508	-1.559	0.004
104	A	457	PHE	0	-0.023	0.018	4.232	-0.477	-0.045	0.001	-0.076	-0.356	0.000
105	A	458	LEU	0	0.029	-0.012	2.383	-3.500	-1.653	2.242	-1.255	-2.834	-0.014
106	A	459	GLY	0	0.052	0.026	4.430	-0.225	-0.119	-0.001	-0.008	-0.097	0.000
107	A	460	GLU	-1	-0.977	-0.991	7.153	-0.424	-0.424	0.000	0.000	0.000	0.000
108	A	461	ALA	0	0.037	0.028	10.772	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	462	GLU	-1	-0.844	-0.931	13.980	-0.326	-0.326	0.000	0.000	0.000	0.000
110	A	463	ILE	0	0.019	0.014	17.658	0.007	0.007	0.000	0.000	0.000	0.000
111	A	464	GLN	0	0.001	-0.003	21.142	0.006	0.006	0.000	0.000	0.000	0.000
112	A	465	MET	0	-0.009	-0.003	23.941	0.007	0.007	0.000	0.000	0.000	0.000
113	A	466	ASP	-1	-0.805	-0.886	27.083	-0.108	-0.108	0.000	0.000	0.000	0.000
114	A	467	SER	0	0.048	0.021	26.814	0.006	0.006	0.000	0.000	0.000	0.000
115	A	468	TRP	0	-0.041	-0.021	26.226	0.007	0.007	0.000	0.000	0.000	0.000
116	A	469	LYS	1	0.806	0.882	28.336	0.119	0.119	0.000	0.000	0.000	0.000
117	A	470	LEU	0	-0.022	0.012	31.527	0.007	0.007	0.000	0.000	0.000	0.000
118	A	471	ASP	-1	-0.850	-0.927	31.967	-0.110	-0.110	0.000	0.000	0.000	0.000
119	A	472	LYS	1	0.749	0.876	29.969	0.113	0.113	0.000	0.000	0.000	0.000
120	A	473	LYS	1	0.912	0.943	24.113	0.206	0.206	0.000	0.000	0.000	0.000
121	A	474	LEU	0	-0.004	-0.002	27.620	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	475	ASP	-1	-0.801	-0.895	24.709	-0.190	-0.190	0.000	0.000	0.000	0.000
123	A	476	HIS	0	-0.032	-0.014	20.982	0.000	0.000	0.000	0.000	0.000	0.000
124	A	477	CYM	-1	-0.706	-0.769	17.744	-0.378	-0.378	0.000	0.000	0.000	0.000
125	A	478	LEU	0	-0.042	-0.017	15.737	0.015	0.015	0.000	0.000	0.000	0.000
126	A	479	PRO	0	0.012	0.006	12.563	-0.039	-0.039	0.000	0.000	0.000	0.000
127	A	480	LEU	0	-0.034	-0.018	8.155	0.030	0.030	0.000	0.000	0.000	0.000
128	A	481	HIS	0	-0.015	-0.005	9.406	0.011	0.011	0.000	0.000	0.000	0.000
129	A	482	GLY	0	0.041	0.007	6.746	-0.281	-0.281	0.000	0.000	0.000	0.000
130	A	483	LYS	1	0.965	0.981	6.508	0.973	0.973	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:354:ILE)