FMO DATABASE

FMODB ID: 721QK

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	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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1218422.585088
FMO2-HF: Nuclear repulsion	1165479.015459
FMO2-HF: Total energy	-52943.569629
FMO2-MP2: Total energy	-53100.155455

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.
-2.041	-5.417	19.374	-4.804	-11.19	-0.01

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 : -0.019 / 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	A	356	VAL	0	-0.028	-0.008	3.031	-1.709	0.565	0.340	-0.747	-1.867	-0.002
4	A	357	THR	0	-0.016	-0.017	3.697	0.424	0.565	0.007	0.016	-0.163	0.000
5	A	358	GLY	0	0.049	0.030	6.694	-0.055	-0.055	0.000	0.000	0.000	0.000
6	A	359	ARG	1	0.826	0.895	9.662	0.410	0.410	0.000	0.000	0.000	0.000
7	A	360	ILE	0	-0.012	-0.005	12.327	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	361	ALA	0	0.081	0.049	14.147	0.024	0.024	0.000	0.000	0.000	0.000
9	A	362	PHE	0	-0.031	-0.029	17.411	0.011	0.011	0.000	0.000	0.000	0.000
10	A	363	SER	0	-0.001	-0.004	20.388	0.005	0.005	0.000	0.000	0.000	0.000
11	A	364	LEU	0	-0.020	0.005	22.614	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	365	LYS	1	0.909	0.947	25.766	0.142	0.142	0.000	0.000	0.000	0.000
13	A	366	TYR	0	-0.006	-0.021	29.231	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	367	GLU	-1	-0.864	-0.918	31.694	-0.096	-0.096	0.000	0.000	0.000	0.000
15	A	368	GLN	0	0.124	0.047	34.461	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	369	GLN	0	-0.062	-0.024	36.039	0.002	0.002	0.000	0.000	0.000	0.000
17	A	370	THR	0	-0.014	-0.025	34.456	0.002	0.002	0.000	0.000	0.000	0.000
18	A	371	GLN	0	0.028	0.027	35.563	0.000	0.000	0.000	0.000	0.000	0.000
19	A	372	SER	0	0.005	0.005	30.709	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	373	LEU	0	-0.007	0.008	24.855	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	374	VAL	0	-0.032	-0.026	27.087	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	375	VAL	0	0.007	-0.014	20.718	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	376	HIS	0	-0.026	-0.001	23.029	0.004	0.004	0.000	0.000	0.000	0.000
24	A	377	VAL	0	-0.002	-0.016	16.484	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	378	LYS	1	0.907	0.953	19.224	0.218	0.218	0.000	0.000	0.000	0.000
26	A	379	GLU	-1	-0.881	-0.952	16.242	-0.252	-0.252	0.000	0.000	0.000	0.000
27	A	380	CYS	0	-0.109	-0.040	10.772	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	381	HIS	0	0.061	0.040	12.419	0.037	0.037	0.000	0.000	0.000	0.000
29	A	382	GLN	0	0.005	-0.010	10.360	-0.124	-0.124	0.000	0.000	0.000	0.000
30	A	383	LEU	0	-0.017	0.010	6.294	-0.135	-0.135	0.000	0.000	0.000	0.000
31	A	384	ALA	0	0.054	0.037	2.409	0.117	-0.316	2.302	-0.631	-1.238	-0.001
32	A	385	TYR	0	0.006	-0.007	4.418	0.047	0.228	-0.001	-0.013	-0.166	0.000
33	A	386	ALA	0	0.000	-0.015	2.394	-2.187	-0.840	1.621	-1.273	-1.694	-0.006
34	A	387	ASP	-1	-0.969	-0.973	3.313	0.456	0.384	0.013	0.556	-0.497	-0.003
35	A	388	GLU	-1	-0.721	-0.869	5.611	-0.336	-0.336	0.000	0.000	0.000	0.000
36	A	389	ALA	0	-0.040	-0.005	7.052	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	390	LYS	1	0.893	0.922	10.189	-0.178	-0.178	0.000	0.000	0.000	0.000
38	A	391	LYS	1	0.805	0.923	9.198	0.011	0.011	0.000	0.000	0.000	0.000
39	A	392	ARG	1	0.954	0.974	8.449	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	393	SER	0	-0.011	-0.016	5.814	0.025	0.025	0.000	0.000	0.000	0.000
41	A	394	ASN	0	-0.052	-0.012	7.636	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	395	PRO	0	0.066	0.048	8.613	0.049	0.049	0.000	0.000	0.000	0.000
43	A	396	TYR	0	-0.068	-0.008	9.761	0.033	0.033	0.000	0.000	0.000	0.000
44	A	397	VAL	0	0.069	0.034	10.912	-0.067	-0.067	0.000	0.000	0.000	0.000
45	A	398	LYS	1	0.876	0.927	12.814	0.318	0.318	0.000	0.000	0.000	0.000
46	A	399	THR	0	0.031	0.010	14.977	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	400	TYR	0	-0.017	-0.016	15.593	0.025	0.025	0.000	0.000	0.000	0.000
48	A	401	LEU	0	0.053	0.047	19.865	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	402	LEU	0	-0.021	0.011	18.082	0.023	0.023	0.000	0.000	0.000	0.000
50	A	403	PRO	0	0.062	0.005	22.110	0.004	0.004	0.000	0.000	0.000	0.000
51	A	404	ASP	-1	-0.748	-0.801	23.438	-0.107	-0.107	0.000	0.000	0.000	0.000
52	A	405	LYS	1	0.880	0.929	15.914	0.237	0.237	0.000	0.000	0.000	0.000
53	A	406	SER	0	-0.042	-0.088	20.166	0.006	0.006	0.000	0.000	0.000	0.000
54	A	407	ARG	1	0.988	0.972	20.860	0.058	0.058	0.000	0.000	0.000	0.000
55	A	408	GLN	0	-0.013	-0.013	21.930	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	409	GLY	0	0.143	0.101	23.507	0.002	0.002	0.000	0.000	0.000	0.000
57	A	410	LYS	1	0.836	0.918	16.703	0.115	0.115	0.000	0.000	0.000	0.000
58	A	411	ARG	1	0.806	0.917	19.514	0.149	0.149	0.000	0.000	0.000	0.000
59	A	412	LYS	1	0.910	0.939	16.106	0.096	0.096	0.000	0.000	0.000	0.000
60	A	413	THR	0	0.062	0.054	15.501	0.006	0.006	0.000	0.000	0.000	0.000
61	A	414	SER	0	-0.133	-0.101	16.650	0.009	0.009	0.000	0.000	0.000	0.000
62	A	415	ILE	0	-0.010	-0.014	12.090	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	416	LYS	1	0.951	0.998	13.367	0.194	0.194	0.000	0.000	0.000	0.000
64	A	417	ARG	1	0.906	0.944	12.638	0.045	0.045	0.000	0.000	0.000	0.000
65	A	418	ASP	-1	-0.899	-0.977	11.834	-0.141	-0.141	0.000	0.000	0.000	0.000
66	A	419	THR	0	0.037	0.020	11.328	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	420	VAL	0	0.006	-0.004	8.001	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	421	ASN	0	0.006	0.009	10.132	-0.110	-0.110	0.000	0.000	0.000	0.000
69	A	422	PRO	0	-0.034	0.002	11.501	0.050	0.050	0.000	0.000	0.000	0.000
70	A	423	LEU	0	0.122	0.070	14.410	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	424	TYR	0	-0.167	-0.130	12.768	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	425	ASP	-1	-0.813	-0.912	18.971	-0.161	-0.161	0.000	0.000	0.000	0.000
73	A	426	GLU	-1	-0.822	-0.865	19.560	-0.150	-0.150	0.000	0.000	0.000	0.000
74	A	427	THR	0	-0.027	-0.018	21.848	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	428	LEU	0	-0.061	-0.026	18.749	0.010	0.010	0.000	0.000	0.000	0.000
76	A	429	ARG	1	0.932	0.960	23.492	0.104	0.104	0.000	0.000	0.000	0.000
77	A	430	TYR	0	-0.053	-0.027	21.647	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	431	GLU	-1	-0.893	-0.953	27.660	-0.080	-0.080	0.000	0.000	0.000	0.000
79	A	432	ILE	0	-0.086	-0.041	29.205	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	433	PRO	0	0.078	0.042	32.390	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	434	GLU	-1	-0.855	-0.928	33.396	-0.101	-0.101	0.000	0.000	0.000	0.000
82	A	435	SER	0	-0.019	-0.008	33.557	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	436	LEU	0	0.014	0.003	32.207	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	437	LEU	0	0.008	0.001	27.727	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	438	ALA	0	-0.018	-0.013	28.663	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	439	GLN	0	0.007	0.007	29.534	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	440	ARG	1	0.853	0.948	25.293	0.124	0.124	0.000	0.000	0.000	0.000
88	A	441	THR	0	0.031	0.023	19.749	0.008	0.008	0.000	0.000	0.000	0.000
89	A	442	LEU	0	-0.042	-0.006	19.739	0.003	0.003	0.000	0.000	0.000	0.000
90	A	443	GLN	0	-0.018	-0.014	14.774	0.006	0.006	0.000	0.000	0.000	0.000
91	A	444	PHE	0	0.015	-0.001	14.223	0.034	0.034	0.000	0.000	0.000	0.000
92	A	445	SER	0	0.013	0.018	10.535	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	446	VAL	0	0.060	0.031	7.819	0.141	0.141	0.000	0.000	0.000	0.000
94	A	447	TRP	0	-0.073	-0.046	6.723	-0.155	-0.155	0.000	0.000	0.000	0.000
95	A	448	HIS	0	0.076	0.043	4.652	-0.223	-0.103	-0.001	-0.005	-0.113	0.000
96	A	449	HIS	0	-0.034	-0.011	6.472	0.135	0.135	0.000	0.000	0.000	0.000
97	A	450	GLY	0	0.043	0.004	8.145	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	451	ARG	1	0.977	0.976	9.077	-0.399	-0.399	0.000	0.000	0.000	0.000
99	A	452	PHE	0	-0.021	-0.013	11.338	0.027	0.027	0.000	0.000	0.000	0.000
100	A	453	GLY	0	0.063	0.043	12.734	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	454	ARG	1	0.922	0.966	7.565	-0.400	-0.400	0.000	0.000	0.000	0.000
102	A	455	ASN	0	0.013	-0.001	8.487	0.008	0.008	0.000	0.000	0.000	0.000
103	A	456	THR	0	-0.041	-0.015	2.125	4.660	-4.126	13.436	-1.888	-2.761	0.009
104	A	457	PHE	0	-0.007	0.010	4.611	-0.367	-0.028	-0.001	-0.048	-0.291	0.000
105	A	458	LEU	0	0.014	-0.018	2.281	-2.062	-0.662	1.659	-0.767	-2.292	-0.007
106	A	459	GLY	0	0.058	0.028	4.324	-0.388	-0.275	-0.001	-0.004	-0.108	0.000
107	A	460	GLU	-1	-0.999	-0.993	6.593	-0.399	-0.399	0.000	0.000	0.000	0.000
108	A	461	ALA	0	0.040	0.024	10.233	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	462	GLU	-1	-0.875	-0.952	13.457	-0.321	-0.321	0.000	0.000	0.000	0.000
110	A	463	ILE	0	0.015	0.009	17.105	0.004	0.004	0.000	0.000	0.000	0.000
111	A	464	GLN	0	0.006	0.000	20.619	0.005	0.005	0.000	0.000	0.000	0.000
112	A	465	MET	0	-0.008	-0.001	23.724	0.008	0.008	0.000	0.000	0.000	0.000
113	A	466	ASP	-1	-0.809	-0.886	26.529	-0.111	-0.111	0.000	0.000	0.000	0.000
114	A	467	SER	0	0.057	0.022	26.597	0.005	0.005	0.000	0.000	0.000	0.000
115	A	468	TRP	0	-0.054	-0.021	25.734	0.007	0.007	0.000	0.000	0.000	0.000
116	A	469	LYS	1	0.810	0.883	27.855	0.120	0.120	0.000	0.000	0.000	0.000
117	A	470	LEU	0	-0.029	0.021	31.025	0.007	0.007	0.000	0.000	0.000	0.000
118	A	471	ASP	-1	-0.827	-0.921	31.870	-0.107	-0.107	0.000	0.000	0.000	0.000
119	A	472	LYS	1	0.747	0.865	29.556	0.111	0.111	0.000	0.000	0.000	0.000
120	A	473	LYS	1	0.930	0.955	23.848	0.205	0.205	0.000	0.000	0.000	0.000
121	A	474	LEU	0	-0.003	0.000	27.250	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	475	ASP	-1	-0.795	-0.882	24.504	-0.182	-0.182	0.000	0.000	0.000	0.000
123	A	476	HIS	0	-0.059	-0.037	20.680	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	477	CYM	-1	-0.772	-0.870	17.697	-0.366	-0.366	0.000	0.000	0.000	0.000
125	A	478	LEU	0	-0.058	-0.021	15.448	0.009	0.009	0.000	0.000	0.000	0.000
126	A	479	PRO	0	-0.008	-0.005	12.375	-0.035	-0.035	0.000	0.000	0.000	0.000
127	A	480	LEU	0	-0.014	-0.010	7.806	0.033	0.033	0.000	0.000	0.000	0.000
128	A	481	HIS	0	-0.017	0.000	9.070	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	482	GLY	0	0.035	0.003	6.271	-0.276	-0.276	0.000	0.000	0.000	0.000
130	A	483	LYS	1	0.969	0.981	6.490	1.050	1.050	0.000	0.000	0.000	0.000

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