FMO DATABASE

FMODB ID: 6YG6Z

Calculation Name: 5HDW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HDW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UK99

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1137774.306945
FMO2-HF: Nuclear repulsion	1085020.296334
FMO2-HF: Total energy	-52754.010612
FMO2-MP2: Total energy	-52906.360579

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:-3:SER)

Summations of interaction energy for fragment #1(A:-3: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.
-5.095	2.183	1.276	-3.753	-4.798	-0.016

Interaction energy analysis for fragmet #1(A:-3:SER)

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 : -0.005

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	-1	PHE	0	-0.011	-0.003	2.701	-1.368	2.650	0.485	-2.074	-2.429	-0.003
4	A	278	VAL	0	0.018	-0.001	6.485	-0.012	-0.012	0.000	0.000	0.000	0.000
5	A	279	ALA	0	0.003	0.012	10.141	0.251	0.251	0.000	0.000	0.000	0.000
6	A	280	THR	0	0.052	0.030	13.559	-0.097	-0.097	0.000	0.000	0.000	0.000
7	A	281	THR	0	-0.049	-0.025	16.871	0.078	0.078	0.000	0.000	0.000	0.000
8	A	282	GLY	0	-0.001	0.007	20.255	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	283	ASP	-1	-0.836	-0.910	22.099	-0.346	-0.346	0.000	0.000	0.000	0.000
10	A	284	ILE	0	-0.019	-0.017	18.759	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	285	THR	0	-0.003	-0.003	13.883	0.045	0.045	0.000	0.000	0.000	0.000
12	A	286	VAL	0	0.002	-0.003	12.555	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	287	SER	0	0.009	-0.012	9.340	0.032	0.032	0.000	0.000	0.000	0.000
14	A	288	VAL	0	0.000	0.002	6.492	0.184	0.184	0.000	0.000	0.000	0.000
15	A	289	SER	0	0.023	0.021	3.923	-0.851	-0.657	0.000	-0.076	-0.117	0.000
16	A	290	THR	0	0.008	0.003	2.546	-1.892	0.112	0.616	-1.064	-1.555	-0.008
17	A	291	SER	0	-0.019	-0.013	3.113	-1.773	-0.763	0.176	-0.538	-0.648	-0.005
18	A	292	PHE	0	0.037	0.014	5.462	0.193	0.193	0.000	0.000	0.000	0.000
19	A	293	LEU	0	0.025	0.007	8.098	0.069	0.069	0.000	0.000	0.000	0.000
20	A	294	PRO	0	0.006	-0.007	11.105	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	295	GLU	-1	-0.942	-0.960	14.045	-0.064	-0.064	0.000	0.000	0.000	0.000
22	A	296	LEU	0	-0.056	-0.021	15.002	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	297	SER	0	-0.046	-0.019	13.904	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	298	SER	0	-0.015	-0.002	16.342	0.034	0.034	0.000	0.000	0.000	0.000
25	A	299	VAL	0	-0.015	-0.015	18.688	0.005	0.005	0.000	0.000	0.000	0.000
26	A	300	HIS	0	-0.034	-0.009	20.080	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	301	PRO	0	0.048	0.011	23.443	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	302	PRO	0	-0.038	-0.006	19.897	0.001	0.001	0.000	0.000	0.000	0.000
29	A	303	HIS	0	0.008	0.005	18.164	-0.055	-0.055	0.000	0.000	0.000	0.000
30	A	304	TYR	0	0.000	-0.009	12.929	0.040	0.040	0.000	0.000	0.000	0.000
31	A	305	PHE	0	0.039	0.012	12.290	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	306	PHE	0	0.016	-0.001	7.031	0.059	0.059	0.000	0.000	0.000	0.000
33	A	307	THR	0	0.011	0.005	8.465	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	308	TYR	0	0.027	-0.008	7.016	-0.600	-0.600	0.000	0.000	0.000	0.000
35	A	309	ARG	1	0.800	0.875	7.227	3.167	3.167	0.000	0.000	0.000	0.000
36	A	310	ILE	0	-0.035	-0.018	8.678	-0.505	-0.505	0.000	0.000	0.000	0.000
37	A	311	ARG	1	0.843	0.908	11.286	1.450	1.450	0.000	0.000	0.000	0.000
38	A	312	ILE	0	-0.006	0.005	12.969	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	313	GLU	-1	-0.831	-0.909	14.617	-0.974	-0.974	0.000	0.000	0.000	0.000
40	A	314	MET	0	0.006	0.018	18.225	0.023	0.023	0.000	0.000	0.000	0.000
41	A	315	SER	0	0.016	-0.006	21.415	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	316	LYS	1	0.958	0.940	22.325	0.388	0.388	0.000	0.000	0.000	0.000
43	A	317	ASP	-1	-0.909	-0.919	25.024	-0.314	-0.314	0.000	0.000	0.000	0.000
44	A	318	ALA	0	0.002	0.024	25.764	0.023	0.023	0.000	0.000	0.000	0.000
45	A	319	LEU	0	0.002	-0.009	27.717	0.006	0.006	0.000	0.000	0.000	0.000
46	A	320	PRO	0	0.020	0.001	30.214	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	321	GLU	-1	-0.880	-0.954	31.716	-0.228	-0.228	0.000	0.000	0.000	0.000
48	A	322	LYS	1	0.789	0.881	28.094	0.299	0.299	0.000	0.000	0.000	0.000
49	A	323	ALA	0	0.018	0.018	28.121	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	324	CYS	0	-0.048	-0.011	25.476	0.008	0.008	0.000	0.000	0.000	0.000
51	A	325	GLN	0	-0.028	-0.029	26.329	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	326	LEU	0	-0.061	0.000	21.079	0.012	0.012	0.000	0.000	0.000	0.000
53	A	327	ASP	-1	-0.792	-0.893	24.389	-0.328	-0.328	0.000	0.000	0.000	0.000
54	A	328	SER	0	-0.049	-0.040	24.143	0.013	0.013	0.000	0.000	0.000	0.000
55	A	329	ARG	1	0.883	0.947	18.739	0.481	0.481	0.000	0.000	0.000	0.000
56	A	330	TYR	0	-0.077	-0.070	19.937	0.036	0.036	0.000	0.000	0.000	0.000
57	A	331	TRP	0	0.001	-0.007	12.247	-0.098	-0.098	0.000	0.000	0.000	0.000
58	A	332	ARG	1	0.949	0.972	16.948	0.296	0.296	0.000	0.000	0.000	0.000
59	A	333	ILE	0	0.002	-0.013	14.600	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	334	THR	0	0.004	0.008	14.819	0.081	0.081	0.000	0.000	0.000	0.000
61	A	335	ASN	0	-0.007	-0.021	14.491	0.009	0.009	0.000	0.000	0.000	0.000
62	A	336	ALA	0	-0.021	-0.024	15.111	0.016	0.016	0.000	0.000	0.000	0.000
63	A	337	LYS	1	0.868	0.933	16.672	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	338	GLY	0	-0.008	0.004	19.279	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	339	ASP	-1	-0.840	-0.891	20.732	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	340	VAL	0	-0.063	-0.049	19.448	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	341	GLU	-1	-0.942	-0.960	19.654	-0.291	-0.291	0.000	0.000	0.000	0.000
68	A	342	GLU	-1	-0.881	-0.911	19.894	-0.290	-0.290	0.000	0.000	0.000	0.000
69	A	343	VAL	0	-0.011	-0.008	19.642	0.010	0.010	0.000	0.000	0.000	0.000
70	A	344	GLN	0	0.005	0.001	21.198	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	345	GLY	0	-0.012	0.000	23.575	0.027	0.027	0.000	0.000	0.000	0.000
72	A	346	PRO	0	-0.004	-0.005	24.059	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	347	GLY	0	0.063	0.023	23.753	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	348	VAL	0	-0.035	-0.018	18.168	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	349	VAL	0	-0.003	-0.003	17.759	0.006	0.006	0.000	0.000	0.000	0.000
76	A	350	GLY	0	0.005	0.009	20.704	0.024	0.024	0.000	0.000	0.000	0.000
77	A	351	GLU	-1	-0.885	-0.903	21.901	-0.515	-0.515	0.000	0.000	0.000	0.000
78	A	352	PHE	0	0.003	-0.008	23.600	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	353	PRO	0	0.015	0.031	21.020	0.043	0.043	0.000	0.000	0.000	0.000
80	A	354	ILE	0	0.014	0.000	24.225	0.003	0.003	0.000	0.000	0.000	0.000
81	A	355	ILE	0	-0.001	0.005	20.533	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	356	SER	0	0.044	0.007	24.128	0.033	0.033	0.000	0.000	0.000	0.000
83	A	357	PRO	0	0.053	0.020	24.552	-0.039	-0.039	0.000	0.000	0.000	0.000
84	A	358	GLY	0	-0.087	-0.044	23.023	0.025	0.025	0.000	0.000	0.000	0.000
85	A	359	ARG	1	0.812	0.919	22.096	0.409	0.409	0.000	0.000	0.000	0.000
86	A	360	VAL	0	0.026	0.002	15.807	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	361	TYR	0	-0.070	-0.052	17.828	0.011	0.011	0.000	0.000	0.000	0.000
88	A	362	GLU	-1	-0.772	-0.863	12.482	-1.668	-1.668	0.000	0.000	0.000	0.000
89	A	363	TYR	0	0.004	-0.005	13.979	0.127	0.127	0.000	0.000	0.000	0.000
90	A	364	THR	0	-0.012	-0.021	11.132	-0.302	-0.302	0.000	0.000	0.000	0.000
91	A	365	SER	0	-0.011	0.005	11.928	0.257	0.257	0.000	0.000	0.000	0.000
92	A	366	CYS	0	-0.043	-0.019	11.666	-0.169	-0.169	0.000	0.000	0.000	0.000
93	A	367	THR	0	0.014	0.006	10.999	0.091	0.091	0.000	0.000	0.000	0.000
94	A	368	THR	0	0.018	0.020	12.965	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	369	PHE	0	0.034	0.020	10.896	0.024	0.024	0.000	0.000	0.000	0.000
96	A	370	SER	0	-0.006	0.006	15.724	0.043	0.043	0.000	0.000	0.000	0.000
97	A	371	THR	0	-0.030	-0.037	15.269	0.020	0.020	0.000	0.000	0.000	0.000
98	A	372	THR	0	0.019	0.010	13.418	-0.074	-0.074	0.000	0.000	0.000	0.000
99	A	373	SER	0	0.009	0.000	10.851	0.108	0.108	0.000	0.000	0.000	0.000
100	A	374	GLY	0	0.071	0.041	10.628	-0.061	-0.061	0.000	0.000	0.000	0.000
101	A	375	TYR	0	-0.062	-0.025	9.979	0.001	0.001	0.000	0.000	0.000	0.000
102	A	376	MET	0	-0.013	0.012	10.500	0.044	0.044	0.000	0.000	0.000	0.000
103	A	377	GLU	-1	-0.785	-0.876	11.395	-0.467	-0.467	0.000	0.000	0.000	0.000
104	A	378	GLY	0	0.038	0.013	13.877	0.065	0.065	0.000	0.000	0.000	0.000
105	A	379	TYR	0	-0.058	-0.019	16.780	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	380	TYR	0	0.054	0.034	14.441	0.028	0.028	0.000	0.000	0.000	0.000
107	A	381	THR	0	-0.013	-0.019	20.525	0.022	0.022	0.000	0.000	0.000	0.000
108	A	382	PHE	0	0.022	0.011	20.369	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	383	HIS	0	0.002	-0.005	25.709	0.040	0.040	0.000	0.000	0.000	0.000
110	A	384	PHE	0	-0.031	-0.024	28.432	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	385	LEU	0	0.011	0.013	30.132	0.013	0.013	0.000	0.000	0.000	0.000
112	A	386	TYR	0	-0.046	-0.029	32.849	0.013	0.013	0.000	0.000	0.000	0.000
113	A	387	PHE	0	-0.036	-0.016	33.269	0.016	0.016	0.000	0.000	0.000	0.000
114	A	388	LYS	1	0.964	0.975	35.224	0.148	0.148	0.000	0.000	0.000	0.000
115	A	389	ASP	-1	-0.881	-0.938	35.392	-0.184	-0.184	0.000	0.000	0.000	0.000
116	A	390	LYS	1	0.865	0.950	32.703	0.189	0.189	0.000	0.000	0.000	0.000
117	A	391	ILE	0	0.061	0.021	28.687	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	392	PHE	0	-0.042	-0.023	23.954	0.015	0.015	0.000	0.000	0.000	0.000
119	A	393	ASN	0	0.033	0.030	22.517	-0.029	-0.029	0.000	0.000	0.000	0.000
120	A	394	VAL	0	0.004	-0.001	18.154	0.018	0.018	0.000	0.000	0.000	0.000
121	A	395	ALA	0	0.000	0.000	16.535	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	396	ILE	0	-0.012	0.002	12.110	-0.098	-0.098	0.000	0.000	0.000	0.000
123	A	397	PRO	0	-0.022	0.004	9.549	0.143	0.143	0.000	0.000	0.000	0.000
124	A	398	ARG	1	0.873	0.917	10.422	0.175	0.175	0.000	0.000	0.000	0.000
125	A	399	PHE	0	-0.024	-0.005	5.828	-0.165	-0.165	0.000	0.000	0.000	0.000
126	A	400	HIS	0	-0.017	-0.017	5.926	0.332	0.332	0.000	0.000	0.000	0.000
127	A	401	MET	0	-0.048	-0.009	5.143	-0.559	-0.507	-0.001	-0.001	-0.049	0.000
128	A	402	ALA	0	0.036	-0.003	6.715	0.063	0.063	0.000	0.000	0.000	0.000
129	A	403	CYS	0	-0.034	0.000	7.339	0.403	0.403	0.000	0.000	0.000	0.000
130	A	404	PRO	0	-0.043	-0.010	7.751	-0.067	-0.067	0.000	0.000	0.000	0.000
131	A	405	THR	0	0.031	0.015	10.246	-0.161	-0.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:SER)