FMO DATABASE

FMODB ID: 2NL2R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1136840.036677
FMO2-HF: Nuclear repulsion	1084086.483345
FMO2-HF: Total energy	-52753.553332
FMO2-MP2: Total energy	-52905.841967

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.
-4.986	2.384	0.844	-3.676	-4.539	-0.012

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 : 0.001 / q_NPA : -0.001

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	-0.021	-0.010	3.150	-2.370	1.761	0.144	-2.024	-2.251	0.000
4	A	278	VAL	0	0.022	0.001	6.193	0.163	0.163	0.000	0.000	0.000	0.000
5	A	279	ALA	0	0.003	0.010	9.807	0.136	0.136	0.000	0.000	0.000	0.000
6	A	280	THR	0	0.070	0.057	13.237	-0.041	-0.041	0.000	0.000	0.000	0.000
7	A	281	THR	0	-0.053	-0.024	16.545	0.037	0.037	0.000	0.000	0.000	0.000
8	A	282	GLY	0	-0.015	0.000	19.972	0.012	0.012	0.000	0.000	0.000	0.000
9	A	283	ASP	-1	-0.905	-0.948	21.801	-0.307	-0.307	0.000	0.000	0.000	0.000
10	A	284	ILE	0	-0.022	-0.026	18.696	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	285	THR	0	-0.019	-0.036	13.888	0.014	0.014	0.000	0.000	0.000	0.000
12	A	286	VAL	0	-0.001	-0.004	12.575	0.007	0.007	0.000	0.000	0.000	0.000
13	A	287	SER	0	0.005	-0.007	9.402	-0.072	-0.072	0.000	0.000	0.000	0.000
14	A	288	VAL	0	-0.009	-0.006	6.523	0.230	0.230	0.000	0.000	0.000	0.000
15	A	289	SER	0	-0.002	0.009	3.997	-0.763	-0.590	-0.001	-0.067	-0.106	0.000
16	A	290	THR	0	-0.002	-0.002	2.593	-1.492	0.529	0.523	-1.053	-1.491	-0.007
17	A	291	SER	0	-0.013	-0.012	3.122	-0.552	0.437	0.179	-0.531	-0.637	-0.005
18	A	292	PHE	0	0.039	0.016	5.450	-0.320	-0.320	0.000	0.000	0.000	0.000
19	A	293	LEU	0	0.016	0.003	8.063	0.204	0.204	0.000	0.000	0.000	0.000
20	A	294	PRO	0	0.001	-0.012	11.064	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	295	GLU	-1	-0.932	-0.957	14.006	0.238	0.238	0.000	0.000	0.000	0.000
22	A	296	LEU	0	-0.052	-0.020	15.146	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	297	SER	0	-0.046	-0.012	13.799	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	298	SER	0	-0.036	-0.023	16.306	0.041	0.041	0.000	0.000	0.000	0.000
25	A	299	VAL	0	-0.010	-0.012	18.645	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	300	HIS	0	-0.038	-0.013	20.313	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	301	PRO	0	0.042	0.010	23.505	0.012	0.012	0.000	0.000	0.000	0.000
28	A	302	PRO	0	-0.015	0.008	19.992	0.014	0.014	0.000	0.000	0.000	0.000
29	A	303	HIS	0	0.006	0.010	18.139	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	304	TYR	0	0.001	-0.008	12.866	0.050	0.050	0.000	0.000	0.000	0.000
31	A	305	PHE	0	0.036	0.012	12.371	-0.138	-0.138	0.000	0.000	0.000	0.000
32	A	306	PHE	0	0.019	0.001	6.952	0.107	0.107	0.000	0.000	0.000	0.000
33	A	307	THR	0	0.004	0.004	8.434	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	308	TYR	0	0.029	-0.003	7.043	-0.391	-0.391	0.000	0.000	0.000	0.000
35	A	309	ARG	1	0.921	0.965	7.042	1.937	1.937	0.000	0.000	0.000	0.000
36	A	310	ILE	0	-0.042	-0.014	8.665	-0.438	-0.438	0.000	0.000	0.000	0.000
37	A	311	ARG	1	0.904	0.963	11.333	0.940	0.940	0.000	0.000	0.000	0.000
38	A	312	ILE	0	-0.007	0.005	12.960	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	313	GLU	-1	-0.898	-0.955	14.913	-0.599	-0.599	0.000	0.000	0.000	0.000
40	A	314	MET	0	0.000	0.012	18.218	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	315	SER	0	0.015	-0.014	21.415	0.013	0.013	0.000	0.000	0.000	0.000
42	A	316	LYS	1	0.955	0.934	22.305	0.216	0.216	0.000	0.000	0.000	0.000
43	A	317	ASP	-1	-0.909	-0.909	25.006	-0.234	-0.234	0.000	0.000	0.000	0.000
44	A	318	ALA	0	0.044	0.043	25.806	0.013	0.013	0.000	0.000	0.000	0.000
45	A	319	LEU	0	-0.024	-0.020	27.717	0.010	0.010	0.000	0.000	0.000	0.000
46	A	320	PRO	0	0.027	0.001	30.214	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	321	GLU	-1	-0.885	-0.951	31.716	-0.177	-0.177	0.000	0.000	0.000	0.000
48	A	322	LYS	1	0.870	0.930	28.171	0.238	0.238	0.000	0.000	0.000	0.000
49	A	323	ALA	0	0.037	0.031	28.116	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	324	CYS	0	-0.043	-0.013	25.521	0.001	0.001	0.000	0.000	0.000	0.000
51	A	325	GLN	0	-0.020	-0.018	26.410	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	326	LEU	0	-0.069	-0.009	20.711	0.001	0.001	0.000	0.000	0.000	0.000
53	A	327	ASP	-1	-0.811	-0.908	24.442	-0.275	-0.275	0.000	0.000	0.000	0.000
54	A	328	SER	0	-0.059	-0.044	24.205	0.010	0.010	0.000	0.000	0.000	0.000
55	A	329	ARG	1	0.901	0.959	18.717	0.423	0.423	0.000	0.000	0.000	0.000
56	A	330	TYR	0	-0.065	-0.059	20.056	0.027	0.027	0.000	0.000	0.000	0.000
57	A	331	TRP	0	-0.004	-0.007	12.488	-0.098	-0.098	0.000	0.000	0.000	0.000
58	A	332	ARG	1	0.990	1.001	17.111	0.553	0.553	0.000	0.000	0.000	0.000
59	A	333	ILE	0	0.008	-0.010	14.774	-0.119	-0.119	0.000	0.000	0.000	0.000
60	A	334	THR	0	-0.003	0.008	14.870	0.106	0.106	0.000	0.000	0.000	0.000
61	A	335	ASN	0	0.026	0.014	14.488	-0.078	-0.078	0.000	0.000	0.000	0.000
62	A	336	ALA	0	-0.029	-0.032	15.041	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	337	LYS	1	0.875	0.934	16.592	0.171	0.171	0.000	0.000	0.000	0.000
64	A	338	GLY	0	-0.010	0.002	19.249	0.021	0.021	0.000	0.000	0.000	0.000
65	A	339	ASP	-1	-0.874	-0.920	20.681	-0.210	-0.210	0.000	0.000	0.000	0.000
66	A	340	VAL	0	-0.055	-0.046	19.546	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	341	GLU	-1	-0.954	-0.965	19.700	-0.318	-0.318	0.000	0.000	0.000	0.000
68	A	342	GLU	-1	-0.889	-0.919	19.974	-0.402	-0.402	0.000	0.000	0.000	0.000
69	A	343	VAL	0	-0.006	-0.003	19.594	0.028	0.028	0.000	0.000	0.000	0.000
70	A	344	GLN	0	0.009	-0.001	21.224	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	345	GLY	0	-0.021	-0.005	23.603	0.030	0.030	0.000	0.000	0.000	0.000
72	A	346	PRO	0	-0.003	-0.002	24.097	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	347	GLY	0	0.058	0.020	23.797	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	348	VAL	0	-0.041	-0.025	18.375	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	349	VAL	0	-0.001	-0.002	17.705	0.015	0.015	0.000	0.000	0.000	0.000
76	A	350	GLY	0	0.008	0.010	20.743	0.028	0.028	0.000	0.000	0.000	0.000
77	A	351	GLU	-1	-0.893	-0.904	22.252	-0.319	-0.319	0.000	0.000	0.000	0.000
78	A	352	PHE	0	0.002	-0.004	23.648	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	353	PRO	0	0.014	0.029	21.054	0.033	0.033	0.000	0.000	0.000	0.000
80	A	354	ILE	0	0.021	0.005	24.214	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	355	ILE	0	0.007	0.016	20.616	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	356	SER	0	0.039	0.004	24.119	0.019	0.019	0.000	0.000	0.000	0.000
83	A	357	PRO	0	0.055	0.024	24.546	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	358	GLY	0	-0.078	-0.041	23.042	0.025	0.025	0.000	0.000	0.000	0.000
85	A	359	ARG	1	0.807	0.906	21.832	0.293	0.293	0.000	0.000	0.000	0.000
86	A	360	VAL	0	0.018	-0.001	15.927	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	361	TYR	0	-0.078	-0.061	17.883	0.019	0.019	0.000	0.000	0.000	0.000
88	A	362	GLU	-1	-0.857	-0.946	12.304	-0.965	-0.965	0.000	0.000	0.000	0.000
89	A	363	TYR	0	-0.002	-0.014	13.952	0.093	0.093	0.000	0.000	0.000	0.000
90	A	364	THR	0	-0.007	-0.014	11.504	-0.207	-0.207	0.000	0.000	0.000	0.000
91	A	365	SER	0	-0.007	0.009	11.960	0.183	0.183	0.000	0.000	0.000	0.000
92	A	366	CYS	0	-0.065	-0.032	11.688	-0.084	-0.084	0.000	0.000	0.000	0.000
93	A	367	THR	0	0.032	0.012	11.076	0.040	0.040	0.000	0.000	0.000	0.000
94	A	368	THR	0	0.013	0.013	12.957	0.041	0.041	0.000	0.000	0.000	0.000
95	A	369	PHE	0	0.036	0.024	10.847	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	370	SER	0	-0.005	0.008	15.700	0.051	0.051	0.000	0.000	0.000	0.000
97	A	371	THR	0	-0.044	-0.054	14.983	0.037	0.037	0.000	0.000	0.000	0.000
98	A	372	THR	0	0.012	0.004	13.627	-0.058	-0.058	0.000	0.000	0.000	0.000
99	A	373	SER	0	0.023	0.008	10.787	0.058	0.058	0.000	0.000	0.000	0.000
100	A	374	GLY	0	0.077	0.052	10.527	0.106	0.106	0.000	0.000	0.000	0.000
101	A	375	TYR	0	-0.045	-0.022	9.951	-0.200	-0.200	0.000	0.000	0.000	0.000
102	A	376	MET	0	-0.020	0.008	10.626	0.157	0.157	0.000	0.000	0.000	0.000
103	A	377	GLU	-1	-0.833	-0.916	11.595	-0.925	-0.925	0.000	0.000	0.000	0.000
104	A	378	GLY	0	0.028	0.012	14.102	0.090	0.090	0.000	0.000	0.000	0.000
105	A	379	TYR	0	-0.053	-0.021	17.065	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	380	TYR	0	0.066	0.040	14.372	0.037	0.037	0.000	0.000	0.000	0.000
107	A	381	THR	0	-0.007	-0.016	20.571	0.012	0.012	0.000	0.000	0.000	0.000
108	A	382	PHE	0	0.011	0.005	20.451	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	383	HIS	0	0.015	0.009	25.761	0.026	0.026	0.000	0.000	0.000	0.000
110	A	384	PHE	0	-0.034	-0.028	28.631	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	385	LEU	0	0.016	0.015	29.978	0.011	0.011	0.000	0.000	0.000	0.000
112	A	386	TYR	0	-0.037	-0.026	32.907	0.012	0.012	0.000	0.000	0.000	0.000
113	A	387	PHE	0	-0.044	-0.019	33.521	0.011	0.011	0.000	0.000	0.000	0.000
114	A	388	LYS	1	0.962	0.969	35.279	0.127	0.127	0.000	0.000	0.000	0.000
115	A	389	ASP	-1	-0.864	-0.921	35.474	-0.175	-0.175	0.000	0.000	0.000	0.000
116	A	390	LYS	1	0.860	0.945	32.622	0.184	0.184	0.000	0.000	0.000	0.000
117	A	391	ILE	0	0.058	0.021	28.803	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	392	PHE	0	-0.049	-0.026	23.933	0.007	0.007	0.000	0.000	0.000	0.000
119	A	393	ASN	0	0.043	0.036	22.752	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	394	VAL	0	0.000	-0.003	18.255	0.012	0.012	0.000	0.000	0.000	0.000
121	A	395	ALA	0	-0.001	-0.001	16.610	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	396	ILE	0	-0.015	0.002	12.396	-0.057	-0.057	0.000	0.000	0.000	0.000
123	A	397	PRO	0	-0.024	0.003	9.720	0.083	0.083	0.000	0.000	0.000	0.000
124	A	398	ARG	1	0.897	0.936	10.541	0.760	0.760	0.000	0.000	0.000	0.000
125	A	399	PHE	0	-0.035	-0.013	6.000	-0.268	-0.268	0.000	0.000	0.000	0.000
126	A	400	HIS	0	-0.009	-0.015	6.106	0.471	0.471	0.000	0.000	0.000	0.000
127	A	401	MET	0	-0.040	-0.005	5.145	-0.861	-0.805	-0.001	-0.001	-0.054	0.000
128	A	402	ALA	0	0.030	-0.005	6.494	0.189	0.189	0.000	0.000	0.000	0.000
129	A	403	CYS	0	-0.019	0.007	7.572	0.457	0.457	0.000	0.000	0.000	0.000
130	A	404	PRO	0	-0.048	-0.010	8.063	-0.133	-0.133	0.000	0.000	0.000	0.000
131	A	405	THR	0	0.025	0.011	10.212	-0.168	-0.168	0.000	0.000	0.000	0.000

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