FMO DATABASE

FMODB ID: ZVNYN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1136017.839056
FMO2-HF: Nuclear repulsion	1083263.514345
FMO2-HF: Total energy	-52754.324711
FMO2-MP2: Total energy	-52906.839955

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.
-6.766	0.099	1.591	-3.547	-4.908	-0.029

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 : -0.002 / 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	0.006	0.010	2.772	-0.778	1.608	0.223	-1.121	-1.488	-0.003
4	A	278	VAL	0	0.014	-0.005	6.477	0.129	0.129	0.000	0.000	0.000	0.000
5	A	279	ALA	0	-0.013	0.004	10.262	0.079	0.079	0.000	0.000	0.000	0.000
6	A	280	THR	0	0.046	0.018	13.728	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	281	THR	0	-0.036	-0.009	17.296	0.006	0.006	0.000	0.000	0.000	0.000
8	A	282	GLY	0	0.014	0.007	20.663	0.006	0.006	0.000	0.000	0.000	0.000
9	A	283	ASP	-1	-0.785	-0.884	22.042	-0.099	-0.099	0.000	0.000	0.000	0.000
10	A	284	ILE	0	-0.004	0.006	19.432	0.007	0.007	0.000	0.000	0.000	0.000
11	A	285	THR	0	-0.018	-0.014	14.489	0.008	0.008	0.000	0.000	0.000	0.000
12	A	286	VAL	0	-0.003	-0.005	13.029	0.000	0.000	0.000	0.000	0.000	0.000
13	A	287	SER	0	0.017	-0.003	9.730	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	288	VAL	0	-0.013	-0.009	7.118	0.153	0.153	0.000	0.000	0.000	0.000
15	A	289	SER	0	0.026	0.002	4.689	-1.049	-0.971	-0.001	-0.024	-0.052	0.000
16	A	290	THR	0	-0.048	-0.037	2.550	-3.058	-0.304	0.936	-1.457	-2.233	-0.014
17	A	291	SER	0	-0.020	-0.021	2.677	-1.573	-0.048	0.435	-0.939	-1.021	-0.012
18	A	292	PHE	0	0.039	0.010	4.905	0.241	0.273	-0.001	-0.002	-0.029	0.000
19	A	293	LEU	0	0.032	0.017	7.956	0.249	0.249	0.000	0.000	0.000	0.000
20	A	294	PRO	0	-0.002	-0.002	10.880	0.081	0.081	0.000	0.000	0.000	0.000
21	A	295	GLU	-1	-0.938	-0.965	13.944	-0.238	-0.238	0.000	0.000	0.000	0.000
22	A	296	LEU	0	-0.063	-0.018	14.772	0.041	0.041	0.000	0.000	0.000	0.000
23	A	297	SER	0	-0.034	-0.022	13.866	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	298	SER	0	-0.033	-0.021	16.344	0.054	0.054	0.000	0.000	0.000	0.000
25	A	299	VAL	0	0.000	-0.001	18.356	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	300	HIS	0	-0.016	-0.004	19.371	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	301	PRO	0	0.036	0.012	22.878	0.014	0.014	0.000	0.000	0.000	0.000
28	A	302	PRO	0	-0.025	-0.001	19.403	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	303	HIS	0	0.001	0.000	17.802	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	304	TYR	0	-0.003	-0.004	12.252	0.037	0.037	0.000	0.000	0.000	0.000
31	A	305	PHE	0	0.075	0.031	12.179	-0.094	-0.094	0.000	0.000	0.000	0.000
32	A	306	PHE	0	-0.031	-0.023	7.243	-0.146	-0.146	0.000	0.000	0.000	0.000
33	A	307	THR	0	-0.002	-0.008	8.012	0.194	0.194	0.000	0.000	0.000	0.000
34	A	308	TYR	0	0.029	-0.008	6.832	-0.760	-0.760	0.000	0.000	0.000	0.000
35	A	309	ARG	1	0.824	0.896	7.549	0.719	0.719	0.000	0.000	0.000	0.000
36	A	310	ILE	0	-0.049	-0.012	9.011	-0.159	-0.159	0.000	0.000	0.000	0.000
37	A	311	ARG	1	0.809	0.881	11.611	0.319	0.319	0.000	0.000	0.000	0.000
38	A	312	ILE	0	0.006	-0.002	13.503	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	313	GLU	-1	-0.837	-0.910	15.340	-0.107	-0.107	0.000	0.000	0.000	0.000
40	A	314	MET	0	-0.009	0.006	18.883	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	315	SER	0	0.010	-0.005	21.827	0.012	0.012	0.000	0.000	0.000	0.000
42	A	316	LYS	1	0.931	0.939	22.748	0.009	0.009	0.000	0.000	0.000	0.000
43	A	317	ASP	-1	-0.893	-0.913	25.352	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	318	ALA	0	0.001	0.024	25.904	0.000	0.000	0.000	0.000	0.000	0.000
45	A	319	LEU	0	0.002	-0.004	27.882	0.004	0.004	0.000	0.000	0.000	0.000
46	A	320	PRO	0	0.016	-0.006	30.625	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	321	GLU	-1	-0.876	-0.950	32.043	-0.065	-0.065	0.000	0.000	0.000	0.000
48	A	322	LYS	1	0.774	0.871	28.083	0.082	0.082	0.000	0.000	0.000	0.000
49	A	323	ALA	0	0.010	0.005	28.408	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	324	CYS	0	-0.045	-0.011	26.119	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	325	GLN	0	-0.044	-0.029	26.912	0.008	0.008	0.000	0.000	0.000	0.000
52	A	326	LEU	0	-0.032	0.017	21.534	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	327	ASP	-1	-0.789	-0.893	24.999	-0.186	-0.186	0.000	0.000	0.000	0.000
54	A	328	SER	0	-0.050	-0.046	24.679	0.000	0.000	0.000	0.000	0.000	0.000
55	A	329	ARG	1	0.880	0.943	19.186	0.382	0.382	0.000	0.000	0.000	0.000
56	A	330	TYR	0	-0.069	-0.059	19.805	0.017	0.017	0.000	0.000	0.000	0.000
57	A	331	TRP	0	0.006	0.004	12.585	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	332	ARG	1	0.922	0.955	16.814	0.470	0.470	0.000	0.000	0.000	0.000
59	A	333	ILE	0	0.024	0.005	14.281	-0.114	-0.114	0.000	0.000	0.000	0.000
60	A	334	THR	0	-0.036	-0.024	14.449	0.118	0.118	0.000	0.000	0.000	0.000
61	A	335	ASN	0	0.001	-0.021	14.000	-0.085	-0.085	0.000	0.000	0.000	0.000
62	A	336	ALA	0	-0.013	-0.009	14.379	0.056	0.056	0.000	0.000	0.000	0.000
63	A	337	LYS	1	0.801	0.894	16.049	0.382	0.382	0.000	0.000	0.000	0.000
64	A	338	GLY	0	-0.001	0.010	18.775	0.033	0.033	0.000	0.000	0.000	0.000
65	A	339	ASP	-1	-0.805	-0.865	19.872	-0.307	-0.307	0.000	0.000	0.000	0.000
66	A	340	VAL	0	-0.064	-0.049	18.896	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	341	GLU	-1	-0.927	-0.957	19.169	-0.439	-0.439	0.000	0.000	0.000	0.000
68	A	342	GLU	-1	-0.876	-0.919	19.457	-0.350	-0.350	0.000	0.000	0.000	0.000
69	A	343	VAL	0	-0.013	-0.004	19.530	0.024	0.024	0.000	0.000	0.000	0.000
70	A	344	GLN	0	-0.002	-0.007	20.808	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	345	GLY	0	-0.014	-0.004	23.503	0.016	0.016	0.000	0.000	0.000	0.000
72	A	346	PRO	0	0.001	-0.004	24.468	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	347	GLY	0	0.068	0.031	24.463	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	348	VAL	0	-0.035	-0.025	18.826	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	349	VAL	0	-0.018	-0.011	17.913	0.020	0.020	0.000	0.000	0.000	0.000
76	A	350	GLY	0	0.021	0.022	20.934	0.022	0.022	0.000	0.000	0.000	0.000
77	A	351	GLU	-1	-0.896	-0.914	21.903	-0.226	-0.226	0.000	0.000	0.000	0.000
78	A	352	PHE	0	0.010	-0.001	24.235	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	353	PRO	0	0.018	0.026	21.204	0.027	0.027	0.000	0.000	0.000	0.000
80	A	354	ILE	0	0.016	0.008	24.358	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	355	ILE	0	-0.016	-0.009	21.285	0.004	0.004	0.000	0.000	0.000	0.000
82	A	356	SER	0	0.039	0.007	24.900	0.008	0.008	0.000	0.000	0.000	0.000
83	A	357	PRO	0	0.058	0.021	25.136	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	358	GLY	0	-0.063	-0.036	23.282	0.010	0.010	0.000	0.000	0.000	0.000
85	A	359	ARG	1	0.819	0.930	22.987	0.136	0.136	0.000	0.000	0.000	0.000
86	A	360	VAL	0	0.014	-0.006	16.878	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	361	TYR	0	-0.053	-0.052	18.211	0.005	0.005	0.000	0.000	0.000	0.000
88	A	362	GLU	-1	-0.795	-0.875	13.492	-0.232	-0.232	0.000	0.000	0.000	0.000
89	A	363	TYR	0	0.007	-0.002	14.341	0.032	0.032	0.000	0.000	0.000	0.000
90	A	364	THR	0	-0.005	-0.015	10.849	-0.099	-0.099	0.000	0.000	0.000	0.000
91	A	365	SER	0	-0.020	-0.004	11.873	0.155	0.155	0.000	0.000	0.000	0.000
92	A	366	CYS	0	-0.027	-0.011	11.493	-0.143	-0.143	0.000	0.000	0.000	0.000
93	A	367	THR	0	0.028	0.012	11.055	0.092	0.092	0.000	0.000	0.000	0.000
94	A	368	THR	0	0.024	0.018	13.156	-0.062	-0.062	0.000	0.000	0.000	0.000
95	A	369	PHE	0	0.024	0.024	10.313	0.087	0.087	0.000	0.000	0.000	0.000
96	A	370	SER	0	0.017	0.011	15.222	0.020	0.020	0.000	0.000	0.000	0.000
97	A	371	THR	0	-0.030	-0.044	14.773	0.078	0.078	0.000	0.000	0.000	0.000
98	A	372	THR	0	0.014	0.008	12.625	-0.089	-0.089	0.000	0.000	0.000	0.000
99	A	373	SER	0	0.014	0.007	10.152	-0.115	-0.115	0.000	0.000	0.000	0.000
100	A	374	GLY	0	0.044	0.027	10.143	0.170	0.170	0.000	0.000	0.000	0.000
101	A	375	TYR	0	-0.057	-0.014	9.453	-0.199	-0.199	0.000	0.000	0.000	0.000
102	A	376	MET	0	-0.004	0.011	10.180	0.100	0.100	0.000	0.000	0.000	0.000
103	A	377	GLU	-1	-0.778	-0.871	11.083	-0.631	-0.631	0.000	0.000	0.000	0.000
104	A	378	GLY	0	0.048	0.016	13.736	0.037	0.037	0.000	0.000	0.000	0.000
105	A	379	TYR	0	-0.054	-0.016	16.854	0.011	0.011	0.000	0.000	0.000	0.000
106	A	380	TYR	0	0.061	0.037	14.886	0.002	0.002	0.000	0.000	0.000	0.000
107	A	381	THR	0	-0.040	-0.023	20.681	0.018	0.018	0.000	0.000	0.000	0.000
108	A	382	PHE	0	0.005	0.000	20.865	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	383	HIS	0	-0.019	-0.018	26.164	0.021	0.021	0.000	0.000	0.000	0.000
110	A	384	PHE	0	-0.005	-0.010	28.206	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	385	LEU	0	-0.013	-0.007	30.440	0.006	0.006	0.000	0.000	0.000	0.000
112	A	386	TYR	0	-0.045	-0.019	33.357	0.006	0.006	0.000	0.000	0.000	0.000
113	A	387	PHE	0	-0.032	-0.012	33.457	0.008	0.008	0.000	0.000	0.000	0.000
114	A	388	LYS	1	0.992	0.996	35.509	0.066	0.066	0.000	0.000	0.000	0.000
115	A	389	ASP	-1	-0.851	-0.921	35.823	-0.099	-0.099	0.000	0.000	0.000	0.000
116	A	390	LYS	1	0.792	0.894	32.932	0.101	0.101	0.000	0.000	0.000	0.000
117	A	391	ILE	0	0.064	0.028	28.923	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	392	PHE	0	-0.047	-0.027	24.350	0.006	0.006	0.000	0.000	0.000	0.000
119	A	393	ASN	0	0.045	0.029	22.816	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	394	VAL	0	0.009	0.007	18.501	0.014	0.014	0.000	0.000	0.000	0.000
121	A	395	ALA	0	0.006	0.000	17.055	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	396	ILE	0	-0.014	0.003	12.248	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	397	PRO	0	-0.046	-0.008	9.638	0.048	0.048	0.000	0.000	0.000	0.000
124	A	398	ARG	1	0.871	0.913	10.734	0.351	0.351	0.000	0.000	0.000	0.000
125	A	399	PHE	0	-0.019	0.001	5.861	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	400	HIS	0	-0.002	-0.014	5.836	0.354	0.354	0.000	0.000	0.000	0.000
127	A	401	MET	0	-0.048	-0.010	4.626	-1.164	-1.074	-0.001	-0.004	-0.085	0.000
128	A	402	ALA	0	0.041	-0.002	5.919	0.712	0.712	0.000	0.000	0.000	0.000
129	A	403	CYS	0	-0.042	-0.003	6.457	-0.385	-0.385	0.000	0.000	0.000	0.000
130	A	404	PRO	0	-0.037	-0.017	6.909	0.207	0.207	0.000	0.000	0.000	0.000
131	A	405	THR	0	0.014	0.021	9.437	0.098	0.098	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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