FMO DATABASE

FMODB ID: LNZ19

Calculation Name: 3HDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HDV

Chain ID: A

ChEMBL ID:

UniProt ID: Q88QX9

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002478.72292
FMO2-HF: Nuclear repulsion	956299.721751
FMO2-HF: Total energy	-46179.001168
FMO2-MP2: Total energy	-46314.829322

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:68:ARG)

Summations of interaction energy for fragment #1(A:68:ARG)

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.
-97.417	-90.313	4.196	-4.269	-7.03	-0.03

Interaction energy analysis for fragmet #1(A:68:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.963

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	70	LEU	0	-0.052	-0.015	3.550	-11.305	-9.429	0.002	-0.904	-0.974	-0.001
4	A	71	VAL	0	0.027	0.017	6.113	4.407	4.407	0.000	0.000	0.000	0.000
5	A	72	LEU	0	-0.015	-0.002	9.051	-1.033	-1.033	0.000	0.000	0.000	0.000
6	A	73	VAL	0	-0.018	-0.018	11.263	1.157	1.157	0.000	0.000	0.000	0.000
7	A	74	VAL	0	-0.003	-0.015	13.852	0.095	0.095	0.000	0.000	0.000	0.000
8	A	75	ASP	-1	-0.823	-0.942	17.514	-14.610	-14.610	0.000	0.000	0.000	0.000
9	A	76	ASP	-1	-0.787	-0.875	20.026	-13.027	-13.027	0.000	0.000	0.000	0.000
10	A	77	ASN	0	-0.019	0.002	22.114	-0.065	-0.065	0.000	0.000	0.000	0.000
11	A	78	ALA	0	0.024	-0.010	19.620	-0.738	-0.738	0.000	0.000	0.000	0.000
12	A	79	VAL	0	0.001	0.002	18.588	-0.832	-0.832	0.000	0.000	0.000	0.000
13	A	80	ASN	0	-0.028	-0.016	18.564	-0.565	-0.565	0.000	0.000	0.000	0.000
14	A	81	ARG	1	0.901	0.958	15.390	16.163	16.163	0.000	0.000	0.000	0.000
15	A	82	GLU	-1	-0.945	-0.979	13.909	-22.784	-22.784	0.000	0.000	0.000	0.000
16	A	83	ALA	0	-0.012	0.004	13.433	-1.397	-1.397	0.000	0.000	0.000	0.000
17	A	84	LEU	0	-0.012	-0.002	12.623	-0.952	-0.952	0.000	0.000	0.000	0.000
18	A	85	ILE	0	0.038	0.014	8.879	-2.403	-2.403	0.000	0.000	0.000	0.000
19	A	86	LEU	0	-0.027	-0.008	8.750	-3.664	-3.664	0.000	0.000	0.000	0.000
20	A	87	TYR	0	0.059	0.018	9.335	-2.113	-2.113	0.000	0.000	0.000	0.000
21	A	88	LEU	0	0.052	0.025	7.275	-1.143	-1.143	0.000	0.000	0.000	0.000
22	A	89	LYS	1	0.951	0.997	4.757	32.920	33.005	-0.001	-0.003	-0.080	0.000
23	A	90	SER	0	-0.112	-0.057	5.503	-2.350	-2.350	0.000	0.000	0.000	0.000
24	A	91	ARG	1	0.876	0.932	7.552	26.491	26.491	0.000	0.000	0.000	0.000
25	A	92	GLY	0	-0.012	0.005	4.373	1.656	1.723	-0.001	-0.014	-0.052	0.000
26	A	93	ILE	0	-0.050	-0.018	2.923	-16.904	-14.662	0.132	-1.280	-1.094	-0.014
27	A	94	ASP	-1	-0.912	-0.973	2.464	-62.441	-61.420	3.710	-1.475	-3.256	-0.011
28	A	95	ALA	0	0.005	-0.007	3.519	5.498	5.612	0.063	0.030	-0.207	0.000
29	A	96	VAL	0	-0.021	-0.006	7.302	-0.453	-0.453	0.000	0.000	0.000	0.000
30	A	97	GLY	0	0.024	0.005	10.577	0.543	0.543	0.000	0.000	0.000	0.000
31	A	98	ALA	0	-0.044	-0.023	14.109	-0.067	-0.067	0.000	0.000	0.000	0.000
32	A	99	ASP	-1	-0.967	-0.995	17.473	-14.344	-14.344	0.000	0.000	0.000	0.000
33	A	100	GLY	0	0.114	0.036	20.684	0.778	0.778	0.000	0.000	0.000	0.000
34	A	101	ALA	0	-0.005	-0.007	21.408	-0.684	-0.684	0.000	0.000	0.000	0.000
35	A	102	GLU	-1	-0.948	-0.970	22.170	-12.435	-12.435	0.000	0.000	0.000	0.000
36	A	103	GLU	-1	-0.813	-0.897	18.362	-16.971	-16.971	0.000	0.000	0.000	0.000
37	A	104	ALA	0	-0.011	-0.004	17.609	-0.956	-0.956	0.000	0.000	0.000	0.000
38	A	105	ARG	1	0.806	0.852	17.315	11.681	11.681	0.000	0.000	0.000	0.000
39	A	106	LEU	0	0.021	0.024	17.931	-0.354	-0.354	0.000	0.000	0.000	0.000
40	A	107	TYR	0	0.030	0.001	11.910	-1.463	-1.463	0.000	0.000	0.000	0.000
41	A	108	LEU	0	-0.034	-0.016	13.375	-1.069	-1.069	0.000	0.000	0.000	0.000
42	A	109	HIS	0	-0.014	0.009	13.978	-0.528	-0.528	0.000	0.000	0.000	0.000
43	A	110	TYR	0	-0.015	-0.023	12.996	-0.652	-0.652	0.000	0.000	0.000	0.000
44	A	111	GLN	0	-0.025	0.003	7.809	-1.323	-1.323	0.000	0.000	0.000	0.000
45	A	112	LYS	1	0.972	0.960	9.134	16.615	16.615	0.000	0.000	0.000	0.000
46	A	113	ARG	1	0.839	0.926	2.642	49.660	51.359	0.291	-0.623	-1.367	-0.004
47	A	114	ILE	0	-0.037	-0.002	5.964	-2.653	-2.653	0.000	0.000	0.000	0.000
48	A	115	GLY	0	0.011	0.016	8.412	2.526	2.526	0.000	0.000	0.000	0.000
49	A	116	LEU	0	-0.027	-0.005	9.597	1.251	1.251	0.000	0.000	0.000	0.000
50	A	117	MET	0	0.001	0.017	11.739	-1.471	-1.471	0.000	0.000	0.000	0.000
51	A	118	ILE	0	-0.019	-0.005	12.101	0.620	0.620	0.000	0.000	0.000	0.000
52	A	119	THR	0	0.001	-0.012	15.545	-0.336	-0.336	0.000	0.000	0.000	0.000
53	A	120	ASP	-1	-0.745	-0.862	18.838	-12.789	-12.789	0.000	0.000	0.000	0.000
54	A	121	LEU	0	-0.064	-0.046	21.776	-0.122	-0.122	0.000	0.000	0.000	0.000
55	A	122	ARG	1	0.812	0.852	25.262	11.276	11.276	0.000	0.000	0.000	0.000
56	A	123	MET	0	-0.080	0.007	22.271	-0.614	-0.614	0.000	0.000	0.000	0.000
57	A	124	GLN	0	-0.042	0.006	26.457	0.685	0.685	0.000	0.000	0.000	0.000
58	A	125	PRO	0	-0.028	-0.028	27.456	-0.323	-0.323	0.000	0.000	0.000	0.000
59	A	126	GLU	-1	-0.763	-0.870	27.193	-11.352	-11.352	0.000	0.000	0.000	0.000
60	A	127	SER	0	0.022	0.022	26.832	-0.492	-0.492	0.000	0.000	0.000	0.000
61	A	128	GLY	0	0.050	0.011	24.122	-0.268	-0.268	0.000	0.000	0.000	0.000
62	A	129	LEU	0	0.008	0.000	24.858	-0.283	-0.283	0.000	0.000	0.000	0.000
63	A	130	ASP	-1	-0.894	-0.952	27.303	-10.311	-10.311	0.000	0.000	0.000	0.000
64	A	131	LEU	0	0.004	0.006	20.412	-0.097	-0.097	0.000	0.000	0.000	0.000
65	A	132	ILE	0	0.004	0.002	22.101	-0.265	-0.265	0.000	0.000	0.000	0.000
66	A	133	ARG	1	0.963	0.985	23.822	10.040	10.040	0.000	0.000	0.000	0.000
67	A	134	THR	0	-0.047	-0.017	24.215	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	135	ILE	0	0.008	0.004	19.150	-0.062	-0.062	0.000	0.000	0.000	0.000
69	A	136	ARG	1	0.802	0.881	19.427	13.733	13.733	0.000	0.000	0.000	0.000
70	A	137	ALA	0	-0.053	-0.012	23.861	0.278	0.278	0.000	0.000	0.000	0.000
71	A	138	SER	0	-0.038	-0.014	20.863	0.034	0.034	0.000	0.000	0.000	0.000
72	A	139	GLU	-1	-0.892	-0.962	18.187	-13.362	-13.362	0.000	0.000	0.000	0.000
73	A	140	ARG	1	0.766	0.869	10.871	19.197	19.197	0.000	0.000	0.000	0.000
74	A	141	ALA	0	0.055	0.035	17.926	-0.445	-0.445	0.000	0.000	0.000	0.000
75	A	142	ALA	0	-0.026	-0.016	17.543	0.056	0.056	0.000	0.000	0.000	0.000
76	A	143	LEU	0	-0.050	0.001	13.538	-0.596	-0.596	0.000	0.000	0.000	0.000
77	A	144	SER	0	0.031	0.002	14.088	0.762	0.762	0.000	0.000	0.000	0.000
78	A	145	ILE	0	-0.017	-0.019	15.328	-1.040	-1.040	0.000	0.000	0.000	0.000
79	A	146	ILE	0	-0.011	0.000	14.424	0.606	0.606	0.000	0.000	0.000	0.000
80	A	147	VAL	0	0.051	0.032	18.095	-0.434	-0.434	0.000	0.000	0.000	0.000
81	A	148	VAL	0	-0.053	-0.028	17.383	0.081	0.081	0.000	0.000	0.000	0.000
82	A	149	SER	0	0.044	0.026	20.558	0.098	0.098	0.000	0.000	0.000	0.000
83	A	150	GLY	0	-0.048	-0.045	23.874	0.040	0.040	0.000	0.000	0.000	0.000
84	A	151	ASP	-1	-0.965	-0.968	26.094	-9.729	-9.729	0.000	0.000	0.000	0.000
85	A	152	THR	0	0.013	0.007	28.101	-0.121	-0.121	0.000	0.000	0.000	0.000
86	A	153	ASP	-1	-0.866	-0.924	30.640	-8.963	-8.963	0.000	0.000	0.000	0.000
87	A	154	VAL	0	-0.003	-0.014	32.373	-0.222	-0.222	0.000	0.000	0.000	0.000
88	A	155	GLU	-1	-0.930	-0.974	33.632	-8.214	-8.214	0.000	0.000	0.000	0.000
89	A	156	GLU	-1	-0.757	-0.843	29.166	-10.763	-10.763	0.000	0.000	0.000	0.000
90	A	157	ALA	0	-0.017	-0.013	29.027	-0.324	-0.324	0.000	0.000	0.000	0.000
91	A	158	VAL	0	-0.022	-0.017	29.601	-0.248	-0.248	0.000	0.000	0.000	0.000
92	A	159	ASP	-1	-0.922	-0.955	31.435	-9.428	-9.428	0.000	0.000	0.000	0.000
93	A	160	VAL	0	-0.035	-0.032	25.250	-0.256	-0.256	0.000	0.000	0.000	0.000
94	A	161	MET	0	-0.046	-0.020	25.323	-0.524	-0.524	0.000	0.000	0.000	0.000
95	A	162	HIS	0	-0.018	-0.006	27.907	-0.201	-0.201	0.000	0.000	0.000	0.000
96	A	163	LEU	0	-0.083	-0.025	25.685	0.032	0.032	0.000	0.000	0.000	0.000
97	A	164	GLY	0	0.010	0.011	24.441	-0.424	-0.424	0.000	0.000	0.000	0.000
98	A	165	VAL	0	-0.075	-0.029	21.421	-0.596	-0.596	0.000	0.000	0.000	0.000
99	A	166	VAL	0	-0.049	-0.022	17.005	0.270	0.270	0.000	0.000	0.000	0.000
100	A	167	ASP	-1	-0.829	-0.938	20.293	-13.266	-13.266	0.000	0.000	0.000	0.000
101	A	168	PHE	0	0.005	0.001	21.349	-0.444	-0.444	0.000	0.000	0.000	0.000
102	A	169	LEU	0	-0.075	-0.039	18.524	0.368	0.368	0.000	0.000	0.000	0.000
103	A	170	LEU	0	0.054	0.021	22.506	-0.092	-0.092	0.000	0.000	0.000	0.000
104	A	171	LYS	1	0.904	0.961	20.982	13.530	13.530	0.000	0.000	0.000	0.000
105	A	172	PRO	0	-0.010	-0.013	23.013	0.424	0.424	0.000	0.000	0.000	0.000
106	A	173	VAL	0	0.029	0.019	17.628	0.136	0.136	0.000	0.000	0.000	0.000
107	A	174	ASP	-1	-0.863	-0.928	20.144	-14.645	-14.645	0.000	0.000	0.000	0.000
108	A	175	LEU	0	-0.006	-0.023	14.491	-0.581	-0.581	0.000	0.000	0.000	0.000
109	A	176	GLY	0	-0.004	0.007	15.370	-1.195	-1.195	0.000	0.000	0.000	0.000
110	A	177	LYS	1	1.020	1.020	16.582	12.687	12.687	0.000	0.000	0.000	0.000
111	A	178	LEU	0	0.004	-0.001	13.606	-0.531	-0.531	0.000	0.000	0.000	0.000
112	A	179	LEU	0	-0.020	-0.019	9.598	-1.149	-1.149	0.000	0.000	0.000	0.000
113	A	180	GLU	-1	-0.970	-0.968	12.438	-17.093	-17.093	0.000	0.000	0.000	0.000
114	A	181	LEU	0	-0.029	-0.018	14.855	-0.445	-0.445	0.000	0.000	0.000	0.000
115	A	182	VAL	0	-0.001	0.001	9.168	-0.473	-0.473	0.000	0.000	0.000	0.000
116	A	183	ASN	0	-0.003	-0.016	9.514	-3.515	-3.515	0.000	0.000	0.000	0.000
117	A	184	LYS	1	0.953	0.989	11.309	15.878	15.878	0.000	0.000	0.000	0.000
118	A	185	GLU	-1	-0.928	-0.961	13.014	-17.344	-17.344	0.000	0.000	0.000	0.000
119	A	186	LEU	0	-0.028	-0.015	6.440	-0.597	-0.597	0.000	0.000	0.000	0.000
120	A	187	LYS	1	0.856	0.949	8.469	18.707	18.707	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:68:ARG)