FMO DATABASE

FMODB ID: MNV5Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1009038.993616
FMO2-HF: Nuclear repulsion	962858.767994
FMO2-HF: Total energy	-46180.225622
FMO2-MP2: Total energy	-46316.082164

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.
-118.33	-110.171	12.081	-8.806	-11.436	-0.085

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 : 0.947 / q_NPA : 0.975

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	-0.039	-0.016	2.640	-14.702	-11.045	0.639	-2.138	-2.158	-0.014
4	A	71	VAL	0	0.028	0.017	5.417	4.097	4.097	0.000	0.000	0.000	0.000
5	A	72	LEU	0	-0.003	0.007	8.729	-1.148	-1.148	0.000	0.000	0.000	0.000
6	A	73	VAL	0	-0.012	-0.009	12.025	1.038	1.038	0.000	0.000	0.000	0.000
7	A	74	VAL	0	0.015	-0.009	14.745	0.145	0.145	0.000	0.000	0.000	0.000
8	A	75	ASP	-1	-0.755	-0.902	18.286	-14.752	-14.752	0.000	0.000	0.000	0.000
9	A	76	ASP	-1	-0.768	-0.874	20.769	-12.887	-12.887	0.000	0.000	0.000	0.000
10	A	77	ASN	0	0.002	0.009	23.053	-0.151	-0.151	0.000	0.000	0.000	0.000
11	A	78	ALA	0	0.035	-0.003	19.544	-0.687	-0.687	0.000	0.000	0.000	0.000
12	A	79	VAL	0	-0.032	-0.011	18.535	-0.910	-0.910	0.000	0.000	0.000	0.000
13	A	80	ASN	0	-0.060	-0.033	18.773	-0.339	-0.339	0.000	0.000	0.000	0.000
14	A	81	ARG	1	0.802	0.921	15.575	16.547	16.547	0.000	0.000	0.000	0.000
15	A	82	GLU	-1	-0.814	-0.914	13.898	-22.651	-22.651	0.000	0.000	0.000	0.000
16	A	83	ALA	0	-0.011	0.009	13.119	-1.577	-1.577	0.000	0.000	0.000	0.000
17	A	84	LEU	0	0.011	0.008	12.742	-1.205	-1.205	0.000	0.000	0.000	0.000
18	A	85	ILE	0	0.005	0.004	9.263	-2.759	-2.759	0.000	0.000	0.000	0.000
19	A	86	LEU	0	-0.020	-0.008	8.478	-3.997	-3.997	0.000	0.000	0.000	0.000
20	A	87	TYR	0	0.023	0.010	8.926	-2.443	-2.443	0.000	0.000	0.000	0.000
21	A	88	LEU	0	0.031	0.016	7.373	-1.589	-1.589	0.000	0.000	0.000	0.000
22	A	89	LYS	1	0.876	0.959	4.281	36.414	36.565	-0.001	-0.009	-0.141	0.000
23	A	90	SER	0	-0.096	-0.057	4.983	-2.917	-2.871	-0.001	0.000	-0.045	0.000
24	A	91	ARG	1	0.885	0.938	7.097	28.983	28.983	0.000	0.000	0.000	0.000
25	A	92	GLY	0	0.003	0.015	3.456	1.985	2.438	0.009	-0.244	-0.218	-0.001
26	A	93	ILE	0	-0.031	-0.003	1.828	-36.403	-37.698	8.765	-3.983	-3.488	-0.056
27	A	94	ASP	-1	-0.800	-0.895	2.647	-65.550	-62.844	1.983	-1.426	-3.263	-0.008
28	A	95	ALA	0	0.002	-0.013	4.230	6.065	6.320	0.017	-0.061	-0.212	0.000
29	A	96	VAL	0	-0.014	-0.005	7.970	-0.967	-0.967	0.000	0.000	0.000	0.000
30	A	97	GLY	0	0.043	0.010	10.819	0.238	0.238	0.000	0.000	0.000	0.000
31	A	98	ALA	0	-0.048	-0.021	14.605	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	99	ASP	-1	-0.937	-0.988	17.869	-14.227	-14.227	0.000	0.000	0.000	0.000
33	A	100	GLY	0	0.114	0.047	21.350	0.655	0.655	0.000	0.000	0.000	0.000
34	A	101	ALA	0	-0.013	-0.005	21.343	-0.659	-0.659	0.000	0.000	0.000	0.000
35	A	102	GLU	-1	-0.946	-0.968	22.187	-12.320	-12.320	0.000	0.000	0.000	0.000
36	A	103	GLU	-1	-0.799	-0.898	18.196	-17.511	-17.511	0.000	0.000	0.000	0.000
37	A	104	ALA	0	0.000	-0.008	17.379	-0.995	-0.995	0.000	0.000	0.000	0.000
38	A	105	ARG	1	0.803	0.840	17.346	11.851	11.851	0.000	0.000	0.000	0.000
39	A	106	LEU	0	0.007	0.018	18.409	-0.306	-0.306	0.000	0.000	0.000	0.000
40	A	107	TYR	0	-0.009	-0.023	12.393	-1.406	-1.406	0.000	0.000	0.000	0.000
41	A	108	LEU	0	-0.029	-0.010	13.775	-1.071	-1.071	0.000	0.000	0.000	0.000
42	A	109	HIS	0	0.031	0.042	14.573	-0.691	-0.691	0.000	0.000	0.000	0.000
43	A	110	TYR	0	0.015	-0.006	12.942	-0.603	-0.603	0.000	0.000	0.000	0.000
44	A	111	GLN	0	0.004	0.010	8.320	-1.147	-1.147	0.000	0.000	0.000	0.000
45	A	112	LYS	1	0.872	0.911	9.456	17.268	17.268	0.000	0.000	0.000	0.000
46	A	113	ARG	1	0.738	0.854	2.730	53.705	55.891	0.670	-0.945	-1.911	-0.006
47	A	114	ILE	0	-0.042	-0.007	6.549	-3.201	-3.201	0.000	0.000	0.000	0.000
48	A	115	GLY	0	0.006	0.014	8.217	2.418	2.418	0.000	0.000	0.000	0.000
49	A	116	LEU	0	-0.023	-0.007	9.686	1.648	1.648	0.000	0.000	0.000	0.000
50	A	117	MET	0	-0.009	0.004	11.229	-1.430	-1.430	0.000	0.000	0.000	0.000
51	A	118	ILE	0	-0.019	-0.009	12.347	0.557	0.557	0.000	0.000	0.000	0.000
52	A	119	THR	0	0.009	-0.010	15.907	-0.306	-0.306	0.000	0.000	0.000	0.000
53	A	120	ASP	-1	-0.710	-0.824	19.371	-12.959	-12.959	0.000	0.000	0.000	0.000
54	A	121	LEU	0	-0.044	-0.031	22.499	-0.173	-0.173	0.000	0.000	0.000	0.000
55	A	122	ARG	1	0.787	0.851	25.917	11.088	11.088	0.000	0.000	0.000	0.000
56	A	123	MET	0	-0.072	-0.003	22.066	-0.553	-0.553	0.000	0.000	0.000	0.000
57	A	124	GLN	0	-0.019	-0.001	27.013	0.713	0.713	0.000	0.000	0.000	0.000
58	A	125	PRO	0	-0.027	-0.020	27.501	-0.365	-0.365	0.000	0.000	0.000	0.000
59	A	126	GLU	-1	-0.799	-0.873	26.769	-11.518	-11.518	0.000	0.000	0.000	0.000
60	A	127	SER	0	0.028	0.003	26.856	-0.513	-0.513	0.000	0.000	0.000	0.000
61	A	128	GLY	0	0.029	-0.001	23.741	-0.258	-0.258	0.000	0.000	0.000	0.000
62	A	129	LEU	0	0.011	0.011	24.102	-0.384	-0.384	0.000	0.000	0.000	0.000
63	A	130	ASP	-1	-0.839	-0.887	26.537	-10.529	-10.529	0.000	0.000	0.000	0.000
64	A	131	LEU	0	0.021	0.034	19.700	-0.102	-0.102	0.000	0.000	0.000	0.000
65	A	132	ILE	0	-0.013	-0.006	21.494	-0.329	-0.329	0.000	0.000	0.000	0.000
66	A	133	ARG	1	0.816	0.884	23.293	10.200	10.200	0.000	0.000	0.000	0.000
67	A	134	THR	0	-0.025	-0.023	24.873	-0.083	-0.083	0.000	0.000	0.000	0.000
68	A	135	ILE	0	-0.008	0.001	18.628	-0.102	-0.102	0.000	0.000	0.000	0.000
69	A	136	ARG	1	0.742	0.852	19.468	14.099	14.099	0.000	0.000	0.000	0.000
70	A	137	ALA	0	-0.024	0.002	24.107	0.370	0.370	0.000	0.000	0.000	0.000
71	A	138	SER	0	-0.039	-0.023	21.251	0.033	0.033	0.000	0.000	0.000	0.000
72	A	139	GLU	-1	-0.880	-0.963	18.447	-14.119	-14.119	0.000	0.000	0.000	0.000
73	A	140	ARG	1	0.781	0.875	11.800	19.699	19.699	0.000	0.000	0.000	0.000
74	A	141	ALA	0	0.037	0.032	18.244	-0.593	-0.593	0.000	0.000	0.000	0.000
75	A	142	ALA	0	-0.023	-0.013	17.334	0.145	0.145	0.000	0.000	0.000	0.000
76	A	143	LEU	0	-0.049	-0.003	13.454	-0.590	-0.590	0.000	0.000	0.000	0.000
77	A	144	SER	0	0.021	0.007	13.814	1.155	1.155	0.000	0.000	0.000	0.000
78	A	145	ILE	0	0.009	-0.004	14.813	-1.211	-1.211	0.000	0.000	0.000	0.000
79	A	146	ILE	0	-0.022	-0.003	14.922	0.619	0.619	0.000	0.000	0.000	0.000
80	A	147	VAL	0	0.036	0.024	18.164	-0.424	-0.424	0.000	0.000	0.000	0.000
81	A	148	VAL	0	-0.051	-0.040	17.396	-0.071	-0.071	0.000	0.000	0.000	0.000
82	A	149	SER	0	0.032	0.009	20.732	-0.185	-0.185	0.000	0.000	0.000	0.000
83	A	150	GLY	0	-0.008	-0.009	24.176	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	151	ASP	-1	-0.877	-0.926	26.267	-9.886	-9.886	0.000	0.000	0.000	0.000
85	A	152	THR	0	-0.046	-0.021	28.649	-0.399	-0.399	0.000	0.000	0.000	0.000
86	A	153	ASP	-1	-0.817	-0.881	31.021	-9.237	-9.237	0.000	0.000	0.000	0.000
87	A	154	VAL	0	-0.005	-0.027	32.590	-0.273	-0.273	0.000	0.000	0.000	0.000
88	A	155	GLU	-1	-0.950	-0.968	33.838	-8.333	-8.333	0.000	0.000	0.000	0.000
89	A	156	GLU	-1	-0.770	-0.869	29.587	-10.892	-10.892	0.000	0.000	0.000	0.000
90	A	157	ALA	0	-0.005	-0.009	29.163	-0.346	-0.346	0.000	0.000	0.000	0.000
91	A	158	VAL	0	-0.022	-0.012	29.374	-0.261	-0.261	0.000	0.000	0.000	0.000
92	A	159	ASP	-1	-0.842	-0.907	30.972	-9.998	-9.998	0.000	0.000	0.000	0.000
93	A	160	VAL	0	0.011	-0.010	24.771	-0.274	-0.274	0.000	0.000	0.000	0.000
94	A	161	MET	0	-0.057	-0.024	25.129	-0.537	-0.537	0.000	0.000	0.000	0.000
95	A	162	HIS	0	-0.019	-0.005	27.682	-0.210	-0.210	0.000	0.000	0.000	0.000
96	A	163	LEU	0	-0.043	-0.006	25.550	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	164	GLY	0	0.004	0.012	24.470	-0.476	-0.476	0.000	0.000	0.000	0.000
98	A	165	VAL	0	-0.028	-0.003	21.132	-0.668	-0.668	0.000	0.000	0.000	0.000
99	A	166	VAL	0	-0.068	-0.039	16.853	0.244	0.244	0.000	0.000	0.000	0.000
100	A	167	ASP	-1	-0.799	-0.910	20.061	-13.852	-13.852	0.000	0.000	0.000	0.000
101	A	168	PHE	0	0.037	0.011	21.519	-0.338	-0.338	0.000	0.000	0.000	0.000
102	A	169	LEU	0	-0.047	-0.020	18.505	0.335	0.335	0.000	0.000	0.000	0.000
103	A	170	LEU	0	0.032	0.013	22.628	0.078	0.078	0.000	0.000	0.000	0.000
104	A	171	LYS	1	0.750	0.864	20.535	14.275	14.275	0.000	0.000	0.000	0.000
105	A	172	PRO	0	-0.027	-0.019	22.993	0.458	0.458	0.000	0.000	0.000	0.000
106	A	173	VAL	0	0.043	0.016	18.021	0.164	0.164	0.000	0.000	0.000	0.000
107	A	174	ASP	-1	-0.840	-0.917	19.624	-15.552	-15.552	0.000	0.000	0.000	0.000
108	A	175	LEU	0	-0.005	-0.020	14.528	-0.674	-0.674	0.000	0.000	0.000	0.000
109	A	176	GLY	0	-0.007	0.009	14.800	-1.368	-1.368	0.000	0.000	0.000	0.000
110	A	177	LYS	1	0.907	0.945	15.935	13.201	13.201	0.000	0.000	0.000	0.000
111	A	178	LEU	0	-0.004	0.001	13.557	-0.557	-0.557	0.000	0.000	0.000	0.000
112	A	179	LEU	0	-0.015	-0.014	9.703	-1.639	-1.639	0.000	0.000	0.000	0.000
113	A	180	GLU	-1	-0.967	-0.962	12.311	-17.388	-17.388	0.000	0.000	0.000	0.000
114	A	181	LEU	0	-0.012	-0.005	14.701	-0.516	-0.516	0.000	0.000	0.000	0.000
115	A	182	VAL	0	0.022	0.002	9.165	-0.541	-0.541	0.000	0.000	0.000	0.000
116	A	183	ASN	0	-0.051	-0.037	9.111	-3.797	-3.797	0.000	0.000	0.000	0.000
117	A	184	LYS	1	0.900	0.961	11.235	16.636	16.636	0.000	0.000	0.000	0.000
118	A	185	GLU	-1	-0.821	-0.922	12.785	-17.871	-17.871	0.000	0.000	0.000	0.000
119	A	186	LEU	0	-0.023	-0.002	5.772	-0.448	-0.448	0.000	0.000	0.000	0.000
120	A	187	LYS	1	0.761	0.904	8.003	19.474	19.474	0.000	0.000	0.000	0.000

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