FMO DATABASE

FMODB ID: 98432

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1004905.646939
FMO2-HF: Nuclear repulsion	958725.751919
FMO2-HF: Total energy	-46179.895021
FMO2-MP2: Total energy	-46315.728368

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.
-100.623	-89.677	3.005	-5.857	-8.093	-0.046

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 : 0.993 / q_NPA : 0.998

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	-0.057	-0.021	3.060	-11.555	-8.153	0.103	-1.856	-1.649	-0.006
4	A	71	VAL	0	0.017	0.013	5.526	4.048	4.048	0.000	0.000	0.000	0.000
5	A	72	LEU	0	-0.011	0.001	8.748	-0.946	-0.946	0.000	0.000	0.000	0.000
6	A	73	VAL	0	-0.019	-0.020	11.810	1.115	1.115	0.000	0.000	0.000	0.000
7	A	74	VAL	0	0.015	-0.007	14.551	0.127	0.127	0.000	0.000	0.000	0.000
8	A	75	ASP	-1	-0.818	-0.944	18.013	-14.653	-14.653	0.000	0.000	0.000	0.000
9	A	76	ASP	-1	-0.779	-0.872	20.621	-12.941	-12.941	0.000	0.000	0.000	0.000
10	A	77	ASN	0	-0.010	0.007	22.514	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	78	ALA	0	0.033	-0.004	19.972	-0.757	-0.757	0.000	0.000	0.000	0.000
12	A	79	VAL	0	-0.003	-0.002	18.906	-0.836	-0.836	0.000	0.000	0.000	0.000
13	A	80	ASN	0	-0.025	-0.011	18.780	-0.479	-0.479	0.000	0.000	0.000	0.000
14	A	81	ARG	1	0.824	0.927	15.637	16.537	16.537	0.000	0.000	0.000	0.000
15	A	82	GLU	-1	-0.856	-0.933	14.406	-22.329	-22.329	0.000	0.000	0.000	0.000
16	A	83	ALA	0	-0.013	0.005	13.667	-1.400	-1.400	0.000	0.000	0.000	0.000
17	A	84	LEU	0	-0.008	-0.003	13.115	-0.981	-0.981	0.000	0.000	0.000	0.000
18	A	85	ILE	0	0.017	0.010	9.437	-2.588	-2.588	0.000	0.000	0.000	0.000
19	A	86	LEU	0	-0.024	-0.006	8.900	-3.601	-3.601	0.000	0.000	0.000	0.000
20	A	87	TYR	0	0.056	0.022	9.346	-2.234	-2.234	0.000	0.000	0.000	0.000
21	A	88	LEU	0	0.049	0.029	7.647	-1.339	-1.339	0.000	0.000	0.000	0.000
22	A	89	LYS	1	0.898	0.975	4.729	33.827	33.915	-0.001	-0.003	-0.084	0.000
23	A	90	SER	0	-0.113	-0.060	5.288	-2.941	-2.941	0.000	0.000	0.000	0.000
24	A	91	ARG	1	0.885	0.936	7.252	27.233	27.233	0.000	0.000	0.000	0.000
25	A	92	GLY	0	-0.009	0.005	3.815	1.526	1.691	0.001	-0.060	-0.105	0.000
26	A	93	ILE	0	-0.050	-0.023	2.330	-25.184	-22.091	1.304	-2.259	-2.138	-0.032
27	A	94	ASP	-1	-0.852	-0.923	2.759	-58.116	-56.178	1.320	-0.832	-2.425	-0.004
28	A	95	ALA	0	0.033	0.003	4.277	4.534	4.741	0.013	-0.058	-0.162	0.000
29	A	96	VAL	0	0.004	-0.006	7.993	-0.631	-0.631	0.000	0.000	0.000	0.000
30	A	97	GLY	0	0.032	0.012	11.069	0.385	0.385	0.000	0.000	0.000	0.000
31	A	98	ALA	0	-0.045	-0.022	14.628	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	99	ASP	-1	-0.952	-0.996	17.642	-14.366	-14.366	0.000	0.000	0.000	0.000
33	A	100	GLY	0	0.108	0.042	20.828	0.782	0.782	0.000	0.000	0.000	0.000
34	A	101	ALA	0	-0.006	-0.007	21.072	-0.700	-0.700	0.000	0.000	0.000	0.000
35	A	102	GLU	-1	-0.941	-0.966	21.932	-12.395	-12.395	0.000	0.000	0.000	0.000
36	A	103	GLU	-1	-0.829	-0.909	18.294	-17.322	-17.322	0.000	0.000	0.000	0.000
37	A	104	ALA	0	-0.003	-0.004	17.341	-0.981	-0.981	0.000	0.000	0.000	0.000
38	A	105	ARG	1	0.800	0.833	17.287	11.847	11.847	0.000	0.000	0.000	0.000
39	A	106	LEU	0	0.012	0.021	17.987	-0.385	-0.385	0.000	0.000	0.000	0.000
40	A	107	TYR	0	0.022	-0.003	12.073	-1.466	-1.466	0.000	0.000	0.000	0.000
41	A	108	LEU	0	-0.026	-0.012	13.424	-1.164	-1.164	0.000	0.000	0.000	0.000
42	A	109	HIS	0	-0.001	0.020	14.041	-0.605	-0.605	0.000	0.000	0.000	0.000
43	A	110	TYR	0	-0.005	-0.031	12.733	-0.628	-0.628	0.000	0.000	0.000	0.000
44	A	111	GLN	0	0.013	0.012	7.781	-1.323	-1.323	0.000	0.000	0.000	0.000
45	A	112	LYS	1	0.906	0.947	9.081	17.354	17.354	0.000	0.000	0.000	0.000
46	A	113	ARG	1	0.769	0.877	2.833	51.806	53.859	0.265	-0.789	-1.530	-0.004
47	A	114	ILE	0	-0.039	-0.007	6.029	-2.963	-2.963	0.000	0.000	0.000	0.000
48	A	115	GLY	0	0.012	0.017	8.244	2.409	2.409	0.000	0.000	0.000	0.000
49	A	116	LEU	0	-0.034	-0.012	9.541	1.403	1.403	0.000	0.000	0.000	0.000
50	A	117	MET	0	0.007	0.018	11.271	-1.471	-1.471	0.000	0.000	0.000	0.000
51	A	118	ILE	0	-0.020	-0.008	12.346	0.647	0.647	0.000	0.000	0.000	0.000
52	A	119	THR	0	0.005	-0.007	15.946	-0.300	-0.300	0.000	0.000	0.000	0.000
53	A	120	ASP	-1	-0.745	-0.845	19.283	-13.057	-13.057	0.000	0.000	0.000	0.000
54	A	121	LEU	0	-0.027	-0.029	22.327	-0.135	-0.135	0.000	0.000	0.000	0.000
55	A	122	ARG	1	0.739	0.836	25.809	11.127	11.127	0.000	0.000	0.000	0.000
56	A	123	MET	0	-0.030	0.010	22.275	-0.624	-0.624	0.000	0.000	0.000	0.000
57	A	124	GLN	0	-0.045	-0.005	27.110	0.713	0.713	0.000	0.000	0.000	0.000
58	A	125	PRO	0	-0.027	-0.026	27.732	-0.325	-0.325	0.000	0.000	0.000	0.000
59	A	126	GLU	-1	-0.778	-0.863	26.620	-11.560	-11.560	0.000	0.000	0.000	0.000
60	A	127	SER	0	0.020	-0.006	26.798	-0.522	-0.522	0.000	0.000	0.000	0.000
61	A	128	GLY	0	0.038	0.007	23.994	-0.282	-0.282	0.000	0.000	0.000	0.000
62	A	129	LEU	0	-0.001	-0.001	24.490	-0.342	-0.342	0.000	0.000	0.000	0.000
63	A	130	ASP	-1	-0.862	-0.909	26.812	-10.463	-10.463	0.000	0.000	0.000	0.000
64	A	131	LEU	0	0.020	0.021	19.939	-0.119	-0.119	0.000	0.000	0.000	0.000
65	A	132	ILE	0	-0.008	-0.006	21.559	-0.301	-0.301	0.000	0.000	0.000	0.000
66	A	133	ARG	1	0.854	0.921	23.397	10.179	10.179	0.000	0.000	0.000	0.000
67	A	134	THR	0	-0.037	-0.014	24.463	-0.077	-0.077	0.000	0.000	0.000	0.000
68	A	135	ILE	0	0.004	0.001	18.729	-0.094	-0.094	0.000	0.000	0.000	0.000
69	A	136	ARG	1	0.795	0.888	19.216	14.055	14.055	0.000	0.000	0.000	0.000
70	A	137	ALA	0	-0.055	-0.012	23.479	0.283	0.283	0.000	0.000	0.000	0.000
71	A	138	SER	0	-0.044	-0.023	20.798	0.044	0.044	0.000	0.000	0.000	0.000
72	A	139	GLU	-1	-0.879	-0.961	17.872	-14.022	-14.022	0.000	0.000	0.000	0.000
73	A	140	ARG	1	0.760	0.869	10.967	19.776	19.776	0.000	0.000	0.000	0.000
74	A	141	ALA	0	0.060	0.039	17.590	-0.470	-0.470	0.000	0.000	0.000	0.000
75	A	142	ALA	0	-0.022	-0.015	16.778	0.065	0.065	0.000	0.000	0.000	0.000
76	A	143	LEU	0	-0.044	0.005	13.421	-0.698	-0.698	0.000	0.000	0.000	0.000
77	A	144	SER	0	0.006	0.001	13.850	0.997	0.997	0.000	0.000	0.000	0.000
78	A	145	ILE	0	0.005	-0.010	14.990	-1.083	-1.083	0.000	0.000	0.000	0.000
79	A	146	ILE	0	-0.015	-0.004	14.687	0.640	0.640	0.000	0.000	0.000	0.000
80	A	147	VAL	0	0.050	0.031	18.223	-0.421	-0.421	0.000	0.000	0.000	0.000
81	A	148	VAL	0	-0.051	-0.030	17.678	0.075	0.075	0.000	0.000	0.000	0.000
82	A	149	SER	0	0.054	0.017	20.912	-0.102	-0.102	0.000	0.000	0.000	0.000
83	A	150	GLY	0	-0.022	-0.023	24.282	0.053	0.053	0.000	0.000	0.000	0.000
84	A	151	ASP	-1	-0.931	-0.967	26.507	-9.860	-9.860	0.000	0.000	0.000	0.000
85	A	152	THR	0	-0.017	0.007	28.669	-0.282	-0.282	0.000	0.000	0.000	0.000
86	A	153	ASP	-1	-0.828	-0.894	31.046	-9.078	-9.078	0.000	0.000	0.000	0.000
87	A	154	VAL	0	0.004	-0.015	32.702	-0.239	-0.239	0.000	0.000	0.000	0.000
88	A	155	GLU	-1	-0.936	-0.965	33.909	-8.322	-8.322	0.000	0.000	0.000	0.000
89	A	156	GLU	-1	-0.775	-0.866	29.569	-10.870	-10.870	0.000	0.000	0.000	0.000
90	A	157	ALA	0	-0.010	-0.012	29.326	-0.325	-0.325	0.000	0.000	0.000	0.000
91	A	158	VAL	0	-0.024	-0.015	29.611	-0.256	-0.256	0.000	0.000	0.000	0.000
92	A	159	ASP	-1	-0.853	-0.919	31.130	-9.856	-9.856	0.000	0.000	0.000	0.000
93	A	160	VAL	0	0.009	-0.011	25.156	-0.270	-0.270	0.000	0.000	0.000	0.000
94	A	161	MET	0	-0.058	-0.022	25.196	-0.545	-0.545	0.000	0.000	0.000	0.000
95	A	162	HIS	0	-0.016	-0.002	27.651	-0.221	-0.221	0.000	0.000	0.000	0.000
96	A	163	LEU	0	-0.060	-0.013	25.511	0.001	0.001	0.000	0.000	0.000	0.000
97	A	164	GLY	0	0.019	0.014	24.407	-0.458	-0.458	0.000	0.000	0.000	0.000
98	A	165	VAL	0	-0.072	-0.030	21.144	-0.647	-0.647	0.000	0.000	0.000	0.000
99	A	166	VAL	0	-0.049	-0.024	16.761	0.253	0.253	0.000	0.000	0.000	0.000
100	A	167	ASP	-1	-0.785	-0.897	20.129	-13.647	-13.647	0.000	0.000	0.000	0.000
101	A	168	PHE	0	0.034	0.009	21.543	-0.409	-0.409	0.000	0.000	0.000	0.000
102	A	169	LEU	0	-0.068	-0.032	18.488	0.366	0.366	0.000	0.000	0.000	0.000
103	A	170	LEU	0	0.049	0.020	22.674	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	171	LYS	1	0.799	0.904	20.809	14.104	14.104	0.000	0.000	0.000	0.000
105	A	172	PRO	0	-0.004	-0.009	23.254	0.453	0.453	0.000	0.000	0.000	0.000
106	A	173	VAL	0	0.021	0.014	17.834	0.103	0.103	0.000	0.000	0.000	0.000
107	A	174	ASP	-1	-0.838	-0.914	20.006	-15.069	-15.069	0.000	0.000	0.000	0.000
108	A	175	LEU	0	-0.020	-0.027	14.803	-0.645	-0.645	0.000	0.000	0.000	0.000
109	A	176	GLY	0	0.000	0.007	15.234	-1.259	-1.259	0.000	0.000	0.000	0.000
110	A	177	LYS	1	0.926	0.955	16.299	13.263	13.263	0.000	0.000	0.000	0.000
111	A	178	LEU	0	-0.002	-0.002	13.648	-0.608	-0.608	0.000	0.000	0.000	0.000
112	A	179	LEU	0	-0.028	-0.022	9.817	-1.283	-1.283	0.000	0.000	0.000	0.000
113	A	180	GLU	-1	-0.962	-0.962	12.139	-17.571	-17.571	0.000	0.000	0.000	0.000
114	A	181	LEU	0	-0.018	-0.013	14.517	-0.454	-0.454	0.000	0.000	0.000	0.000
115	A	182	VAL	0	-0.006	-0.006	9.073	-0.520	-0.520	0.000	0.000	0.000	0.000
116	A	183	ASN	0	-0.003	-0.017	9.009	-3.732	-3.732	0.000	0.000	0.000	0.000
117	A	184	LYS	1	0.910	0.972	10.916	16.493	16.493	0.000	0.000	0.000	0.000
118	A	185	GLU	-1	-0.856	-0.937	13.144	-17.946	-17.946	0.000	0.000	0.000	0.000
119	A	186	LEU	0	-0.007	0.013	6.387	-0.495	-0.495	0.000	0.000	0.000	0.000
120	A	187	LYS	1	0.783	0.903	8.475	20.017	20.017	0.000	0.000	0.000	0.000

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