FMO DATABASE

FMODB ID: V5R71

Calculation Name: 3V4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V4H

Chain ID: A

ChEMBL ID:

UniProt ID: Q8CLE0

Base Structure: X-ray

Registration Date: 2023-06-21

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1266608.759254
FMO2-HF: Nuclear repulsion	1210235.038142
FMO2-HF: Total energy	-56373.721111
FMO2-MP2: Total energy	-56536.703465

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:4:ASP)

Summations of interaction energy for fragment #1(A:4:ASP)

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.
-55.882	-50.925	22.653	-12.579	-15.029	0.113

Interaction energy analysis for fragmet #1(A:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.851 / q_NPA : -0.921

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	6	PHE	0	-0.011	0.000	2.461	-2.192	2.214	2.698	-2.519	-4.585	0.025
4	A	7	ILE	0	0.005	0.003	6.542	-4.013	-4.013	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.857	0.929	10.212	-23.322	-23.322	0.000	0.000	0.000	0.000
6	A	9	ILE	0	0.039	0.006	12.691	-1.190	-1.190	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.824	-0.910	16.013	15.645	15.645	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.055	-0.035	19.222	-0.538	-0.538	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.035	-0.014	16.628	-0.486	-0.486	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.828	-0.887	15.054	20.133	20.133	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.026	0.005	11.866	-0.595	-0.595	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.847	-0.945	11.155	21.995	21.995	0.000	0.000	0.000	0.000
13	A	16	SER	0	0.000	0.001	5.800	1.236	1.236	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.045	0.001	8.107	-3.551	-3.551	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.712	-0.832	4.634	55.852	56.063	-0.001	-0.014	-0.196	0.000
16	A	19	ALA	0	-0.084	-0.045	6.544	-5.289	-5.289	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.001	-0.006	7.349	-4.570	-4.570	0.000	0.000	0.000	0.000
18	A	21	HIS	1	0.760	0.857	6.076	-41.860	-41.860	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.852	0.931	8.529	-29.403	-29.403	0.000	0.000	0.000	0.000
20	A	23	ASN	0	-0.049	-0.042	10.823	-0.678	-0.678	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.771	-0.835	8.804	28.354	28.354	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.011	-0.016	9.498	1.136	1.136	0.000	0.000	0.000	0.000
23	A	26	GLN	0	0.021	0.032	2.177	-22.619	-20.569	2.268	-1.988	-2.329	0.031
24	A	27	VAL	0	-0.057	-0.021	5.802	-5.408	-5.408	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.007	0.000	5.418	5.424	5.424	0.000	0.000	0.000	0.000
26	A	29	ALA	0	-0.007	-0.008	7.802	-0.641	-0.641	0.000	0.000	0.000	0.000
27	A	30	TRP	0	0.012	-0.013	8.387	-0.787	-0.787	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.069	-0.026	11.897	-1.037	-1.037	0.000	0.000	0.000	0.000
29	A	32	TRP	0	0.013	-0.010	14.993	0.271	0.271	0.000	0.000	0.000	0.000
30	A	33	ASP	-1	-0.904	-0.907	17.647	13.405	13.405	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.036	0.022	20.576	-0.340	-0.340	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.013	0.017	23.469	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	36	GLN	0	-0.019	-0.022	26.702	-0.219	-0.219	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.025	0.024	29.990	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	50	LYS	1	0.879	0.954	30.223	-10.053	-10.053	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.028	-0.019	27.082	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	52	SER	0	-0.003	0.000	28.278	-0.149	-0.149	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.046	-0.033	22.678	0.201	0.201	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.004	-0.031	21.325	0.039	0.039	0.000	0.000	0.000	0.000
40	A	55	ASP	-1	-0.765	-0.870	20.954	13.260	13.260	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.042	-0.013	11.730	0.257	0.257	0.000	0.000	0.000	0.000
42	A	57	CYS	0	0.003	0.006	16.065	-0.761	-0.761	0.000	0.000	0.000	0.000
43	A	58	PHE	0	-0.004	-0.026	11.075	1.419	1.419	0.000	0.000	0.000	0.000
44	A	59	ALA	0	0.052	0.042	11.535	-1.592	-1.592	0.000	0.000	0.000	0.000
45	A	60	HIS	1	0.744	0.854	10.278	-19.601	-19.601	0.000	0.000	0.000	0.000
46	A	61	TYR	0	0.031	-0.004	9.415	-0.748	-0.748	0.000	0.000	0.000	0.000
47	A	62	ILE	0	-0.012	0.007	12.999	0.151	0.151	0.000	0.000	0.000	0.000
48	A	63	ASP	-1	-0.793	-0.890	12.200	24.516	24.516	0.000	0.000	0.000	0.000
49	A	64	LYS	1	0.822	0.895	15.256	-21.310	-21.310	0.000	0.000	0.000	0.000
50	A	65	ALA	0	0.009	0.005	14.750	-1.165	-1.165	0.000	0.000	0.000	0.000
51	A	66	SER	0	0.002	-0.030	16.619	-0.495	-0.495	0.000	0.000	0.000	0.000
52	A	67	PRO	0	0.012	0.017	18.457	-0.772	-0.772	0.000	0.000	0.000	0.000
53	A	68	ASN	0	-0.036	-0.008	19.560	-1.365	-1.365	0.000	0.000	0.000	0.000
54	A	69	LEU	0	0.012	-0.005	15.727	-0.531	-0.531	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.048	0.026	20.464	-0.544	-0.544	0.000	0.000	0.000	0.000
56	A	71	SER	0	-0.037	-0.030	23.389	-0.757	-0.757	0.000	0.000	0.000	0.000
57	A	72	TYR	0	-0.022	-0.025	22.911	-0.703	-0.703	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.054	-0.006	23.632	-0.403	-0.403	0.000	0.000	0.000	0.000
59	A	74	LEU	0	-0.014	-0.009	25.499	-0.470	-0.470	0.000	0.000	0.000	0.000
60	A	75	LEU	0	-0.062	-0.036	28.403	-0.410	-0.410	0.000	0.000	0.000	0.000
61	A	76	GLY	0	0.021	0.036	28.417	-0.310	-0.310	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.848	0.931	25.706	-12.350	-12.350	0.000	0.000	0.000	0.000
63	A	78	HIS	0	-0.038	-0.032	25.844	0.214	0.214	0.000	0.000	0.000	0.000
64	A	79	ILE	0	-0.022	-0.015	19.861	0.015	0.015	0.000	0.000	0.000	0.000
65	A	80	LYS	1	0.922	0.969	23.204	-11.700	-11.700	0.000	0.000	0.000	0.000
66	A	81	ASN	0	-0.030	-0.028	19.033	-0.475	-0.475	0.000	0.000	0.000	0.000
67	A	82	VAL	0	0.035	0.031	15.086	0.459	0.459	0.000	0.000	0.000	0.000
68	A	83	GLN	0	-0.006	0.005	11.504	-1.966	-1.966	0.000	0.000	0.000	0.000
69	A	84	PHE	0	0.013	0.011	7.955	1.623	1.623	0.000	0.000	0.000	0.000
70	A	85	VAL	0	0.002	-0.007	6.088	-2.106	-2.106	0.000	0.000	0.000	0.000
71	A	86	LEU	0	-0.013	0.013	4.635	4.959	5.012	-0.001	-0.033	-0.019	0.000
72	A	87	ARG	1	0.773	0.842	1.693	-99.794	-103.099	16.596	-6.852	-6.439	0.073
73	A	88	LYS	1	0.867	0.953	2.411	-28.122	-26.788	1.094	-1.144	-1.284	-0.016
74	A	89	ALA	0	0.027	0.019	4.309	2.907	3.115	-0.001	-0.029	-0.177	0.000
75	A	90	GLY	0	-0.019	-0.010	6.322	3.906	3.906	0.000	0.000	0.000	0.000
76	A	91	GLY	0	-0.034	-0.004	8.960	-1.379	-1.379	0.000	0.000	0.000	0.000
77	A	92	ASP	-1	-0.793	-0.911	10.968	23.087	23.087	0.000	0.000	0.000	0.000
78	A	93	PRO	0	-0.113	-0.054	6.020	0.657	0.657	0.000	0.000	0.000	0.000
79	A	94	LEU	0	0.053	0.031	7.565	1.143	1.143	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.808	-0.919	6.117	39.766	39.766	0.000	0.000	0.000	0.000
81	A	96	TYR	0	-0.015	-0.007	4.923	-3.905	-3.905	0.000	0.000	0.000	0.000
82	A	97	LEU	0	0.024	0.015	8.453	-2.347	-2.347	0.000	0.000	0.000	0.000
83	A	98	THR	0	-0.030	-0.003	9.215	2.016	2.016	0.000	0.000	0.000	0.000
84	A	99	ILE	0	0.038	0.014	11.648	-1.691	-1.691	0.000	0.000	0.000	0.000
85	A	100	LYS	1	0.851	0.932	13.865	-18.397	-18.397	0.000	0.000	0.000	0.000
86	A	101	PHE	0	0.034	0.005	14.292	-0.830	-0.830	0.000	0.000	0.000	0.000
87	A	102	THR	0	-0.036	-0.033	19.065	0.132	0.132	0.000	0.000	0.000	0.000
88	A	103	ASP	-1	-0.914	-0.942	22.350	11.302	11.302	0.000	0.000	0.000	0.000
89	A	104	VAL	0	0.007	0.005	19.490	-0.185	-0.185	0.000	0.000	0.000	0.000
90	A	105	ILE	0	0.034	0.014	22.752	-0.238	-0.238	0.000	0.000	0.000	0.000
91	A	106	ILE	0	-0.008	0.005	20.030	0.303	0.303	0.000	0.000	0.000	0.000
92	A	107	THR	0	-0.008	-0.030	22.551	-0.350	-0.350	0.000	0.000	0.000	0.000
93	A	108	ARG	1	0.895	0.947	21.929	-13.301	-13.301	0.000	0.000	0.000	0.000
94	A	109	VAL	0	0.013	0.000	20.120	0.739	0.739	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.892	-0.923	20.281	12.764	12.764	0.000	0.000	0.000	0.000
96	A	111	MET	0	-0.031	-0.026	19.591	0.825	0.825	0.000	0.000	0.000	0.000
97	A	112	ALA	0	-0.013	-0.011	19.917	-0.794	-0.794	0.000	0.000	0.000	0.000
98	A	113	GLY	0	0.025	0.002	19.731	1.009	1.009	0.000	0.000	0.000	0.000
99	A	114	SER	0	-0.065	-0.046	21.555	-0.483	-0.483	0.000	0.000	0.000	0.000
100	A	115	LEU	0	0.010	-0.003	22.238	0.364	0.364	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.956	-0.938	21.507	12.878	12.878	0.000	0.000	0.000	0.000
102	A	117	ASP	-1	-0.809	-0.904	18.574	17.072	17.072	0.000	0.000	0.000	0.000
103	A	118	GLU	-1	-0.851	-0.892	12.574	23.614	23.614	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.118	-0.089	13.968	1.942	1.942	0.000	0.000	0.000	0.000
105	A	120	ARG	1	0.838	0.925	11.846	-24.281	-24.281	0.000	0.000	0.000	0.000
106	A	121	PRO	0	0.049	0.044	16.497	0.427	0.427	0.000	0.000	0.000	0.000
107	A	122	ARG	1	0.812	0.873	12.815	-19.799	-19.799	0.000	0.000	0.000	0.000
108	A	123	GLU	-1	-0.759	-0.863	15.158	16.149	16.149	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.834	-0.887	14.985	17.589	17.589	0.000	0.000	0.000	0.000
110	A	125	ILE	0	-0.040	-0.024	15.371	-0.999	-0.999	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.830	0.892	16.554	-14.144	-14.144	0.000	0.000	0.000	0.000
112	A	127	PHE	0	-0.056	-0.030	15.325	-0.234	-0.234	0.000	0.000	0.000	0.000
113	A	128	SER	0	0.050	0.023	20.686	-0.136	-0.136	0.000	0.000	0.000	0.000
114	A	129	PHE	0	-0.023	-0.024	20.252	0.496	0.496	0.000	0.000	0.000	0.000
115	A	130	THR	0	0.022	0.022	23.447	-0.358	-0.358	0.000	0.000	0.000	0.000
116	A	131	LYS	1	0.924	0.974	24.142	-11.786	-11.786	0.000	0.000	0.000	0.000
117	A	132	MET	0	-0.035	0.006	18.276	0.289	0.289	0.000	0.000	0.000	0.000
118	A	133	THR	0	0.015	-0.001	18.618	-0.902	-0.902	0.000	0.000	0.000	0.000
119	A	134	GLN	0	-0.004	0.002	14.583	1.557	1.557	0.000	0.000	0.000	0.000
120	A	135	ASP	-1	-0.857	-0.907	14.731	15.736	15.736	0.000	0.000	0.000	0.000
121	A	136	TYR	0	0.018	0.002	11.800	1.877	1.877	0.000	0.000	0.000	0.000
122	A	137	VAL	0	-0.029	-0.019	12.396	-1.435	-1.435	0.000	0.000	0.000	0.000
123	A	138	MET	0	-0.024	-0.005	13.119	0.635	0.635	0.000	0.000	0.000	0.000
124	A	139	GLN	0	0.053	0.023	13.164	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	140	ASN	0	-0.067	-0.048	16.097	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	141	ALA	0	0.075	0.024	18.531	0.366	0.366	0.000	0.000	0.000	0.000
127	A	142	GLU	-1	-0.921	-0.950	19.548	12.886	12.886	0.000	0.000	0.000	0.000
128	A	143	GLY	0	-0.011	0.008	17.036	0.909	0.909	0.000	0.000	0.000	0.000
129	A	144	HIS	0	-0.026	-0.013	16.472	-0.126	-0.126	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.916	0.971	15.628	-15.258	-15.258	0.000	0.000	0.000	0.000
131	A	146	SER	0	-0.019	-0.016	17.238	-0.479	-0.479	0.000	0.000	0.000	0.000
132	A	147	GLY	0	-0.012	-0.021	18.394	-0.738	-0.738	0.000	0.000	0.000	0.000
133	A	148	VAL	0	-0.020	-0.019	16.328	0.993	0.993	0.000	0.000	0.000	0.000
134	A	149	ILE	0	-0.038	-0.002	17.423	-0.866	-0.866	0.000	0.000	0.000	0.000
135	A	150	SER	0	0.017	-0.029	17.817	0.701	0.701	0.000	0.000	0.000	0.000
136	A	151	ALA	0	-0.040	0.000	19.656	-0.721	-0.721	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.005	-0.008	20.506	0.526	0.526	0.000	0.000	0.000	0.000
138	A	153	TYR	0	0.010	-0.002	22.800	-0.661	-0.661	0.000	0.000	0.000	0.000
139	A	154	ASP	-1	-0.836	-0.896	24.733	11.091	11.091	0.000	0.000	0.000	0.000
140	A	155	VAL	0	-0.064	-0.067	26.776	-0.777	-0.777	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASP)