FMO DATABASE

FMODB ID: 174ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1268768.847031
FMO2-HF: Nuclear repulsion	1212394.365776
FMO2-HF: Total energy	-56374.481255
FMO2-MP2: Total energy	-56537.472404

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.
-77.805	-78.16	30.94	-14.404	-16.18	0.176

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 : -0.793 / q_NPA : -0.899

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	-0.018	-0.006	2.550	-5.757	-1.136	3.551	-3.218	-4.954	0.037
4	A	7	ILE	0	-0.004	-0.001	6.445	-4.096	-4.096	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.869	0.938	10.204	-25.379	-25.379	0.000	0.000	0.000	0.000
6	A	9	ILE	0	0.045	0.006	12.684	-1.027	-1.027	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.819	-0.905	16.107	15.913	15.913	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.056	-0.033	19.455	-0.661	-0.661	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.044	-0.022	16.463	-0.555	-0.555	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.799	-0.870	14.919	20.431	20.431	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.036	0.012	12.039	-0.783	-0.783	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.808	-0.910	11.291	21.770	21.770	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.027	-0.011	5.777	1.031	1.031	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.060	0.008	8.291	-2.541	-2.541	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.734	-0.839	5.080	55.725	55.873	-0.001	-0.003	-0.144	0.000
16	A	19	ALA	0	-0.058	-0.028	6.977	-5.917	-5.917	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.048	-0.028	6.964	-5.494	-5.494	0.000	0.000	0.000	0.000
18	A	21	HIS	1	0.745	0.841	5.380	-47.189	-47.189	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.871	0.938	8.302	-29.127	-29.127	0.000	0.000	0.000	0.000
20	A	23	ASN	0	-0.063	-0.048	10.760	-0.902	-0.902	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.768	-0.845	8.549	30.885	30.885	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.004	-0.003	9.559	0.743	0.743	0.000	0.000	0.000	0.000
23	A	26	GLN	0	0.004	0.013	1.898	-25.986	-27.011	6.812	-2.882	-2.904	0.041
24	A	27	VAL	0	-0.070	-0.030	5.633	-5.908	-5.908	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.008	-0.002	5.474	4.636	4.636	0.000	0.000	0.000	0.000
26	A	29	ALA	0	-0.005	-0.008	7.754	-0.312	-0.312	0.000	0.000	0.000	0.000
27	A	30	TRP	0	0.003	-0.012	8.342	-0.788	-0.788	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.060	-0.027	11.861	-1.255	-1.255	0.000	0.000	0.000	0.000
29	A	32	TRP	0	0.012	-0.001	15.072	0.342	0.342	0.000	0.000	0.000	0.000
30	A	33	ASP	-1	-0.876	-0.894	17.600	13.652	13.652	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.022	0.002	20.419	-0.292	-0.292	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.002	0.011	23.436	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	36	GLN	0	-0.005	-0.021	26.813	-0.153	-0.153	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.015	0.022	30.282	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	50	LYS	1	0.860	0.923	30.460	-10.227	-10.227	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.021	-0.013	27.270	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	52	SER	0	0.008	0.010	28.367	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.033	-0.022	22.602	0.222	0.222	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.012	-0.027	21.341	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	55	ASP	-1	-0.739	-0.840	21.139	13.311	13.311	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.033	-0.006	12.030	0.370	0.370	0.000	0.000	0.000	0.000
42	A	57	CYS	0	-0.033	-0.011	16.363	-0.607	-0.607	0.000	0.000	0.000	0.000
43	A	58	PHE	0	0.007	-0.013	11.282	1.370	1.370	0.000	0.000	0.000	0.000
44	A	59	ALA	0	0.044	0.026	11.463	-1.455	-1.455	0.000	0.000	0.000	0.000
45	A	60	HIS	1	0.740	0.850	10.212	-19.759	-19.759	0.000	0.000	0.000	0.000
46	A	61	TYR	0	0.029	0.000	9.799	-0.688	-0.688	0.000	0.000	0.000	0.000
47	A	62	ILE	0	-0.012	0.005	13.305	0.096	0.096	0.000	0.000	0.000	0.000
48	A	63	ASP	-1	-0.800	-0.894	12.182	24.429	24.429	0.000	0.000	0.000	0.000
49	A	64	LYS	1	0.802	0.883	15.005	-21.577	-21.577	0.000	0.000	0.000	0.000
50	A	65	ALA	0	0.013	0.009	14.699	-1.044	-1.044	0.000	0.000	0.000	0.000
51	A	66	SER	0	-0.012	-0.027	16.527	-0.620	-0.620	0.000	0.000	0.000	0.000
52	A	67	PRO	0	0.005	0.012	18.390	-0.772	-0.772	0.000	0.000	0.000	0.000
53	A	68	ASN	0	-0.039	-0.004	19.340	-1.402	-1.402	0.000	0.000	0.000	0.000
54	A	69	LEU	0	0.015	-0.002	15.571	-0.527	-0.527	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.045	0.026	20.279	-0.575	-0.575	0.000	0.000	0.000	0.000
56	A	71	SER	0	-0.030	-0.032	23.267	-0.763	-0.763	0.000	0.000	0.000	0.000
57	A	72	TYR	0	-0.034	-0.037	22.670	-0.746	-0.746	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.061	-0.008	23.537	-0.453	-0.453	0.000	0.000	0.000	0.000
59	A	74	LEU	0	-0.005	-0.010	25.401	-0.502	-0.502	0.000	0.000	0.000	0.000
60	A	75	LEU	0	-0.066	-0.024	28.173	-0.477	-0.477	0.000	0.000	0.000	0.000
61	A	76	GLY	0	0.015	0.023	28.339	-0.262	-0.262	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.844	0.933	25.330	-12.553	-12.553	0.000	0.000	0.000	0.000
63	A	78	HIS	0	-0.024	-0.029	25.374	0.283	0.283	0.000	0.000	0.000	0.000
64	A	79	ILE	0	-0.035	-0.017	19.681	0.059	0.059	0.000	0.000	0.000	0.000
65	A	80	LYS	1	0.925	0.971	23.062	-11.758	-11.758	0.000	0.000	0.000	0.000
66	A	81	ASN	0	-0.028	-0.028	19.718	-0.515	-0.515	0.000	0.000	0.000	0.000
67	A	82	VAL	0	0.032	0.026	15.065	0.377	0.377	0.000	0.000	0.000	0.000
68	A	83	GLN	0	-0.020	-0.008	12.176	-2.154	-2.154	0.000	0.000	0.000	0.000
69	A	84	PHE	0	0.044	0.031	8.205	1.837	1.837	0.000	0.000	0.000	0.000
70	A	85	VAL	0	-0.030	-0.027	6.897	-2.150	-2.150	0.000	0.000	0.000	0.000
71	A	86	LEU	0	0.000	0.017	4.982	4.478	4.478	0.000	0.000	0.000	0.000
72	A	87	ARG	1	0.717	0.832	1.739	-111.738	-116.966	20.529	-7.737	-7.564	0.103
73	A	88	LYS	1	0.849	0.938	3.170	-29.907	-28.926	0.050	-0.556	-0.476	-0.005
74	A	89	ALA	0	0.014	0.002	4.656	1.970	2.118	-0.001	-0.008	-0.138	0.000
75	A	90	GLY	0	-0.004	-0.007	6.538	3.902	3.902	0.000	0.000	0.000	0.000
76	A	91	GLY	0	-0.032	-0.004	9.053	-1.546	-1.546	0.000	0.000	0.000	0.000
77	A	92	ASP	-1	-0.792	-0.910	10.832	23.936	23.936	0.000	0.000	0.000	0.000
78	A	93	PRO	0	-0.074	-0.022	6.084	0.878	0.878	0.000	0.000	0.000	0.000
79	A	94	LEU	0	0.050	0.019	6.920	3.410	3.410	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.782	-0.886	6.526	46.161	46.161	0.000	0.000	0.000	0.000
81	A	96	TYR	0	-0.005	-0.017	5.027	-4.613	-4.613	0.000	0.000	0.000	0.000
82	A	97	LEU	0	0.024	0.019	8.835	-2.677	-2.677	0.000	0.000	0.000	0.000
83	A	98	THR	0	-0.036	-0.003	9.458	2.331	2.331	0.000	0.000	0.000	0.000
84	A	99	ILE	0	0.032	0.008	12.095	-1.776	-1.776	0.000	0.000	0.000	0.000
85	A	100	LYS	1	0.851	0.934	14.478	-18.920	-18.920	0.000	0.000	0.000	0.000
86	A	101	PHE	0	0.023	0.001	14.740	-0.819	-0.819	0.000	0.000	0.000	0.000
87	A	102	THR	0	-0.021	-0.025	19.722	0.187	0.187	0.000	0.000	0.000	0.000
88	A	103	ASP	-1	-0.910	-0.940	23.078	11.428	11.428	0.000	0.000	0.000	0.000
89	A	104	VAL	0	0.025	0.014	19.766	-0.201	-0.201	0.000	0.000	0.000	0.000
90	A	105	ILE	0	0.022	0.004	23.025	-0.240	-0.240	0.000	0.000	0.000	0.000
91	A	106	ILE	0	-0.026	-0.017	19.973	0.213	0.213	0.000	0.000	0.000	0.000
92	A	107	THR	0	-0.015	-0.031	22.782	-0.354	-0.354	0.000	0.000	0.000	0.000
93	A	108	ARG	1	0.843	0.904	22.166	-13.485	-13.485	0.000	0.000	0.000	0.000
94	A	109	VAL	0	0.007	-0.005	19.855	0.782	0.782	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.826	-0.879	20.236	12.649	12.649	0.000	0.000	0.000	0.000
96	A	111	MET	0	-0.046	-0.040	19.490	0.824	0.824	0.000	0.000	0.000	0.000
97	A	112	ALA	0	-0.021	-0.006	19.691	-0.838	-0.838	0.000	0.000	0.000	0.000
98	A	113	GLY	0	0.013	-0.002	19.328	1.054	1.054	0.000	0.000	0.000	0.000
99	A	114	SER	0	-0.087	-0.059	20.905	-0.567	-0.567	0.000	0.000	0.000	0.000
100	A	115	LEU	0	0.009	0.000	22.072	0.350	0.350	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.903	-0.920	21.185	12.619	12.619	0.000	0.000	0.000	0.000
102	A	117	ASP	-1	-0.816	-0.907	18.194	16.619	16.619	0.000	0.000	0.000	0.000
103	A	118	GLU	-1	-0.842	-0.881	12.306	22.364	22.364	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.110	-0.077	14.036	1.850	1.850	0.000	0.000	0.000	0.000
105	A	120	ARG	1	0.807	0.885	12.369	-23.271	-23.271	0.000	0.000	0.000	0.000
106	A	121	PRO	0	0.049	0.048	16.151	0.615	0.615	0.000	0.000	0.000	0.000
107	A	122	ARG	1	0.811	0.871	13.085	-18.808	-18.808	0.000	0.000	0.000	0.000
108	A	123	GLU	-1	-0.717	-0.844	15.136	16.217	16.217	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.845	-0.900	14.834	18.054	18.054	0.000	0.000	0.000	0.000
110	A	125	ILE	0	-0.048	-0.019	15.282	-1.057	-1.057	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.834	0.890	16.881	-14.579	-14.579	0.000	0.000	0.000	0.000
112	A	127	PHE	0	-0.022	-0.013	15.608	-0.315	-0.315	0.000	0.000	0.000	0.000
113	A	128	SER	0	0.051	0.023	20.894	0.066	0.066	0.000	0.000	0.000	0.000
114	A	129	PHE	0	-0.027	-0.034	20.337	0.457	0.457	0.000	0.000	0.000	0.000
115	A	130	THR	0	-0.012	0.011	23.777	-0.420	-0.420	0.000	0.000	0.000	0.000
116	A	131	LYS	1	0.920	0.963	24.734	-11.911	-11.911	0.000	0.000	0.000	0.000
117	A	132	MET	0	-0.030	0.009	18.616	0.297	0.297	0.000	0.000	0.000	0.000
118	A	133	THR	0	0.028	-0.004	19.322	-1.021	-1.021	0.000	0.000	0.000	0.000
119	A	134	GLN	0	-0.013	0.006	14.722	1.676	1.676	0.000	0.000	0.000	0.000
120	A	135	ASP	-1	-0.836	-0.901	15.060	16.680	16.680	0.000	0.000	0.000	0.000
121	A	136	TYR	0	0.012	0.008	11.770	2.103	2.103	0.000	0.000	0.000	0.000
122	A	137	VAL	0	-0.036	-0.024	12.731	-1.451	-1.451	0.000	0.000	0.000	0.000
123	A	138	MET	0	-0.030	-0.007	13.729	0.402	0.402	0.000	0.000	0.000	0.000
124	A	139	GLN	0	0.017	0.002	13.581	0.553	0.553	0.000	0.000	0.000	0.000
125	A	140	ASN	0	-0.079	-0.045	16.622	-0.500	-0.500	0.000	0.000	0.000	0.000
126	A	141	ALA	0	0.034	0.033	18.504	0.509	0.509	0.000	0.000	0.000	0.000
127	A	142	GLU	-1	-0.891	-0.965	19.599	12.723	12.723	0.000	0.000	0.000	0.000
128	A	143	GLY	0	0.003	0.003	16.778	0.968	0.968	0.000	0.000	0.000	0.000
129	A	144	HIS	0	0.029	0.029	16.162	-0.131	-0.131	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.917	0.955	15.693	-16.857	-16.857	0.000	0.000	0.000	0.000
131	A	146	SER	0	-0.005	-0.002	17.217	-0.495	-0.495	0.000	0.000	0.000	0.000
132	A	147	GLY	0	0.006	-0.009	18.836	-0.854	-0.854	0.000	0.000	0.000	0.000
133	A	148	VAL	0	-0.057	-0.037	16.625	1.132	1.132	0.000	0.000	0.000	0.000
134	A	149	ILE	0	-0.008	0.014	17.653	-0.911	-0.911	0.000	0.000	0.000	0.000
135	A	150	SER	0	-0.006	-0.036	17.936	0.859	0.859	0.000	0.000	0.000	0.000
136	A	151	ALA	0	-0.038	-0.009	19.912	-0.782	-0.782	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.014	-0.007	20.687	0.651	0.651	0.000	0.000	0.000	0.000
138	A	153	TYR	0	-0.017	-0.016	23.077	-0.636	-0.636	0.000	0.000	0.000	0.000
139	A	154	ASP	-1	-0.848	-0.906	25.106	11.174	11.174	0.000	0.000	0.000	0.000
140	A	155	VAL	0	-0.034	-0.019	27.236	-0.818	-0.818	0.000	0.000	0.000	0.000

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