FMO DATABASE

FMODB ID: 39K8L

Calculation Name: 5V3N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V3N

Chain ID: A

ChEMBL ID:

UniProt ID: P25651

Base Structure: X-ray

Registration Date: 2023-06-22

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-887693.889308
FMO2-HF: Nuclear repulsion	842972.379934
FMO2-HF: Total energy	-44721.509374
FMO2-MP2: Total energy	-44853.514535

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:70:ASN)

Summations of interaction energy for fragment #1(A:70:ASN)

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.
-4.53	0.378	0.411	-1.801	-3.519	0.006

Interaction energy analysis for fragmet #1(A:70:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : -0.002

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	72	GLU	-1	-0.902	-0.952	3.083	-1.729	0.576	0.004	-0.969	-1.341	0.002
4	A	73	VAL	0	0.044	0.033	3.095	-0.507	0.470	0.096	-0.247	-0.826	0.000
5	A	74	ILE	0	-0.002	-0.003	2.811	-1.830	-0.204	0.311	-0.585	-1.352	0.004
6	A	75	LYS	1	0.854	0.924	5.920	-0.587	-0.587	0.000	0.000	0.000	0.000
7	A	76	ASP	-1	-0.824	-0.894	7.862	0.603	0.603	0.000	0.000	0.000	0.000
8	A	77	LEU	0	-0.032	-0.015	8.520	-0.108	-0.108	0.000	0.000	0.000	0.000
9	A	78	TYR	0	-0.036	-0.034	8.934	-0.177	-0.177	0.000	0.000	0.000	0.000
10	A	79	GLU	-1	-0.843	-0.893	12.128	0.287	0.287	0.000	0.000	0.000	0.000
11	A	80	TYR	0	-0.009	-0.011	11.457	-0.041	-0.041	0.000	0.000	0.000	0.000
12	A	81	LEU	0	-0.060	-0.024	12.992	-0.056	-0.056	0.000	0.000	0.000	0.000
13	A	82	CYS	0	-0.054	-0.018	15.265	-0.078	-0.078	0.000	0.000	0.000	0.000
14	A	83	ASN	0	0.007	0.034	17.324	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	84	VAL	0	-0.018	-0.028	16.320	-0.046	-0.046	0.000	0.000	0.000	0.000
16	A	85	ARG	1	0.845	0.906	10.165	-0.361	-0.361	0.000	0.000	0.000	0.000
17	A	86	VAL	0	0.025	0.022	14.232	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	87	HIS	0	0.002	-0.018	13.678	0.030	0.030	0.000	0.000	0.000	0.000
19	A	88	LYS	1	0.914	0.946	14.204	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	89	SER	0	-0.019	-0.003	16.009	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	90	TYR	0	-0.056	-0.012	18.040	0.010	0.010	0.000	0.000	0.000	0.000
22	A	91	GLU	-1	-0.913	-0.958	20.701	-0.098	-0.098	0.000	0.000	0.000	0.000
23	A	92	ASP	-1	-0.875	-0.954	23.405	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	93	ASP	-1	-0.949	-0.968	26.987	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	94	SER	0	-0.034	-0.018	29.562	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	95	GLY	0	0.008	-0.004	27.221	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	96	LEU	0	-0.013	0.022	19.508	0.001	0.001	0.000	0.000	0.000	0.000
28	A	97	TRP	0	-0.031	-0.012	22.519	0.011	0.011	0.000	0.000	0.000	0.000
29	A	98	PHE	0	-0.023	-0.018	16.547	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	99	ASP	-1	-0.829	-0.890	19.157	0.058	0.058	0.000	0.000	0.000	0.000
31	A	100	ILE	0	-0.023	-0.021	18.447	0.015	0.015	0.000	0.000	0.000	0.000
32	A	101	SER	0	-0.007	-0.004	18.942	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	102	GLN	0	-0.002	0.024	19.502	0.004	0.004	0.000	0.000	0.000	0.000
34	A	103	GLY	0	0.001	-0.011	21.296	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	104	THR	0	-0.019	-0.006	21.180	0.030	0.030	0.000	0.000	0.000	0.000
36	A	105	HIS	0	0.092	0.048	20.485	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	106	SER	0	-0.041	-0.019	23.696	0.006	0.006	0.000	0.000	0.000	0.000
38	A	107	GLY	0	0.041	0.005	25.230	0.017	0.017	0.000	0.000	0.000	0.000
39	A	108	GLY	0	-0.031	-0.083	27.443	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	109	SER	0	-0.018	0.022	29.834	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	110	SER	0	-0.023	0.023	27.605	0.005	0.005	0.000	0.000	0.000	0.000
42	A	111	ASP	-1	-0.924	-0.949	27.810	0.123	0.123	0.000	0.000	0.000	0.000
43	A	112	ASP	-1	-0.997	-0.989	29.930	0.126	0.126	0.000	0.000	0.000	0.000
44	A	113	TYR	0	-0.026	-0.039	25.297	0.015	0.015	0.000	0.000	0.000	0.000
45	A	114	SER	0	-0.036	-0.012	26.238	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	115	ILE	0	0.015	0.003	22.369	0.010	0.010	0.000	0.000	0.000	0.000
47	A	116	MET	0	-0.034	0.006	24.882	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	117	ASP	-1	-0.776	-0.868	23.040	0.129	0.129	0.000	0.000	0.000	0.000
49	A	118	TYR	0	-0.067	-0.084	22.889	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	119	LYS	1	0.839	0.912	23.329	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	120	LEU	0	-0.043	-0.026	22.000	0.000	0.000	0.000	0.000	0.000	0.000
52	A	121	GLY	0	0.063	0.023	23.664	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	122	PHE	0	-0.052	-0.028	22.097	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	123	VAL	0	0.063	0.026	26.112	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	124	LYS	1	0.853	0.940	28.165	0.077	0.077	0.000	0.000	0.000	0.000
56	A	125	GLY	0	0.071	0.043	31.606	0.005	0.005	0.000	0.000	0.000	0.000
57	A	126	GLN	0	0.011	-0.011	34.763	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	127	ALA	0	0.004	-0.006	36.227	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	128	GLN	0	-0.007	0.002	32.755	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	129	VAL	0	0.009	0.008	31.632	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	130	THR	0	-0.053	-0.035	26.149	0.002	0.002	0.000	0.000	0.000	0.000
62	A	131	GLU	-1	-0.906	-0.946	29.490	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	132	VAL	0	-0.018	-0.013	26.320	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	133	ILE	0	-0.005	0.001	28.245	0.005	0.005	0.000	0.000	0.000	0.000
65	A	134	TYR	0	-0.047	-0.039	27.168	0.004	0.004	0.000	0.000	0.000	0.000
66	A	135	ALA	0	0.063	0.024	28.149	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	136	PRO	0	0.013	0.021	28.134	0.005	0.005	0.000	0.000	0.000	0.000
68	A	137	VAL	0	-0.080	-0.048	25.775	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	138	LEU	0	0.048	0.002	28.321	0.006	0.006	0.000	0.000	0.000	0.000
70	A	139	LYS	1	0.902	0.957	30.894	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	140	GLN	0	-0.002	-0.010	27.002	0.002	0.002	0.000	0.000	0.000	0.000
72	A	141	ARG	1	0.801	0.909	27.456	-0.101	-0.101	0.000	0.000	0.000	0.000
73	A	142	SER	0	0.040	0.030	31.229	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	143	THR	0	0.029	-0.012	34.086	0.002	0.002	0.000	0.000	0.000	0.000
75	A	144	GLU	-1	-0.907	-0.947	35.356	0.075	0.075	0.000	0.000	0.000	0.000
76	A	145	GLU	-1	-0.745	-0.851	28.809	0.105	0.105	0.000	0.000	0.000	0.000
77	A	146	LEU	0	0.005	-0.004	32.869	0.001	0.001	0.000	0.000	0.000	0.000
78	A	147	TYR	0	0.006	0.021	34.689	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	148	SER	0	0.020	0.004	32.927	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	149	LEU	0	0.011	0.004	29.196	0.000	0.000	0.000	0.000	0.000	0.000
81	A	150	GLN	0	-0.038	-0.029	33.163	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	151	SER	0	-0.093	-0.025	36.066	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	152	LYS	1	0.899	0.962	31.367	-0.104	-0.104	0.000	0.000	0.000	0.000
84	A	153	LEU	0	-0.034	-0.022	29.899	0.001	0.001	0.000	0.000	0.000	0.000
85	A	154	PRO	0	-0.040	-0.017	33.065	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	155	GLU	-1	-0.846	-0.941	35.463	0.034	0.034	0.000	0.000	0.000	0.000
87	A	156	TYR	0	0.085	0.041	33.198	0.002	0.002	0.000	0.000	0.000	0.000
88	A	157	LEU	0	-0.058	-0.026	30.290	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	158	PHE	0	-0.027	-0.001	32.333	0.005	0.005	0.000	0.000	0.000	0.000
90	A	159	GLU	-1	-0.933	-0.956	34.754	0.023	0.023	0.000	0.000	0.000	0.000
91	A	160	THR	0	-0.051	-0.035	32.642	0.001	0.001	0.000	0.000	0.000	0.000
92	A	161	LEU	0	-0.040	-0.005	32.073	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	162	SER	0	0.025	0.009	32.390	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	163	PHE	0	-0.011	-0.015	27.424	0.003	0.003	0.000	0.000	0.000	0.000
95	A	164	PRO	0	0.083	0.047	31.090	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	165	LEU	0	0.075	0.031	24.057	0.005	0.005	0.000	0.000	0.000	0.000
97	A	166	SER	0	-0.041	-0.027	26.534	0.002	0.002	0.000	0.000	0.000	0.000
98	A	167	SER	0	-0.011	-0.009	28.240	0.005	0.005	0.000	0.000	0.000	0.000
99	A	168	LEU	0	0.023	0.026	21.997	0.010	0.010	0.000	0.000	0.000	0.000
100	A	169	ASN	0	0.019	-0.003	21.874	0.009	0.009	0.000	0.000	0.000	0.000
101	A	170	GLN	0	0.008	0.003	24.323	0.014	0.014	0.000	0.000	0.000	0.000
102	A	171	PHE	0	0.028	0.022	26.466	0.009	0.009	0.000	0.000	0.000	0.000
103	A	172	TYR	0	-0.017	-0.023	19.919	0.000	0.000	0.000	0.000	0.000	0.000
104	A	173	ASN	0	0.026	-0.004	24.401	0.025	0.025	0.000	0.000	0.000	0.000
105	A	174	LYS	1	0.884	0.960	26.077	-0.045	-0.045	0.000	0.000	0.000	0.000
106	A	175	ILE	0	0.062	0.052	25.814	0.004	0.004	0.000	0.000	0.000	0.000
107	A	176	ALA	0	0.029	0.021	23.694	0.007	0.007	0.000	0.000	0.000	0.000
108	A	177	LYS	1	0.918	0.950	25.460	-0.075	-0.075	0.000	0.000	0.000	0.000
109	A	178	SER	0	-0.085	-0.084	28.406	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	179	LEU	0	-0.007	-0.005	25.160	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	180	ASN	0	-0.012	0.005	24.135	0.013	0.013	0.000	0.000	0.000	0.000
112	A	181	LYS	1	0.838	0.944	27.980	-0.075	-0.075	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:70:ASN)