FMO DATABASE

FMODB ID: VQVJ1

Calculation Name: 3VBZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VBZ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG57

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-968331.689449
FMO2-HF: Nuclear repulsion	917827.051061
FMO2-HF: Total energy	-50504.638388
FMO2-MP2: Total energy	-50638.98511

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:1:ASN)

Summations of interaction energy for fragment #1(A:1: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.
-55.331	-53.742	41.907	-19.756	-23.739	-0.035

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.020

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	3	VAL	0	-0.002	0.013	2.142	-9.273	-7.019	5.083	-3.090	-4.247	0.034
4	A	4	GLN	0	-0.041	-0.026	2.219	-14.859	-11.238	3.826	-2.135	-5.313	0.028
5	A	5	PHE	0	0.040	0.033	3.817	-3.403	-2.917	0.002	-0.197	-0.291	0.001
6	A	6	GLY	0	0.053	0.025	5.512	-0.914	-0.914	0.000	0.000	0.000	0.000
7	A	7	PHE	0	-0.002	-0.021	5.688	-0.737	-0.737	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.039	-0.005	5.807	-0.889	-0.889	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.015	0.022	9.293	-0.420	-0.420	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.866	-0.936	11.565	1.818	1.818	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.120	-0.034	12.315	-0.295	-0.295	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.023	-0.020	13.322	-0.174	-0.174	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.037	0.001	15.138	-0.134	-0.134	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.885	0.920	16.463	-0.707	-0.707	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.029	-0.027	15.045	-0.127	-0.127	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.955	0.998	17.605	-0.526	-0.526	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.877	0.945	18.102	-0.719	-0.719	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.006	0.024	15.183	0.104	0.104	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.063	0.012	10.733	-0.123	-0.123	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.020	-0.016	12.766	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.867	-0.939	14.182	0.699	0.699	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.022	-0.025	13.899	-0.179	-0.179	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.038	-0.012	10.704	0.027	0.027	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.010	-0.012	14.693	-0.105	-0.105	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.034	-0.035	18.145	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.033	0.004	19.292	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.123	-0.025	21.130	0.024	0.024	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.020	-0.034	16.546	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.065	0.013	13.729	-0.057	-0.057	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.052	0.021	13.720	0.095	0.095	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.090	-0.058	14.624	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.068	-0.046	16.945	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.060	0.057	17.178	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.884	0.937	17.878	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.036	0.020	21.470	0.033	0.033	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.040	-0.009	23.674	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.022	0.017	21.547	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.071	-0.037	23.274	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.785	-0.864	22.707	0.242	0.242	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.754	-0.881	22.529	0.046	0.046	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.027	0.029	17.938	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.717	-0.880	18.082	0.209	0.209	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.831	0.908	18.262	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.029	0.010	14.559	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	46	GLN	0	-0.004	0.008	14.256	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.007	-0.010	14.888	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	48	HIS	0	-0.078	-0.047	6.962	0.159	0.159	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.856	-0.926	11.264	-0.357	-0.357	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.907	-0.948	12.700	-0.365	-0.365	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.093	-0.033	7.766	0.159	0.159	0.000	0.000	0.000	0.000
51	A	52	TYR	0	0.000	-0.066	4.821	-0.464	-0.381	-0.001	-0.004	-0.077	0.000
52	A	53	ALA	0	0.054	0.045	10.151	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.034	-0.022	13.426	0.038	0.038	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.011	0.002	9.541	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.928	-0.969	10.879	-0.878	-0.878	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.776	0.890	12.339	0.761	0.761	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.050	-0.011	12.908	0.104	0.104	0.000	0.000	0.000	0.000
58	A	59	GLY	0	-0.021	0.003	14.179	0.012	0.012	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.029	-0.021	8.245	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.069	0.021	7.936	0.312	0.312	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.012	0.028	5.352	-0.966	-0.966	0.000	0.000	0.000	0.000
62	A	63	SER	0	0.035	0.008	3.014	-3.897	-2.304	0.179	-0.738	-1.035	-0.007
63	A	64	LEU	0	-0.026	-0.025	2.687	-2.060	0.231	1.556	-1.757	-2.090	-0.018
64	A	65	THR	0	-0.032	-0.002	3.361	-1.560	-0.037	0.063	-0.656	-0.931	-0.002
65	A	66	THR	0	0.008	0.008	1.660	-14.208	-25.559	27.497	-9.415	-6.730	-0.065
66	A	67	TYR	0	-0.026	-0.046	2.097	2.455	2.897	3.694	-1.459	-2.677	-0.004
67	A	68	GLN	0	-0.109	-0.053	5.250	0.622	0.669	-0.001	0.000	-0.045	0.000
68	A	69	TRP	0	0.071	0.020	6.591	-0.412	-0.412	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.884	-0.932	9.526	0.238	0.238	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.834	0.896	13.846	-0.069	-0.069	0.000	0.000	0.000	0.000
71	A	73	GLN	0	-0.025	-0.020	17.345	0.035	0.035	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.022	-0.032	20.184	0.017	0.017	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.020	0.024	17.171	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.007	0.000	10.607	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.807	-0.872	12.747	-0.206	-0.206	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.030	0.014	5.478	0.327	0.327	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.040	-0.045	10.807	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	80	SER	0	0.013	0.016	8.465	-0.178	-0.178	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.957	0.988	10.341	1.086	1.086	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.052	-0.055	9.633	0.120	0.120	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.033	0.012	10.965	-0.082	-0.082	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.792	-0.867	6.211	-2.507	-2.507	0.000	0.000	0.000	0.000
83	A	86	VAL	0	-0.026	-0.026	7.153	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.012	0.001	9.756	0.121	0.121	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.052	0.021	3.891	0.077	0.231	0.002	-0.036	-0.119	0.000
86	A	90	ALA	0	-0.004	-0.006	6.392	0.497	0.497	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.700	-0.794	3.520	-4.299	-3.853	0.007	-0.269	-0.184	-0.002
88	A	93	LEU	0	-0.023	-0.034	7.089	0.542	0.542	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.055	-0.029	9.689	0.184	0.184	0.000	0.000	0.000	0.000
90	A	95	ALA	0	0.054	0.039	9.784	0.120	0.120	0.000	0.000	0.000	0.000
91	A	96	ALA	0	-0.013	-0.004	9.749	0.149	0.149	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.932	0.960	11.699	0.044	0.044	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.020	-0.015	12.308	0.039	0.039	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.086	-0.042	15.703	0.038	0.038	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.107	-0.055	17.391	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.914	-0.939	19.611	0.110	0.110	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.898	-0.943	21.488	0.259	0.259	0.000	0.000	0.000	0.000
98	A	104	TYR	0	-0.089	-0.062	19.019	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.045	0.014	23.080	0.007	0.007	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.043	0.009	25.240	0.016	0.016	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.039	-0.009	26.318	0.013	0.013	0.000	0.000	0.000	0.000
102	A	108	HIS	0	-0.085	-0.072	24.191	-0.036	-0.036	0.000	0.000	0.000	0.000
103	A	109	PHE	0	0.016	0.021	19.177	0.006	0.006	0.000	0.000	0.000	0.000
104	A	110	ASN	0	-0.051	-0.008	22.272	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	111	ILE	0	-0.024	0.007	23.695	-0.039	-0.039	0.000	0.000	0.000	0.000
106	A	112	ASN	0	0.001	-0.010	25.684	0.008	0.008	0.000	0.000	0.000	0.000
107	A	113	THR	0	0.079	0.011	22.261	-0.031	-0.031	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.011	0.016	25.612	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.956	-0.990	28.281	0.109	0.109	0.000	0.000	0.000	0.000
110	A	116	ARG	1	0.890	0.939	27.240	-0.195	-0.195	0.000	0.000	0.000	0.000
111	A	118	LYS	1	0.901	0.959	25.534	-0.106	-0.106	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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