FMO DATABASE

FMODB ID: 4969N

Calculation Name: 1VJQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJQ

Chain ID: A

ChEMBL ID:

UniProt ID:

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-447901.120058
FMO2-HF: Nuclear repulsion	419238.473936
FMO2-HF: Total energy	-28662.646122
FMO2-MP2: Total energy	-28746.858149

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:LYS)

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

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.
-217.456	-215.514	16.758	-7.557	-11.145	-0.058

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.939

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	ILE	0	0.029	0.033	3.829	-0.060	1.755	-0.021	-0.897	-0.898	0.001
4	A	4	PHE	0	-0.008	0.005	6.181	1.363	1.363	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.002	0.000	9.405	0.313	0.313	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.005	-0.012	11.696	0.659	0.659	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.002	-0.012	14.793	0.261	0.261	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.025	0.040	18.213	0.330	0.330	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.027	-0.024	20.893	0.416	0.416	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.018	0.008	24.431	0.173	0.173	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.769	-0.904	24.835	-10.580	-10.580	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.932	-0.966	25.587	-9.936	-9.936	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.029	-0.025	21.398	-0.587	-0.587	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.048	0.028	20.817	-0.707	-0.707	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.029	0.023	21.170	-0.386	-0.386	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.049	-0.041	17.591	-0.107	-0.107	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.004	-0.010	15.380	-0.462	-0.462	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.906	-0.953	17.315	-12.321	-12.321	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.068	-0.032	19.448	-0.109	-0.109	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.021	-0.013	14.739	-0.095	-0.095	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.032	0.018	14.758	-0.386	-0.386	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.868	0.941	15.796	11.903	11.903	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.105	-0.044	16.096	0.559	0.559	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.940	-0.964	14.976	-18.374	-18.374	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.959	-0.973	11.466	-20.393	-20.393	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.028	-0.006	10.183	-1.131	-1.131	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.051	-0.037	5.935	-2.035	-2.035	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.014	0.004	5.898	-4.018	-4.018	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.893	-0.944	6.124	-25.705	-25.705	0.000	0.000	0.000	0.000
30	A	30	TRP	0	0.024	0.004	8.048	-0.503	-0.503	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.035	-0.027	7.657	1.430	1.430	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.031	-0.014	11.565	0.273	0.273	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.003	0.010	14.689	-0.460	-0.460	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.004	-0.017	16.437	0.142	0.142	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.033	-0.013	18.991	0.354	0.354	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.865	-0.931	22.410	-9.677	-9.677	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.055	-0.032	22.963	-0.516	-0.516	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.053	-0.029	23.208	0.240	0.240	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.060	-0.016	20.824	0.074	0.074	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.031	-0.027	16.317	-0.301	-0.301	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.008	0.008	13.564	0.177	0.177	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.018	-0.011	9.234	-0.619	-0.619	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.003	0.012	7.557	0.309	0.309	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.012	-0.009	2.856	-2.020	-1.318	0.537	-0.409	-0.830	0.003
45	A	45	ILE	0	0.024	0.026	3.500	1.399	1.897	0.003	-0.175	-0.327	-0.001
46	A	46	PRO	0	0.009	-0.005	2.097	-16.050	-13.456	4.547	-3.732	-3.410	-0.034
47	A	47	SER	0	0.019	-0.057	1.938	-0.540	-4.766	11.560	-2.487	-4.847	-0.025
48	A	48	ASP	-1	-0.945	-0.970	3.102	-31.311	-31.501	0.131	0.409	-0.350	0.000
49	A	49	MET	0	0.005	0.016	5.952	5.002	5.002	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.025	-0.003	5.353	2.524	2.524	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.938	-0.978	7.982	-16.872	-16.872	0.000	0.000	0.000	0.000
52	A	52	TRP	0	0.063	0.011	10.773	1.695	1.695	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.012	0.011	10.126	1.339	1.339	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.021	-0.003	11.368	1.189	1.189	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.915	-0.952	13.406	-14.234	-14.234	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.029	0.008	14.187	1.387	1.387	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.006	-0.010	12.914	1.063	1.063	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.931	0.965	17.034	15.984	15.984	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.041	0.000	19.359	0.764	0.764	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.833	0.924	19.763	12.951	12.951	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.017	-0.002	21.858	0.388	0.388	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.046	-0.024	17.795	0.392	0.392	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.010	-0.004	18.381	-0.620	-0.620	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.014	0.002	13.262	-0.463	-0.463	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.060	-0.026	13.969	0.135	0.135	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.051	0.030	8.594	-0.627	-0.627	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.035	-0.014	8.915	1.563	1.563	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.010	-0.015	6.500	-3.274	-3.274	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.949	-0.972	3.724	-60.276	-59.527	0.001	-0.266	-0.483	-0.002
70	A	70	GLU	-1	-0.958	-0.975	6.461	-20.293	-20.293	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.019	-0.015	9.041	1.751	1.751	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.019	0.011	9.574	-1.119	-1.119	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.051	-0.016	10.485	1.209	1.209	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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