FMO DATABASE

FMODB ID: YZ1Y2

Calculation Name: 1VJQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-446991.10001
FMO2-HF: Nuclear repulsion	418327.754399
FMO2-HF: Total energy	-28663.345611
FMO2-MP2: Total energy	-28747.511588

3D Structure Molmil

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.
-301.258	-298.845	28.336	-16.576	-14.175	-0.167

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 : 0.854 / q_NPA : 0.908

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

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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	0.026	0.030	3.878	-0.854	1.490	-0.020	-1.312	-1.012	0.004
4	A	4	PHE	0	0.009	0.009	6.322	2.080	2.080	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.015	-0.012	9.884	0.007	0.007	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.028	0.005	12.861	0.846	0.846	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.019	-0.008	15.571	0.134	0.134	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.002	0.025	19.247	0.369	0.369	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.031	-0.042	21.797	0.382	0.382	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.017	-0.022	25.388	0.066	0.066	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.779	-0.905	25.716	-10.689	-10.689	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.906	-0.952	26.204	-10.095	-10.095	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.025	0.001	22.163	-0.463	-0.463	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.029	0.019	21.653	-0.653	-0.653	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.051	0.019	21.805	-0.444	-0.444	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.010	-0.015	19.134	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.032	0.008	16.198	-0.431	-0.431	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.847	-0.899	17.909	-12.238	-12.238	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.042	-0.021	20.220	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.026	-0.012	15.888	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.023	0.008	15.444	-0.441	-0.441	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.758	0.866	16.494	11.951	11.951	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.090	-0.041	16.458	0.731	0.731	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.932	-0.956	15.209	-17.725	-17.725	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.968	-0.979	12.307	-19.030	-19.030	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.005	-0.012	10.912	-1.319	-1.319	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.027	-0.023	6.227	-1.674	-1.674	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.010	-0.004	6.343	-3.591	-3.591	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.874	-0.923	6.969	-24.429	-24.429	0.000	0.000	0.000	0.000
30	A	30	TRP	0	0.021	-0.004	8.561	-1.210	-1.210	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.070	-0.043	8.643	0.829	0.829	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.066	-0.042	11.660	0.252	0.252	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.013	0.020	15.122	-0.364	-0.364	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.005	-0.017	17.362	0.068	0.068	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.044	-0.026	19.793	0.269	0.269	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.884	-0.932	23.274	-9.908	-9.908	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.023	-0.016	23.753	-0.570	-0.570	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.050	-0.022	23.762	0.226	0.226	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.039	-0.015	21.341	-0.224	-0.224	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.024	-0.023	16.499	-0.277	-0.277	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.006	0.010	14.513	0.254	0.254	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.015	-0.003	9.635	-0.703	-0.703	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.013	-0.003	8.087	0.443	0.443	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.011	0.001	2.465	-3.712	-3.301	0.964	-0.421	-0.954	-0.001
45	A	45	ILE	0	0.015	0.014	3.961	3.017	3.275	-0.001	-0.050	-0.208	0.000
46	A	46	PRO	0	0.014	0.002	2.469	-13.652	-10.664	0.915	-2.124	-1.779	-0.020
47	A	47	SER	0	0.005	-0.026	2.462	-2.491	-1.105	1.851	-1.077	-2.160	-0.016
48	A	48	ASP	-1	-0.934	-0.975	3.992	-29.406	-29.218	0.005	-0.035	-0.159	0.000
49	A	49	MET	0	-0.013	0.009	6.583	3.825	3.825	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.014	0.002	6.164	1.888	1.888	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.898	-0.954	8.871	-17.276	-17.276	0.000	0.000	0.000	0.000
52	A	52	TRP	0	0.019	-0.016	11.278	1.356	1.356	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.023	0.019	10.702	1.122	1.122	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.002	0.002	12.160	0.903	0.903	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.796	-0.884	14.101	-13.877	-13.877	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.044	-0.010	14.610	1.304	1.304	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.015	-0.001	13.862	0.932	0.932	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.830	0.885	18.010	15.422	15.422	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.051	-0.017	20.218	0.716	0.716	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.829	0.933	21.274	12.930	12.930	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.000	0.001	23.081	0.247	0.247	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.030	-0.009	19.009	0.351	0.351	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.014	-0.004	19.396	-0.579	-0.579	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.004	-0.005	13.912	-0.440	-0.440	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.036	-0.003	13.828	0.341	0.341	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.017	0.003	9.052	-0.663	-0.663	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.010	0.002	8.546	1.621	1.621	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.021	0.000	5.862	-3.576	-3.576	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.838	-0.901	1.747	-141.032	-146.194	24.622	-11.557	-7.903	-0.134
70	A	70	GLU	-1	-0.977	-0.977	5.551	-22.961	-22.961	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.011	-0.011	7.697	2.485	2.485	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.005	0.005	7.637	-3.252	-3.252	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.044	-0.011	8.939	1.758	1.758	0.000	0.000	0.000	0.000

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