FMO DATABASE

FMODB ID: 52Y2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-447612.81184
FMO2-HF: Nuclear repulsion	418949.598262
FMO2-HF: Total energy	-28663.213579
FMO2-MP2: Total energy	-28747.401895

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.
-293.364	-290.702	30.933	-17.763	-15.832	-0.17

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 : 0.798 / q_NPA : 0.882

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	0.000	0.008	3.838	0.080	2.464	-0.022	-1.288	-1.075	0.005
4	A	4	PHE	0	0.001	0.009	6.180	1.902	1.902	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.012	-0.006	9.633	0.313	0.313	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.009	-0.010	11.927	0.786	0.786	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.005	-0.009	15.005	0.245	0.245	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.016	0.031	18.451	0.371	0.371	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.028	-0.027	21.080	0.362	0.362	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.006	-0.007	24.628	0.073	0.073	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.779	-0.907	24.997	-10.673	-10.673	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.898	-0.955	25.717	-10.082	-10.082	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.009	-0.002	21.523	-0.449	-0.449	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.038	0.022	20.944	-0.675	-0.675	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.013	0.013	21.286	-0.356	-0.356	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.016	-0.026	17.867	0.005	0.005	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.017	-0.002	15.458	-0.372	-0.372	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.824	-0.902	17.389	-12.193	-12.193	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.064	-0.024	19.493	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.013	-0.004	14.963	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.027	0.017	14.774	-0.280	-0.280	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.774	0.877	15.827	11.951	11.951	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.115	-0.048	16.070	0.687	0.687	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.935	-0.960	14.719	-17.273	-17.273	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.974	-0.983	11.668	-18.636	-18.636	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.026	-0.001	10.189	-1.028	-1.028	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.043	-0.039	5.864	-0.451	-0.451	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.008	0.003	5.770	-3.650	-3.650	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.866	-0.930	6.385	-24.193	-24.193	0.000	0.000	0.000	0.000
30	A	30	TRP	0	0.008	0.009	8.062	-1.231	-1.231	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.060	-0.052	8.258	0.847	0.847	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.059	-0.038	11.503	0.193	0.193	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.015	0.017	14.841	-0.429	-0.429	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.002	-0.016	16.703	0.082	0.082	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.038	-0.020	19.143	0.361	0.361	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.892	-0.940	22.576	-9.876	-9.876	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.044	-0.026	23.161	-0.577	-0.577	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.044	-0.026	23.426	0.236	0.236	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.047	-0.013	20.812	-0.063	-0.063	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.029	-0.025	16.126	-0.267	-0.267	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.012	0.013	13.710	0.248	0.248	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.007	-0.003	9.037	-0.746	-0.746	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.006	0.011	7.583	0.486	0.486	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.007	0.000	2.055	-3.503	-3.917	2.582	-0.854	-1.313	-0.003
45	A	45	ILE	0	0.016	0.023	3.631	2.662	3.091	0.002	-0.127	-0.303	-0.001
46	A	46	PRO	0	0.025	0.010	2.113	-14.515	-11.826	3.023	-3.088	-2.626	-0.026
47	A	47	SER	0	0.055	0.006	2.086	-1.170	-1.929	5.005	-1.062	-3.184	-0.014
48	A	48	ASP	-1	-0.940	-0.964	3.359	-28.449	-28.399	0.053	0.144	-0.246	0.000
49	A	49	MET	0	-0.004	0.013	6.207	3.979	3.979	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.013	0.001	5.744	2.030	2.030	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.922	-0.967	8.371	-17.051	-17.051	0.000	0.000	0.000	0.000
52	A	52	TRP	0	0.031	-0.010	10.888	1.472	1.472	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.007	0.010	10.517	1.196	1.196	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.012	0.002	11.562	0.935	0.935	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.773	-0.866	13.841	-14.150	-14.150	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.027	0.008	14.171	1.356	1.356	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.008	-0.010	13.038	1.001	1.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.812	0.882	17.220	15.758	15.758	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.052	-0.006	19.701	0.740	0.740	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.823	0.922	20.267	12.855	12.855	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.012	-0.001	21.974	0.369	0.369	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.054	-0.029	18.247	0.381	0.381	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.011	-0.003	18.551	-0.652	-0.652	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.018	0.006	13.717	-0.501	-0.501	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.056	-0.024	14.166	0.108	0.108	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.036	0.024	8.990	-0.731	-0.731	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.023	-0.009	8.676	1.677	1.677	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.014	0.000	6.486	-3.679	-3.679	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.863	-0.910	1.677	-140.669	-142.386	20.290	-11.488	-7.085	-0.131
70	A	70	GLU	-1	-0.939	-0.967	5.612	-22.551	-22.551	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.016	-0.012	7.300	2.587	2.587	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.000	0.001	8.080	-2.114	-2.114	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.037	-0.008	9.040	1.621	1.621	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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