FMO DATABASE

FMODB ID: 3GYZL

Calculation Name: 1VQO-1-Xray549

Preferred Name:

Target Type:

Ligand 3-letter code: PPU | 1MA | PSU | OMG | UR3 | OMU | CD | MG | SR | CL | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VQO

Chain ID: 1

ChEMBL ID:

UniProt ID: P60617

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-246733.895108
FMO2-HF: Nuclear repulsion	224230.583665
FMO2-HF: Total energy	-22503.311443
FMO2-MP2: Total energy	-22566.142359

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(1:1:THR)

Summations of interaction energy for fragment #1(1:1:THR)

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.
148.296	152.148	0.829	-1.638	-3.043	-0.011

Interaction energy analysis for fragmet #1(1:1:THR)

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 : 0.928

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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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	1	3	ALA	0	0.061	0.030	2.935	-1.632	0.623	0.187	-1.061	-1.381	-0.008
6	1	6	PRO	0	0.015	0.012	2.598	0.770	1.440	0.570	-0.274	-0.966	-0.001
7	1	7	SER	0	-0.047	-0.035	2.858	-3.034	-2.240	0.074	-0.288	-0.580	-0.002
8	1	8	GLN	0	-0.036	-0.015	4.690	5.973	5.987	-0.001	-0.005	-0.007	0.000
10	1	10	LYS	1	0.975	0.986	3.944	43.023	43.142	-0.001	-0.010	-0.109	0.000
4	1	4	GLY	0	0.070	0.041	5.485	4.592	4.592	0.000	0.000	0.000	0.000
5	1	5	THR	0	0.075	0.024	5.945	-2.228	-2.228	0.000	0.000	0.000	0.000
9	1	9	GLY	0	0.044	0.023	7.606	2.012	2.012	0.000	0.000	0.000	0.000
11	1	11	LYS	1	0.823	0.915	8.675	26.255	26.255	0.000	0.000	0.000	0.000
12	1	12	ASN	0	0.076	0.039	11.797	0.725	0.725	0.000	0.000	0.000	0.000
13	1	13	THR	0	-0.040	-0.010	14.638	1.131	1.131	0.000	0.000	0.000	0.000
14	1	14	THR	0	0.034	0.018	16.523	0.193	0.193	0.000	0.000	0.000	0.000
15	1	15	THR	0	-0.011	-0.025	18.502	0.213	0.213	0.000	0.000	0.000	0.000
16	1	16	HIS	0	0.003	0.009	21.247	0.842	0.842	0.000	0.000	0.000	0.000
17	1	17	THR	0	-0.023	-0.028	23.801	0.020	0.020	0.000	0.000	0.000	0.000
18	1	18	LYS	1	0.944	0.964	26.701	9.174	9.174	0.000	0.000	0.000	0.000
19	1	19	CYS	0	-0.036	-0.058	30.352	0.216	0.216	0.000	0.000	0.000	0.000
20	1	20	ARG	1	0.980	0.986	32.462	8.489	8.489	0.000	0.000	0.000	0.000
21	1	21	ARG	1	0.839	0.923	35.777	8.226	8.226	0.000	0.000	0.000	0.000
22	1	22	CYS	0	-0.006	-0.007	33.812	0.136	0.136	0.000	0.000	0.000	0.000
23	1	23	GLY	0	0.058	0.056	34.710	0.063	0.063	0.000	0.000	0.000	0.000
24	1	24	GLU	-1	-0.819	-0.919	30.561	-9.673	-9.673	0.000	0.000	0.000	0.000
25	1	25	LYS	1	0.869	0.936	23.071	12.152	12.152	0.000	0.000	0.000	0.000
26	1	26	SER	0	0.056	0.028	26.119	-0.636	-0.636	0.000	0.000	0.000	0.000
27	1	27	TYR	0	0.011	0.011	27.693	-0.078	-0.078	0.000	0.000	0.000	0.000
28	1	28	HIS	0	0.062	0.035	20.774	0.014	0.014	0.000	0.000	0.000	0.000
29	1	29	THR	0	0.021	0.004	23.891	0.301	0.301	0.000	0.000	0.000	0.000
30	1	30	LYS	1	0.943	0.968	19.359	14.378	14.378	0.000	0.000	0.000	0.000
31	1	31	LYS	1	0.952	0.977	22.546	13.074	13.074	0.000	0.000	0.000	0.000
32	1	32	LYS	1	0.898	0.965	26.825	10.899	10.899	0.000	0.000	0.000	0.000
33	1	33	VAL	0	0.038	0.021	28.770	0.375	0.375	0.000	0.000	0.000	0.000
34	1	34	CYS	-1	-0.852	-0.746	28.699	-10.028	-10.028	0.000	0.000	0.000	0.000
35	1	35	SER	0	-0.060	-0.046	26.695	0.068	0.068	0.000	0.000	0.000	0.000
36	1	36	SER	0	0.033	0.001	28.733	0.092	0.092	0.000	0.000	0.000	0.000
37	1	37	CYS	0	-0.022	-0.112	31.319	0.247	0.247	0.000	0.000	0.000	0.000
38	1	38	GLY	0	0.100	0.044	33.191	0.282	0.282	0.000	0.000	0.000	0.000
39	1	39	PHE	0	0.020	-0.003	33.961	0.168	0.168	0.000	0.000	0.000	0.000
40	1	40	GLY	0	0.009	0.004	33.408	-0.312	-0.312	0.000	0.000	0.000	0.000
41	1	41	LYS	1	0.941	0.981	32.623	9.261	9.261	0.000	0.000	0.000	0.000
42	1	42	SER	0	0.022	-0.002	35.145	0.080	0.080	0.000	0.000	0.000	0.000
43	1	43	ALA	0	0.026	0.024	38.540	-0.030	-0.030	0.000	0.000	0.000	0.000
44	1	44	LYS	1	0.997	0.998	41.294	7.056	7.056	0.000	0.000	0.000	0.000
45	1	45	ARG	1	0.948	0.970	38.470	7.570	7.570	0.000	0.000	0.000	0.000
46	1	46	ARG	1	0.852	0.921	30.307	9.814	9.814	0.000	0.000	0.000	0.000
47	1	47	ASP	-1	-0.888	-0.942	36.648	-7.848	-7.848	0.000	0.000	0.000	0.000
48	1	48	TYR	0	-0.066	-0.044	33.671	-0.200	-0.200	0.000	0.000	0.000	0.000
49	1	49	GLU	-1	-0.808	-0.901	38.085	-7.471	-7.471	0.000	0.000	0.000	0.000
50	1	50	TRP	0	-0.066	-0.018	31.088	-0.164	-0.164	0.000	0.000	0.000	0.000
51	1	51	GLN	0	-0.090	-0.060	34.192	-0.168	-0.168	0.000	0.000	0.000	0.000
52	1	52	SER	0	0.001	-0.001	36.185	-0.114	-0.114	0.000	0.000	0.000	0.000
53	1	53	LYS	1	0.927	0.954	36.534	8.239	8.239	0.000	0.000	0.000	0.000
54	1	54	ALA	0	0.015	-0.010	40.491	0.110	0.110	0.000	0.000	0.000	0.000
55	1	55	GLY	0	-0.039	-0.008	42.627	0.117	0.117	0.000	0.000	0.000	0.000
56	1	56	GLU	-2	-1.847	-1.881	42.224	-14.438	-14.438	0.000	0.000	0.000	0.000

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