FMO DATABASE

FMODB ID: 3GYML

Calculation Name: 1VQO-X-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: X

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-543055.33647
FMO2-HF: Nuclear repulsion	510820.310939
FMO2-HF: Total energy	-32235.025531
FMO2-MP2: Total energy	-32330.593151

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(X:7:GLU)

Summations of interaction energy for fragment #1(X:7:GLU)

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.
-31.164	-23.116	10.255	-8.295	-10.005	-0.033

Interaction energy analysis for fragmet #1(X:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.099 / q_NPA : -0.056

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	X	9	VAL	0	0.033	0.044	3.676	2.783	4.729	-0.023	-0.824	-1.099	0.001
35	X	41	PHE	0	-0.009	-0.011	3.257	-2.398	-2.122	0.021	-0.064	-0.233	0.000
67	X	73	ARG	1	0.864	0.951	2.440	-28.279	-25.566	1.493	-1.686	-2.519	0.022
68	X	74	ALA	0	0.038	0.015	4.035	0.896	1.625	0.000	-0.196	-0.533	0.000
69	X	75	ALA	0	0.002	-0.008	2.165	-20.583	-17.818	8.687	-6.449	-5.002	-0.055
70	X	76	ARG	1	0.912	0.962	3.125	10.312	9.769	0.078	0.942	-0.477	-0.001
71	X	77	PHE	0	-0.076	-0.036	4.492	-4.940	-4.778	-0.001	-0.018	-0.142	0.000
4	X	10	VAL	0	-0.019	-0.018	5.933	-2.388	-2.388	0.000	0.000	0.000	0.000
5	X	11	THR	0	-0.052	-0.024	9.125	1.244	1.244	0.000	0.000	0.000	0.000
6	X	12	ILE	0	0.034	0.024	11.060	-0.588	-0.588	0.000	0.000	0.000	0.000
7	X	13	PRO	0	-0.062	-0.031	14.719	0.376	0.376	0.000	0.000	0.000	0.000
8	X	14	LEU	0	0.073	0.024	16.891	-0.088	-0.088	0.000	0.000	0.000	0.000
9	X	15	ARG	1	0.913	0.951	20.428	0.675	0.675	0.000	0.000	0.000	0.000
10	X	16	ASP	-1	-0.853	-0.917	22.776	-0.614	-0.614	0.000	0.000	0.000	0.000
11	X	17	ALA	0	0.008	0.001	23.099	0.003	0.003	0.000	0.000	0.000	0.000
12	X	18	ARG	1	0.833	0.899	24.993	0.237	0.237	0.000	0.000	0.000	0.000
13	X	19	ALA	0	0.008	0.016	27.765	0.005	0.005	0.000	0.000	0.000	0.000
14	X	20	GLU	-1	-0.851	-0.903	27.596	-0.116	-0.116	0.000	0.000	0.000	0.000
15	X	21	PRO	0	-0.021	-0.011	29.593	0.038	0.038	0.000	0.000	0.000	0.000
16	X	22	ASN	0	0.053	-0.008	30.777	0.035	0.035	0.000	0.000	0.000	0.000
17	X	23	HIS	0	0.013	0.005	30.559	0.050	0.050	0.000	0.000	0.000	0.000
18	X	24	LYS	1	0.854	0.919	28.652	0.027	0.027	0.000	0.000	0.000	0.000
19	X	25	ARG	1	0.903	0.964	25.889	-0.290	-0.290	0.000	0.000	0.000	0.000
20	X	26	ALA	0	0.039	0.024	22.910	-0.036	-0.036	0.000	0.000	0.000	0.000
21	X	27	ASP	-1	-0.770	-0.855	21.940	0.369	0.369	0.000	0.000	0.000	0.000
22	X	28	LYS	1	0.963	0.986	22.281	0.370	0.370	0.000	0.000	0.000	0.000
23	X	29	ALA	0	-0.002	-0.003	19.627	-0.121	-0.121	0.000	0.000	0.000	0.000
24	X	30	MET	0	-0.002	0.012	17.242	-0.008	-0.008	0.000	0.000	0.000	0.000
25	X	31	ILE	0	-0.035	0.008	17.560	-0.072	-0.072	0.000	0.000	0.000	0.000
26	X	32	LEU	0	0.018	0.005	17.992	-0.151	-0.151	0.000	0.000	0.000	0.000
27	X	33	ILE	0	-0.033	-0.025	12.742	-0.269	-0.269	0.000	0.000	0.000	0.000
28	X	34	ARG	1	0.877	0.936	13.346	0.109	0.109	0.000	0.000	0.000	0.000
29	X	35	GLU	-1	-0.841	-0.925	14.036	-1.349	-1.349	0.000	0.000	0.000	0.000
30	X	36	HIS	0	-0.051	-0.038	11.869	-0.231	-0.231	0.000	0.000	0.000	0.000
31	X	37	LEU	0	-0.013	-0.018	8.066	-0.727	-0.727	0.000	0.000	0.000	0.000
32	X	38	ALA	0	0.077	0.054	10.227	-1.215	-1.215	0.000	0.000	0.000	0.000
33	X	39	LYS	1	0.958	0.984	12.479	1.793	1.793	0.000	0.000	0.000	0.000
34	X	40	HIS	0	-0.108	-0.064	10.231	-0.235	-0.235	0.000	0.000	0.000	0.000
36	X	42	SER	0	-0.061	-0.018	8.272	-0.978	-0.978	0.000	0.000	0.000	0.000
37	X	43	VAL	0	-0.039	-0.011	9.207	-0.523	-0.523	0.000	0.000	0.000	0.000
38	X	44	ASP	-1	-0.827	-0.905	12.245	-2.144	-2.144	0.000	0.000	0.000	0.000
39	X	45	GLU	-1	-0.930	-0.993	14.538	-1.445	-1.445	0.000	0.000	0.000	0.000
40	X	46	ASP	-1	-0.937	-0.962	15.845	-0.834	-0.834	0.000	0.000	0.000	0.000
41	X	47	ALA	0	0.028	0.028	13.522	0.308	0.308	0.000	0.000	0.000	0.000
42	X	48	VAL	0	-0.013	-0.005	10.347	-0.411	-0.411	0.000	0.000	0.000	0.000
43	X	49	ARG	1	0.917	0.960	10.782	-2.755	-2.755	0.000	0.000	0.000	0.000
44	X	50	LEU	0	-0.021	-0.025	10.289	0.399	0.399	0.000	0.000	0.000	0.000
45	X	51	ASP	-1	-0.781	-0.870	10.736	4.612	4.612	0.000	0.000	0.000	0.000
46	X	52	PRO	0	-0.007	-0.009	12.586	-0.275	-0.275	0.000	0.000	0.000	0.000
47	X	53	SER	0	0.041	0.011	11.807	-0.221	-0.221	0.000	0.000	0.000	0.000
48	X	54	ILE	0	-0.015	-0.008	9.943	-0.360	-0.360	0.000	0.000	0.000	0.000
49	X	55	ASN	0	0.006	-0.014	14.296	-0.582	-0.582	0.000	0.000	0.000	0.000
50	X	56	GLU	-1	-0.930	-0.975	17.532	2.288	2.288	0.000	0.000	0.000	0.000
51	X	57	ALA	0	-0.003	0.000	15.987	-0.221	-0.221	0.000	0.000	0.000	0.000
52	X	58	ALA	0	-0.062	-0.037	17.970	-0.242	-0.242	0.000	0.000	0.000	0.000
53	X	59	TRP	0	0.033	-0.009	19.856	-0.213	-0.213	0.000	0.000	0.000	0.000
54	X	60	ALA	0	-0.015	0.013	21.234	-0.098	-0.098	0.000	0.000	0.000	0.000
55	X	61	ARG	1	0.881	0.941	21.248	-1.082	-1.082	0.000	0.000	0.000	0.000
56	X	62	GLY	0	0.045	0.023	26.281	-0.107	-0.107	0.000	0.000	0.000	0.000
57	X	63	ARG	1	0.828	0.869	26.494	-0.351	-0.351	0.000	0.000	0.000	0.000
58	X	64	ALA	0	0.010	0.017	27.257	-0.056	-0.056	0.000	0.000	0.000	0.000
59	X	65	ASN	0	-0.083	-0.031	27.047	-0.110	-0.110	0.000	0.000	0.000	0.000
60	X	66	THR	0	0.070	0.040	21.200	0.132	0.132	0.000	0.000	0.000	0.000
61	X	67	PRO	0	-0.046	0.006	19.430	-0.090	-0.090	0.000	0.000	0.000	0.000
62	X	68	SER	0	0.008	-0.019	21.521	-0.072	-0.072	0.000	0.000	0.000	0.000
63	X	69	LYS	1	0.914	0.949	17.223	-0.303	-0.303	0.000	0.000	0.000	0.000
64	X	70	ILE	0	0.037	0.025	13.522	0.124	0.124	0.000	0.000	0.000	0.000
65	X	71	ARG	1	0.905	0.968	11.183	-2.529	-2.529	0.000	0.000	0.000	0.000
66	X	72	VAL	0	0.029	0.014	8.349	0.246	0.246	0.000	0.000	0.000	0.000
72	X	78	GLU	-1	-0.881	-0.940	7.263	-0.311	-0.311	0.000	0.000	0.000	0.000
73	X	79	GLU	-1	-0.954	-0.965	11.101	-2.580	-2.580	0.000	0.000	0.000	0.000
74	X	80	GLU	-1	-0.951	-0.972	14.115	-1.803	-1.803	0.000	0.000	0.000	0.000
75	X	81	GLY	0	-0.060	-0.027	10.744	-0.377	-0.377	0.000	0.000	0.000	0.000
76	X	82	GLU	-1	-0.867	-0.945	9.154	-1.588	-1.588	0.000	0.000	0.000	0.000
77	X	83	ALA	0	-0.013	-0.028	6.990	-2.510	-2.510	0.000	0.000	0.000	0.000
78	X	84	ILE	0	-0.016	0.014	6.613	1.760	1.760	0.000	0.000	0.000	0.000
79	X	85	VAL	0	-0.039	-0.021	5.475	0.608	0.608	0.000	0.000	0.000	0.000
80	X	86	GLU	-1	-0.866	-0.941	5.799	15.845	15.845	0.000	0.000	0.000	0.000
81	X	87	ALA	0	-0.013	-0.012	8.422	-0.509	-0.509	0.000	0.000	0.000	0.000
82	X	88	GLU	-2	-1.749	-1.883	6.979	13.570	13.570	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:7:GLU)