FMO DATABASE

FMODB ID: 5GG5Z

Calculation Name: 1VMG-A-Xray547

Preferred Name:

Target Type:

Ligand Name: lithium ion

Ligand 3-letter code: LI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VMG

Chain ID: A

ChEMBL ID:

UniProt ID: Q97U11

Base Structure: X-ray

Registration Date: 2025-10-06

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-535201.475095
FMO2-HF: Nuclear repulsion	501521.408619
FMO2-HF: Total energy	-33680.066476
FMO2-MP2: Total energy	-33777.742015

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:MET)

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

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.
-142.373	-139.102	0.325	-1.797	-1.797	-0.015

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.810 / q_NPA : 0.895

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	LEU	0	-0.036	-0.003	2.746	-15.749	-12.665	0.327	-1.783	-1.627	-0.015
4	A	4	GLU	-1	-0.877	-0.944	4.918	-33.575	-33.402	-0.001	-0.008	-0.163	0.000
7	A	7	GLU	-1	-0.872	-0.919	4.631	-52.827	-52.813	-0.001	-0.006	-0.007	0.000
5	A	5	LEU	0	0.033	0.012	7.024	2.206	2.206	0.000	0.000	0.000	0.000
6	A	6	LYS	1	1.014	1.013	9.375	30.820	30.820	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.007	0.001	9.110	1.505	1.505	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.016	-0.010	10.953	1.173	1.173	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.023	-0.034	11.762	1.089	1.089	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.939	0.960	6.812	40.023	40.023	0.000	0.000	0.000	0.000
12	A	12	MET	0	0.026	0.017	13.342	1.547	1.547	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.863	0.950	15.985	16.113	16.113	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.980	-1.003	14.693	-19.883	-19.883	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.065	-0.018	14.556	0.719	0.719	0.000	0.000	0.000	0.000
16	A	16	TYR	0	0.032	0.014	18.134	1.015	1.015	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.051	0.020	21.175	0.715	0.715	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.943	-0.951	22.906	-11.100	-11.100	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.992	0.989	25.439	12.676	12.676	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.785	-0.873	22.993	-13.175	-13.175	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.012	-0.031	26.206	0.429	0.429	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.098	-0.039	28.476	0.204	0.204	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.770	0.873	25.981	12.216	12.216	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.029	0.028	30.713	0.303	0.303	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.041	0.019	27.985	-0.163	-0.163	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.022	0.002	30.141	-0.197	-0.197	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.025	0.030	32.316	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.030	0.011	25.603	-0.198	-0.198	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.013	-0.001	27.587	-0.265	-0.265	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.048	-0.040	29.308	0.097	0.097	0.000	0.000	0.000	0.000
31	A	31	TRP	0	-0.011	0.001	27.185	0.149	0.149	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.009	0.018	23.788	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.042	-0.028	26.887	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	34	GLU	0	-0.093	-0.078	27.993	0.250	0.250	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.756	-0.853	24.729	-12.598	-12.598	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.066	-0.035	26.623	-0.168	-0.168	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.050	-0.020	28.074	0.184	0.184	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.841	-0.914	26.997	-10.489	-10.489	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.015	-0.013	23.217	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.047	-0.029	26.427	0.072	0.072	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.922	-0.957	29.780	-9.778	-9.778	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.033	0.030	24.860	0.147	0.147	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.055	-0.034	24.648	0.017	0.017	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.062	-0.029	27.600	0.280	0.280	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.073	-0.049	28.899	0.211	0.211	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.111	-0.059	27.299	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.032	0.038	24.500	-0.564	-0.564	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.017	-0.004	18.909	-0.307	-0.307	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.929	-0.962	19.648	-14.005	-14.005	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.055	0.011	20.241	-0.374	-0.374	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.035	-0.015	20.343	-0.378	-0.378	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.089	-0.046	13.876	-0.240	-0.240	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.947	-0.953	17.649	-15.212	-15.212	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.795	-0.914	19.703	-13.576	-13.576	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.101	-0.054	18.547	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.046	-0.014	16.105	-0.752	-0.752	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.841	-0.909	17.473	-16.123	-16.123	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.020	-0.018	20.527	0.144	0.144	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.046	-0.008	15.363	0.075	0.075	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.009	0.000	17.314	-0.065	-0.065	0.000	0.000	0.000	0.000
61	A	61	TRP	0	0.044	0.007	18.198	0.520	0.520	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.044	-0.033	20.275	0.813	0.813	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.037	-0.016	15.558	0.184	0.184	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.036	-0.031	18.775	-0.105	-0.105	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.026	-0.014	21.345	0.525	0.525	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.023	-0.004	19.617	0.410	0.410	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.022	-0.034	17.201	0.232	0.232	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.099	-0.034	21.304	0.369	0.369	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.923	-0.970	25.058	-10.722	-10.722	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.061	-0.018	23.120	0.218	0.218	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.061	-0.024	21.661	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.839	-0.908	16.447	-19.549	-19.549	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.037	-0.006	15.009	0.597	0.597	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.878	-0.924	12.488	-24.550	-24.550	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.841	-0.932	15.904	-17.053	-17.053	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.060	-0.025	19.169	0.940	0.940	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.036	-0.009	16.503	0.784	0.784	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.850	0.902	14.696	20.932	20.932	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.897	0.964	20.320	12.557	12.557	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.873	0.943	23.117	12.674	12.674	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.033	-0.027	21.237	0.722	0.722	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.923	0.960	21.609	13.008	13.008	0.000	0.000	0.000	0.000
83	A	83	LEU	-1	-0.884	-0.927	16.579	-18.321	-18.321	0.000	0.000	0.000	0.000

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