FMO DATABASE

FMODB ID: 3KZVL

Calculation Name: 6MZD-H-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6MZD

Chain ID: H

ChEMBL ID:

UniProt ID: Q12962

Base Structure: ElectronMicroscopy

Registration Date: 2025-09-02

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-379396.901735
FMO2-HF: Nuclear repulsion	350039.00684
FMO2-HF: Total energy	-29357.894895
FMO2-MP2: Total energy	-29440.369333

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(H:6:LYS)

Summations of interaction energy for fragment #1(H:6: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.
-8.392	-5.065	0.297	-2.014	-1.611	-0.014

Interaction energy analysis for fragmet #1(H:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.836 / q_NPA : 1.909

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	H	8	LYS	1	0.988	0.983	2.838	34.466	37.793	0.297	-2.014	-1.611	-0.014
4	H	9	LEU	0	0.017	0.016	5.600	3.160	3.160	0.000	0.000	0.000	0.000
5	H	10	SER	0	-0.020	-0.009	9.016	0.810	0.810	0.000	0.000	0.000	0.000
6	H	11	ASN	0	0.053	0.025	12.049	-0.990	-0.990	0.000	0.000	0.000	0.000
7	H	12	THR	0	-0.024	-0.022	15.622	-1.205	-1.205	0.000	0.000	0.000	0.000
8	H	13	VAL	0	0.052	0.039	17.711	0.786	0.786	0.000	0.000	0.000	0.000
9	H	14	LEU	0	0.022	0.015	20.582	-0.273	-0.273	0.000	0.000	0.000	0.000
10	H	15	PRO	0	0.025	0.012	23.811	0.212	0.212	0.000	0.000	0.000	0.000
11	H	16	SER	0	0.048	0.023	25.726	1.008	1.008	0.000	0.000	0.000	0.000
12	H	17	GLU	-1	-0.878	-0.942	27.979	-18.878	-18.878	0.000	0.000	0.000	0.000
13	H	18	SER	0	-0.055	-0.036	28.524	0.494	0.494	0.000	0.000	0.000	0.000
14	H	19	MET	0	0.012	0.003	28.091	0.290	0.290	0.000	0.000	0.000	0.000
15	H	20	LYS	1	0.915	0.969	31.187	18.655	18.655	0.000	0.000	0.000	0.000
16	H	21	VAL	0	0.020	0.019	34.042	0.503	0.503	0.000	0.000	0.000	0.000
17	H	22	VAL	0	-0.018	-0.009	32.904	0.449	0.449	0.000	0.000	0.000	0.000
18	H	23	ALA	0	0.003	0.014	35.049	0.446	0.446	0.000	0.000	0.000	0.000
19	H	24	GLU	-1	-0.920	-0.983	36.795	-15.518	-15.518	0.000	0.000	0.000	0.000
20	H	25	SER	0	-0.105	-0.055	38.590	0.491	0.491	0.000	0.000	0.000	0.000
21	H	26	MET	0	-0.031	-0.019	39.789	0.364	0.364	0.000	0.000	0.000	0.000
22	H	27	GLY	0	-0.028	-0.004	41.915	0.289	0.289	0.000	0.000	0.000	0.000
23	H	28	ILE	0	-0.057	-0.022	38.126	0.211	0.211	0.000	0.000	0.000	0.000
24	H	29	ALA	0	-0.005	-0.013	40.135	0.302	0.302	0.000	0.000	0.000	0.000
25	H	30	GLN	0	0.018	0.019	39.938	-0.173	-0.173	0.000	0.000	0.000	0.000
26	H	31	ILE	0	0.013	0.010	33.926	-0.079	-0.079	0.000	0.000	0.000	0.000
27	H	32	GLN	0	0.019	0.001	33.508	-0.466	-0.466	0.000	0.000	0.000	0.000
28	H	33	GLU	-1	-0.907	-0.963	28.788	-19.856	-19.856	0.000	0.000	0.000	0.000
29	H	34	GLU	-1	-0.896	-0.942	27.540	-20.532	-20.532	0.000	0.000	0.000	0.000
30	H	35	THR	0	-0.033	-0.026	27.999	-0.382	-0.382	0.000	0.000	0.000	0.000
31	H	36	CYS	0	0.001	0.001	29.259	-0.110	-0.110	0.000	0.000	0.000	0.000
32	H	37	GLN	0	-0.013	-0.002	24.217	-0.774	-0.774	0.000	0.000	0.000	0.000
33	H	38	LEU	0	0.091	0.060	24.119	-0.782	-0.782	0.000	0.000	0.000	0.000
34	H	39	LEU	0	0.027	0.021	25.332	-0.416	-0.416	0.000	0.000	0.000	0.000
35	H	40	THR	0	-0.090	-0.067	23.896	-0.457	-0.457	0.000	0.000	0.000	0.000
36	H	41	ASP	-1	-0.900	-0.945	20.318	-28.508	-28.508	0.000	0.000	0.000	0.000
37	H	42	GLU	-1	-0.907	-0.953	21.561	-22.500	-22.500	0.000	0.000	0.000	0.000
38	H	43	VAL	0	-0.022	-0.012	23.983	-0.168	-0.168	0.000	0.000	0.000	0.000
39	H	44	SER	0	-0.093	-0.055	19.540	-1.101	-1.101	0.000	0.000	0.000	0.000
40	H	45	TYR	0	-0.036	-0.022	17.544	-1.062	-1.062	0.000	0.000	0.000	0.000
41	H	46	ARG	1	1.046	1.023	20.424	21.063	21.063	0.000	0.000	0.000	0.000
42	H	47	ILE	0	-0.005	0.004	21.008	-0.031	-0.031	0.000	0.000	0.000	0.000
43	H	48	LYS	1	0.853	0.917	14.409	36.099	36.099	0.000	0.000	0.000	0.000
44	H	49	GLU	-1	-0.927	-0.957	18.864	-27.661	-27.661	0.000	0.000	0.000	0.000
45	H	50	ILE	0	0.069	0.027	20.834	-0.135	-0.135	0.000	0.000	0.000	0.000
46	H	51	ALA	0	-0.021	-0.005	19.439	0.168	0.168	0.000	0.000	0.000	0.000
47	H	52	GLN	0	-0.030	-0.022	15.272	0.266	0.266	0.000	0.000	0.000	0.000
48	H	53	ASP	-1	-0.837	-0.911	19.535	-25.798	-25.798	0.000	0.000	0.000	0.000
49	H	54	ALA	0	0.028	0.014	23.171	0.397	0.397	0.000	0.000	0.000	0.000
50	H	55	LEU	0	-0.029	-0.016	16.871	-0.003	-0.003	0.000	0.000	0.000	0.000
51	H	56	LYS	1	0.853	0.932	20.145	27.513	27.513	0.000	0.000	0.000	0.000
52	H	57	PHE	0	0.020	0.013	21.836	0.555	0.555	0.000	0.000	0.000	0.000
53	H	58	MET	0	0.008	0.019	22.924	0.782	0.782	0.000	0.000	0.000	0.000
54	H	59	HIS	0	-0.083	-0.048	17.587	-1.036	-1.036	0.000	0.000	0.000	0.000
55	H	60	MET	0	-0.047	-0.020	21.464	0.432	0.432	0.000	0.000	0.000	0.000
56	H	61	GLY	0	-0.005	-0.006	24.867	0.876	0.876	0.000	0.000	0.000	0.000
57	H	62	LYS	1	0.870	0.942	22.795	23.561	23.561	0.000	0.000	0.000	0.000
58	H	63	ARG	1	0.961	0.977	23.083	21.768	21.768	0.000	0.000	0.000	0.000
59	H	64	GLN	0	0.011	0.014	16.439	0.008	0.008	0.000	0.000	0.000	0.000
60	H	65	LYS	1	0.910	0.939	20.051	24.326	24.326	0.000	0.000	0.000	0.000
61	H	66	LEU	0	0.015	0.023	21.625	0.283	0.283	0.000	0.000	0.000	0.000
62	H	67	THR	0	-0.066	-0.055	24.553	0.428	0.428	0.000	0.000	0.000	0.000
63	H	68	THR	0	0.044	0.012	28.134	-0.444	-0.444	0.000	0.000	0.000	0.000
64	H	69	SER	0	0.045	0.034	30.582	-0.038	-0.038	0.000	0.000	0.000	0.000
65	H	70	ASP	-1	-0.836	-0.913	27.225	-22.089	-22.089	0.000	0.000	0.000	0.000
66	H	71	ILE	0	-0.017	-0.009	25.357	-0.482	-0.482	0.000	0.000	0.000	0.000
67	H	72	ASP	-1	-0.862	-0.942	28.608	-19.024	-19.024	0.000	0.000	0.000	0.000
68	H	73	TYR	0	-0.087	-0.065	31.307	0.703	0.703	0.000	0.000	0.000	0.000
69	H	74	ALA	0	-0.006	-0.006	27.253	0.070	0.070	0.000	0.000	0.000	0.000
70	H	75	LEU	0	-0.032	-0.003	29.340	-0.179	-0.179	0.000	0.000	0.000	0.000
71	H	76	LYS	1	0.829	0.923	31.502	19.174	19.174	0.000	0.000	0.000	0.000
72	H	77	LEU	-1	-0.923	-0.939	27.705	-18.650	-18.650	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:6:LYS)