FMO DATABASE

FMODB ID: VVMN1

Calculation Name: 1Z8M-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Z8M

Chain ID: A

ChEMBL ID:

UniProt ID: O25554

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-646127.939281
FMO2-HF: Nuclear repulsion	610408.666327
FMO2-HF: Total energy	-35719.272954
FMO2-MP2: Total energy	-35825.183428

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.
-31.263	-26.318	0.802	-2.182	-3.564	-0.017

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 : 0.842 / q_NPA : 0.916

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	LYS	1	0.949	0.985	2.876	19.609	22.125	0.235	-1.411	-1.339	-0.011
37	A	37	LYS	1	0.909	0.932	4.345	31.755	32.022	0.001	-0.034	-0.234	0.000
38	A	38	GLU	-1	-0.915	-0.937	3.289	-36.581	-35.484	0.063	-0.480	-0.679	-0.004
39	A	39	PRO	0	-0.057	-0.022	2.501	-1.905	-0.961	0.503	-0.219	-1.229	-0.002
40	A	40	LEU	0	0.007	-0.007	4.335	3.165	3.286	0.000	-0.038	-0.083	0.000
4	A	4	LEU	0	0.051	0.029	5.660	2.591	2.591	0.000	0.000	0.000	0.000
5	A	5	ASN	0	-0.017	-0.011	7.124	1.592	1.592	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.044	0.033	10.982	0.087	0.087	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.934	0.968	14.099	18.466	18.466	0.000	0.000	0.000	0.000
8	A	8	LYS	1	1.000	0.994	17.642	11.660	11.660	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.086	-0.042	20.614	0.609	0.609	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.086	0.038	13.941	0.018	0.018	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.036	-0.039	17.845	-0.113	-0.113	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.869	0.929	19.312	11.672	11.672	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.722	-0.856	20.066	-13.258	-13.258	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.003	0.008	14.771	-0.391	-0.391	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.926	-0.962	19.575	-12.738	-12.738	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.842	0.909	22.217	11.647	11.647	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.064	0.046	22.149	0.479	0.479	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.019	0.022	21.041	0.349	0.349	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.024	-0.016	25.015	0.396	0.396	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.102	-0.057	27.912	0.675	0.675	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.022	0.020	29.599	0.112	0.112	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.028	0.000	20.552	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.783	-0.865	24.939	-11.630	-11.630	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.929	-0.978	22.751	-12.204	-12.204	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.050	-0.055	21.809	-0.644	-0.644	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.004	-0.004	20.133	-0.681	-0.681	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.013	0.006	17.289	-0.952	-0.952	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.010	-0.007	16.698	-1.554	-1.554	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.834	-0.902	16.011	-16.559	-16.559	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.001	0.014	13.093	-1.312	-1.312	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.018	-0.021	11.922	-2.144	-2.144	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.017	0.017	11.484	-2.093	-2.093	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.029	-0.014	8.986	-1.199	-1.199	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.007	-0.003	7.264	-2.677	-2.677	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.880	0.937	6.779	20.233	20.233	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.879	0.954	8.361	24.336	24.336	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.870	-0.926	7.511	-23.697	-23.697	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.009	-0.013	9.527	0.939	0.939	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.064	-0.028	12.294	1.214	1.214	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.045	-0.020	11.445	0.771	0.771	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.010	-0.013	14.902	-0.105	-0.105	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.863	-0.915	11.679	-19.960	-19.960	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.051	0.000	14.930	0.118	0.118	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.088	-0.027	17.278	-0.297	-0.297	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.032	0.035	19.447	0.535	0.535	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.955	0.962	22.509	11.313	11.313	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.039	0.022	26.322	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.944	0.953	27.760	9.893	9.893	0.000	0.000	0.000	0.000
53	A	53	TRP	0	0.060	0.022	22.854	-0.312	-0.312	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.984	1.004	22.373	10.978	10.978	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.042	-0.015	21.533	-0.283	-0.283	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.006	-0.013	18.079	-0.385	-0.385	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.900	0.958	13.538	18.236	18.236	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.888	-0.963	16.306	-15.098	-15.098	0.000	0.000	0.000	0.000
59	A	59	CYS	0	0.006	0.020	12.703	-0.867	-0.867	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.077	0.052	15.011	-0.085	-0.085	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.022	-0.017	11.752	0.248	0.248	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.873	0.921	14.686	15.388	15.388	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.009	-0.010	18.187	0.048	0.048	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.831	-0.920	21.310	-11.140	-11.140	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.046	-0.015	17.014	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.017	0.014	18.302	-0.349	-0.349	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.027	-0.007	11.835	0.031	0.031	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.012	-0.006	15.413	-0.269	-0.269	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.003	-0.025	10.242	-0.365	-0.365	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.035	-0.026	13.137	1.251	1.251	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.015	0.006	9.697	-1.709	-1.709	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.823	0.908	11.007	23.593	23.593	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.804	-0.907	10.952	-21.867	-21.867	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.876	-0.927	8.238	-33.862	-33.862	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-1.019	-1.012	7.262	-33.502	-33.502	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.003	0.004	6.482	3.116	3.116	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.108	-0.071	8.663	0.571	0.571	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.049	0.025	9.895	0.778	0.778	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.079	-0.039	12.912	0.759	0.759	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.917	0.949	16.611	13.773	13.773	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.042	-0.012	16.316	-0.995	-0.995	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.086	0.043	18.946	0.616	0.616	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.056	0.025	20.759	-0.618	-0.618	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.060	-0.030	23.313	0.147	0.147	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.012	-0.010	25.390	0.379	0.379	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.949	-0.972	25.324	-11.091	-11.091	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.113	-0.057	21.291	-0.070	-0.070	0.000	0.000	0.000	0.000
88	A	88	PHE	-1	-0.954	-0.957	24.951	-9.752	-9.752	0.000	0.000	0.000	0.000

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