FMO DATABASE

FMODB ID: 3Z8NL

Calculation Name: 4ZGL-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine monophosphate

Ligand 3-letter code: AMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZGL

Chain ID: A

ChEMBL ID:

UniProt ID: P64382

Base Structure: X-ray

Registration Date: 2025-10-04

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	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-778743.345554
FMO2-HF: Nuclear repulsion	738330.455707
FMO2-HF: Total energy	-40412.889847
FMO2-MP2: Total energy	-40529.614669

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.
-113.172	-112.056	13.77	-8.102	-6.783	-0.094

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 : 0.822 / q_NPA : 0.885

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

Sort

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	VAL	0	0.034	0.018	3.775	-5.862	-4.368	-0.013	-0.743	-0.738	0.001
5	A	5	GLU	-1	-0.751	-0.860	1.723	-118.911	-120.556	13.751	-7.027	-5.079	-0.094
6	A	6	LYS	1	0.895	0.955	3.337	57.627	58.444	0.035	-0.251	-0.601	-0.001
7	A	7	ILE	0	0.002	0.004	4.803	5.279	5.351	-0.001	-0.006	-0.065	0.000
9	A	9	GLN	0	-0.109	-0.050	4.218	2.621	2.866	-0.001	-0.058	-0.186	0.000
11	A	11	GLU	-1	-0.940	-0.980	4.501	-59.636	-59.503	-0.001	-0.017	-0.114	0.000
4	A	4	PHE	0	0.080	0.011	6.383	1.298	1.298	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.054	-0.017	7.206	3.362	3.362	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.014	0.026	7.621	2.291	2.291	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.049	-0.027	7.932	2.170	2.170	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.015	0.016	10.174	-0.144	-0.144	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.013	0.001	12.732	-0.282	-0.282	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.024	0.013	14.629	0.764	0.764	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.902	0.935	16.841	16.913	16.913	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.040	0.000	18.169	0.916	0.916	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.004	-0.006	19.546	0.855	0.855	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.810	-0.895	15.650	-20.127	-20.127	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.055	0.040	18.302	0.198	0.198	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.874	-0.943	17.757	-15.926	-15.926	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.916	0.967	16.261	14.187	14.187	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.009	0.007	15.354	-1.328	-1.328	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.033	0.013	12.139	0.459	0.459	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.021	-0.014	15.548	0.085	0.085	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.038	0.005	11.775	0.183	0.183	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.010	-0.001	17.279	0.159	0.159	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.847	-0.920	16.992	-19.641	-19.641	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.019	-0.016	14.396	0.739	0.739	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.066	-0.030	18.115	1.256	1.256	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.015	-0.006	20.360	0.122	0.122	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.966	0.974	21.811	15.019	15.019	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.048	-0.021	24.958	0.443	0.443	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.836	0.910	26.582	9.431	9.431	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.022	0.019	25.131	-0.147	-0.147	0.000	0.000	0.000	0.000
36	A	36	HIS	0	0.007	0.009	19.611	0.707	0.707	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.003	0.001	20.087	-0.363	-0.363	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.014	0.017	14.307	0.088	0.088	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.010	0.004	16.939	0.146	0.146	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.023	0.007	10.144	-0.238	-0.238	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.001	0.011	12.032	1.165	1.165	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.855	0.887	10.992	18.038	18.038	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.010	0.003	9.999	-1.365	-1.365	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.012	-0.004	5.964	1.516	1.516	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.012	0.005	8.512	2.611	2.611	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.005	0.013	9.975	-1.217	-1.217	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.802	-0.921	10.947	-19.360	-19.360	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.023	-0.012	14.460	0.142	0.142	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.041	-0.016	17.631	1.473	1.473	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.013	0.006	15.301	0.435	0.435	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.045	-0.014	16.183	-0.596	-0.596	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.029	0.012	17.904	0.733	0.733	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.040	0.001	20.999	-0.177	-0.177	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.897	-0.941	23.191	-11.799	-11.799	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.016	0.000	16.078	0.035	0.035	0.000	0.000	0.000	0.000
56	A	56	MET	0	0.051	0.029	20.763	-0.538	-0.538	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.005	0.018	21.818	0.232	0.232	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.009	-0.016	21.840	-0.333	-0.333	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.018	-0.003	16.283	0.070	0.070	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.026	-0.029	21.169	0.105	0.105	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.004	0.008	24.580	0.467	0.467	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.006	-0.004	18.399	0.060	0.060	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.004	-0.010	20.958	-0.060	-0.060	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.023	-0.021	23.763	0.269	0.269	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.863	-0.936	24.910	-12.454	-12.454	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.017	-0.017	21.195	0.163	0.163	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.008	-0.002	24.650	0.222	0.222	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.902	-0.942	27.390	-9.851	-9.851	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.860	0.933	24.061	12.966	12.966	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.045	-0.025	23.424	0.026	0.026	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.010	0.004	27.793	0.186	0.186	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.055	-0.045	26.491	0.317	0.317	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.861	0.941	30.888	10.127	10.127	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.859	-0.942	31.777	-9.091	-9.091	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.865	0.938	33.602	9.504	9.504	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.005	0.028	33.470	0.155	0.155	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.032	-0.024	26.970	-0.087	-0.087	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.926	0.963	26.948	11.027	11.027	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.034	0.012	22.781	-0.373	-0.373	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.023	-0.008	21.429	0.482	0.482	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.028	-0.018	17.313	-0.750	-0.750	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.010	0.008	17.581	1.290	1.290	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.009	0.001	16.862	-1.167	-1.167	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.088	0.040	15.683	0.811	0.811	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.916	0.942	14.651	16.932	16.932	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.023	-0.016	16.491	0.039	0.039	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.006	0.019	19.600	0.791	0.791	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.036	0.020	19.120	0.099	0.099	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.072	-0.044	12.492	0.843	0.843	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.927	-0.964	13.786	-19.467	-19.467	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.008	-0.003	8.826	-2.009	-2.009	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.030	-0.005	8.040	1.948	1.948	0.000	0.000	0.000	0.000
93	A	93	HIS	0	-0.030	-0.034	7.423	-7.229	-7.229	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.021	0.012	9.408	1.941	1.941	0.000	0.000	0.000	0.000
95	A	95	HIS	0	-0.012	-0.025	12.731	0.695	0.695	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.011	0.014	14.737	0.956	0.956	0.000	0.000	0.000	0.000
97	A	97	HIS	0	0.001	-0.001	17.012	0.336	0.336	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.008	0.000	20.101	0.680	0.680	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.020	-0.008	23.168	-0.152	-0.152	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.038	0.011	25.834	0.231	0.231	0.000	0.000	0.000	0.000
101	A	101	GLY	-1	-0.848	-0.902	29.278	-9.928	-9.928	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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