FMO DATABASE

FMODB ID: 8Q6MY

Calculation Name: 3GLV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine monophosphate | sulfate ion

Ligand 3-letter code: AMP | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GLV

Chain ID: A

ChEMBL ID:

UniProt ID: Q979C2

Base Structure: X-ray

Registration Date: 2025-10-05

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1018539.139029
FMO2-HF: Nuclear repulsion	970743.207765
FMO2-HF: Total energy	-47795.931264
FMO2-MP2: Total energy	-47935.628503

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-42.834	-42.04	-0.006	-0.241	-0.547	-0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.890

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	2	ILE	0	0.014	0.016	3.831	5.316	6.110	-0.006	-0.241	-0.547	-0.001
4	A	3	ARG	1	0.837	0.908	6.349	31.082	31.082	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.002	-0.004	9.568	1.456	1.456	0.000	0.000	0.000	0.000
6	A	5	MET	0	-0.029	-0.007	12.811	0.978	0.978	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.024	0.005	16.115	0.434	0.434	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.033	-0.016	19.477	0.353	0.353	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.055	0.015	22.922	0.176	0.176	0.000	0.000	0.000	0.000
10	A	9	VAL	0	-0.036	-0.019	26.505	0.011	0.011	0.000	0.000	0.000	0.000
11	A	10	PHE	0	-0.003	-0.001	23.762	0.063	0.063	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.751	-0.876	29.291	-9.058	-9.058	0.000	0.000	0.000	0.000
13	A	12	ILE	0	0.025	0.023	32.995	0.044	0.044	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.000	-0.004	27.755	-0.163	-0.163	0.000	0.000	0.000	0.000
15	A	14	HIS	0	0.048	0.017	30.393	0.182	0.182	0.000	0.000	0.000	0.000
16	A	15	LEU	0	0.052	0.009	29.009	-0.464	-0.464	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.073	0.051	27.756	-0.414	-0.414	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.019	-0.011	26.291	-0.516	-0.516	0.000	0.000	0.000	0.000
19	A	18	ILE	0	-0.003	-0.001	24.489	-0.691	-0.691	0.000	0.000	0.000	0.000
20	A	19	HIS	0	-0.019	-0.007	23.214	-0.774	-0.774	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.024	-0.010	21.783	-0.723	-0.723	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.010	0.020	20.097	-0.887	-0.887	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.961	0.975	18.618	12.964	12.964	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.834	-0.903	17.814	-16.849	-16.849	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.020	-0.016	16.494	-1.000	-1.000	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.783	0.889	12.323	21.985	21.985	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.799	0.879	13.048	14.919	14.919	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.063	-0.024	12.306	-0.929	-0.929	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.020	-0.020	8.405	-2.049	-2.049	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.866	-0.911	5.568	-54.375	-54.375	0.000	0.000	0.000	0.000
31	A	30	GLU	-1	-0.804	-0.878	8.633	-23.306	-23.306	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.040	-0.018	10.810	0.036	0.036	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.027	-0.017	13.582	1.032	1.032	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.010	-0.008	16.180	0.314	0.314	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.016	-0.005	19.778	0.388	0.388	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.019	0.000	22.212	0.317	0.317	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.029	-0.020	25.770	0.132	0.132	0.000	0.000	0.000	0.000
38	A	37	ARG	1	0.935	0.949	28.648	10.791	10.791	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.767	-0.874	31.272	-9.196	-9.196	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.049	-0.023	34.673	0.119	0.119	0.000	0.000	0.000	0.000
41	A	40	THR	0	0.011	-0.012	29.966	0.116	0.116	0.000	0.000	0.000	0.000
42	A	41	ALA	0	-0.030	-0.007	32.952	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.969	0.983	34.156	8.114	8.114	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.016	-0.010	35.764	0.335	0.335	0.000	0.000	0.000	0.000
45	A	44	ASN	0	-0.052	-0.011	31.791	0.199	0.199	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.027	0.014	35.808	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.888	0.944	31.749	9.965	9.965	0.000	0.000	0.000	0.000
48	A	47	ILE	0	-0.017	-0.017	36.701	-0.161	-0.161	0.000	0.000	0.000	0.000
49	A	48	PRO	0	-0.055	-0.005	34.808	0.040	0.040	0.000	0.000	0.000	0.000
50	A	49	ILE	0	-0.021	-0.025	36.941	0.230	0.230	0.000	0.000	0.000	0.000
51	A	50	PHE	0	-0.028	-0.007	34.690	0.132	0.132	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.764	-0.852	34.485	-9.389	-9.389	0.000	0.000	0.000	0.000
53	A	52	GLU	-1	-0.795	-0.918	30.784	-10.232	-10.232	0.000	0.000	0.000	0.000
54	A	53	ASN	0	-0.032	-0.015	30.017	-0.688	-0.688	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.026	-0.040	30.242	-0.314	-0.314	0.000	0.000	0.000	0.000
56	A	55	ARG	1	0.703	0.835	29.917	9.904	9.904	0.000	0.000	0.000	0.000
57	A	56	LEU	0	-0.032	-0.012	23.830	-0.405	-0.405	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.007	0.010	25.897	-0.520	-0.520	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.021	0.007	27.023	-0.309	-0.309	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.026	-0.027	22.919	-0.276	-0.276	0.000	0.000	0.000	0.000
61	A	60	SER	0	-0.049	-0.035	22.529	-0.828	-0.828	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.935	-0.947	22.928	-12.380	-12.380	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.081	-0.031	22.650	0.019	0.019	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.966	0.960	20.591	12.809	12.809	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.033	-0.013	17.844	-0.690	-0.690	0.000	0.000	0.000	0.000
66	A	65	VAL	0	-0.001	0.003	16.773	-1.268	-1.268	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.777	-0.852	13.836	-23.012	-23.012	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.865	0.915	13.740	20.860	20.860	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.020	0.022	17.582	-0.224	-0.224	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.016	-0.006	19.900	0.116	0.116	0.000	0.000	0.000	0.000
71	A	70	LEU	0	0.014	0.018	22.687	0.104	0.104	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.000	-0.009	24.218	-0.425	-0.425	0.000	0.000	0.000	0.000
73	A	72	HIS	1	0.721	0.820	24.067	12.718	12.718	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.784	-0.882	27.161	-10.853	-10.853	0.000	0.000	0.000	0.000
75	A	74	GLY	0	0.019	0.014	30.361	0.302	0.302	0.000	0.000	0.000	0.000
76	A	75	ASP	-1	-0.892	-0.937	26.574	-11.610	-11.610	0.000	0.000	0.000	0.000
77	A	76	MET	0	0.051	0.022	23.148	-0.407	-0.407	0.000	0.000	0.000	0.000
78	A	77	MET	0	0.010	0.004	20.722	-0.611	-0.611	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.957	0.991	21.644	10.873	10.873	0.000	0.000	0.000	0.000
80	A	79	THR	0	0.008	-0.005	20.646	-0.342	-0.342	0.000	0.000	0.000	0.000
81	A	80	VAL	0	0.008	0.009	17.052	-0.774	-0.774	0.000	0.000	0.000	0.000
82	A	81	ILE	0	-0.033	-0.017	16.946	-1.135	-1.135	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.855	-0.917	17.792	-13.850	-13.850	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.041	-0.024	14.750	-0.671	-0.671	0.000	0.000	0.000	0.000
85	A	84	LYS	1	0.899	0.958	12.611	17.273	17.273	0.000	0.000	0.000	0.000
86	A	85	PRO	0	-0.014	-0.001	11.460	-1.920	-1.920	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.794	-0.888	7.542	-36.834	-36.834	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.044	-0.024	10.358	1.672	1.672	0.000	0.000	0.000	0.000
89	A	88	ILE	0	0.001	0.002	13.170	0.319	0.319	0.000	0.000	0.000	0.000
90	A	89	THR	0	-0.005	0.003	16.798	0.152	0.152	0.000	0.000	0.000	0.000
91	A	90	LEU	0	-0.018	-0.004	18.779	0.707	0.707	0.000	0.000	0.000	0.000
92	A	91	GLY	0	0.071	0.031	22.581	-0.292	-0.292	0.000	0.000	0.000	0.000
93	A	92	TYR	0	0.003	0.003	25.487	0.086	0.086	0.000	0.000	0.000	0.000
94	A	93	ASP	-1	-0.884	-0.971	26.649	-11.014	-11.014	0.000	0.000	0.000	0.000
95	A	94	GLN	0	0.019	0.019	25.949	-0.111	-0.111	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.890	0.921	26.915	10.538	10.538	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.021	0.013	28.500	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.781	-0.898	26.671	-11.239	-11.239	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.846	-0.907	22.997	-13.770	-13.770	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.030	0.018	24.242	-0.383	-0.383	0.000	0.000	0.000	0.000
101	A	100	GLU	-1	-0.908	-0.951	26.756	-10.435	-10.435	0.000	0.000	0.000	0.000
102	A	101	LEU	0	-0.029	-0.020	20.159	0.068	0.068	0.000	0.000	0.000	0.000
103	A	102	GLN	0	0.012	-0.009	19.516	-0.499	-0.499	0.000	0.000	0.000	0.000
104	A	103	SER	0	-0.029	-0.024	23.055	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	104	LYS	1	0.852	0.932	23.982	11.657	11.657	0.000	0.000	0.000	0.000
106	A	105	ILE	0	-0.012	-0.002	18.267	0.054	0.054	0.000	0.000	0.000	0.000
107	A	106	ASN	0	0.013	0.002	21.090	-0.689	-0.689	0.000	0.000	0.000	0.000
108	A	107	LYS	1	0.927	0.971	22.929	10.642	10.642	0.000	0.000	0.000	0.000
109	A	108	LEU	0	-0.036	-0.019	20.963	0.285	0.285	0.000	0.000	0.000	0.000
110	A	109	GLY	0	0.025	0.022	20.384	-0.104	-0.104	0.000	0.000	0.000	0.000
111	A	110	ILE	0	-0.053	-0.016	16.231	-0.697	-0.697	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.011	-0.016	11.756	0.200	0.200	0.000	0.000	0.000	0.000
113	A	112	VAL	0	0.004	0.006	12.626	-1.282	-1.282	0.000	0.000	0.000	0.000
114	A	113	LYS	1	0.931	0.976	13.338	23.299	23.299	0.000	0.000	0.000	0.000
115	A	114	ILE	0	0.017	0.015	15.065	-0.165	-0.165	0.000	0.000	0.000	0.000
116	A	115	VAL	0	-0.011	-0.014	15.484	-0.287	-0.287	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.790	0.904	18.616	13.012	13.012	0.000	0.000	0.000	0.000
118	A	117	ILE	0	-0.018	0.000	18.319	-0.270	-0.270	0.000	0.000	0.000	0.000
119	A	118	SER	0	0.027	0.003	21.745	0.602	0.602	0.000	0.000	0.000	0.000
120	A	119	LYS	1	0.906	0.944	24.320	9.930	9.930	0.000	0.000	0.000	0.000
121	A	120	TYR	0	-0.052	-0.022	27.518	-0.392	-0.392	0.000	0.000	0.000	0.000
122	A	121	ASP	-2	-1.817	-1.902	28.973	-20.021	-20.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)