FMO DATABASE

FMODB ID: 3KYRL

Calculation Name: 2DCL-B-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine monophosphate

Ligand 3-letter code: AMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DCL

Chain ID: B

ChEMBL ID:

UniProt ID: O59172

Base Structure: X-ray

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-708319.267239
FMO2-HF: Nuclear repulsion	669386.114686
FMO2-HF: Total energy	-38933.152553
FMO2-MP2: Total energy	-39047.508118

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-27.816	-24.168	0.223	-2.013	-1.858	-0.018

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.762 / q_NPA : 0.866

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	4	VAL	0	-0.024	-0.029	2.727	-13.096	-9.492	0.224	-2.009	-1.819	-0.018
95	A	107	LEU	0	-0.007	-0.021	4.348	-2.309	-2.265	-0.001	-0.004	-0.039	0.000
4	A	5	GLU	-1	-0.870	-0.924	5.497	-26.585	-26.585	0.000	0.000	0.000	0.000
5	A	6	HIS	0	-0.007	-0.013	9.206	3.878	3.878	0.000	0.000	0.000	0.000
6	A	7	TRP	0	0.038	0.015	9.205	-0.237	-0.237	0.000	0.000	0.000	0.000
7	A	8	ASN	0	-0.044	-0.018	10.991	1.484	1.484	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.001	0.001	13.370	1.237	1.237	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.022	-0.005	15.313	-0.167	-0.167	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.870	0.929	15.356	17.858	17.858	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.012	-0.005	19.143	0.510	0.510	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.861	0.910	21.578	13.925	13.925	0.000	0.000	0.000	0.000
13	A	14	ILE	0	0.007	0.006	25.229	0.305	0.305	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.030	-0.019	25.964	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.023	0.005	31.360	0.191	0.191	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.101	0.054	34.748	-0.128	-0.128	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.877	-0.909	37.002	-8.678	-8.678	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.126	-0.100	37.893	0.194	0.194	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.788	-0.873	38.206	-8.037	-8.037	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.861	0.926	39.980	7.139	7.139	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.006	0.009	39.890	0.009	0.009	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.893	-0.954	41.796	-7.447	-7.447	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.000	0.009	44.801	0.077	0.077	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.836	0.908	38.079	8.164	8.164	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.004	-0.012	38.147	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.038	0.020	35.801	-0.170	-0.170	0.000	0.000	0.000	0.000
27	A	28	TYR	0	0.070	0.014	32.591	-0.211	-0.211	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.897	0.962	32.862	8.207	8.207	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.039	0.028	34.485	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.004	0.009	30.254	-0.160	-0.160	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.002	-0.007	28.935	-0.278	-0.278	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.871	-0.926	30.388	-8.857	-8.857	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.886	0.921	32.150	8.905	8.905	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.017	-0.016	26.193	-0.176	-0.176	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.944	0.975	27.565	10.382	10.382	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.863	-0.912	29.101	-9.271	-9.271	0.000	0.000	0.000	0.000
37	A	38	MET	0	-0.054	-0.018	28.538	0.011	0.011	0.000	0.000	0.000	0.000
38	A	39	GLY	0	-0.027	-0.006	26.427	-0.198	-0.198	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.073	-0.036	22.346	-0.400	-0.400	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.010	-0.001	18.239	0.154	0.154	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.017	0.005	20.395	-0.159	-0.159	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.040	-0.030	21.448	0.041	0.041	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.014	0.014	20.906	0.067	0.067	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.033	-0.017	23.863	0.242	0.242	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.045	-0.041	21.354	0.089	0.089	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.825	0.876	28.292	9.140	9.140	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.009	0.007	31.619	-0.165	-0.165	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.015	-0.014	32.769	0.221	0.221	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.008	-0.007	35.312	0.339	0.339	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.009	-0.011	35.118	-0.351	-0.351	0.000	0.000	0.000	0.000
51	A	52	PHE	0	-0.041	-0.015	36.551	0.247	0.247	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.077	0.046	36.601	-0.294	-0.294	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.891	0.939	38.070	8.360	8.360	0.000	0.000	0.000	0.000
54	A	55	LYS	0	0.091	0.057	37.844	-0.515	-0.515	0.000	0.000	0.000	0.000
55	A	67	SER	0	0.020	-0.007	40.352	0.043	0.043	0.000	0.000	0.000	0.000
56	A	68	THR	0	-0.036	-0.019	42.983	0.024	0.024	0.000	0.000	0.000	0.000
57	A	69	ASP	-1	-0.815	-0.892	40.307	-8.002	-8.002	0.000	0.000	0.000	0.000
58	A	70	LEU	0	-0.014	0.010	36.547	-0.106	-0.106	0.000	0.000	0.000	0.000
59	A	71	PRO	0	0.009	0.009	33.136	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	72	ILE	0	-0.001	-0.001	31.341	-0.220	-0.220	0.000	0.000	0.000	0.000
61	A	73	ILE	0	-0.026	-0.017	26.566	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	74	VAL	0	-0.012	-0.004	26.683	-0.192	-0.192	0.000	0.000	0.000	0.000
63	A	75	GLU	-1	-0.797	-0.874	19.927	-15.556	-15.556	0.000	0.000	0.000	0.000
64	A	76	VAL	0	0.004	-0.002	21.671	0.107	0.107	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.006	-0.004	15.216	-0.155	-0.155	0.000	0.000	0.000	0.000
66	A	78	ASP	-1	-0.734	-0.848	17.659	-16.172	-16.172	0.000	0.000	0.000	0.000
67	A	79	ARG	1	0.917	0.945	16.138	18.225	18.225	0.000	0.000	0.000	0.000
68	A	80	GLY	0	0.038	0.011	18.338	0.857	0.857	0.000	0.000	0.000	0.000
69	A	81	HIS	0	-0.026	-0.010	20.680	0.332	0.332	0.000	0.000	0.000	0.000
70	A	82	ASN	0	-0.031	-0.029	21.433	0.896	0.896	0.000	0.000	0.000	0.000
71	A	83	ILE	0	-0.009	-0.005	21.019	0.676	0.676	0.000	0.000	0.000	0.000
72	A	84	GLU	-1	-0.900	-0.949	23.875	-10.873	-10.873	0.000	0.000	0.000	0.000
73	A	85	LYS	1	0.908	0.960	26.329	12.319	12.319	0.000	0.000	0.000	0.000
74	A	86	VAL	0	0.012	0.010	25.396	0.473	0.473	0.000	0.000	0.000	0.000
75	A	87	VAL	0	0.010	0.000	26.896	0.462	0.462	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.041	-0.031	29.485	0.561	0.561	0.000	0.000	0.000	0.000
77	A	89	VAL	0	-0.013	-0.004	31.694	0.368	0.368	0.000	0.000	0.000	0.000
78	A	90	ILE	0	0.022	0.004	29.590	0.284	0.284	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.934	0.969	32.439	9.774	9.774	0.000	0.000	0.000	0.000
80	A	92	PRO	0	-0.058	-0.027	34.980	0.211	0.211	0.000	0.000	0.000	0.000
81	A	93	MET	0	-0.032	-0.004	34.648	0.223	0.223	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.002	0.018	33.038	0.087	0.087	0.000	0.000	0.000	0.000
83	A	95	LYS	1	0.850	0.910	37.362	7.947	7.947	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.894	-0.937	39.244	-7.676	-7.676	0.000	0.000	0.000	0.000
85	A	97	GLY	0	0.047	0.041	35.651	-0.115	-0.115	0.000	0.000	0.000	0.000
86	A	98	MET	0	-0.079	-0.040	29.461	0.067	0.067	0.000	0.000	0.000	0.000
87	A	99	ILE	0	-0.006	-0.008	27.777	-0.170	-0.170	0.000	0.000	0.000	0.000
88	A	100	THR	0	-0.012	-0.001	24.576	0.202	0.202	0.000	0.000	0.000	0.000
89	A	101	VAL	0	0.005	-0.008	22.125	-0.167	-0.167	0.000	0.000	0.000	0.000
90	A	102	GLU	-1	-0.839	-0.901	19.021	-14.467	-14.467	0.000	0.000	0.000	0.000
91	A	103	PRO	0	0.019	-0.001	15.993	-0.382	-0.382	0.000	0.000	0.000	0.000
92	A	104	THR	0	-0.026	-0.015	12.777	0.352	0.352	0.000	0.000	0.000	0.000
93	A	105	ILE	0	0.000	0.008	6.986	0.056	0.056	0.000	0.000	0.000	0.000
94	A	106	VAL	0	-0.010	-0.003	9.702	0.898	0.898	0.000	0.000	0.000	0.000
96	A	108	TRP	0	0.009	0.006	6.417	-4.553	-4.553	0.000	0.000	0.000	0.000
97	A	109	VAL	0	-0.045	-0.019	9.169	1.975	1.975	0.000	0.000	0.000	0.000
98	A	110	GLY	-1	-0.936	-0.943	12.905	-19.622	-19.622	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)