FMO DATABASE

FMODB ID: 559YZ

Calculation Name: 1LFD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester

Ligand 3-letter code: GNP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LFD

Chain ID: A

ChEMBL ID:

UniProt ID: Q03386

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-620263.499157
FMO2-HF: Nuclear repulsion	584511.02274
FMO2-HF: Total energy	-35752.476417
FMO2-MP2: Total energy	-35854.163013

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:14:GLY)

Summations of interaction energy for fragment #1(A:14: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.
-17.434	-16.312	0.007	-0.403	-0.725	-0.001

Interaction energy analysis for fragmet #1(A:14:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / q_NPA : 0.877

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	16	CYS	0	0.002	-0.013	3.473	9.574	10.542	0.007	-0.362	-0.612	-0.001
25	A	38	SER	0	0.029	0.011	3.575	4.305	4.459	0.000	-0.041	-0.113	0.000
4	A	17	CYS	0	0.007	0.022	6.887	0.834	0.834	0.000	0.000	0.000	0.000
5	A	18	ILE	0	-0.004	-0.004	10.599	0.361	0.361	0.000	0.000	0.000	0.000
6	A	19	ILE	0	0.000	0.004	13.510	0.480	0.480	0.000	0.000	0.000	0.000
7	A	20	ARG	1	0.890	0.959	16.305	14.784	14.784	0.000	0.000	0.000	0.000
8	A	21	VAL	0	0.024	0.005	19.002	0.046	0.046	0.000	0.000	0.000	0.000
9	A	22	SER	0	0.013	0.004	21.713	0.442	0.442	0.000	0.000	0.000	0.000
10	A	23	LEU	0	0.028	0.004	25.201	-0.412	-0.412	0.000	0.000	0.000	0.000
11	A	24	ASP	-1	-0.887	-0.948	27.792	-10.257	-10.257	0.000	0.000	0.000	0.000
12	A	25	VAL	0	-0.030	-0.013	31.032	0.394	0.394	0.000	0.000	0.000	0.000
13	A	26	ASP	-1	-0.924	-0.955	32.942	-8.887	-8.887	0.000	0.000	0.000	0.000
14	A	27	ASN	0	0.012	-0.012	30.261	0.097	0.097	0.000	0.000	0.000	0.000
15	A	28	GLY	0	0.009	0.011	33.834	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	29	ASN	0	-0.092	-0.057	26.528	-0.389	-0.389	0.000	0.000	0.000	0.000
17	A	30	MET	0	0.031	0.023	28.255	0.028	0.028	0.000	0.000	0.000	0.000
18	A	31	TYR	0	0.014	-0.011	22.430	-0.264	-0.264	0.000	0.000	0.000	0.000
19	A	32	LYS	1	0.880	0.964	22.363	12.390	12.390	0.000	0.000	0.000	0.000
20	A	33	SER	0	-0.012	-0.006	17.659	-0.117	-0.117	0.000	0.000	0.000	0.000
21	A	34	ILE	0	-0.025	-0.010	15.529	0.124	0.124	0.000	0.000	0.000	0.000
22	A	35	LEU	0	-0.003	0.005	8.492	-0.282	-0.282	0.000	0.000	0.000	0.000
23	A	36	VAL	0	0.018	0.016	10.655	0.543	0.543	0.000	0.000	0.000	0.000
24	A	37	THR	0	0.006	-0.035	5.322	-3.291	-3.291	0.000	0.000	0.000	0.000
26	A	39	GLN	0	-0.021	-0.009	5.417	4.167	4.167	0.000	0.000	0.000	0.000
27	A	40	ASP	-1	-0.815	-0.864	7.994	-24.651	-24.651	0.000	0.000	0.000	0.000
28	A	41	LYS	1	0.968	0.983	10.821	21.098	21.098	0.000	0.000	0.000	0.000
29	A	42	ALA	0	0.048	0.023	14.332	0.023	0.023	0.000	0.000	0.000	0.000
30	A	43	PRO	0	0.079	0.041	17.467	0.003	0.003	0.000	0.000	0.000	0.000
31	A	44	THR	0	-0.066	-0.021	12.784	0.100	0.100	0.000	0.000	0.000	0.000
32	A	45	VAL	0	-0.016	-0.019	13.632	-0.084	-0.084	0.000	0.000	0.000	0.000
33	A	46	ILE	0	0.008	0.020	16.079	0.294	0.294	0.000	0.000	0.000	0.000
34	A	47	ARG	1	0.868	0.921	18.911	13.325	13.325	0.000	0.000	0.000	0.000
35	A	48	LYS	1	0.800	0.881	11.394	24.857	24.857	0.000	0.000	0.000	0.000
36	A	49	ALA	0	-0.023	-0.023	17.760	0.146	0.146	0.000	0.000	0.000	0.000
37	A	50	MET	0	-0.006	0.009	20.097	0.326	0.326	0.000	0.000	0.000	0.000
38	A	51	ASP	-1	-0.793	-0.882	20.686	-13.808	-13.808	0.000	0.000	0.000	0.000
39	A	52	LYS	1	0.827	0.928	18.813	16.308	16.308	0.000	0.000	0.000	0.000
40	A	53	HIS	0	-0.062	-0.062	22.009	0.668	0.668	0.000	0.000	0.000	0.000
41	A	54	ASN	0	-0.085	-0.024	25.130	0.533	0.533	0.000	0.000	0.000	0.000
42	A	55	LEU	0	0.033	0.021	26.032	0.394	0.394	0.000	0.000	0.000	0.000
43	A	56	ASP	-1	-0.895	-0.968	25.575	-12.216	-12.216	0.000	0.000	0.000	0.000
44	A	57	GLU	-1	-1.003	-0.988	27.163	-9.180	-9.180	0.000	0.000	0.000	0.000
45	A	58	ASP	-1	-0.794	-0.874	28.380	-10.189	-10.189	0.000	0.000	0.000	0.000
46	A	59	GLU	-1	-0.907	-0.960	27.330	-10.679	-10.679	0.000	0.000	0.000	0.000
47	A	60	PRO	0	-0.054	-0.055	22.559	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.915	-0.960	24.745	-12.581	-12.581	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.913	-0.934	26.929	-9.819	-9.819	0.000	0.000	0.000	0.000
50	A	63	TYR	0	-0.067	-0.055	25.142	0.068	0.068	0.000	0.000	0.000	0.000
51	A	64	GLU	-1	-0.836	-0.908	24.809	-11.743	-11.743	0.000	0.000	0.000	0.000
52	A	65	LEU	0	0.006	-0.005	18.017	-0.147	-0.147	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.031	-0.018	22.600	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	67	GLN	0	0.043	0.005	18.454	-0.071	-0.071	0.000	0.000	0.000	0.000
55	A	68	ILE	0	-0.029	-0.029	22.068	0.702	0.702	0.000	0.000	0.000	0.000
56	A	69	ILE	0	-0.083	-0.028	21.951	-0.510	-0.510	0.000	0.000	0.000	0.000
57	A	70	SER	0	-0.026	-0.025	24.968	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	71	GLU	-1	-0.937	-0.962	28.548	-9.618	-9.618	0.000	0.000	0.000	0.000
59	A	72	ASP	-1	-0.897	-0.943	31.662	-9.468	-9.468	0.000	0.000	0.000	0.000
60	A	73	HIS	0	-0.037	-0.020	26.167	0.059	0.059	0.000	0.000	0.000	0.000
61	A	74	LYS	1	0.866	0.926	25.663	12.012	12.012	0.000	0.000	0.000	0.000
62	A	75	LEU	0	-0.021	0.011	19.777	0.324	0.324	0.000	0.000	0.000	0.000
63	A	76	LYS	1	0.861	0.906	23.137	11.117	11.117	0.000	0.000	0.000	0.000
64	A	77	ILE	0	-0.017	-0.002	18.052	-0.391	-0.391	0.000	0.000	0.000	0.000
65	A	78	PRO	0	-0.011	-0.013	19.809	0.363	0.363	0.000	0.000	0.000	0.000
66	A	79	GLU	-1	-0.809	-0.904	20.217	-13.120	-13.120	0.000	0.000	0.000	0.000
67	A	80	ASN	0	0.013	-0.003	19.354	-0.646	-0.646	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.042	-0.004	17.315	-0.773	-0.773	0.000	0.000	0.000	0.000
69	A	82	ASN	0	-0.030	-0.036	9.500	-0.358	-0.358	0.000	0.000	0.000	0.000
70	A	83	VAL	0	0.039	0.011	13.110	0.222	0.222	0.000	0.000	0.000	0.000
71	A	84	PHE	0	-0.005	-0.002	6.629	-0.638	-0.638	0.000	0.000	0.000	0.000
72	A	85	TYR	0	-0.023	-0.023	6.442	-1.451	-1.451	0.000	0.000	0.000	0.000
73	A	86	ALA	0	-0.016	0.009	12.099	1.345	1.345	0.000	0.000	0.000	0.000
74	A	87	MET	0	-0.046	-0.003	13.666	0.759	0.759	0.000	0.000	0.000	0.000
75	A	88	ASN	0	0.033	0.008	15.726	-1.123	-1.123	0.000	0.000	0.000	0.000
76	A	89	SER	0	0.009	0.004	13.375	0.899	0.899	0.000	0.000	0.000	0.000
77	A	90	ALA	0	0.018	0.016	15.296	-0.430	-0.430	0.000	0.000	0.000	0.000
78	A	91	ALA	0	-0.019	0.005	18.364	1.046	1.046	0.000	0.000	0.000	0.000
79	A	92	ASN	0	0.039	0.021	18.879	-1.154	-1.154	0.000	0.000	0.000	0.000
80	A	93	TYR	0	-0.067	-0.036	13.459	-1.009	-1.009	0.000	0.000	0.000	0.000
81	A	94	ASP	-1	-0.834	-0.922	18.421	-14.589	-14.589	0.000	0.000	0.000	0.000
82	A	95	PHE	0	-0.001	-0.022	16.826	-0.030	-0.030	0.000	0.000	0.000	0.000
83	A	96	ILE	0	-0.025	0.008	22.124	0.328	0.328	0.000	0.000	0.000	0.000
84	A	97	LEU	0	-0.021	-0.002	22.573	-0.395	-0.395	0.000	0.000	0.000	0.000
85	A	98	LYS	1	0.941	0.973	24.662	10.686	10.686	0.000	0.000	0.000	0.000
86	A	99	LYS	1	0.887	0.949	27.591	9.633	9.633	0.000	0.000	0.000	0.000
87	A	100	ARG	0	-0.057	-0.031	27.464	1.320	1.320	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:GLY)