FMO DATABASE

FMODB ID: 46G9N

Calculation Name: 4LHW-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | (4s)-2-methyl-2,4-pentanediol | magnesium ion

Ligand 3-letter code: GNP | MPD | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LHW

Chain ID: A

ChEMBL ID:

UniProt ID: P61006

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1873416.193489
FMO2-HF: Nuclear repulsion	1804218.124685
FMO2-HF: Total energy	-69198.068804
FMO2-MP2: Total energy	-69398.848956

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:6:ASP)

Summations of interaction energy for fragment #1(A:6:ASP)

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.
-22.74	-20.08	5.864	-4.418	-4.105	-0.054

Interaction energy analysis for fragmet #1(A:6:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.145 / q_NPA : -0.079

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	8	LEU	0	-0.022	-0.014	3.807	-0.387	0.907	-0.004	-0.516	-0.774	0.003
50	A	55	LYS	1	0.894	0.948	4.080	11.001	11.201	-0.001	-0.019	-0.181	0.000
51	A	56	ARG	1	1.000	0.993	3.117	6.019	6.700	0.040	-0.202	-0.519	0.000
52	A	57	ILE	0	0.009	0.003	1.947	-28.338	-28.046	5.830	-3.668	-2.453	-0.057
53	A	58	LYS	1	0.955	0.982	4.518	-0.288	-0.095	-0.001	-0.013	-0.178	0.000
4	A	9	PHE	0	0.010	-0.013	5.905	0.474	0.474	0.000	0.000	0.000	0.000
5	A	10	LYS	1	0.963	0.973	9.484	-1.155	-1.155	0.000	0.000	0.000	0.000
6	A	11	LEU	0	0.006	0.006	12.489	-0.087	-0.087	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.027	0.014	15.238	0.240	0.240	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.024	-0.004	18.872	-0.132	-0.132	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.001	0.006	21.909	0.120	0.120	0.000	0.000	0.000	0.000
10	A	15	GLY	0	0.079	0.040	25.316	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.777	-0.868	28.850	-0.216	-0.216	0.000	0.000	0.000	0.000
12	A	17	SER	0	-0.014	-0.027	30.817	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.035	0.022	32.402	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	19	VAL	0	-0.017	-0.006	28.461	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	20	GLY	0	0.026	0.017	28.738	-0.046	-0.046	0.000	0.000	0.000	0.000
16	A	21	LYS	1	0.839	0.929	24.331	0.272	0.272	0.000	0.000	0.000	0.000
17	A	22	THR	0	0.039	0.004	23.668	-0.080	-0.080	0.000	0.000	0.000	0.000
18	A	23	CYS	0	-0.033	-0.012	24.074	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	24	VAL	0	0.022	0.009	21.466	-0.050	-0.050	0.000	0.000	0.000	0.000
20	A	25	LEU	0	0.023	0.011	17.404	-0.125	-0.125	0.000	0.000	0.000	0.000
21	A	26	PHE	0	-0.026	0.009	19.902	-0.065	-0.065	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.821	0.909	21.841	0.732	0.732	0.000	0.000	0.000	0.000
23	A	28	PHE	0	-0.004	-0.014	13.208	-0.093	-0.093	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.059	-0.054	16.868	-0.139	-0.139	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.841	-0.911	17.904	-0.301	-0.301	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.879	-0.909	20.709	-0.853	-0.853	0.000	0.000	0.000	0.000
27	A	32	ALA	0	0.003	0.014	22.364	0.063	0.063	0.000	0.000	0.000	0.000
28	A	33	PHE	0	-0.026	-0.038	25.325	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	34	ASN	0	0.013	0.012	28.080	0.015	0.015	0.000	0.000	0.000	0.000
30	A	35	SER	0	-0.002	-0.010	30.826	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	36	THR	0	-0.004	0.004	32.395	0.011	0.011	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.021	-0.006	32.513	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	38	ILE	0	0.055	0.019	31.679	0.023	0.023	0.000	0.000	0.000	0.000
34	A	39	SER	0	-0.068	-0.027	30.905	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	40	THR	0	0.002	-0.008	25.014	0.033	0.033	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.005	0.004	28.389	0.004	0.004	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.017	0.020	27.163	0.036	0.036	0.000	0.000	0.000	0.000
38	A	43	ILE	0	-0.045	-0.015	20.982	-0.079	-0.079	0.000	0.000	0.000	0.000
39	A	44	ASP	-1	-0.843	-0.897	19.940	0.569	0.569	0.000	0.000	0.000	0.000
40	A	45	PHE	0	-0.053	-0.047	13.857	-0.087	-0.087	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.862	0.928	16.057	0.336	0.336	0.000	0.000	0.000	0.000
42	A	47	ILE	0	-0.031	-0.024	9.871	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.812	0.869	11.339	2.243	2.243	0.000	0.000	0.000	0.000
44	A	49	THR	0	-0.069	-0.032	5.524	-0.183	-0.183	0.000	0.000	0.000	0.000
45	A	50	ILE	0	-0.002	0.011	7.715	0.714	0.714	0.000	0.000	0.000	0.000
46	A	51	GLU	-1	-0.942	-0.983	6.643	-8.919	-8.919	0.000	0.000	0.000	0.000
47	A	52	LEU	0	0.008	0.006	7.394	1.671	1.671	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.840	-0.912	8.115	-7.322	-7.322	0.000	0.000	0.000	0.000
49	A	54	GLY	0	0.051	0.041	9.168	-0.146	-0.146	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.027	0.013	6.240	0.631	0.631	0.000	0.000	0.000	0.000
55	A	60	GLN	0	-0.006	-0.010	9.733	0.767	0.767	0.000	0.000	0.000	0.000
56	A	61	ILE	0	-0.019	-0.009	11.799	-0.082	-0.082	0.000	0.000	0.000	0.000
57	A	62	TRP	0	0.005	0.003	14.408	0.228	0.228	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.773	-0.890	18.212	-0.414	-0.414	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.006	-0.034	21.858	0.119	0.119	0.000	0.000	0.000	0.000
60	A	65	ALA	0	0.028	0.025	25.175	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	66	GLY	0	0.025	0.016	28.846	0.000	0.000	0.000	0.000	0.000	0.000
62	A	67	GLN	0	-0.045	-0.030	30.530	0.014	0.014	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.910	-0.962	32.678	-0.103	-0.103	0.000	0.000	0.000	0.000
64	A	69	ARG	1	0.924	0.969	35.433	-0.066	-0.066	0.000	0.000	0.000	0.000
65	A	70	PHE	0	0.073	0.023	32.224	0.018	0.018	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.901	0.964	31.146	0.166	0.166	0.000	0.000	0.000	0.000
67	A	72	THR	0	0.048	0.012	30.908	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.004	0.018	29.971	0.008	0.008	0.000	0.000	0.000	0.000
69	A	74	THR	0	-0.040	-0.032	27.091	0.016	0.016	0.000	0.000	0.000	0.000
70	A	75	THR	0	-0.003	0.005	26.116	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	76	ALA	0	0.039	0.013	25.386	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	77	TYR	0	-0.003	-0.023	21.854	0.069	0.069	0.000	0.000	0.000	0.000
73	A	78	TYR	0	0.004	0.003	20.629	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	79	ARG	1	0.917	0.967	20.620	-0.201	-0.201	0.000	0.000	0.000	0.000
75	A	80	GLY	0	-0.024	0.001	17.093	0.046	0.046	0.000	0.000	0.000	0.000
76	A	81	ALA	0	-0.055	-0.022	15.538	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	82	MET	0	0.004	0.025	9.732	0.110	0.110	0.000	0.000	0.000	0.000
78	A	83	GLY	0	0.037	0.010	14.961	-0.259	-0.259	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.037	-0.023	16.610	0.145	0.145	0.000	0.000	0.000	0.000
80	A	85	MET	0	-0.020	0.013	17.625	-0.049	-0.049	0.000	0.000	0.000	0.000
81	A	86	LEU	0	-0.004	-0.009	21.611	0.127	0.127	0.000	0.000	0.000	0.000
82	A	87	VAL	0	-0.026	-0.012	24.430	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	88	TYR	0	0.034	0.005	26.894	0.058	0.058	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.796	-0.861	30.169	-0.420	-0.420	0.000	0.000	0.000	0.000
85	A	90	ILE	0	0.018	0.011	32.324	0.025	0.025	0.000	0.000	0.000	0.000
86	A	91	THR	0	-0.045	-0.043	34.834	0.027	0.027	0.000	0.000	0.000	0.000
87	A	92	ASN	0	-0.029	-0.014	36.108	0.035	0.035	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.652	-0.761	36.802	-0.361	-0.361	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.965	0.991	38.075	0.172	0.172	0.000	0.000	0.000	0.000
90	A	95	SER	0	-0.025	-0.022	33.330	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	96	PHE	0	0.000	-0.004	33.285	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	97	ASP	0	-0.052	-0.060	34.626	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	98	ASN	0	-0.011	-0.032	34.317	0.009	0.009	0.000	0.000	0.000	0.000
94	A	99	ILE	0	-0.031	-0.001	29.205	0.006	0.006	0.000	0.000	0.000	0.000
95	A	100	ARG	1	0.925	0.970	31.412	0.396	0.396	0.000	0.000	0.000	0.000
96	A	101	ASN	0	0.014	0.008	33.258	0.021	0.021	0.000	0.000	0.000	0.000
97	A	102	TRP	0	-0.057	-0.050	28.555	0.019	0.019	0.000	0.000	0.000	0.000
98	A	103	ILE	0	0.010	0.000	27.848	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.860	0.926	28.675	0.332	0.332	0.000	0.000	0.000	0.000
100	A	105	ASN	0	0.030	0.012	28.597	0.050	0.050	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.026	-0.017	23.453	0.017	0.017	0.000	0.000	0.000	0.000
102	A	107	GLU	-1	-0.891	-0.927	25.627	-0.396	-0.396	0.000	0.000	0.000	0.000
103	A	108	GLU	-1	-0.937	-0.961	27.932	-0.132	-0.132	0.000	0.000	0.000	0.000
104	A	109	HIS	0	-0.011	-0.004	26.187	0.076	0.076	0.000	0.000	0.000	0.000
105	A	110	ALA	0	-0.045	-0.023	21.499	0.065	0.065	0.000	0.000	0.000	0.000
106	A	111	SER	0	0.006	0.007	18.525	0.099	0.099	0.000	0.000	0.000	0.000
107	A	112	ALA	0	0.019	0.003	21.402	-0.104	-0.104	0.000	0.000	0.000	0.000
108	A	113	ASP	-1	-0.924	-0.966	17.888	-0.899	-0.899	0.000	0.000	0.000	0.000
109	A	114	VAL	0	0.001	0.027	17.789	-0.218	-0.218	0.000	0.000	0.000	0.000
110	A	115	GLU	-1	-0.853	-0.921	16.091	-1.597	-1.597	0.000	0.000	0.000	0.000
111	A	116	LYS	1	0.884	0.923	18.671	0.956	0.956	0.000	0.000	0.000	0.000
112	A	117	MET	0	-0.021	0.000	19.018	-0.056	-0.056	0.000	0.000	0.000	0.000
113	A	118	ILE	0	0.019	0.017	22.521	0.068	0.068	0.000	0.000	0.000	0.000
114	A	119	LEU	0	-0.019	-0.023	21.689	-0.063	-0.063	0.000	0.000	0.000	0.000
115	A	120	GLY	0	0.061	0.024	26.081	0.077	0.077	0.000	0.000	0.000	0.000
116	A	121	ASN	0	-0.034	-0.022	27.820	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	122	LYS	1	0.833	0.893	29.400	0.412	0.412	0.000	0.000	0.000	0.000
118	A	123	CYS	0	0.022	0.013	30.692	0.015	0.015	0.000	0.000	0.000	0.000
119	A	124	ASP	-1	-0.807	-0.872	32.504	-0.496	-0.496	0.000	0.000	0.000	0.000
120	A	125	VAL	0	-0.017	-0.001	34.327	0.027	0.027	0.000	0.000	0.000	0.000
121	A	126	ASN	0	0.041	0.020	37.027	0.000	0.000	0.000	0.000	0.000	0.000
122	A	127	ASP	-1	-0.837	-0.904	38.365	-0.324	-0.324	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.818	0.884	39.934	0.312	0.312	0.000	0.000	0.000	0.000
124	A	129	ARG	1	0.758	0.834	34.477	0.522	0.522	0.000	0.000	0.000	0.000
125	A	130	GLN	0	-0.013	0.005	39.050	0.016	0.016	0.000	0.000	0.000	0.000
126	A	131	VAL	0	-0.029	-0.002	35.376	0.005	0.005	0.000	0.000	0.000	0.000
127	A	132	SER	0	0.032	0.016	37.171	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	133	LYS	1	0.967	0.987	31.866	0.705	0.705	0.000	0.000	0.000	0.000
129	A	134	GLU	-1	-0.893	-0.932	33.930	-0.482	-0.482	0.000	0.000	0.000	0.000
130	A	135	ARG	1	0.824	0.873	35.834	0.373	0.373	0.000	0.000	0.000	0.000
131	A	136	GLY	0	0.024	0.014	32.163	0.006	0.006	0.000	0.000	0.000	0.000
132	A	137	GLU	-1	-0.911	-0.974	30.911	-0.738	-0.738	0.000	0.000	0.000	0.000
133	A	138	LYS	1	0.856	0.911	31.873	0.454	0.454	0.000	0.000	0.000	0.000
134	A	139	LEU	0	-0.028	-0.014	31.400	0.011	0.011	0.000	0.000	0.000	0.000
135	A	140	ALA	0	-0.016	-0.017	27.705	0.002	0.002	0.000	0.000	0.000	0.000
136	A	141	LEU	0	0.006	-0.003	29.302	-0.023	-0.023	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.865	-0.909	31.463	-0.478	-0.478	0.000	0.000	0.000	0.000
138	A	143	TYR	0	-0.050	-0.028	28.889	0.054	0.054	0.000	0.000	0.000	0.000
139	A	144	GLY	0	0.001	0.018	28.214	-0.028	-0.028	0.000	0.000	0.000	0.000
140	A	145	ILE	0	-0.057	-0.019	24.404	-0.090	-0.090	0.000	0.000	0.000	0.000
141	A	146	LYS	1	0.856	0.906	19.246	1.886	1.886	0.000	0.000	0.000	0.000
142	A	147	PHE	0	0.021	-0.006	24.409	0.051	0.051	0.000	0.000	0.000	0.000
143	A	148	MET	0	-0.061	-0.003	20.768	-0.056	-0.056	0.000	0.000	0.000	0.000
144	A	149	GLU	-1	-0.775	-0.849	26.210	-0.560	-0.560	0.000	0.000	0.000	0.000
145	A	150	THR	0	0.005	-0.018	24.061	-0.069	-0.069	0.000	0.000	0.000	0.000
146	A	151	SER	0	-0.021	-0.047	26.892	0.078	0.078	0.000	0.000	0.000	0.000
147	A	152	ALA	0	0.020	0.018	25.473	-0.048	-0.048	0.000	0.000	0.000	0.000
148	A	153	LYS	1	0.865	0.950	26.477	0.410	0.410	0.000	0.000	0.000	0.000
149	A	154	ALA	0	0.012	-0.012	29.299	0.003	0.003	0.000	0.000	0.000	0.000
150	A	155	ASN	0	0.016	0.016	22.481	-0.072	-0.072	0.000	0.000	0.000	0.000
151	A	156	ILE	0	0.017	0.019	25.090	-0.082	-0.082	0.000	0.000	0.000	0.000
152	A	157	ASN	0	0.016	-0.027	23.166	-0.070	-0.070	0.000	0.000	0.000	0.000
153	A	158	VAL	0	0.005	0.018	20.000	-0.110	-0.110	0.000	0.000	0.000	0.000
154	A	159	GLU	-1	-0.721	-0.831	16.478	-2.223	-2.223	0.000	0.000	0.000	0.000
155	A	160	ASN	0	-0.013	-0.019	17.149	-0.418	-0.418	0.000	0.000	0.000	0.000
156	A	161	ALA	0	0.071	0.031	18.363	-0.169	-0.169	0.000	0.000	0.000	0.000
157	A	162	PHE	0	0.015	0.003	14.595	-0.100	-0.100	0.000	0.000	0.000	0.000
158	A	163	PHE	0	0.022	0.003	12.295	-0.479	-0.479	0.000	0.000	0.000	0.000
159	A	164	THR	0	-0.072	-0.031	13.952	-0.369	-0.369	0.000	0.000	0.000	0.000
160	A	165	LEU	0	0.033	0.018	15.310	-0.137	-0.137	0.000	0.000	0.000	0.000
161	A	166	ALA	0	-0.007	-0.005	10.093	-0.158	-0.158	0.000	0.000	0.000	0.000
162	A	167	ARG	1	0.943	0.952	11.189	2.340	2.340	0.000	0.000	0.000	0.000
163	A	168	ASP	-1	-0.814	-0.871	13.090	-2.282	-2.282	0.000	0.000	0.000	0.000
164	A	169	ILE	0	0.029	0.009	11.088	0.092	0.092	0.000	0.000	0.000	0.000
165	A	170	LYS	1	0.771	0.869	7.317	7.684	7.684	0.000	0.000	0.000	0.000
166	A	171	ALA	0	-0.008	-0.002	10.729	0.133	0.133	0.000	0.000	0.000	0.000
167	A	172	LYS	1	0.817	0.911	14.031	1.759	1.759	0.000	0.000	0.000	0.000
168	A	173	MET	0	0.001	-0.005	8.706	-0.274	-0.274	0.000	0.000	0.000	0.000
169	A	174	ASP	-1	-0.801	-0.869	9.271	-6.632	-6.632	0.000	0.000	0.000	0.000
170	A	175	LYS	1	0.872	0.942	11.986	2.173	2.173	0.000	0.000	0.000	0.000
171	A	176	LYS	0	0.009	0.031	12.404	0.227	0.227	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ASP)