FMO DATABASE

FMODB ID: QKJVY

Calculation Name: 1K5D-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | magnesium ion

Ligand 3-letter code: GNP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K5D

Chain ID: B

ChEMBL ID:

UniProt ID: P43487

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1391782.75646
FMO2-HF: Nuclear repulsion	1330526.535223
FMO2-HF: Total energy	-61256.221237
FMO2-MP2: Total energy	-61432.798882

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:22:ASN)

Summations of interaction energy for fragment #1(A:22:ASN)

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.
-53.528	-49.718	0.702	-1.459	-3.054	-0.01

Interaction energy analysis for fragmet #1(A:22:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.901

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	24	ASP	-1	-0.827	-0.908	3.232	-37.880	-35.677	0.017	-0.900	-1.320	-0.004
4	A	25	PRO	0	-0.118	-0.055	2.362	-5.561	-4.181	0.679	-0.484	-1.575	-0.005
5	A	26	GLN	0	0.019	0.019	3.919	6.749	6.976	0.006	-0.075	-0.159	-0.001
6	A	27	PHE	0	-0.019	-0.019	7.113	-0.943	-0.943	0.000	0.000	0.000	0.000
7	A	28	GLU	-1	-0.926	-0.950	10.013	-17.768	-17.768	0.000	0.000	0.000	0.000
8	A	29	PRO	0	-0.033	-0.028	13.745	-0.223	-0.223	0.000	0.000	0.000	0.000
9	A	30	ILE	0	0.015	0.012	15.932	0.800	0.800	0.000	0.000	0.000	0.000
10	A	31	VAL	0	-0.024	-0.011	18.574	0.941	0.941	0.000	0.000	0.000	0.000
11	A	32	SER	0	-0.017	-0.006	20.290	-0.678	-0.678	0.000	0.000	0.000	0.000
12	A	33	LEU	0	-0.005	-0.013	22.465	0.545	0.545	0.000	0.000	0.000	0.000
13	A	34	PRO	0	-0.023	-0.014	24.510	-0.259	-0.259	0.000	0.000	0.000	0.000
14	A	35	GLU	-1	-0.896	-0.936	25.383	-12.625	-12.625	0.000	0.000	0.000	0.000
15	A	36	GLN	0	-0.057	-0.039	27.374	0.555	0.555	0.000	0.000	0.000	0.000
16	A	37	GLU	-1	-0.926	-0.953	29.685	-9.509	-9.509	0.000	0.000	0.000	0.000
17	A	38	ILE	0	-0.033	-0.010	29.264	0.289	0.289	0.000	0.000	0.000	0.000
18	A	39	LYS	1	0.900	0.953	32.659	8.730	8.730	0.000	0.000	0.000	0.000
19	A	40	THR	0	-0.043	-0.029	34.479	-0.278	-0.278	0.000	0.000	0.000	0.000
20	A	41	LEU	0	-0.036	-0.027	35.794	0.029	0.029	0.000	0.000	0.000	0.000
21	A	42	GLU	-1	-0.808	-0.924	37.127	-8.592	-8.592	0.000	0.000	0.000	0.000
22	A	43	GLU	-1	-0.716	-0.843	37.812	-8.585	-8.585	0.000	0.000	0.000	0.000
23	A	44	ASP	-1	-0.888	-0.926	41.646	-7.044	-7.044	0.000	0.000	0.000	0.000
24	A	45	GLU	-1	-0.992	-1.024	41.428	-7.628	-7.628	0.000	0.000	0.000	0.000
25	A	46	GLU	-1	-0.886	-0.983	44.411	-6.410	-6.410	0.000	0.000	0.000	0.000
26	A	47	GLU	-1	-0.862	-0.917	39.454	-8.330	-8.330	0.000	0.000	0.000	0.000
27	A	48	LEU	0	0.007	0.022	43.937	0.044	0.044	0.000	0.000	0.000	0.000
28	A	49	PHE	0	-0.036	-0.038	42.545	0.082	0.082	0.000	0.000	0.000	0.000
29	A	50	LYS	1	0.945	0.972	34.869	8.911	8.911	0.000	0.000	0.000	0.000
30	A	51	MET	0	-0.085	-0.019	38.771	0.092	0.092	0.000	0.000	0.000	0.000
31	A	52	ARG	1	0.872	0.936	29.369	10.306	10.306	0.000	0.000	0.000	0.000
32	A	53	ALA	0	-0.014	-0.009	35.501	0.236	0.236	0.000	0.000	0.000	0.000
33	A	54	LYS	1	0.800	0.881	31.050	9.633	9.633	0.000	0.000	0.000	0.000
34	A	55	LEU	0	0.017	0.011	35.059	0.274	0.274	0.000	0.000	0.000	0.000
35	A	56	PHE	0	-0.037	-0.029	35.512	-0.334	-0.334	0.000	0.000	0.000	0.000
36	A	57	ARG	1	0.825	0.880	36.847	8.249	8.249	0.000	0.000	0.000	0.000
37	A	58	PHE	0	0.017	0.004	38.921	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	59	ALA	0	0.001	0.010	41.333	0.009	0.009	0.000	0.000	0.000	0.000
39	A	60	SER	0	-0.020	-0.015	40.282	-0.260	-0.260	0.000	0.000	0.000	0.000
40	A	61	GLU	-1	-0.888	-0.916	42.432	-6.726	-6.726	0.000	0.000	0.000	0.000
41	A	62	ASN	0	-0.076	-0.063	39.013	-0.186	-0.186	0.000	0.000	0.000	0.000
42	A	63	ASP	-1	-0.840	-0.913	43.013	-6.773	-6.773	0.000	0.000	0.000	0.000
43	A	64	LEU	0	-0.028	-0.008	40.968	0.096	0.096	0.000	0.000	0.000	0.000
44	A	65	PRO	0	-0.079	-0.050	42.922	-0.171	-0.171	0.000	0.000	0.000	0.000
45	A	66	GLU	-1	-0.914	-0.940	38.987	-8.163	-8.163	0.000	0.000	0.000	0.000
46	A	67	TRP	0	-0.037	-0.026	39.538	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	68	LYS	1	0.976	0.999	35.122	8.490	8.490	0.000	0.000	0.000	0.000
48	A	69	GLU	-1	-0.823	-0.898	30.916	-10.001	-10.001	0.000	0.000	0.000	0.000
49	A	70	ARG	1	0.840	0.927	33.336	8.899	8.899	0.000	0.000	0.000	0.000
50	A	71	GLY	0	0.032	-0.004	31.197	-0.305	-0.305	0.000	0.000	0.000	0.000
51	A	72	THR	0	-0.042	-0.032	30.017	0.253	0.253	0.000	0.000	0.000	0.000
52	A	73	GLY	0	0.049	0.044	30.230	-0.449	-0.449	0.000	0.000	0.000	0.000
53	A	74	ASP	-1	-0.854	-0.920	32.059	-9.100	-9.100	0.000	0.000	0.000	0.000
54	A	75	VAL	0	-0.033	-0.024	35.023	-0.051	-0.051	0.000	0.000	0.000	0.000
55	A	76	LYS	1	0.798	0.874	36.779	8.683	8.683	0.000	0.000	0.000	0.000
56	A	77	LEU	0	-0.022	0.000	40.580	0.021	0.021	0.000	0.000	0.000	0.000
57	A	78	LEU	0	-0.017	-0.010	40.256	0.031	0.031	0.000	0.000	0.000	0.000
58	A	79	LYS	1	0.860	0.939	44.859	6.222	6.222	0.000	0.000	0.000	0.000
59	A	80	HIS	0	-0.080	-0.043	47.176	0.026	0.026	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.948	0.983	45.960	7.145	7.145	0.000	0.000	0.000	0.000
61	A	82	GLU	-1	-0.900	-0.942	50.080	-6.225	-6.225	0.000	0.000	0.000	0.000
62	A	83	LYS	1	0.845	0.918	49.207	6.623	6.623	0.000	0.000	0.000	0.000
63	A	84	GLY	0	0.082	0.047	53.155	0.042	0.042	0.000	0.000	0.000	0.000
64	A	85	ALA	0	-0.098	-0.037	50.057	0.018	0.018	0.000	0.000	0.000	0.000
65	A	86	ILE	0	0.059	0.028	47.565	-0.112	-0.112	0.000	0.000	0.000	0.000
66	A	87	ARG	1	0.860	0.937	40.529	7.905	7.905	0.000	0.000	0.000	0.000
67	A	88	LEU	0	0.010	0.023	40.542	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	89	LEU	0	-0.027	-0.015	36.954	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	90	MET	0	-0.030	-0.004	34.005	0.033	0.033	0.000	0.000	0.000	0.000
70	A	91	ARG	1	0.896	0.947	31.272	9.381	9.381	0.000	0.000	0.000	0.000
71	A	92	ARG	1	0.862	0.926	28.163	10.607	10.607	0.000	0.000	0.000	0.000
72	A	93	ASP	-1	-0.765	-0.883	26.179	-11.424	-11.424	0.000	0.000	0.000	0.000
73	A	94	LYS	1	0.922	0.967	21.244	13.397	13.397	0.000	0.000	0.000	0.000
74	A	95	THR	0	0.009	0.002	23.280	-0.092	-0.092	0.000	0.000	0.000	0.000
75	A	96	LEU	0	0.024	0.012	24.495	0.088	0.088	0.000	0.000	0.000	0.000
76	A	97	LYS	1	0.922	0.963	26.747	11.601	11.601	0.000	0.000	0.000	0.000
77	A	98	ILE	0	0.034	0.025	29.377	0.013	0.013	0.000	0.000	0.000	0.000
78	A	99	CYS	0	-0.095	-0.043	32.456	-0.233	-0.233	0.000	0.000	0.000	0.000
79	A	100	ALA	0	0.024	0.012	34.275	0.145	0.145	0.000	0.000	0.000	0.000
80	A	101	ASN	0	-0.029	-0.029	38.046	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	102	HIS	0	0.029	0.009	40.159	0.157	0.157	0.000	0.000	0.000	0.000
82	A	103	TYR	0	-0.009	-0.009	43.970	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	104	ILE	0	0.027	0.012	46.827	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	105	THR	0	-0.038	-0.024	49.359	0.116	0.116	0.000	0.000	0.000	0.000
85	A	106	PRO	0	0.105	0.042	52.828	-0.033	-0.033	0.000	0.000	0.000	0.000
86	A	107	MET	0	-0.057	-0.018	55.554	0.090	0.090	0.000	0.000	0.000	0.000
87	A	108	MET	0	-0.028	0.014	48.127	-0.105	-0.105	0.000	0.000	0.000	0.000
88	A	109	GLU	-1	-0.901	-0.956	51.787	-6.182	-6.182	0.000	0.000	0.000	0.000
89	A	110	LEU	0	0.009	0.003	46.849	-0.178	-0.178	0.000	0.000	0.000	0.000
90	A	111	LYS	1	0.967	0.997	50.129	6.067	6.067	0.000	0.000	0.000	0.000
91	A	112	PRO	0	0.038	0.005	49.313	-0.159	-0.159	0.000	0.000	0.000	0.000
92	A	113	ASN	0	-0.029	-0.004	44.955	0.034	0.034	0.000	0.000	0.000	0.000
93	A	114	ALA	0	-0.022	-0.014	47.698	-0.085	-0.085	0.000	0.000	0.000	0.000
94	A	115	GLY	0	0.021	0.029	48.775	0.122	0.122	0.000	0.000	0.000	0.000
95	A	116	SER	0	-0.045	-0.043	44.556	-0.087	-0.087	0.000	0.000	0.000	0.000
96	A	117	ASP	-1	-0.806	-0.908	46.132	-6.869	-6.869	0.000	0.000	0.000	0.000
97	A	118	ARG	1	0.852	0.923	39.369	7.795	7.795	0.000	0.000	0.000	0.000
98	A	119	ALA	0	-0.038	-0.026	43.111	-0.210	-0.210	0.000	0.000	0.000	0.000
99	A	120	TRP	0	-0.020	0.001	44.466	0.218	0.218	0.000	0.000	0.000	0.000
100	A	121	VAL	0	-0.004	-0.015	44.617	-0.221	-0.221	0.000	0.000	0.000	0.000
101	A	122	TRP	0	-0.002	-0.005	41.667	0.068	0.068	0.000	0.000	0.000	0.000
102	A	123	ASN	0	0.017	-0.002	46.529	-0.227	-0.227	0.000	0.000	0.000	0.000
103	A	124	THR	0	0.019	0.012	44.574	0.135	0.135	0.000	0.000	0.000	0.000
104	A	125	HIS	0	0.041	0.013	46.720	-0.142	-0.142	0.000	0.000	0.000	0.000
105	A	126	ALA	0	0.002	-0.005	45.674	0.005	0.005	0.000	0.000	0.000	0.000
106	A	127	ASP	-1	-0.815	-0.891	39.460	-8.139	-8.139	0.000	0.000	0.000	0.000
107	A	128	PHE	0	0.034	0.006	39.823	0.022	0.022	0.000	0.000	0.000	0.000
108	A	129	ALA	0	-0.031	-0.016	35.465	-0.149	-0.149	0.000	0.000	0.000	0.000
109	A	130	ASP	-1	-0.874	-0.932	34.233	-9.476	-9.476	0.000	0.000	0.000	0.000
110	A	131	GLU	-1	-0.959	-0.979	34.399	-9.336	-9.336	0.000	0.000	0.000	0.000
111	A	132	CYS	0	0.002	0.006	37.718	0.195	0.195	0.000	0.000	0.000	0.000
112	A	133	PRO	0	-0.041	-0.020	40.207	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	134	LYS	1	0.890	0.938	37.369	8.474	8.474	0.000	0.000	0.000	0.000
114	A	135	PRO	0	0.015	0.019	43.599	-0.027	-0.027	0.000	0.000	0.000	0.000
115	A	136	GLU	-1	-0.824	-0.896	39.648	-8.256	-8.256	0.000	0.000	0.000	0.000
116	A	137	LEU	0	0.004	0.012	43.844	0.124	0.124	0.000	0.000	0.000	0.000
117	A	138	LEU	0	-0.019	-0.005	40.002	-0.240	-0.240	0.000	0.000	0.000	0.000
118	A	139	ALA	0	0.052	0.019	41.258	0.213	0.213	0.000	0.000	0.000	0.000
119	A	140	ILE	0	-0.051	-0.010	39.093	-0.284	-0.284	0.000	0.000	0.000	0.000
120	A	141	ARG	1	0.938	0.971	37.419	8.522	8.522	0.000	0.000	0.000	0.000
121	A	142	PHE	0	0.048	0.018	38.646	-0.247	-0.247	0.000	0.000	0.000	0.000
122	A	143	LEU	0	0.000	-0.001	36.764	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	144	ASN	0	0.013	-0.006	39.553	0.009	0.009	0.000	0.000	0.000	0.000
124	A	145	ALA	0	0.039	0.013	43.223	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	146	GLU	-1	-0.831	-0.916	44.704	-7.154	-7.154	0.000	0.000	0.000	0.000
126	A	147	ASN	0	0.014	-0.009	41.841	-0.097	-0.097	0.000	0.000	0.000	0.000
127	A	148	ALA	0	0.032	0.032	44.643	0.004	0.004	0.000	0.000	0.000	0.000
128	A	149	GLN	0	0.042	0.017	45.798	0.165	0.165	0.000	0.000	0.000	0.000
129	A	150	LYS	1	0.917	0.963	45.477	7.107	7.107	0.000	0.000	0.000	0.000
130	A	151	PHE	0	0.026	0.012	43.592	0.011	0.011	0.000	0.000	0.000	0.000
131	A	152	LYS	1	0.928	0.974	46.160	6.194	6.194	0.000	0.000	0.000	0.000
132	A	153	THR	0	-0.022	-0.009	49.205	0.112	0.112	0.000	0.000	0.000	0.000
133	A	154	LYS	1	0.885	0.933	47.682	6.606	6.606	0.000	0.000	0.000	0.000
134	A	155	PHE	0	0.033	0.012	46.277	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	156	GLU	-1	-0.883	-0.964	49.523	-6.116	-6.116	0.000	0.000	0.000	0.000
136	A	157	GLU	-1	-0.916	-0.942	52.330	-6.085	-6.085	0.000	0.000	0.000	0.000
137	A	158	CYS	0	-0.014	-0.002	49.770	0.024	0.024	0.000	0.000	0.000	0.000
138	A	159	ARG	1	0.835	0.910	52.127	5.772	5.772	0.000	0.000	0.000	0.000
139	A	160	LYS	1	0.934	0.980	53.705	5.666	5.666	0.000	0.000	0.000	0.000
140	A	161	GLU	-1	-0.794	-0.892	54.443	-5.959	-5.959	0.000	0.000	0.000	0.000
141	A	162	ILE	0	-0.084	-0.055	51.103	0.047	0.047	0.000	0.000	0.000	0.000
142	A	163	GLU	-1	-0.947	-0.974	55.638	-5.365	-5.365	0.000	0.000	0.000	0.000
143	A	164	GLU	-1	-0.905	-0.941	58.657	-5.261	-5.261	0.000	0.000	0.000	0.000
144	A	165	ARG	1	0.912	0.981	53.835	5.959	5.959	0.000	0.000	0.000	0.000
145	A	166	GLU	0	-0.188	-0.121	58.828	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	167	LYS	0	0.097	0.059	61.065	0.164	0.164	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:ASN)