FMO DATABASE

FMODB ID: 973N2

Calculation Name: 6KYH-F-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: 6KYH

Chain ID: F

ChEMBL ID:

UniProt ID: Q61411

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1784425.759887
FMO2-HF: Nuclear repulsion	1717085.564427
FMO2-HF: Total energy	-67340.19546
FMO2-MP2: Total energy	-67534.43574

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:1:MET)

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

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.
-147.191	-141.562	9.272	-5.836	-9.064	-0.041

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.769 / q_NPA : 0.889

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	3	GLU	-1	-0.858	-0.920	3.485	-29.268	-27.272	0.008	-0.771	-1.232	-0.004
4	A	4	TYR	0	0.010	-0.023	5.301	2.332	2.367	-0.001	-0.004	-0.031	0.000
43	A	43	GLN	0	-0.020	-0.004	2.458	-2.730	-3.510	4.666	-1.594	-2.292	-0.002
50	A	50	THR	0	-0.046	-0.028	2.229	2.406	2.921	3.132	-1.329	-2.317	-0.008
51	A	51	CYS	0	-0.011	0.008	2.479	-17.785	-15.401	1.342	-1.747	-1.979	-0.025
52	A	52	LEU	0	-0.033	-0.030	3.281	2.901	4.375	0.125	-0.377	-1.222	-0.002
53	A	53	LEU	0	-0.014	-0.004	4.557	-0.403	-0.398	0.000	-0.014	0.009	0.000
5	A	5	LYS	1	0.852	0.934	8.520	25.732	25.732	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.011	0.009	11.550	1.114	1.114	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.023	0.016	14.080	0.336	0.336	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.015	0.003	17.672	0.360	0.360	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.001	0.013	20.289	0.457	0.457	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.071	0.026	23.688	0.072	0.072	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.040	0.025	27.273	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.025	0.012	29.423	-0.280	-0.280	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.002	-0.003	31.271	0.121	0.121	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.054	-0.038	27.069	0.120	0.120	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.017	0.010	27.208	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.846	0.945	23.114	10.899	10.899	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.060	0.028	22.065	-0.408	-0.408	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.005	0.004	22.305	-0.383	-0.383	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.030	-0.020	20.871	-0.184	-0.184	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.019	0.008	17.017	-0.787	-0.787	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.000	-0.001	18.044	-0.695	-0.695	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.019	-0.019	19.634	-0.577	-0.577	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.026	0.004	13.551	-0.315	-0.315	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.031	-0.010	13.735	-0.988	-0.988	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.016	-0.017	15.674	-0.777	-0.777	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.078	-0.015	18.312	0.571	0.571	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.035	0.014	20.066	0.146	0.146	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.007	-0.011	23.219	-0.193	-0.193	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.010	0.008	25.262	0.147	0.147	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.930	-0.969	27.756	-9.107	-9.107	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.970	-0.977	31.491	-8.517	-8.517	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.079	-0.056	30.809	-0.311	-0.311	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.877	-0.932	27.696	-10.017	-10.017	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.099	-0.058	29.018	-0.256	-0.256	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.020	0.014	23.419	0.213	0.213	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.039	-0.010	25.861	0.248	0.248	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.866	-0.987	21.373	-12.940	-12.940	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.858	-0.903	20.122	-12.386	-12.386	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.044	-0.032	14.714	-0.504	-0.504	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.044	-0.024	14.285	0.111	0.111	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.820	0.902	6.596	26.340	26.340	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.872	0.928	9.219	19.572	19.572	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.006	0.001	6.242	2.687	2.687	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.019	-0.015	6.067	-4.171	-4.171	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.031	0.021	8.011	2.551	2.551	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.785	-0.862	9.652	-22.992	-22.992	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.002	0.003	10.198	-0.062	-0.062	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.782	-0.839	5.311	-50.365	-50.365	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.810	-0.912	8.194	-22.904	-22.904	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.001	0.000	10.222	0.584	0.584	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.012	0.010	13.666	0.295	0.295	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.771	-0.873	17.131	-12.181	-12.181	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.009	-0.022	20.417	0.248	0.248	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.058	0.028	23.352	0.280	0.280	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.062	-0.030	27.070	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.035	-0.020	29.326	0.085	0.085	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.874	-0.944	31.711	-8.869	-8.869	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.928	-0.922	33.639	-8.523	-8.523	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.010	-0.036	28.772	-0.099	-0.099	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.018	-0.042	29.143	-0.410	-0.410	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.057	-0.033	30.084	-0.185	-0.185	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.013	0.009	25.298	-0.130	-0.130	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.929	0.975	25.093	9.583	9.583	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.824	-0.892	24.626	-11.872	-11.872	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.016	0.004	20.727	-0.793	-0.793	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.111	0.047	19.822	-0.483	-0.483	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.058	-0.019	19.610	-0.585	-0.585	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.850	0.912	21.109	11.676	11.676	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.038	-0.017	16.417	-0.817	-0.817	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.005	0.014	15.388	-1.317	-1.317	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.843	-0.923	10.857	-27.547	-27.547	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.040	0.015	14.864	0.532	0.532	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.030	-0.014	16.450	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.020	0.006	17.997	0.302	0.302	0.000	0.000	0.000	0.000
80	A	80	CYS	0	-0.035	-0.016	20.335	0.292	0.292	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.000	-0.001	23.222	0.245	0.245	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.034	0.011	25.778	0.328	0.328	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.013	0.006	29.213	-0.179	-0.179	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.041	0.028	31.541	0.301	0.301	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.004	-0.005	33.938	0.046	0.046	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.017	-0.005	34.781	0.311	0.311	0.000	0.000	0.000	0.000
87	A	87	THR	0	0.095	0.047	35.547	-0.160	-0.160	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.883	0.936	36.980	7.497	7.497	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.009	-0.012	31.913	-0.231	-0.231	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.012	-0.004	32.104	-0.265	-0.265	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.845	-0.913	33.491	-7.885	-7.885	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.897	-0.957	32.361	-8.889	-8.889	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.050	-0.025	28.013	-0.255	-0.255	0.000	0.000	0.000	0.000
94	A	94	HIS	0	0.048	0.039	29.791	-0.416	-0.416	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.021	-0.014	31.829	-0.156	-0.156	0.000	0.000	0.000	0.000
96	A	96	TYR	0	0.020	0.000	26.734	-0.222	-0.222	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.887	0.964	25.333	11.368	11.368	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.812	-0.922	27.842	-10.237	-10.237	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.041	-0.027	27.781	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.001	-0.006	22.454	-0.129	-0.129	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.883	0.955	24.806	10.167	10.167	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.880	0.953	26.711	9.735	9.735	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.064	-0.029	24.315	0.048	0.048	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.771	0.875	17.838	16.097	16.097	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.977	-0.969	24.064	-11.131	-11.131	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.020	-0.015	23.836	0.083	0.083	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.933	-0.987	25.887	-11.244	-11.244	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.913	-0.940	22.279	-14.848	-14.848	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.014	0.002	20.810	-0.324	-0.324	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.019	0.024	16.394	0.451	0.451	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.005	0.006	18.787	0.369	0.369	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.033	0.016	19.358	0.132	0.132	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.043	0.003	21.966	0.163	0.163	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.006	-0.016	22.031	-0.064	-0.064	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.050	0.038	25.389	0.275	0.275	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.050	-0.044	25.579	0.193	0.193	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.916	0.957	28.259	9.725	9.725	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.024	-0.009	29.078	0.273	0.273	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.836	-0.885	31.102	-9.312	-9.312	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.075	-0.036	33.471	0.318	0.318	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.026	0.006	36.141	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.035	-0.009	39.105	0.082	0.082	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.778	0.847	33.263	8.813	8.813	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.050	-0.036	38.019	0.181	0.181	0.000	0.000	0.000	0.000
125	A	125	VAL	0	0.004	0.023	34.461	0.107	0.107	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.920	-0.972	36.417	-7.870	-7.870	0.000	0.000	0.000	0.000
127	A	127	SER	0	0.001	-0.015	32.486	-0.191	-0.191	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.944	0.974	33.762	7.751	7.751	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.101	0.055	35.484	-0.132	-0.132	0.000	0.000	0.000	0.000
130	A	130	ALA	0	0.016	0.022	31.290	-0.090	-0.090	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.010	-0.009	30.096	-0.358	-0.358	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.934	-0.966	32.022	-8.717	-8.717	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.017	0.003	31.430	-0.065	-0.065	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.015	0.017	27.809	-0.120	-0.120	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.962	0.975	28.974	9.632	9.632	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.094	-0.045	31.122	-0.032	-0.032	0.000	0.000	0.000	0.000
137	A	137	TYR	0	-0.030	-0.042	27.943	-0.041	-0.041	0.000	0.000	0.000	0.000
138	A	138	GLY	0	0.027	0.024	27.826	-0.287	-0.287	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.028	-0.003	23.849	-0.401	-0.401	0.000	0.000	0.000	0.000
140	A	140	PRO	0	0.010	0.003	21.377	0.607	0.607	0.000	0.000	0.000	0.000
141	A	141	TYR	0	-0.063	-0.069	24.546	0.093	0.093	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.023	-0.008	21.856	-0.041	-0.041	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.741	-0.808	25.320	-9.345	-9.345	0.000	0.000	0.000	0.000
144	A	144	THR	0	0.053	0.022	22.796	-0.318	-0.318	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.080	-0.070	26.085	0.425	0.425	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.025	0.013	24.800	-0.282	-0.282	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.956	0.997	25.818	8.638	8.638	0.000	0.000	0.000	0.000
148	A	148	THR	0	-0.019	-0.036	28.107	0.023	0.023	0.000	0.000	0.000	0.000
149	A	149	ARG	1	0.873	0.921	17.680	14.207	14.207	0.000	0.000	0.000	0.000
150	A	150	GLN	0	-0.018	0.001	23.264	-0.449	-0.449	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.103	0.039	22.678	0.076	0.076	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.022	-0.006	18.927	-0.368	-0.368	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.825	-0.906	15.494	-17.256	-17.256	0.000	0.000	0.000	0.000
154	A	154	ASP	-1	-0.906	-0.944	16.823	-15.093	-15.093	0.000	0.000	0.000	0.000
155	A	155	ALA	0	0.016	0.026	18.668	-0.366	-0.366	0.000	0.000	0.000	0.000
156	A	156	PHE	0	0.023	0.005	14.264	-0.329	-0.329	0.000	0.000	0.000	0.000
157	A	157	TYR	0	-0.031	-0.037	12.502	-1.680	-1.680	0.000	0.000	0.000	0.000
158	A	158	THR	0	-0.045	-0.037	14.551	-0.678	-0.678	0.000	0.000	0.000	0.000
159	A	159	LEU	0	-0.016	0.008	15.171	-0.295	-0.295	0.000	0.000	0.000	0.000
160	A	160	VAL	0	-0.001	-0.003	9.760	-0.584	-0.584	0.000	0.000	0.000	0.000
161	A	161	ARG	1	0.786	0.867	12.635	17.580	17.580	0.000	0.000	0.000	0.000
162	A	162	GLU	-1	-0.817	-0.920	14.913	-15.673	-15.673	0.000	0.000	0.000	0.000
163	A	163	ILE	0	-0.056	-0.034	11.887	-0.003	-0.003	0.000	0.000	0.000	0.000
164	A	164	ARG	1	0.765	0.851	8.799	28.830	28.830	0.000	0.000	0.000	0.000
165	A	165	GLN	0	-0.094	-0.036	13.395	0.072	0.072	0.000	0.000	0.000	0.000
166	A	166	HIS	0	-0.086	-0.044	16.513	0.385	0.385	0.000	0.000	0.000	0.000
167	A	167	LYS	0	-0.099	-0.039	9.338	5.075	5.075	0.000	0.000	0.000	0.000

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