FMO DATABASE

FMODB ID: LQ3Q9

Calculation Name: 1R2Q-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: 1R2Q

Chain ID: A

ChEMBL ID:

UniProt ID: P20339

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1771738.138258
FMO2-HF: Nuclear repulsion	1705049.698011
FMO2-HF: Total energy	-66688.440247
FMO2-MP2: Total energy	-66882.509309

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:15:GLY)

Summations of interaction energy for fragment #1(A:15: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.
-39.567	-34.644	7.629	-6.876	-5.675	-0.077

Interaction energy analysis for fragmet #1(A:15:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / 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	17	LYS	1	0.927	0.978	3.545	49.995	51.961	-0.015	-0.921	-1.030	-0.004
49	A	63	CYS	0	-0.026	-0.012	4.869	-6.918	-6.835	0.001	-0.025	-0.059	0.000
52	A	66	ASP	-1	-0.841	-0.901	2.557	-68.821	-67.025	1.028	-1.465	-1.359	-0.013
53	A	67	THR	0	-0.058	-0.049	2.258	-27.731	-26.769	6.616	-4.455	-3.123	-0.060
54	A	68	THR	0	-0.017	0.000	4.123	1.439	1.555	-0.001	-0.010	-0.104	0.000
4	A	18	ILE	0	0.034	0.015	5.390	-5.023	-5.023	0.000	0.000	0.000	0.000
5	A	19	CYS	0	-0.039	-0.013	8.137	2.017	2.017	0.000	0.000	0.000	0.000
6	A	20	GLN	0	-0.013	-0.003	10.842	-1.495	-1.495	0.000	0.000	0.000	0.000
7	A	21	PHE	0	-0.017	-0.004	13.802	0.797	0.797	0.000	0.000	0.000	0.000
8	A	22	LYS	1	0.881	0.961	16.703	12.321	12.321	0.000	0.000	0.000	0.000
9	A	23	LEU	0	-0.001	0.004	18.836	0.089	0.089	0.000	0.000	0.000	0.000
10	A	24	VAL	0	-0.005	-0.005	21.227	0.333	0.333	0.000	0.000	0.000	0.000
11	A	25	LEU	0	-0.002	0.012	23.314	-0.080	-0.080	0.000	0.000	0.000	0.000
12	A	26	LEU	0	0.018	0.026	26.674	0.426	0.426	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.088	0.029	30.073	-0.169	-0.169	0.000	0.000	0.000	0.000
14	A	28	GLU	0	-0.065	-0.071	32.835	0.008	0.008	0.000	0.000	0.000	0.000
15	A	29	SER	0	0.013	-0.002	34.789	-0.258	-0.258	0.000	0.000	0.000	0.000
16	A	30	ALA	0	0.017	0.007	36.067	0.060	0.060	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.024	0.025	31.779	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	32	GLY	0	0.037	0.026	31.320	-0.208	-0.208	0.000	0.000	0.000	0.000
19	A	33	LYS	1	0.819	0.928	28.228	9.712	9.712	0.000	0.000	0.000	0.000
20	A	34	SER	0	0.037	-0.014	26.991	-0.351	-0.351	0.000	0.000	0.000	0.000
21	A	35	SER	0	-0.021	-0.010	27.006	-0.270	-0.270	0.000	0.000	0.000	0.000
22	A	36	LEU	0	0.015	0.015	24.290	-0.350	-0.350	0.000	0.000	0.000	0.000
23	A	37	VAL	0	0.012	0.008	22.055	-0.677	-0.677	0.000	0.000	0.000	0.000
24	A	38	LEU	0	-0.018	-0.012	22.229	-0.653	-0.653	0.000	0.000	0.000	0.000
25	A	39	ARG	1	0.841	0.933	22.393	12.214	12.214	0.000	0.000	0.000	0.000
26	A	40	PHE	0	-0.003	-0.001	14.444	-0.369	-0.369	0.000	0.000	0.000	0.000
27	A	41	VAL	0	-0.037	-0.018	18.059	-0.927	-0.927	0.000	0.000	0.000	0.000
28	A	42	LYS	1	0.914	0.959	19.242	12.312	12.312	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.056	0.046	21.179	0.247	0.247	0.000	0.000	0.000	0.000
30	A	44	GLN	0	-0.047	-0.028	22.238	0.566	0.566	0.000	0.000	0.000	0.000
31	A	45	PHE	0	0.008	-0.011	25.887	-0.202	-0.202	0.000	0.000	0.000	0.000
32	A	46	HIS	0	-0.037	-0.020	28.853	0.080	0.080	0.000	0.000	0.000	0.000
33	A	47	GLU	-1	-0.829	-0.894	32.352	-9.009	-9.009	0.000	0.000	0.000	0.000
34	A	48	PHE	0	-0.021	-0.014	35.478	0.141	0.141	0.000	0.000	0.000	0.000
35	A	49	GLN	0	-0.005	0.009	31.397	-0.182	-0.182	0.000	0.000	0.000	0.000
36	A	50	GLU	-1	-0.914	-0.949	34.671	-8.399	-8.399	0.000	0.000	0.000	0.000
37	A	51	SER	0	-0.067	-0.038	34.566	-0.352	-0.352	0.000	0.000	0.000	0.000
38	A	52	THR	0	0.017	0.006	31.154	0.214	0.214	0.000	0.000	0.000	0.000
39	A	53	ILE	0	0.002	0.001	34.248	0.235	0.235	0.000	0.000	0.000	0.000
40	A	54	GLY	0	0.001	-0.002	34.634	-0.147	-0.147	0.000	0.000	0.000	0.000
41	A	55	ALA	0	-0.025	-0.022	29.417	-0.102	-0.102	0.000	0.000	0.000	0.000
42	A	56	ALA	0	0.008	0.027	28.443	0.132	0.132	0.000	0.000	0.000	0.000
43	A	57	PHE	0	-0.011	-0.011	21.125	-0.244	-0.244	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.022	-0.013	21.806	0.153	0.153	0.000	0.000	0.000	0.000
45	A	59	THR	0	-0.036	-0.028	16.976	-0.476	-0.476	0.000	0.000	0.000	0.000
46	A	60	GLN	0	0.044	0.021	14.202	-0.353	-0.353	0.000	0.000	0.000	0.000
47	A	61	THR	0	-0.038	-0.026	9.904	-0.356	-0.356	0.000	0.000	0.000	0.000
48	A	62	VAL	0	0.018	0.016	9.015	0.430	0.430	0.000	0.000	0.000	0.000
50	A	64	LEU	0	0.000	-0.008	5.252	5.762	5.762	0.000	0.000	0.000	0.000
51	A	65	ASP	-1	-0.764	-0.883	5.391	-37.196	-37.196	0.000	0.000	0.000	0.000
55	A	69	VAL	0	-0.016	-0.022	5.863	4.224	4.224	0.000	0.000	0.000	0.000
56	A	70	LYS	1	0.858	0.929	9.208	19.911	19.911	0.000	0.000	0.000	0.000
57	A	71	PHE	0	0.049	0.017	12.448	0.986	0.986	0.000	0.000	0.000	0.000
58	A	72	GLU	-1	-0.850	-0.917	15.738	-16.388	-16.388	0.000	0.000	0.000	0.000
59	A	73	ILE	0	0.001	0.000	18.322	0.484	0.484	0.000	0.000	0.000	0.000
60	A	74	TRP	0	-0.002	-0.006	21.598	0.705	0.705	0.000	0.000	0.000	0.000
61	A	75	ASP	-1	-0.757	-0.869	25.356	-10.997	-10.997	0.000	0.000	0.000	0.000
62	A	76	THR	0	-0.021	-0.036	27.410	0.480	0.480	0.000	0.000	0.000	0.000
63	A	77	ALA	0	0.019	0.007	30.790	0.065	0.065	0.000	0.000	0.000	0.000
64	A	78	GLY	0	-0.017	-0.015	34.262	0.091	0.091	0.000	0.000	0.000	0.000
65	A	79	GLN	0	-0.054	-0.033	35.449	0.324	0.324	0.000	0.000	0.000	0.000
66	A	80	GLU	-1	-0.711	-0.842	38.944	-8.057	-8.057	0.000	0.000	0.000	0.000
67	A	81	ARG	1	0.941	0.963	40.829	7.692	7.692	0.000	0.000	0.000	0.000
68	A	82	TYR	0	0.053	0.026	36.741	0.080	0.080	0.000	0.000	0.000	0.000
69	A	83	HIS	1	0.774	0.855	36.970	8.046	8.046	0.000	0.000	0.000	0.000
70	A	84	SER	0	0.016	-0.001	37.286	-0.213	-0.213	0.000	0.000	0.000	0.000
71	A	85	LEU	0	0.015	0.006	35.188	-0.038	-0.038	0.000	0.000	0.000	0.000
72	A	86	ALA	0	0.022	0.024	32.814	-0.297	-0.297	0.000	0.000	0.000	0.000
73	A	87	PRO	0	0.012	0.002	31.815	-0.381	-0.381	0.000	0.000	0.000	0.000
74	A	88	MET	0	-0.011	0.000	31.867	-0.154	-0.154	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.004	-0.004	28.578	-0.328	-0.328	0.000	0.000	0.000	0.000
76	A	90	TYR	0	0.013	-0.033	27.120	-0.535	-0.535	0.000	0.000	0.000	0.000
77	A	91	ARG	1	0.942	0.977	27.380	9.391	9.391	0.000	0.000	0.000	0.000
78	A	92	GLY	0	0.009	0.001	25.718	-0.123	-0.123	0.000	0.000	0.000	0.000
79	A	93	ALA	0	-0.049	-0.009	22.858	-0.575	-0.575	0.000	0.000	0.000	0.000
80	A	94	GLN	0	0.018	0.006	18.508	-0.176	-0.176	0.000	0.000	0.000	0.000
81	A	95	ALA	0	0.028	0.015	19.499	-0.115	-0.115	0.000	0.000	0.000	0.000
82	A	96	ALA	0	-0.008	-0.015	21.496	0.319	0.319	0.000	0.000	0.000	0.000
83	A	97	ILE	0	0.013	0.023	21.448	-0.184	-0.184	0.000	0.000	0.000	0.000
84	A	98	VAL	0	-0.048	-0.010	25.228	0.349	0.349	0.000	0.000	0.000	0.000
85	A	99	VAL	0	-0.036	-0.024	27.488	-0.068	-0.068	0.000	0.000	0.000	0.000
86	A	100	TYR	0	-0.004	-0.004	30.098	0.403	0.403	0.000	0.000	0.000	0.000
87	A	101	ASP	-1	-0.801	-0.870	32.433	-9.060	-9.060	0.000	0.000	0.000	0.000
88	A	102	ILE	0	0.039	0.025	33.162	0.247	0.247	0.000	0.000	0.000	0.000
89	A	103	THR	0	-0.062	-0.038	35.924	0.270	0.270	0.000	0.000	0.000	0.000
90	A	104	ASN	0	-0.003	-0.003	38.491	0.355	0.355	0.000	0.000	0.000	0.000
91	A	105	GLU	-1	-0.835	-0.909	38.951	-7.591	-7.591	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.806	-0.852	40.384	-7.910	-7.910	0.000	0.000	0.000	0.000
93	A	107	SER	0	-0.042	-0.034	36.750	-0.244	-0.244	0.000	0.000	0.000	0.000
94	A	108	PHE	0	0.059	0.018	34.498	-0.255	-0.255	0.000	0.000	0.000	0.000
95	A	109	ALA	0	0.031	0.021	36.959	-0.124	-0.124	0.000	0.000	0.000	0.000
96	A	110	ARG	1	0.811	0.905	37.039	8.353	8.353	0.000	0.000	0.000	0.000
97	A	111	ALA	0	0.003	-0.007	33.057	-0.135	-0.135	0.000	0.000	0.000	0.000
98	A	112	LYS	1	0.944	0.987	34.192	8.255	8.255	0.000	0.000	0.000	0.000
99	A	113	ASN	0	-0.011	-0.009	36.150	-0.023	-0.023	0.000	0.000	0.000	0.000
100	A	114	TRP	0	-0.021	-0.011	32.620	0.004	0.004	0.000	0.000	0.000	0.000
101	A	115	VAL	0	0.016	0.017	30.628	-0.184	-0.184	0.000	0.000	0.000	0.000
102	A	116	LYS	1	0.958	0.980	32.703	7.998	7.998	0.000	0.000	0.000	0.000
103	A	117	GLU	-1	-0.852	-0.875	34.544	-8.704	-8.704	0.000	0.000	0.000	0.000
104	A	118	LEU	0	-0.010	-0.015	27.955	-0.065	-0.065	0.000	0.000	0.000	0.000
105	A	119	GLN	0	0.014	-0.009	31.110	0.104	0.104	0.000	0.000	0.000	0.000
106	A	120	ARG	1	0.892	0.955	32.406	8.557	8.557	0.000	0.000	0.000	0.000
107	A	121	GLN	0	-0.038	-0.007	33.585	0.372	0.372	0.000	0.000	0.000	0.000
108	A	122	ALA	0	-0.011	0.006	28.217	-0.076	-0.076	0.000	0.000	0.000	0.000
109	A	123	SER	0	-0.002	0.000	24.797	0.286	0.286	0.000	0.000	0.000	0.000
110	A	124	PRO	0	0.036	0.008	27.454	-0.156	-0.156	0.000	0.000	0.000	0.000
111	A	125	ASN	0	-0.022	-0.009	23.472	0.035	0.035	0.000	0.000	0.000	0.000
112	A	126	ILE	0	-0.066	-0.014	22.944	-0.684	-0.684	0.000	0.000	0.000	0.000
113	A	127	VAL	0	0.043	0.012	19.176	0.322	0.322	0.000	0.000	0.000	0.000
114	A	128	ILE	0	-0.018	-0.004	22.325	-0.112	-0.112	0.000	0.000	0.000	0.000
115	A	129	ALA	0	0.027	0.017	22.511	-0.055	-0.055	0.000	0.000	0.000	0.000
116	A	130	LEU	0	-0.035	-0.017	24.639	0.466	0.466	0.000	0.000	0.000	0.000
117	A	131	SER	0	0.018	-0.003	26.054	-0.168	-0.168	0.000	0.000	0.000	0.000
118	A	132	GLY	0	0.069	0.025	27.802	0.385	0.385	0.000	0.000	0.000	0.000
119	A	133	ASN	0	-0.019	-0.029	28.984	-0.398	-0.398	0.000	0.000	0.000	0.000
120	A	134	LYS	1	0.820	0.892	30.511	9.388	9.388	0.000	0.000	0.000	0.000
121	A	135	ALA	0	0.075	0.035	30.287	0.314	0.314	0.000	0.000	0.000	0.000
122	A	136	ASP	-1	-0.851	-0.907	32.304	-9.699	-9.699	0.000	0.000	0.000	0.000
123	A	137	LEU	0	-0.052	-0.028	33.779	0.335	0.335	0.000	0.000	0.000	0.000
124	A	138	ALA	0	0.059	0.026	35.483	0.242	0.242	0.000	0.000	0.000	0.000
125	A	139	ASN	0	-0.035	-0.024	37.376	0.016	0.016	0.000	0.000	0.000	0.000
126	A	140	LYS	1	0.894	0.945	40.143	8.042	8.042	0.000	0.000	0.000	0.000
127	A	141	ARG	1	0.769	0.843	34.041	9.039	9.039	0.000	0.000	0.000	0.000
128	A	142	ALA	0	-0.008	-0.002	39.875	0.187	0.187	0.000	0.000	0.000	0.000
129	A	143	VAL	0	-0.002	0.007	36.277	0.105	0.105	0.000	0.000	0.000	0.000
130	A	144	ASP	-1	-0.780	-0.888	37.649	-8.578	-8.578	0.000	0.000	0.000	0.000
131	A	145	PHE	0	-0.006	-0.001	29.656	-0.154	-0.154	0.000	0.000	0.000	0.000
132	A	146	GLN	0	0.002	-0.008	33.821	-0.378	-0.378	0.000	0.000	0.000	0.000
133	A	147	GLU	-1	-0.928	-0.964	35.779	-7.893	-7.893	0.000	0.000	0.000	0.000
134	A	148	ALA	0	-0.081	-0.044	33.047	-0.061	-0.061	0.000	0.000	0.000	0.000
135	A	149	GLN	0	-0.060	-0.042	28.310	-0.380	-0.380	0.000	0.000	0.000	0.000
136	A	150	SER	0	0.039	0.030	32.049	-0.190	-0.190	0.000	0.000	0.000	0.000
137	A	151	TYR	0	0.031	0.005	32.906	0.027	0.027	0.000	0.000	0.000	0.000
138	A	152	ALA	0	-0.011	-0.017	29.149	-0.060	-0.060	0.000	0.000	0.000	0.000
139	A	153	ASP	-1	-0.853	-0.914	29.270	-11.010	-11.010	0.000	0.000	0.000	0.000
140	A	154	ASP	-1	-0.916	-0.949	30.934	-8.987	-8.987	0.000	0.000	0.000	0.000
141	A	155	ASN	0	-0.136	-0.079	31.989	0.177	0.177	0.000	0.000	0.000	0.000
142	A	156	SER	0	-0.052	-0.023	27.470	-0.243	-0.243	0.000	0.000	0.000	0.000
143	A	157	LEU	0	-0.061	-0.029	26.640	-0.430	-0.430	0.000	0.000	0.000	0.000
144	A	158	LEU	0	-0.006	-0.010	19.578	-0.040	-0.040	0.000	0.000	0.000	0.000
145	A	159	PHE	0	-0.001	-0.008	24.246	-0.109	-0.109	0.000	0.000	0.000	0.000
146	A	160	MET	0	-0.027	0.003	20.055	-0.451	-0.451	0.000	0.000	0.000	0.000
147	A	161	GLU	-1	-0.742	-0.818	26.112	-9.521	-9.521	0.000	0.000	0.000	0.000
148	A	162	THR	0	0.002	-0.008	24.511	-0.435	-0.435	0.000	0.000	0.000	0.000
149	A	163	SER	0	-0.042	-0.053	26.611	0.469	0.469	0.000	0.000	0.000	0.000
150	A	164	ALA	0	0.005	0.009	26.223	-0.355	-0.355	0.000	0.000	0.000	0.000
151	A	165	LYS	1	0.850	0.928	27.308	8.891	8.891	0.000	0.000	0.000	0.000
152	A	166	THR	0	0.042	-0.003	28.606	-0.157	-0.157	0.000	0.000	0.000	0.000
153	A	167	SER	0	-0.061	-0.020	23.009	-0.513	-0.513	0.000	0.000	0.000	0.000
154	A	168	MET	0	0.036	0.022	23.327	-0.501	-0.501	0.000	0.000	0.000	0.000
155	A	169	ASN	0	0.009	-0.015	22.035	-0.017	-0.017	0.000	0.000	0.000	0.000
156	A	170	VAL	0	-0.001	0.006	21.182	-0.226	-0.226	0.000	0.000	0.000	0.000
157	A	171	ASN	0	0.007	-0.001	14.680	-0.970	-0.970	0.000	0.000	0.000	0.000
158	A	172	GLU	-1	-0.850	-0.931	16.792	-17.572	-17.572	0.000	0.000	0.000	0.000
159	A	173	ILE	0	0.048	0.011	17.920	-0.547	-0.547	0.000	0.000	0.000	0.000
160	A	174	PHE	0	-0.032	-0.015	16.613	-0.054	-0.054	0.000	0.000	0.000	0.000
161	A	175	MET	0	0.003	-0.004	9.862	-0.796	-0.796	0.000	0.000	0.000	0.000
162	A	176	ALA	0	-0.018	-0.001	13.972	-1.108	-1.108	0.000	0.000	0.000	0.000
163	A	177	ILE	0	0.011	-0.006	16.632	-0.018	-0.018	0.000	0.000	0.000	0.000
164	A	178	ALA	0	-0.024	-0.011	12.197	-0.137	-0.137	0.000	0.000	0.000	0.000
165	A	179	LYS	1	0.813	0.902	10.043	27.866	27.866	0.000	0.000	0.000	0.000
166	A	180	LYS	1	0.945	0.976	13.496	16.768	16.768	0.000	0.000	0.000	0.000
167	A	181	LEU	0	-0.029	0.009	14.208	0.997	0.997	0.000	0.000	0.000	0.000
168	A	182	PRO	0	0.000	0.001	15.060	-0.990	-0.990	0.000	0.000	0.000	0.000
169	A	183	LYS	1	0.883	0.922	10.387	24.876	24.876	0.000	0.000	0.000	0.000
170	A	184	ASN	-1	-0.923	-0.933	13.366	-18.074	-18.074	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:GLY)