FMO DATABASE

FMODB ID: RQGL8

Calculation Name: 1RDS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2'-fluoroguanylyl-(3'-5')-phosphocytidine

Ligand 3-letter code: GPC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RDS

Chain ID: A

ChEMBL ID:

UniProt ID: P00653

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-775373.022561
FMO2-HF: Nuclear repulsion	734153.821171
FMO2-HF: Total energy	-41219.20139
FMO2-MP2: Total energy	-41336.407604

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:GLU)

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

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.
-18.848	-13.74	3.641	-3.016	-5.733	-0.015

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.139 / q_NPA : -0.080

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	CYS	0	-0.057	-0.014	3.839	-3.131	-1.439	-0.017	-0.694	-0.981	0.001
12	A	13	TRP	0	-0.003	-0.009	2.509	-9.977	-6.561	3.658	-2.322	-4.752	-0.016
4	A	4	GLU	-1	-0.846	-0.897	6.698	-4.837	-4.837	0.000	0.000	0.000	0.000
5	A	5	TYR	0	0.031	-0.001	8.178	0.854	0.854	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.030	-0.022	10.290	0.207	0.207	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.107	-0.023	12.358	0.097	0.097	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.035	0.009	15.221	0.181	0.181	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.074	-0.041	14.374	0.026	0.026	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.006	0.008	11.131	0.592	0.592	0.000	0.000	0.000	0.000
11	A	12	TYR	0	0.040	-0.010	7.947	0.286	0.286	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.014	-0.032	5.490	0.596	0.596	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.072	-0.021	6.264	0.331	0.331	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.790	-0.897	7.353	-2.400	-2.400	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.017	0.012	9.708	0.592	0.592	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.037	-0.033	10.497	0.475	0.475	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.029	-0.010	12.093	0.336	0.336	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.024	0.012	13.863	0.270	0.270	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.778	0.886	15.279	1.891	1.891	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.020	0.010	16.465	0.158	0.158	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.887	0.966	17.991	0.800	0.800	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.049	0.018	19.759	0.109	0.109	0.000	0.000	0.000	0.000
24	A	25	TYR	0	-0.019	-0.020	20.966	0.090	0.090	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.048	-0.034	22.274	0.089	0.089	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.048	-0.003	23.892	0.072	0.072	0.000	0.000	0.000	0.000
27	A	28	TYR	0	-0.015	-0.009	25.584	0.043	0.043	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.985	-0.990	26.202	-0.773	-0.773	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.074	-0.053	28.167	0.045	0.045	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.050	-0.015	30.098	0.042	0.042	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.959	-0.965	29.516	-0.373	-0.373	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.045	-0.041	28.179	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.045	-0.023	24.650	0.031	0.031	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.891	-0.951	26.931	-0.205	-0.205	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.910	-0.956	28.488	-0.280	-0.280	0.000	0.000	0.000	0.000
36	A	37	TYR	0	-0.020	0.007	24.078	-0.026	-0.026	0.000	0.000	0.000	0.000
37	A	38	PRO	0	-0.008	-0.005	24.073	0.004	0.004	0.000	0.000	0.000	0.000
38	A	39	HIS	1	0.848	0.932	25.594	0.383	0.383	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.878	-0.909	26.793	-0.429	-0.429	0.000	0.000	0.000	0.000
40	A	41	TYR	0	0.008	-0.028	25.038	0.016	0.016	0.000	0.000	0.000	0.000
41	A	42	HIS	1	0.817	0.855	27.647	0.334	0.334	0.000	0.000	0.000	0.000
42	A	43	ASP	-1	-0.831	-0.897	27.063	-0.504	-0.504	0.000	0.000	0.000	0.000
43	A	44	TYR	0	-0.116	-0.070	28.609	0.006	0.006	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.814	-0.895	27.249	-0.294	-0.294	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.049	0.000	28.932	0.019	0.019	0.000	0.000	0.000	0.000
46	A	47	PHE	0	-0.045	-0.041	23.407	0.007	0.007	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.966	-0.984	25.539	-0.669	-0.669	0.000	0.000	0.000	0.000
48	A	49	PHE	0	-0.002	0.004	20.840	-0.073	-0.073	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.055	-0.022	19.071	0.042	0.042	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.009	0.015	20.737	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.018	0.019	23.602	0.063	0.063	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.034	0.030	26.207	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.071	-0.059	28.181	0.001	0.001	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.004	-0.016	24.303	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	56	TYR	0	-0.009	0.003	24.410	0.107	0.107	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.834	-0.924	22.189	-0.506	-0.506	0.000	0.000	0.000	0.000
57	A	58	TYR	0	-0.020	-0.048	18.952	0.081	0.081	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.046	-0.011	19.389	-0.072	-0.072	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.018	0.001	11.611	-0.136	-0.136	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.008	0.021	14.499	0.119	0.119	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.013	0.000	12.680	-0.114	-0.114	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.939	-0.970	12.706	0.481	0.481	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.118	-0.078	8.468	0.549	0.549	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.912	-0.933	11.595	-0.588	-0.588	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.054	-0.038	14.594	-0.137	-0.137	0.000	0.000	0.000	0.000
66	A	67	TYR	0	0.019	-0.003	16.466	0.080	0.080	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.017	-0.017	19.401	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.046	0.033	22.687	0.041	0.041	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.028	-0.006	23.754	0.026	0.026	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.051	-0.034	23.972	-0.041	-0.041	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.053	0.035	22.009	0.017	0.017	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.014	0.008	20.488	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.018	-0.016	20.109	-0.044	-0.044	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.732	-0.802	15.727	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.807	0.898	18.426	0.353	0.353	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.011	0.013	15.327	-0.070	-0.070	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.021	-0.010	17.392	0.131	0.131	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.012	0.002	19.131	-0.154	-0.154	0.000	0.000	0.000	0.000
79	A	80	ASN	0	0.017	-0.013	21.150	0.073	0.073	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.024	0.004	24.276	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.941	-0.961	25.193	-0.785	-0.785	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.855	-0.917	19.825	-1.524	-1.524	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.867	-0.913	19.614	-1.318	-1.318	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.056	-0.040	13.609	0.048	0.048	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.011	-0.005	17.820	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.026	0.004	16.317	0.004	0.004	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.031	-0.015	13.149	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.008	0.014	16.423	0.057	0.057	0.000	0.000	0.000	0.000
89	A	90	THR	0	0.005	-0.046	18.234	0.045	0.045	0.000	0.000	0.000	0.000
90	A	91	HIS	1	0.844	0.917	20.308	0.181	0.181	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.047	-0.023	19.045	0.098	0.098	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.011	-0.010	21.308	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.022	0.005	23.924	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.058	-0.038	26.407	0.045	0.045	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.009	-0.020	28.981	0.029	0.029	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.932	-0.960	27.800	-0.102	-0.102	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.880	-0.912	28.303	-0.146	-0.146	0.000	0.000	0.000	0.000
98	A	99	PHE	0	-0.038	-0.016	22.637	0.026	0.026	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.027	-0.009	21.294	0.010	0.010	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.043	0.019	19.537	-0.043	-0.043	0.000	0.000	0.000	0.000
101	A	103	SER	0	-0.028	-0.023	14.532	-0.099	-0.099	0.000	0.000	0.000	0.000
102	A	104	SER	0	0.030	0.014	11.776	0.010	0.010	0.000	0.000	0.000	0.000
103	A	105	SER	-1	-0.910	-0.928	9.703	-0.272	-0.272	0.000	0.000	0.000	0.000

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