FMO DATABASE

FMODB ID: Q5VNY

Calculation Name: 5IT7-A-Other547

Preferred Name:

Target Type:

Ligand Name: phosphomethylphosphonic acid guanylate ester | (2s)-1-amino-n,n,n-trimethyl-1-oxobutan-2-aminium

Ligand 3-letter code: GCP | 6EM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5IT7

Chain ID: A

ChEMBL ID:

UniProt ID: P38665

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-570435.613354
FMO2-HF: Nuclear repulsion	533092.821389
FMO2-HF: Total energy	-37342.791965
FMO2-MP2: Total energy	-37454.047082

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:3:VAL)

Summations of interaction energy for fragment #1(A:3:VAL)

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.
185.377	190.978	4.145	-4.598	-5.149	-0.041

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.922

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	5	SER	0	0.071	0.021	2.929	-1.004	1.611	0.220	-1.343	-1.492	-0.010
4	A	6	GLY	0	-0.015	0.000	5.155	2.328	2.425	-0.001	-0.003	-0.093	0.000
10	A	12	ASN	0	-0.015	-0.019	2.981	5.597	6.308	0.025	-0.166	-0.570	0.000
14	A	16	LYS	1	0.924	0.951	3.140	40.009	40.324	0.028	-0.069	-0.274	0.000
17	A	19	GLN	0	-0.050	-0.039	2.278	-12.766	-10.903	3.873	-3.017	-2.720	-0.031
5	A	7	ILE	0	0.039	0.031	7.587	2.599	2.599	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.030	0.005	10.180	-2.136	-2.136	0.000	0.000	0.000	0.000
7	A	9	VAL	0	0.034	0.016	12.422	0.172	0.172	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.053	0.021	10.832	-1.185	-1.185	0.000	0.000	0.000	0.000
9	A	11	LEU	0	0.011	0.006	8.527	-0.607	-0.607	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.919	0.991	5.440	17.350	17.350	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.010	0.002	7.738	-1.402	-1.402	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.998	0.991	7.132	19.533	19.533	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.006	-0.005	6.180	3.695	3.695	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.072	0.036	6.586	-5.060	-5.060	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.004	0.016	5.609	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	21	THR	0	0.079	0.020	9.156	0.386	0.386	0.000	0.000	0.000	0.000
20	A	22	PRO	0	-0.040	0.011	10.301	1.928	1.928	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.068	0.032	13.374	-0.628	-0.628	0.000	0.000	0.000	0.000
22	A	24	PRO	0	-0.010	-0.007	15.687	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.990	0.992	16.991	17.545	17.545	0.000	0.000	0.000	0.000
24	A	26	ILE	0	0.064	0.018	19.778	-0.125	-0.125	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.027	-0.012	22.229	0.070	0.070	0.000	0.000	0.000	0.000
26	A	28	TYR	0	-0.007	-0.016	15.470	0.270	0.270	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.965	1.002	20.069	12.321	12.321	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.970	0.966	21.910	11.448	11.448	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.028	0.037	23.894	0.533	0.533	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.004	0.006	24.705	-0.142	-0.142	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.032	0.017	26.288	0.279	0.279	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.016	0.002	29.873	0.424	0.424	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.115	0.056	31.540	0.235	0.235	0.000	0.000	0.000	0.000
34	A	36	ARG	1	1.008	1.019	35.044	8.222	8.222	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.057	-0.058	32.969	0.186	0.186	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.011	-0.023	33.153	0.179	0.179	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.061	0.035	35.946	0.119	0.119	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.016	0.003	39.228	0.153	0.153	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.912	0.943	32.526	9.424	9.424	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.002	0.014	39.429	0.041	0.041	0.000	0.000	0.000	0.000
41	A	43	ILE	0	0.085	0.049	41.113	0.108	0.108	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.107	-0.057	42.216	0.132	0.132	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.846	0.919	37.270	8.338	8.338	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.914	-0.936	43.608	-6.723	-6.723	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.034	-0.004	46.746	0.187	0.187	0.000	0.000	0.000	0.000
46	A	48	ALA	0	0.023	0.001	46.240	-0.146	-0.146	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.022	-0.009	47.895	0.110	0.110	0.000	0.000	0.000	0.000
48	A	50	LEU	0	0.026	0.013	43.469	-0.097	-0.097	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.048	0.020	44.213	0.167	0.167	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.017	-0.017	46.087	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	53	TYR	0	-0.052	-0.033	40.079	0.026	0.026	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.778	-0.885	40.738	-7.877	-7.877	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.959	0.987	44.111	6.431	6.431	0.000	0.000	0.000	0.000
54	A	56	ARG	1	1.021	1.000	46.657	6.684	6.684	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.044	-0.009	40.360	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	58	ILE	0	0.041	0.020	42.783	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.949	-0.959	44.821	-6.336	-6.336	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.067	-0.028	43.453	0.028	0.028	0.000	0.000	0.000	0.000
59	A	61	ILE	0	-0.026	-0.025	40.288	0.007	0.007	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.919	0.953	43.797	6.788	6.788	0.000	0.000	0.000	0.000
61	A	63	ASN	0	0.019	0.035	46.908	0.127	0.127	0.000	0.000	0.000	0.000
62	A	64	ALA	0	0.008	0.002	45.851	-0.087	-0.087	0.000	0.000	0.000	0.000
63	A	65	GLY	0	-0.032	-0.004	43.217	-0.099	-0.099	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.691	-0.856	37.171	-8.856	-8.856	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.959	0.993	37.569	8.347	8.347	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.940	0.948	38.580	6.944	6.944	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.091	0.048	39.682	0.045	0.045	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.865	0.910	32.925	9.301	9.301	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.949	0.973	37.292	7.499	7.499	0.000	0.000	0.000	0.000
70	A	72	VAL	0	-0.018	-0.007	39.229	0.067	0.067	0.000	0.000	0.000	0.000
71	A	73	ALA	0	0.046	0.021	37.595	0.041	0.041	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.945	0.967	34.500	8.926	8.926	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.933	0.972	37.142	7.451	7.451	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.891	0.937	40.343	7.487	7.487	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.023	0.036	35.467	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.053	0.022	35.603	0.149	0.149	0.000	0.000	0.000	0.000
77	A	79	THR	0	-0.014	-0.009	30.151	0.045	0.045	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.058	0.011	29.796	0.149	0.149	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.051	0.024	28.243	0.008	0.008	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.953	0.972	29.069	9.967	9.967	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.007	0.001	31.851	0.186	0.186	0.000	0.000	0.000	0.000
82	A	84	LYS	0	-0.011	0.015	28.676	0.319	0.319	0.000	0.000	0.000	0.000
83	A	85	ALA	0	0.087	0.047	29.896	0.207	0.207	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.792	0.889	31.671	8.726	8.726	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.018	-0.027	35.207	0.237	0.237	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.957	-0.965	29.860	-10.575	-10.575	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.755	-0.866	34.330	-8.577	-8.577	0.000	0.000	0.000	0.000
88	A	90	MET	0	-0.079	-0.045	36.001	0.328	0.328	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.016	-0.009	36.687	0.418	0.418	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.921	-0.920	33.550	-9.314	-9.314	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.034	-0.022	38.207	0.198	0.198	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.085	-0.046	41.400	0.287	0.287	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.052	-0.075	39.413	0.139	0.139	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.048	0.039	39.757	0.055	0.055	0.000	0.000	0.000	0.000
95	A	97	SER	0	-0.027	0.000	41.788	0.132	0.132	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.868	0.929	45.175	7.042	7.042	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.857	0.941	44.143	7.230	7.230	0.000	0.000	0.000	0.000
98	A	100	HIS	-1	-0.835	-0.902	41.809	-6.870	-6.870	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL)