FMO DATABASE

FMODB ID: VZQY1

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1070709.788836
FMO2-HF: Nuclear repulsion	1020749.243559
FMO2-HF: Total energy	-49960.545277
FMO2-MP2: Total energy	-50102.384772

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:5:GLY)

Summations of interaction energy for fragment #1(A:5: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.
123.558	127.292	0.952	-2.476	-2.208	-0.02

Interaction energy analysis for fragmet #1(A:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.896

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	7	GLN	0	0.008	0.013	3.511	-15.208	-14.086	-0.001	-0.619	-0.502	-0.002
53	A	57	MET	0	-0.054	-0.014	4.494	0.686	0.725	-0.001	-0.009	-0.028	0.000
102	A	106	LYS	1	0.905	0.962	2.600	27.239	28.482	0.356	-0.594	-1.004	-0.003
103	A	107	GLY	0	0.041	0.019	2.738	-14.273	-13.048	0.594	-1.174	-0.644	-0.014
104	A	108	GLU	-1	-0.959	-0.985	5.034	-29.216	-29.236	-0.001	-0.003	0.024	0.000
122	A	126	TRP	0	-0.030	-0.029	3.689	-12.800	-12.675	0.005	-0.077	-0.054	-0.001
4	A	8	GLY	0	0.039	0.022	5.945	6.885	6.885	0.000	0.000	0.000	0.000
5	A	9	THR	0	-0.030	-0.021	7.317	-2.530	-2.530	0.000	0.000	0.000	0.000
6	A	10	LYS	1	0.855	0.934	9.481	25.346	25.346	0.000	0.000	0.000	0.000
7	A	11	PHE	0	0.041	0.014	11.188	1.515	1.515	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.918	0.960	14.957	15.902	15.902	0.000	0.000	0.000	0.000
9	A	13	ILE	0	0.046	0.031	16.079	0.821	0.821	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.050	-0.044	18.777	-0.060	-0.060	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.016	-0.007	17.356	-0.378	-0.378	0.000	0.000	0.000	0.000
12	A	16	GLY	0	0.019	-0.009	19.658	0.743	0.743	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.001	0.016	18.109	0.374	0.374	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.015	0.017	18.762	-0.896	-0.896	0.000	0.000	0.000	0.000
15	A	19	THR	0	0.057	0.013	19.020	-0.105	-0.105	0.000	0.000	0.000	0.000
16	A	20	GLY	0	-0.032	-0.012	20.845	0.637	0.637	0.000	0.000	0.000	0.000
17	A	21	ALA	0	-0.019	-0.007	21.415	0.220	0.220	0.000	0.000	0.000	0.000
18	A	22	ILE	0	-0.042	-0.029	21.226	-0.667	-0.667	0.000	0.000	0.000	0.000
19	A	23	MET	0	-0.003	0.025	15.365	0.067	0.067	0.000	0.000	0.000	0.000
20	A	24	ASN	0	0.025	0.011	21.660	0.213	0.213	0.000	0.000	0.000	0.000
21	A	25	CYS	0	-0.087	-0.022	18.782	-1.108	-1.108	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.054	0.028	18.048	0.687	0.687	0.000	0.000	0.000	0.000
23	A	27	ASP	-1	-0.731	-0.835	16.101	-17.648	-17.648	0.000	0.000	0.000	0.000
24	A	28	ASN	0	0.018	-0.004	18.787	0.040	0.040	0.000	0.000	0.000	0.000
25	A	29	SER	0	-0.053	-0.050	17.816	0.658	0.658	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.005	-0.012	19.972	0.553	0.553	0.000	0.000	0.000	0.000
27	A	31	ALA	0	-0.015	-0.003	19.757	0.530	0.530	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.974	0.967	21.729	10.670	10.670	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.016	0.010	22.836	0.693	0.693	0.000	0.000	0.000	0.000
30	A	34	LEU	0	0.015	0.010	16.412	0.014	0.014	0.000	0.000	0.000	0.000
31	A	35	TYR	0	0.026	0.013	20.195	0.717	0.717	0.000	0.000	0.000	0.000
32	A	36	ILE	0	0.038	0.021	16.371	-0.751	-0.751	0.000	0.000	0.000	0.000
33	A	37	MET	0	-0.034	-0.014	17.329	0.693	0.693	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.021	0.002	15.430	0.602	0.602	0.000	0.000	0.000	0.000
35	A	39	VAL	0	0.020	0.013	12.449	-0.604	-0.604	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.895	0.946	7.843	29.271	29.271	0.000	0.000	0.000	0.000
37	A	41	GLY	0	0.076	0.038	9.834	-1.182	-1.182	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.037	-0.001	10.756	1.207	1.207	0.000	0.000	0.000	0.000
39	A	43	GLY	0	0.042	0.021	14.455	-0.210	-0.210	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.009	-0.025	17.134	0.043	0.043	0.000	0.000	0.000	0.000
41	A	45	ARG	1	0.884	0.952	20.210	11.546	11.546	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.077	0.034	23.730	-0.100	-0.100	0.000	0.000	0.000	0.000
43	A	47	ASN	0	0.030	0.001	26.798	0.011	0.011	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.945	0.990	21.412	13.301	13.301	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.036	0.027	22.346	-0.313	-0.313	0.000	0.000	0.000	0.000
46	A	50	PRO	0	-0.013	-0.008	16.945	-0.245	-0.245	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.004	-0.013	17.827	0.486	0.486	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.011	0.007	14.326	-0.587	-0.587	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.045	-0.020	14.789	-0.413	-0.413	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.026	0.010	14.088	-1.325	-1.325	0.000	0.000	0.000	0.000
51	A	55	GLY	0	0.013	0.000	11.259	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.845	-0.914	9.422	-28.103	-28.103	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.000	-0.013	9.026	0.962	0.962	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.031	-0.007	11.159	-1.986	-1.986	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.035	0.009	13.436	1.241	1.241	0.000	0.000	0.000	0.000
57	A	61	THR	0	-0.001	-0.011	16.313	0.306	0.306	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.053	0.027	19.519	0.236	0.236	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.904	0.978	21.576	13.129	13.129	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.941	0.964	24.880	11.445	11.445	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.013	0.001	24.451	-0.493	-0.493	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.930	0.981	23.424	13.018	13.018	0.000	0.000	0.000	0.000
63	A	67	PRO	0	0.033	0.012	24.173	-0.520	-0.520	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.812	-0.910	22.794	-12.233	-12.233	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.034	-0.027	18.738	-0.806	-0.806	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.828	0.921	20.592	11.025	11.025	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.927	0.953	23.340	10.818	10.818	0.000	0.000	0.000	0.000
68	A	72	LYS	1	0.940	0.990	18.290	15.041	15.041	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.014	0.006	15.197	-0.058	-0.058	0.000	0.000	0.000	0.000
70	A	74	MET	0	-0.031	-0.009	13.888	-0.129	-0.129	0.000	0.000	0.000	0.000
71	A	75	PRO	0	0.021	0.003	9.019	0.604	0.604	0.000	0.000	0.000	0.000
72	A	76	ALA	0	-0.010	0.007	11.159	1.119	1.119	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.010	0.018	7.227	-1.067	-1.067	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.015	0.006	11.212	1.853	1.853	0.000	0.000	0.000	0.000
75	A	79	VAL	0	0.052	0.003	13.625	-0.993	-0.993	0.000	0.000	0.000	0.000
76	A	80	ARG	1	0.832	0.870	15.735	14.854	14.854	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.016	-0.016	18.500	-1.072	-1.072	0.000	0.000	0.000	0.000
78	A	82	SER	0	0.023	0.031	20.645	0.415	0.415	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.896	0.941	22.625	12.558	12.558	0.000	0.000	0.000	0.000
80	A	84	ALA	0	0.033	0.027	23.188	-0.587	-0.587	0.000	0.000	0.000	0.000
81	A	85	TRP	0	-0.075	-0.044	19.948	0.124	0.124	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.946	0.991	23.009	12.147	12.147	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.850	0.917	20.140	14.201	14.201	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.908	0.942	20.278	15.641	15.641	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.836	-0.929	23.289	-12.949	-12.949	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.028	0.020	25.573	0.533	0.533	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.007	0.008	25.890	0.314	0.314	0.000	0.000	0.000	0.000
88	A	92	PHE	0	-0.001	-0.020	26.073	-0.558	-0.558	0.000	0.000	0.000	0.000
89	A	93	LEU	0	-0.007	0.007	22.324	0.287	0.287	0.000	0.000	0.000	0.000
90	A	94	TYR	0	-0.011	-0.015	24.471	-0.448	-0.448	0.000	0.000	0.000	0.000
91	A	95	PHE	0	-0.004	0.004	19.872	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.866	-0.937	25.398	-10.184	-10.184	0.000	0.000	0.000	0.000
93	A	97	ASP	-1	-0.802	-0.891	23.517	-13.192	-13.192	0.000	0.000	0.000	0.000
94	A	98	ASN	0	-0.051	-0.021	21.197	-0.168	-0.168	0.000	0.000	0.000	0.000
95	A	99	ALA	0	0.000	-0.010	19.750	0.414	0.414	0.000	0.000	0.000	0.000
96	A	100	GLY	0	0.046	0.012	15.820	-0.857	-0.857	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.008	0.012	12.232	1.123	1.123	0.000	0.000	0.000	0.000
98	A	102	ILE	0	-0.030	-0.028	13.026	-1.372	-1.372	0.000	0.000	0.000	0.000
99	A	103	ALA	0	0.032	0.008	8.460	0.077	0.077	0.000	0.000	0.000	0.000
100	A	104	ASN	0	0.016	0.008	6.691	-2.080	-2.080	0.000	0.000	0.000	0.000
101	A	105	PRO	0	0.032	-0.013	5.695	-2.538	-2.538	0.000	0.000	0.000	0.000
105	A	109	MET	0	-0.011	-0.004	8.036	0.027	0.027	0.000	0.000	0.000	0.000
106	A	110	LYS	1	0.924	0.971	11.467	18.254	18.254	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.016	0.004	14.236	1.025	1.025	0.000	0.000	0.000	0.000
108	A	112	SER	0	-0.003	-0.004	15.848	-0.888	-0.888	0.000	0.000	0.000	0.000
109	A	113	ALA	0	0.014	0.011	18.087	0.055	0.055	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.008	-0.020	15.798	-0.395	-0.395	0.000	0.000	0.000	0.000
111	A	115	THR	0	-0.015	0.005	19.044	0.601	0.601	0.000	0.000	0.000	0.000
112	A	116	GLY	0	0.039	0.019	21.662	-0.426	-0.426	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.008	0.014	22.122	-0.259	-0.259	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.016	-0.007	15.300	-0.402	-0.402	0.000	0.000	0.000	0.000
115	A	119	GLY	0	0.032	0.017	17.668	0.725	0.725	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.966	0.971	16.246	16.070	16.070	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.783	-0.858	15.037	-17.995	-17.995	0.000	0.000	0.000	0.000
118	A	122	CYS	0	-0.074	-0.034	11.953	-2.389	-2.389	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.001	0.009	11.605	-1.915	-1.915	0.000	0.000	0.000	0.000
120	A	124	ASP	-1	-0.855	-0.947	12.049	-22.022	-22.022	0.000	0.000	0.000	0.000
121	A	125	LEU	0	-0.044	-0.001	7.703	-1.414	-1.414	0.000	0.000	0.000	0.000
123	A	127	PRO	0	0.071	0.037	7.047	3.305	3.305	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.910	0.967	8.534	28.021	28.021	0.000	0.000	0.000	0.000
125	A	129	ILE	0	0.050	0.018	10.228	1.979	1.979	0.000	0.000	0.000	0.000
126	A	130	ALA	0	0.004	0.022	12.333	1.900	1.900	0.000	0.000	0.000	0.000
127	A	131	SER	0	-0.058	-0.032	13.187	1.268	1.268	0.000	0.000	0.000	0.000
128	A	132	ASN	0	-0.026	-0.010	14.737	0.693	0.693	0.000	0.000	0.000	0.000
129	A	133	SER	0	-0.015	-0.029	15.876	0.764	0.764	0.000	0.000	0.000	0.000
130	A	134	GLY	0	0.030	0.029	18.335	0.327	0.327	0.000	0.000	0.000	0.000
131	A	135	VAL	0	-0.009	-0.007	21.807	-0.073	-0.073	0.000	0.000	0.000	0.000
132	A	136	VAL	-1	-0.842	-0.907	17.950	-15.996	-15.996	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLY)