FMO DATABASE

FMODB ID: N7NNQ

Calculation Name: 3V0R-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 2,5,6-triaminopyrimidin-4-ol | sulfate ion | 8-aminooctanoic acid | unknown atom or ion

Ligand 3-letter code: 0FU | SO4 | 8AC | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3V0R

Chain ID: A

ChEMBL ID:

UniProt ID: P79085

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1043810.867963
FMO2-HF: Nuclear repulsion	992978.150265
FMO2-HF: Total energy	-50832.717697
FMO2-MP2: Total energy	-50978.275256

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:28:ALA)

Summations of interaction energy for fragment #1(A:28:ALA)

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.
-177.841	-193.023	47.539	-22.316	-10.042	-0.245

Interaction energy analysis for fragmet #1(A:28:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.627 / q_NPA : 0.741

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	30	CYS	-1	-0.664	-0.760	1.967	-114.254	-129.742	47.539	-22.165	-9.887	-0.244
4	A	31	PRO	0	-0.016	0.007	3.637	-1.339	-1.029	0.001	-0.150	-0.161	-0.001
6	A	33	THR	0	-0.009	0.004	4.907	-7.023	-7.027	-0.001	-0.001	0.006	0.000
5	A	32	VAL	0	-0.024	-0.024	4.932	6.597	6.597	0.000	0.000	0.000	0.000
7	A	34	THR	0	-0.023	-0.024	5.078	-0.553	-0.553	0.000	0.000	0.000	0.000
8	A	35	GLU	-1	-0.903	-0.972	7.513	-23.333	-23.333	0.000	0.000	0.000	0.000
9	A	36	GLY	0	0.075	0.042	10.085	-0.326	-0.326	0.000	0.000	0.000	0.000
10	A	37	ASP	-1	-0.893	-0.934	13.502	-16.805	-16.805	0.000	0.000	0.000	0.000
11	A	38	TYR	0	-0.052	-0.022	16.556	0.614	0.614	0.000	0.000	0.000	0.000
12	A	39	VAL	0	-0.019	0.008	10.424	0.205	0.205	0.000	0.000	0.000	0.000
13	A	40	TRP	0	-0.012	-0.001	13.868	0.306	0.306	0.000	0.000	0.000	0.000
14	A	41	LYS	1	0.875	0.930	11.067	22.942	22.942	0.000	0.000	0.000	0.000
15	A	42	ILE	0	-0.035	-0.019	13.351	1.915	1.915	0.000	0.000	0.000	0.000
16	A	43	SER	0	-0.019	-0.036	14.324	-1.397	-1.397	0.000	0.000	0.000	0.000
17	A	44	GLU	-1	-0.873	-0.915	16.231	-17.000	-17.000	0.000	0.000	0.000	0.000
18	A	45	PHE	0	-0.027	-0.008	18.913	0.776	0.776	0.000	0.000	0.000	0.000
19	A	46	TYR	0	0.029	0.003	20.821	0.223	0.223	0.000	0.000	0.000	0.000
20	A	47	GLY	0	0.034	0.015	24.454	0.118	0.118	0.000	0.000	0.000	0.000
21	A	48	ARG	1	0.804	0.897	27.478	8.998	8.998	0.000	0.000	0.000	0.000
22	A	49	LYS	1	0.951	0.981	28.248	11.180	11.180	0.000	0.000	0.000	0.000
23	A	50	PRO	0	-0.029	0.004	32.782	0.067	0.067	0.000	0.000	0.000	0.000
24	A	51	GLU	-1	-0.821	-0.918	36.378	-7.769	-7.769	0.000	0.000	0.000	0.000
25	A	52	GLY	0	0.025	0.018	33.926	0.130	0.130	0.000	0.000	0.000	0.000
26	A	53	THR	0	-0.067	-0.031	33.009	-0.285	-0.285	0.000	0.000	0.000	0.000
27	A	54	TYR	0	0.019	0.010	32.169	-0.335	-0.335	0.000	0.000	0.000	0.000
28	A	55	TYR	0	0.050	0.006	25.750	0.035	0.035	0.000	0.000	0.000	0.000
29	A	56	ASN	0	0.008	-0.007	32.050	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	57	SER	0	-0.012	-0.003	31.114	0.062	0.062	0.000	0.000	0.000	0.000
31	A	58	LEU	0	0.015	0.001	25.635	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	59	GLY	0	0.039	0.014	25.317	0.341	0.341	0.000	0.000	0.000	0.000
33	A	60	PHE	0	0.001	-0.001	19.847	-0.380	-0.380	0.000	0.000	0.000	0.000
34	A	61	ASN	0	0.037	0.039	19.101	1.206	1.206	0.000	0.000	0.000	0.000
35	A	62	ILE	0	0.005	-0.005	18.137	-0.986	-0.986	0.000	0.000	0.000	0.000
36	A	63	LYS	1	0.899	0.962	15.431	18.727	18.727	0.000	0.000	0.000	0.000
37	A	64	ALA	0	-0.018	-0.001	15.529	-1.267	-1.267	0.000	0.000	0.000	0.000
38	A	65	THR	0	-0.041	-0.043	11.279	-0.213	-0.213	0.000	0.000	0.000	0.000
39	A	66	ASN	0	0.013	0.006	13.408	-0.628	-0.628	0.000	0.000	0.000	0.000
40	A	67	GLY	0	-0.032	-0.020	15.361	0.971	0.971	0.000	0.000	0.000	0.000
41	A	68	GLY	0	-0.007	0.007	17.221	1.035	1.035	0.000	0.000	0.000	0.000
42	A	69	THR	0	-0.034	-0.041	19.446	-0.391	-0.391	0.000	0.000	0.000	0.000
43	A	70	LEU	0	-0.046	-0.002	20.457	0.357	0.357	0.000	0.000	0.000	0.000
44	A	71	ASP	-1	-0.840	-0.942	19.581	-17.213	-17.213	0.000	0.000	0.000	0.000
45	A	72	PHE	0	-0.026	-0.009	21.010	0.819	0.819	0.000	0.000	0.000	0.000
46	A	73	THR	0	0.009	-0.004	22.206	-0.452	-0.452	0.000	0.000	0.000	0.000
47	A	74	CYS	0	-0.107	-0.033	23.481	0.423	0.423	0.000	0.000	0.000	0.000
48	A	75	SER	0	-0.035	-0.032	25.162	-0.147	-0.147	0.000	0.000	0.000	0.000
49	A	76	ALA	0	0.048	0.025	27.844	0.270	0.270	0.000	0.000	0.000	0.000
50	A	77	GLN	0	-0.033	-0.027	30.909	0.019	0.019	0.000	0.000	0.000	0.000
51	A	78	ALA	0	-0.010	-0.007	33.974	0.189	0.189	0.000	0.000	0.000	0.000
52	A	79	ASP	-1	-0.916	-0.946	36.657	-7.970	-7.970	0.000	0.000	0.000	0.000
53	A	80	LYS	1	0.798	0.886	36.449	8.746	8.746	0.000	0.000	0.000	0.000
54	A	81	LEU	0	-0.050	-0.002	30.880	0.083	0.083	0.000	0.000	0.000	0.000
55	A	82	GLU	-1	-0.881	-0.949	33.770	-8.622	-8.622	0.000	0.000	0.000	0.000
56	A	83	ASP	-1	-0.795	-0.874	29.656	-10.883	-10.883	0.000	0.000	0.000	0.000
57	A	84	HIS	1	0.831	0.919	29.461	10.451	10.451	0.000	0.000	0.000	0.000
58	A	85	LYS	1	0.946	0.993	30.580	9.200	9.200	0.000	0.000	0.000	0.000
59	A	86	TRP	0	0.001	0.006	26.773	-0.333	-0.333	0.000	0.000	0.000	0.000
60	A	87	TYR	0	0.003	0.000	30.049	0.533	0.533	0.000	0.000	0.000	0.000
61	A	88	SER	0	0.078	0.039	29.614	-0.493	-0.493	0.000	0.000	0.000	0.000
62	A	90	GLY	0	0.072	0.036	28.166	-0.185	-0.185	0.000	0.000	0.000	0.000
63	A	91	GLU	-1	-0.943	-0.964	30.995	-9.571	-9.571	0.000	0.000	0.000	0.000
64	A	92	ASN	0	-0.035	-0.023	33.138	0.401	0.401	0.000	0.000	0.000	0.000
65	A	93	SER	0	-0.052	-0.010	28.038	-0.181	-0.181	0.000	0.000	0.000	0.000
66	A	94	PHE	0	0.015	0.009	24.386	0.221	0.221	0.000	0.000	0.000	0.000
67	A	95	MET	0	-0.036	-0.004	22.725	-0.233	-0.233	0.000	0.000	0.000	0.000
68	A	96	ASP	-1	-0.807	-0.894	27.021	-10.045	-10.045	0.000	0.000	0.000	0.000
69	A	97	PHE	0	-0.028	-0.037	24.605	-0.665	-0.665	0.000	0.000	0.000	0.000
70	A	98	SER	0	-0.031	-0.044	25.457	0.631	0.631	0.000	0.000	0.000	0.000
71	A	99	PHE	0	0.026	0.002	22.051	-0.575	-0.575	0.000	0.000	0.000	0.000
72	A	100	ASP	-1	-0.803	-0.895	25.083	-10.932	-10.932	0.000	0.000	0.000	0.000
73	A	101	SER	0	-0.064	-0.073	25.128	-0.498	-0.498	0.000	0.000	0.000	0.000
74	A	102	ASP	-1	-0.864	-0.906	26.362	-12.000	-12.000	0.000	0.000	0.000	0.000
75	A	103	ARG	1	0.802	0.871	22.540	12.221	12.221	0.000	0.000	0.000	0.000
76	A	104	SER	0	-0.019	-0.001	20.949	-0.677	-0.677	0.000	0.000	0.000	0.000
77	A	105	GLY	0	0.004	0.011	20.610	-0.933	-0.933	0.000	0.000	0.000	0.000
78	A	106	LEU	0	-0.013	-0.005	18.555	0.747	0.747	0.000	0.000	0.000	0.000
79	A	107	LEU	0	-0.033	-0.013	20.751	-0.469	-0.469	0.000	0.000	0.000	0.000
80	A	108	LEU	0	0.030	0.002	19.370	0.419	0.419	0.000	0.000	0.000	0.000
81	A	109	LYS	1	0.842	0.916	23.055	10.402	10.402	0.000	0.000	0.000	0.000
82	A	110	GLN	0	0.072	0.034	23.953	-0.249	-0.249	0.000	0.000	0.000	0.000
83	A	111	LYS	1	0.909	0.962	26.416	9.275	9.275	0.000	0.000	0.000	0.000
84	A	112	VAL	0	-0.014	-0.004	26.406	0.088	0.088	0.000	0.000	0.000	0.000
85	A	113	SER	0	-0.005	-0.012	29.712	0.142	0.142	0.000	0.000	0.000	0.000
86	A	114	ASP	-1	-0.835	-0.916	33.037	-8.931	-8.931	0.000	0.000	0.000	0.000
87	A	115	ASP	-1	-0.897	-0.930	33.567	-8.840	-8.840	0.000	0.000	0.000	0.000
88	A	116	ILE	0	-0.007	0.006	27.658	-0.242	-0.242	0.000	0.000	0.000	0.000
89	A	117	THR	0	-0.009	-0.013	27.789	0.153	0.153	0.000	0.000	0.000	0.000
90	A	118	TYR	0	0.007	0.012	22.666	-0.133	-0.133	0.000	0.000	0.000	0.000
91	A	119	VAL	0	0.003	-0.009	22.911	0.385	0.385	0.000	0.000	0.000	0.000
92	A	120	ALA	0	0.044	0.027	17.924	-0.570	-0.570	0.000	0.000	0.000	0.000
93	A	121	THR	0	-0.013	-0.013	18.250	0.460	0.460	0.000	0.000	0.000	0.000
94	A	122	ALA	0	0.034	0.025	15.320	-1.234	-1.234	0.000	0.000	0.000	0.000
95	A	123	THR	0	-0.019	0.000	15.842	1.424	1.424	0.000	0.000	0.000	0.000
96	A	124	LEU	0	0.012	0.011	15.786	-1.359	-1.359	0.000	0.000	0.000	0.000
97	A	125	PRO	0	0.005	0.007	13.736	1.263	1.263	0.000	0.000	0.000	0.000
98	A	126	ASN	0	-0.038	-0.029	17.063	0.409	0.409	0.000	0.000	0.000	0.000
99	A	127	TYR	0	0.010	0.011	20.136	0.350	0.350	0.000	0.000	0.000	0.000
100	A	128	CYS	0	-0.076	-0.030	22.672	0.152	0.152	0.000	0.000	0.000	0.000
101	A	129	ARG	1	0.966	0.977	26.443	11.236	11.236	0.000	0.000	0.000	0.000
102	A	130	ALA	0	0.029	0.012	29.134	0.056	0.056	0.000	0.000	0.000	0.000
103	A	131	GLY	0	-0.024	-0.016	32.391	-0.178	-0.178	0.000	0.000	0.000	0.000
104	A	132	GLY	0	-0.011	-0.001	33.488	0.096	0.096	0.000	0.000	0.000	0.000
105	A	133	ASN	0	-0.049	-0.023	36.878	0.455	0.455	0.000	0.000	0.000	0.000
106	A	134	GLY	0	0.061	0.015	38.830	0.044	0.044	0.000	0.000	0.000	0.000
107	A	135	PRO	0	-0.035	-0.021	39.001	-0.177	-0.177	0.000	0.000	0.000	0.000
108	A	136	LYS	1	0.822	0.903	37.423	8.008	8.008	0.000	0.000	0.000	0.000
109	A	137	ASP	-1	-0.749	-0.834	35.592	-9.372	-9.372	0.000	0.000	0.000	0.000
110	A	138	PHE	0	-0.026	-0.016	30.160	-0.102	-0.102	0.000	0.000	0.000	0.000
111	A	139	VAL	0	-0.005	0.003	28.670	0.031	0.031	0.000	0.000	0.000	0.000
112	A	141	GLN	0	0.025	0.009	21.600	0.634	0.634	0.000	0.000	0.000	0.000
113	A	142	GLY	0	0.022	0.008	18.541	-0.186	-0.186	0.000	0.000	0.000	0.000
114	A	143	VAL	0	-0.072	-0.044	16.010	0.343	0.343	0.000	0.000	0.000	0.000
115	A	144	ALA	0	-0.025	-0.017	11.516	-0.977	-0.977	0.000	0.000	0.000	0.000
116	A	145	ASP	-1	-0.811	-0.880	10.205	-24.043	-24.043	0.000	0.000	0.000	0.000
117	A	146	ALA	0	-0.047	-0.022	11.200	-1.516	-1.516	0.000	0.000	0.000	0.000
118	A	147	TYR	0	0.022	0.002	8.144	-0.249	-0.249	0.000	0.000	0.000	0.000
119	A	148	ILE	0	-0.038	-0.004	11.765	0.577	0.577	0.000	0.000	0.000	0.000
120	A	149	THR	0	0.023	-0.004	13.025	-1.074	-1.074	0.000	0.000	0.000	0.000
121	A	150	LEU	0	-0.052	-0.021	15.339	0.853	0.853	0.000	0.000	0.000	0.000
122	A	151	VAL	0	0.012	0.001	18.566	-0.188	-0.188	0.000	0.000	0.000	0.000
123	A	152	THR	0	-0.037	-0.024	21.005	0.234	0.234	0.000	0.000	0.000	0.000
124	A	153	LEU	0	0.008	0.005	24.749	-0.061	-0.061	0.000	0.000	0.000	0.000
125	A	154	PRO	0	-0.004	-0.007	27.148	0.171	0.171	0.000	0.000	0.000	0.000
126	A	155	LYS	1	0.811	0.910	29.954	9.071	9.071	0.000	0.000	0.000	0.000
127	A	156	SER	0	-0.058	-0.052	33.228	0.181	0.181	0.000	0.000	0.000	0.000
128	A	157	SER	-1	-0.930	-0.952	32.357	-9.302	-9.302	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:ALA)