FMO DATABASE

FMODB ID: 9RL72

Calculation Name: 2F59-D-Xray547

Preferred Name:

Target Type:

Ligand Name: 5-nitro-6-ribityl-amino-2,4(1h,3h)-pyrimidinedione | calcium ion

Ligand 3-letter code: INI | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F59

Chain ID: D

ChEMBL ID:

UniProt ID: Q2YNC6

Base Structure: X-ray

Registration Date: 2025-10-05

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1255963.58612
FMO2-HF: Nuclear repulsion	1201688.490618
FMO2-HF: Total energy	-54275.095502
FMO2-MP2: Total energy	-54435.475959

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:11:ASP)

Summations of interaction energy for fragment #1(A:11:ASP)

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.
-28.474	-26.469	0.035	-1.066	-0.974	-0.003

Interaction energy analysis for fragmet #1(A:11:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.099 / q_NPA : -0.059

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	13	PRO	0	-0.035	-0.010	3.225	-8.935	-6.930	0.035	-1.066	-0.974	-0.003
4	A	14	HIS	0	0.000	0.014	5.539	0.640	0.640	0.000	0.000	0.000	0.000
5	A	15	LEU	0	-0.013	-0.013	7.563	0.947	0.947	0.000	0.000	0.000	0.000
6	A	16	LEU	0	0.013	0.018	11.253	0.156	0.156	0.000	0.000	0.000	0.000
7	A	17	ILE	0	-0.039	-0.024	14.560	0.196	0.196	0.000	0.000	0.000	0.000
8	A	18	VAL	0	-0.003	0.007	17.457	0.130	0.130	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.751	-0.847	20.634	-1.100	-1.100	0.000	0.000	0.000	0.000
10	A	20	ALA	0	0.003	-0.005	23.627	0.058	0.058	0.000	0.000	0.000	0.000
11	A	21	ARG	1	0.644	0.768	25.452	0.987	0.987	0.000	0.000	0.000	0.000
12	A	22	PHE	0	-0.029	-0.009	29.027	0.059	0.059	0.000	0.000	0.000	0.000
13	A	23	TYR	0	-0.023	-0.025	31.704	0.053	0.053	0.000	0.000	0.000	0.000
14	A	24	ASP	-1	-0.812	-0.898	30.484	-0.773	-0.773	0.000	0.000	0.000	0.000
15	A	25	ASP	-1	-0.874	-0.934	29.880	-0.645	-0.645	0.000	0.000	0.000	0.000
16	A	26	LEU	0	-0.040	-0.024	30.477	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	27	ALA	0	-0.008	0.003	26.880	-0.055	-0.055	0.000	0.000	0.000	0.000
18	A	28	ASP	-1	-0.796	-0.888	25.693	-0.995	-0.995	0.000	0.000	0.000	0.000
19	A	29	ALA	0	-0.046	-0.013	25.500	-0.055	-0.055	0.000	0.000	0.000	0.000
20	A	30	LEU	0	-0.024	0.000	24.505	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	31	LEU	0	-0.004	-0.005	19.931	-0.157	-0.157	0.000	0.000	0.000	0.000
22	A	32	ASP	-1	-0.865	-0.932	20.744	-1.151	-1.151	0.000	0.000	0.000	0.000
23	A	33	GLY	0	0.039	0.017	21.091	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	34	ALA	0	-0.063	-0.036	18.622	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	35	LYS	1	0.946	0.979	16.509	1.281	1.281	0.000	0.000	0.000	0.000
26	A	36	ALA	0	0.030	0.030	16.089	-0.200	-0.200	0.000	0.000	0.000	0.000
27	A	37	ALA	0	-0.013	-0.005	16.737	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	38	LEU	0	-0.055	-0.018	12.132	-0.213	-0.213	0.000	0.000	0.000	0.000
29	A	39	ASP	-1	-0.814	-0.896	12.048	-2.538	-2.538	0.000	0.000	0.000	0.000
30	A	40	GLU	-1	-1.039	-1.014	12.714	-1.248	-1.248	0.000	0.000	0.000	0.000
31	A	41	ALA	0	-0.057	-0.029	11.470	0.219	0.219	0.000	0.000	0.000	0.000
32	A	42	GLY	0	-0.053	-0.019	8.573	-0.459	-0.459	0.000	0.000	0.000	0.000
33	A	43	ALA	0	-0.062	-0.034	7.387	-1.576	-1.576	0.000	0.000	0.000	0.000
34	A	44	THR	0	-0.022	-0.026	6.833	0.462	0.462	0.000	0.000	0.000	0.000
35	A	45	TYR	0	-0.044	-0.071	8.942	-0.060	-0.060	0.000	0.000	0.000	0.000
36	A	46	ASP	-1	-0.795	-0.838	11.940	-3.039	-3.039	0.000	0.000	0.000	0.000
37	A	47	VAL	0	-0.046	-0.044	14.376	0.014	0.014	0.000	0.000	0.000	0.000
38	A	48	VAL	0	-0.011	-0.002	17.994	0.125	0.125	0.000	0.000	0.000	0.000
39	A	49	THR	0	-0.028	-0.022	20.838	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	50	VAL	0	-0.045	-0.018	24.262	0.040	0.040	0.000	0.000	0.000	0.000
41	A	51	PRO	0	-0.022	-0.009	26.854	0.016	0.016	0.000	0.000	0.000	0.000
42	A	52	GLY	0	0.039	0.007	30.392	0.030	0.030	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.017	-0.016	28.361	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	54	LEU	0	-0.029	-0.013	28.392	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	55	GLU	-1	-0.810	-0.913	27.983	-0.801	-0.801	0.000	0.000	0.000	0.000
46	A	56	ILE	0	-0.003	0.020	22.954	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	57	PRO	0	0.000	-0.001	23.392	-0.101	-0.101	0.000	0.000	0.000	0.000
48	A	58	ALA	0	0.012	0.007	23.922	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	59	THR	0	0.000	-0.016	21.185	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	60	ILE	0	-0.017	-0.010	18.430	-0.098	-0.098	0.000	0.000	0.000	0.000
51	A	61	SER	0	0.035	0.019	19.682	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	62	PHE	0	-0.056	-0.037	21.488	0.020	0.020	0.000	0.000	0.000	0.000
53	A	63	ALA	0	-0.026	-0.005	16.569	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	64	LEU	0	-0.009	0.006	16.293	-0.180	-0.180	0.000	0.000	0.000	0.000
55	A	65	ASP	-1	-0.850	-0.927	18.189	-1.111	-1.111	0.000	0.000	0.000	0.000
56	A	66	GLY	0	-0.061	-0.038	18.663	0.104	0.104	0.000	0.000	0.000	0.000
57	A	67	ALA	0	-0.033	-0.001	14.098	0.066	0.066	0.000	0.000	0.000	0.000
58	A	68	ASP	-1	-0.876	-0.933	15.770	-1.318	-1.318	0.000	0.000	0.000	0.000
59	A	69	ASN	0	-0.169	-0.081	18.214	0.242	0.242	0.000	0.000	0.000	0.000
60	A	70	GLY	0	-0.060	-0.030	16.115	0.134	0.134	0.000	0.000	0.000	0.000
61	A	71	GLY	0	-0.047	-0.021	15.908	0.024	0.024	0.000	0.000	0.000	0.000
62	A	72	THR	0	-0.087	-0.056	10.933	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	73	GLU	-1	-0.866	-0.923	9.387	-3.018	-3.018	0.000	0.000	0.000	0.000
64	A	74	TYR	0	-0.073	-0.077	9.454	-0.789	-0.789	0.000	0.000	0.000	0.000
65	A	75	ASP	-1	-0.876	-0.931	6.203	-10.932	-10.932	0.000	0.000	0.000	0.000
66	A	76	GLY	0	-0.006	-0.026	9.550	0.779	0.779	0.000	0.000	0.000	0.000
67	A	77	PHE	0	0.025	0.013	12.818	-0.235	-0.235	0.000	0.000	0.000	0.000
68	A	78	VAL	0	-0.015	-0.018	15.263	0.115	0.115	0.000	0.000	0.000	0.000
69	A	79	ALA	0	0.031	0.033	17.869	0.077	0.077	0.000	0.000	0.000	0.000
70	A	80	LEU	0	-0.008	-0.003	20.804	0.072	0.072	0.000	0.000	0.000	0.000
71	A	81	GLY	0	0.087	0.036	23.781	0.029	0.029	0.000	0.000	0.000	0.000
72	A	82	THR	0	-0.058	-0.033	27.526	0.018	0.018	0.000	0.000	0.000	0.000
73	A	83	VAL	0	-0.011	0.004	31.073	0.023	0.023	0.000	0.000	0.000	0.000
74	A	84	ILE	0	0.014	0.014	34.245	0.006	0.006	0.000	0.000	0.000	0.000
75	A	85	ARG	1	0.862	0.922	37.494	0.453	0.453	0.000	0.000	0.000	0.000
76	A	86	GLY	0	0.042	0.026	40.311	0.017	0.017	0.000	0.000	0.000	0.000
77	A	87	GLU	-1	-0.958	-0.987	43.413	-0.337	-0.337	0.000	0.000	0.000	0.000
78	A	88	THR	0	-0.057	-0.024	42.609	0.016	0.016	0.000	0.000	0.000	0.000
79	A	89	TYR	0	0.058	0.014	42.651	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	90	HIS	0	0.007	-0.002	37.368	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	91	PHE	0	0.007	0.019	37.795	-0.023	-0.023	0.000	0.000	0.000	0.000
82	A	92	ASP	-1	-0.845	-0.920	36.799	-0.523	-0.523	0.000	0.000	0.000	0.000
83	A	93	ILE	0	-0.018	-0.002	36.826	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	94	VAL	0	0.013	0.007	32.947	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	95	SER	0	0.007	0.014	32.453	-0.063	-0.063	0.000	0.000	0.000	0.000
86	A	96	ASN	0	-0.065	-0.036	31.918	-0.050	-0.050	0.000	0.000	0.000	0.000
87	A	97	GLU	-1	-0.876	-0.958	32.164	-0.672	-0.672	0.000	0.000	0.000	0.000
88	A	98	SER	0	-0.018	-0.009	28.313	-0.050	-0.050	0.000	0.000	0.000	0.000
89	A	99	CYS	0	-0.007	0.005	27.584	-0.086	-0.086	0.000	0.000	0.000	0.000
90	A	100	ARG	1	0.823	0.929	27.907	0.670	0.670	0.000	0.000	0.000	0.000
91	A	101	ALA	0	0.013	0.001	28.183	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	102	LEU	0	0.001	-0.003	22.392	-0.063	-0.063	0.000	0.000	0.000	0.000
93	A	103	THR	0	-0.058	-0.026	23.811	-0.083	-0.083	0.000	0.000	0.000	0.000
94	A	104	ASP	-1	-0.818	-0.899	25.198	-0.832	-0.832	0.000	0.000	0.000	0.000
95	A	105	LEU	0	0.026	0.016	21.600	-0.022	-0.022	0.000	0.000	0.000	0.000
96	A	106	SER	0	-0.072	-0.049	20.577	-0.088	-0.088	0.000	0.000	0.000	0.000
97	A	107	VAL	0	-0.049	-0.026	20.919	-0.056	-0.056	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-0.991	-1.003	23.079	-0.840	-0.840	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.880	-0.938	19.562	-1.212	-1.212	0.000	0.000	0.000	0.000
100	A	110	SER	0	-0.097	-0.035	18.809	-0.109	-0.109	0.000	0.000	0.000	0.000
101	A	111	ILE	0	-0.031	-0.003	15.594	-0.261	-0.261	0.000	0.000	0.000	0.000
102	A	112	ALA	0	-0.038	-0.024	13.693	0.182	0.182	0.000	0.000	0.000	0.000
103	A	113	ILE	0	0.021	0.011	15.662	-0.212	-0.212	0.000	0.000	0.000	0.000
104	A	114	GLY	0	-0.032	0.004	17.863	0.151	0.151	0.000	0.000	0.000	0.000
105	A	115	ASN	0	-0.014	-0.029	19.304	0.023	0.023	0.000	0.000	0.000	0.000
106	A	116	GLY	0	0.017	-0.010	22.929	0.073	0.073	0.000	0.000	0.000	0.000
107	A	117	ILE	0	-0.012	-0.002	24.308	0.040	0.040	0.000	0.000	0.000	0.000
108	A	118	LEU	0	-0.058	-0.031	27.248	0.037	0.037	0.000	0.000	0.000	0.000
109	A	119	THR	0	0.020	0.001	30.448	0.001	0.001	0.000	0.000	0.000	0.000
110	A	120	VAL	0	-0.043	-0.027	33.761	0.011	0.011	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.842	-0.925	36.575	-0.476	-0.476	0.000	0.000	0.000	0.000
112	A	122	ASN	0	-0.025	-0.014	39.232	0.009	0.009	0.000	0.000	0.000	0.000
113	A	123	GLU	-1	-0.784	-0.897	37.261	-0.523	-0.523	0.000	0.000	0.000	0.000
114	A	124	GLU	-1	-0.959	-0.963	37.218	-0.422	-0.422	0.000	0.000	0.000	0.000
115	A	125	GLN	0	0.019	-0.005	36.892	0.002	0.002	0.000	0.000	0.000	0.000
116	A	126	ALA	0	0.017	0.023	34.002	-0.038	-0.038	0.000	0.000	0.000	0.000
117	A	127	TRP	0	-0.007	-0.023	31.727	-0.063	-0.063	0.000	0.000	0.000	0.000
118	A	128	VAL	0	-0.033	-0.004	32.516	-0.032	-0.032	0.000	0.000	0.000	0.000
119	A	129	HIS	0	-0.076	-0.075	30.678	-0.027	-0.027	0.000	0.000	0.000	0.000
120	A	130	ALA	0	0.035	0.011	28.449	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	131	ARG	1	0.821	0.907	27.415	0.537	0.537	0.000	0.000	0.000	0.000
122	A	132	ARG	1	0.887	0.939	22.069	0.999	0.999	0.000	0.000	0.000	0.000
123	A	133	GLU	-1	-0.908	-0.955	26.473	-0.691	-0.691	0.000	0.000	0.000	0.000
124	A	134	ASP	-1	-0.894	-0.930	29.522	-0.515	-0.515	0.000	0.000	0.000	0.000
125	A	135	LYS	1	0.848	0.930	29.481	0.595	0.595	0.000	0.000	0.000	0.000
126	A	136	ASP	-1	-0.746	-0.844	23.088	-1.276	-1.276	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.880	0.952	24.442	0.964	0.964	0.000	0.000	0.000	0.000
128	A	138	GLY	0	0.058	0.025	22.849	-0.072	-0.072	0.000	0.000	0.000	0.000
129	A	139	GLY	0	0.060	0.026	19.992	-0.178	-0.178	0.000	0.000	0.000	0.000
130	A	140	PHE	0	-0.098	-0.056	19.727	-0.137	-0.137	0.000	0.000	0.000	0.000
131	A	141	ALA	0	-0.005	0.008	20.533	-0.080	-0.080	0.000	0.000	0.000	0.000
132	A	142	ALA	0	0.063	0.038	16.135	-0.163	-0.163	0.000	0.000	0.000	0.000
133	A	143	ARG	1	0.872	0.918	15.637	1.088	1.088	0.000	0.000	0.000	0.000
134	A	144	ALA	0	-0.023	0.004	16.783	-0.078	-0.078	0.000	0.000	0.000	0.000
135	A	145	ALA	0	0.048	0.022	14.735	-0.026	-0.026	0.000	0.000	0.000	0.000
136	A	146	LEU	0	0.020	0.010	10.632	-0.333	-0.333	0.000	0.000	0.000	0.000
137	A	147	THR	0	-0.063	-0.041	12.749	-0.054	-0.054	0.000	0.000	0.000	0.000
138	A	148	MET	0	-0.012	-0.011	15.135	0.129	0.129	0.000	0.000	0.000	0.000
139	A	149	ILE	0	0.016	0.021	8.919	0.025	0.025	0.000	0.000	0.000	0.000
140	A	150	GLY	0	-0.038	-0.016	11.273	-0.064	-0.064	0.000	0.000	0.000	0.000
141	A	151	LEU	0	-0.057	-0.043	12.216	0.328	0.328	0.000	0.000	0.000	0.000
142	A	152	ARG	1	0.964	0.993	12.113	3.182	3.182	0.000	0.000	0.000	0.000
143	A	153	LYS	1	0.981	0.992	5.442	7.946	7.946	0.000	0.000	0.000	0.000
144	A	154	LYS	1	0.811	0.920	11.687	1.371	1.371	0.000	0.000	0.000	0.000
145	A	155	PHE	0	-0.048	-0.061	14.258	0.341	0.341	0.000	0.000	0.000	0.000
146	A	156	GLY	0	-0.048	0.001	14.454	0.176	0.176	0.000	0.000	0.000	0.000
147	A	157	ALA	-1	-0.916	-0.939	14.827	-1.549	-1.549	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:ASP)