FMO DATABASE

FMODB ID: 87JMY

Calculation Name: 2VI5-A-Xray547

Preferred Name: 6,7-dimethyl-8-ribityllumazine synthase

Target Type: SINGLE PROTEIN

Ligand Name: 1-deoxy-1-{[(5s)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-d-ribitol | phosphate ion | potassium ion

Ligand 3-letter code: Y19 | PO4 | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VI5

Chain ID: A

ChEMBL ID: CHEMBL1075177

UniProt ID: P9WHE9

Base Structure: X-ray

Registration Date: 2025-10-04

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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1228891.543289
FMO2-HF: Nuclear repulsion	1174898.937484
FMO2-HF: Total energy	-53992.605806
FMO2-MP2: Total energy	-54151.093458

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:PRO)

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

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.
-188.366	-176.753	13.125	-11.71	-13.027	-0.128

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.881

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	LEU	0	-0.007	0.015	3.100	6.408	10.148	-0.011	-1.769	-1.960	-0.005
4	A	14	ASP	-1	-0.856	-0.934	1.909	-104.185	-100.368	8.145	-6.418	-5.543	-0.082
5	A	15	ALA	0	0.022	-0.009	3.039	-19.082	-17.415	0.153	-1.012	-0.808	-0.010
134	A	144	VAL	0	0.002	0.001	4.691	-3.697	-3.640	-0.001	-0.004	-0.052	0.000
135	A	145	ALA	0	-0.007	0.004	4.738	-6.609	-6.526	-0.001	-0.004	-0.078	0.000
137	A	147	LEU	0	0.031	0.016	4.716	-0.892	-0.786	-0.001	-0.010	-0.095	0.000
138	A	148	ALA	0	-0.007	-0.006	2.683	-8.834	-7.498	0.641	-0.696	-1.281	-0.003
139	A	149	THR	0	-0.022	-0.013	3.405	0.950	1.260	0.026	0.035	-0.371	-0.002
141	A	151	LEU	0	-0.032	-0.015	1.988	-0.771	-0.429	4.175	-1.822	-2.694	-0.026
142	A	152	THR	0	-0.020	-0.017	4.093	3.421	3.576	-0.001	-0.010	-0.145	0.000
6	A	16	SER	0	0.047	0.026	5.499	3.727	3.727	0.000	0.000	0.000	0.000
7	A	17	GLY	0	-0.017	0.002	8.812	2.761	2.761	0.000	0.000	0.000	0.000
8	A	18	VAL	0	-0.080	-0.031	6.192	1.064	1.064	0.000	0.000	0.000	0.000
9	A	19	ARG	1	0.898	0.933	9.491	20.501	20.501	0.000	0.000	0.000	0.000
10	A	20	LEU	0	0.011	0.005	10.139	0.177	0.177	0.000	0.000	0.000	0.000
11	A	21	ALA	0	0.018	0.015	12.295	1.391	1.391	0.000	0.000	0.000	0.000
12	A	22	ILE	0	-0.024	-0.021	13.928	-0.932	-0.932	0.000	0.000	0.000	0.000
13	A	23	VAL	0	0.008	0.013	16.570	0.987	0.987	0.000	0.000	0.000	0.000
14	A	24	ALA	0	0.028	0.009	19.591	-0.262	-0.262	0.000	0.000	0.000	0.000
15	A	25	SER	0	-0.036	-0.011	21.408	0.655	0.655	0.000	0.000	0.000	0.000
16	A	26	SER	0	0.001	-0.027	24.719	-0.296	-0.296	0.000	0.000	0.000	0.000
17	A	27	TRP	0	-0.017	-0.003	27.523	0.365	0.365	0.000	0.000	0.000	0.000
18	A	28	HIS	0	-0.006	-0.018	27.548	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	29	GLY	0	0.059	0.038	27.279	-0.333	-0.333	0.000	0.000	0.000	0.000
20	A	30	LYS	1	0.983	0.993	26.103	10.043	10.043	0.000	0.000	0.000	0.000
21	A	31	ILE	0	-0.003	0.001	23.412	-0.318	-0.318	0.000	0.000	0.000	0.000
22	A	32	CYS	0	-0.039	-0.003	22.378	-0.699	-0.699	0.000	0.000	0.000	0.000
23	A	33	ASP	-1	-0.843	-0.918	21.427	-12.693	-12.693	0.000	0.000	0.000	0.000
24	A	34	ALA	0	-0.023	0.001	21.354	-0.488	-0.488	0.000	0.000	0.000	0.000
25	A	35	LEU	0	0.032	0.027	17.904	-0.793	-0.793	0.000	0.000	0.000	0.000
26	A	36	LEU	0	0.000	-0.007	16.645	-1.202	-1.202	0.000	0.000	0.000	0.000
27	A	37	ASP	-1	-0.851	-0.899	17.392	-16.320	-16.320	0.000	0.000	0.000	0.000
28	A	38	GLY	0	0.057	0.033	15.673	-0.776	-0.776	0.000	0.000	0.000	0.000
29	A	39	ALA	0	-0.039	-0.025	12.718	-1.622	-1.622	0.000	0.000	0.000	0.000
30	A	40	ARG	1	0.950	0.966	12.614	14.104	14.104	0.000	0.000	0.000	0.000
31	A	41	LYS	1	0.826	0.895	14.175	15.387	15.387	0.000	0.000	0.000	0.000
32	A	42	VAL	0	-0.025	-0.003	7.873	-1.227	-1.227	0.000	0.000	0.000	0.000
33	A	43	ALA	0	-0.005	0.004	9.388	-3.111	-3.111	0.000	0.000	0.000	0.000
34	A	44	ALA	0	0.058	0.035	10.495	-1.801	-1.801	0.000	0.000	0.000	0.000
35	A	45	GLY	0	-0.033	-0.006	10.624	-0.242	-0.242	0.000	0.000	0.000	0.000
36	A	46	CYS	0	-0.080	-0.042	6.147	-5.009	-5.009	0.000	0.000	0.000	0.000
37	A	47	GLY	0	-0.010	-0.010	7.727	-1.849	-1.849	0.000	0.000	0.000	0.000
38	A	48	LEU	0	-0.097	-0.044	8.579	1.313	1.313	0.000	0.000	0.000	0.000
39	A	49	ASP	-1	-0.871	-0.952	12.041	-19.451	-19.451	0.000	0.000	0.000	0.000
40	A	50	ASP	-1	-1.012	-0.998	15.549	-14.739	-14.739	0.000	0.000	0.000	0.000
41	A	51	PRO	0	-0.036	-0.003	13.665	-0.274	-0.274	0.000	0.000	0.000	0.000
42	A	52	THR	0	0.007	-0.030	15.588	1.244	1.244	0.000	0.000	0.000	0.000
43	A	53	VAL	0	-0.062	-0.019	17.983	-0.168	-0.168	0.000	0.000	0.000	0.000
44	A	54	VAL	0	0.008	0.004	19.955	0.802	0.802	0.000	0.000	0.000	0.000
45	A	55	ARG	1	0.754	0.860	22.217	12.301	12.301	0.000	0.000	0.000	0.000
46	A	56	VAL	0	0.020	0.015	24.490	0.338	0.338	0.000	0.000	0.000	0.000
47	A	57	LEU	0	0.037	0.025	26.907	-0.042	-0.042	0.000	0.000	0.000	0.000
48	A	58	GLY	0	0.029	0.008	28.658	-0.119	-0.119	0.000	0.000	0.000	0.000
49	A	59	ALA	0	0.039	-0.005	25.164	-0.297	-0.297	0.000	0.000	0.000	0.000
50	A	60	ILE	0	0.001	0.002	25.558	-0.358	-0.358	0.000	0.000	0.000	0.000
51	A	61	GLU	-1	-0.834	-0.930	27.704	-10.364	-10.364	0.000	0.000	0.000	0.000
52	A	62	ILE	0	-0.013	0.012	20.906	-0.193	-0.193	0.000	0.000	0.000	0.000
53	A	63	PRO	0	-0.009	-0.005	22.352	-0.398	-0.398	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.032	0.017	23.289	-0.277	-0.277	0.000	0.000	0.000	0.000
55	A	65	VAL	0	0.025	0.014	22.460	-0.065	-0.065	0.000	0.000	0.000	0.000
56	A	66	ALA	0	0.002	-0.006	19.097	-0.418	-0.418	0.000	0.000	0.000	0.000
57	A	67	GLN	0	-0.020	-0.015	19.970	-0.323	-0.323	0.000	0.000	0.000	0.000
58	A	68	GLU	-1	-0.909	-0.957	22.177	-12.361	-12.361	0.000	0.000	0.000	0.000
59	A	69	LEU	0	-0.003	-0.002	18.575	-0.235	-0.235	0.000	0.000	0.000	0.000
60	A	70	ALA	0	0.020	0.004	17.596	-0.618	-0.618	0.000	0.000	0.000	0.000
61	A	71	ARG	1	0.867	0.950	18.634	12.235	12.235	0.000	0.000	0.000	0.000
62	A	72	ASN	0	-0.050	-0.032	19.369	0.140	0.140	0.000	0.000	0.000	0.000
63	A	73	HIS	0	-0.036	0.009	14.831	-0.347	-0.347	0.000	0.000	0.000	0.000
64	A	74	ASP	-1	-0.809	-0.886	11.005	-22.957	-22.957	0.000	0.000	0.000	0.000
65	A	75	ALA	0	-0.006	-0.021	9.725	-1.735	-1.735	0.000	0.000	0.000	0.000
66	A	76	VAL	0	-0.024	0.003	11.862	0.979	0.979	0.000	0.000	0.000	0.000
67	A	77	VAL	0	-0.019	0.000	11.505	-0.698	-0.698	0.000	0.000	0.000	0.000
68	A	78	ALA	0	0.006	0.009	14.179	1.154	1.154	0.000	0.000	0.000	0.000
69	A	79	LEU	0	0.002	0.006	15.354	-0.236	-0.236	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.056	-0.002	19.038	0.695	0.695	0.000	0.000	0.000	0.000
71	A	81	VAL	0	0.001	0.008	22.150	-0.341	-0.341	0.000	0.000	0.000	0.000
72	A	82	VAL	0	-0.002	0.006	24.926	0.514	0.514	0.000	0.000	0.000	0.000
73	A	83	ILE	0	0.021	0.015	27.264	-0.184	-0.184	0.000	0.000	0.000	0.000
74	A	84	ARG	1	0.786	0.873	29.913	9.712	9.712	0.000	0.000	0.000	0.000
75	A	85	GLY	0	0.031	0.021	32.642	0.144	0.144	0.000	0.000	0.000	0.000
76	A	86	GLN	0	-0.021	-0.029	35.929	0.075	0.075	0.000	0.000	0.000	0.000
77	A	87	THR	0	0.004	0.002	37.839	0.105	0.105	0.000	0.000	0.000	0.000
78	A	88	PRO	0	0.062	0.015	36.200	-0.193	-0.193	0.000	0.000	0.000	0.000
79	A	89	HIS	0	-0.007	0.012	34.292	-0.105	-0.105	0.000	0.000	0.000	0.000
80	A	90	PHE	0	-0.015	-0.001	28.148	-0.212	-0.212	0.000	0.000	0.000	0.000
81	A	91	ASP	-1	-0.784	-0.875	30.292	-9.724	-9.724	0.000	0.000	0.000	0.000
82	A	92	TYR	0	0.049	0.019	30.081	-0.184	-0.184	0.000	0.000	0.000	0.000
83	A	93	VAL	0	-0.018	0.001	28.186	-0.195	-0.195	0.000	0.000	0.000	0.000
84	A	94	CYS	0	-0.027	-0.010	26.097	-0.511	-0.511	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.883	-0.922	25.737	-10.788	-10.788	0.000	0.000	0.000	0.000
86	A	96	ALA	0	-0.013	-0.010	26.882	-0.336	-0.336	0.000	0.000	0.000	0.000
87	A	97	VAL	0	-0.007	-0.007	22.265	-0.297	-0.297	0.000	0.000	0.000	0.000
88	A	98	THR	0	-0.010	-0.010	22.047	-0.754	-0.754	0.000	0.000	0.000	0.000
89	A	99	GLN	0	-0.033	-0.016	22.602	-0.355	-0.355	0.000	0.000	0.000	0.000
90	A	100	GLY	0	0.011	0.011	24.295	-0.178	-0.178	0.000	0.000	0.000	0.000
91	A	101	LEU	0	-0.012	-0.017	18.647	-0.270	-0.270	0.000	0.000	0.000	0.000
92	A	102	THR	0	-0.002	-0.006	19.444	-0.818	-0.818	0.000	0.000	0.000	0.000
93	A	103	ARG	1	0.851	0.917	20.241	11.121	11.121	0.000	0.000	0.000	0.000
94	A	104	VAL	0	0.007	0.015	19.750	-0.149	-0.149	0.000	0.000	0.000	0.000
95	A	105	SER	0	-0.035	-0.008	16.016	-0.461	-0.461	0.000	0.000	0.000	0.000
96	A	106	LEU	0	-0.035	-0.013	17.332	-0.541	-0.541	0.000	0.000	0.000	0.000
97	A	107	ASP	-1	-0.850	-0.917	19.742	-12.239	-12.239	0.000	0.000	0.000	0.000
98	A	108	SER	0	-0.027	-0.036	18.627	-0.100	-0.100	0.000	0.000	0.000	0.000
99	A	109	SER	0	-0.038	-0.005	16.772	-0.584	-0.584	0.000	0.000	0.000	0.000
100	A	110	THR	0	-0.002	0.009	13.871	-1.536	-1.536	0.000	0.000	0.000	0.000
101	A	111	PRO	0	-0.027	-0.021	9.834	0.864	0.864	0.000	0.000	0.000	0.000
102	A	112	ILE	0	0.020	0.020	12.596	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	113	ALA	0	-0.020	0.002	10.971	0.575	0.575	0.000	0.000	0.000	0.000
104	A	114	ASN	0	0.013	-0.004	13.081	0.756	0.756	0.000	0.000	0.000	0.000
105	A	115	GLY	0	0.055	0.020	15.291	-0.676	-0.676	0.000	0.000	0.000	0.000
106	A	116	VAL	0	-0.075	-0.033	16.281	0.644	0.644	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.046	-0.009	19.776	0.061	0.061	0.000	0.000	0.000	0.000
108	A	118	THR	0	0.044	0.015	22.089	0.345	0.345	0.000	0.000	0.000	0.000
109	A	119	THR	0	-0.054	-0.035	24.785	-0.116	-0.116	0.000	0.000	0.000	0.000
110	A	120	ASN	0	0.024	0.003	27.180	0.321	0.321	0.000	0.000	0.000	0.000
111	A	121	THR	0	0.018	0.003	29.754	0.281	0.281	0.000	0.000	0.000	0.000
112	A	122	GLU	-1	-0.863	-0.934	29.100	-10.110	-10.110	0.000	0.000	0.000	0.000
113	A	123	GLU	-1	-0.885	-0.934	28.353	-10.058	-10.058	0.000	0.000	0.000	0.000
114	A	124	GLN	0	0.015	-0.006	26.403	-0.373	-0.373	0.000	0.000	0.000	0.000
115	A	125	ALA	0	0.033	0.018	24.207	-0.577	-0.577	0.000	0.000	0.000	0.000
116	A	126	LEU	0	0.007	-0.004	23.681	-0.574	-0.574	0.000	0.000	0.000	0.000
117	A	127	ASP	-1	-0.812	-0.901	24.302	-12.850	-12.850	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.818	0.900	20.327	12.651	12.651	0.000	0.000	0.000	0.000
119	A	129	ALA	0	0.032	0.006	19.243	-0.763	-0.763	0.000	0.000	0.000	0.000
120	A	130	GLY	0	0.028	0.022	18.682	-0.228	-0.228	0.000	0.000	0.000	0.000
121	A	131	LEU	0	-0.039	-0.008	19.479	0.272	0.272	0.000	0.000	0.000	0.000
122	A	132	PRO	0	-0.026	-0.026	22.848	-0.156	-0.156	0.000	0.000	0.000	0.000
123	A	133	THR	0	-0.028	-0.014	24.506	0.072	0.072	0.000	0.000	0.000	0.000
124	A	134	SER	0	-0.084	-0.035	21.464	0.305	0.305	0.000	0.000	0.000	0.000
125	A	135	ALA	0	0.003	0.012	21.880	-0.335	-0.335	0.000	0.000	0.000	0.000
126	A	136	GLU	-1	-0.865	-0.912	16.949	-17.260	-17.260	0.000	0.000	0.000	0.000
127	A	137	ASP	-1	-0.763	-0.900	15.355	-17.850	-17.850	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.803	0.878	14.554	16.015	16.015	0.000	0.000	0.000	0.000
129	A	139	GLY	0	0.037	0.028	14.207	-0.752	-0.752	0.000	0.000	0.000	0.000
130	A	140	ALA	0	0.023	0.014	11.855	-1.549	-1.549	0.000	0.000	0.000	0.000
131	A	141	GLN	0	-0.036	-0.036	10.056	-2.339	-2.339	0.000	0.000	0.000	0.000
132	A	142	ALA	0	0.012	0.011	9.444	-2.388	-2.388	0.000	0.000	0.000	0.000
133	A	143	THR	0	0.022	-0.009	8.889	-1.079	-1.079	0.000	0.000	0.000	0.000
136	A	146	ALA	0	-0.007	0.008	6.820	-1.680	-1.680	0.000	0.000	0.000	0.000
140	A	150	ALA	0	0.033	0.014	6.518	1.976	1.976	0.000	0.000	0.000	0.000
143	A	153	LEU	0	-0.019	-0.021	6.048	3.878	3.878	0.000	0.000	0.000	0.000
144	A	154	ARG	1	0.927	0.967	6.978	37.705	37.705	0.000	0.000	0.000	0.000
145	A	155	GLU	-1	-0.930	-0.971	6.312	-28.886	-28.886	0.000	0.000	0.000	0.000
146	A	156	LEU	0	-0.015	0.000	8.959	2.585	2.585	0.000	0.000	0.000	0.000
147	A	157	ARG	1	0.848	0.931	11.808	23.053	23.053	0.000	0.000	0.000	0.000
148	A	158	ALA	0	-0.011	-0.016	13.998	-0.230	-0.230	0.000	0.000	0.000	0.000
149	A	159	HIS	1	0.822	0.912	11.193	23.396	23.396	0.000	0.000	0.000	0.000
150	A	160	SER	-1	-0.923	-0.941	15.435	-16.302	-16.302	0.000	0.000	0.000	0.000

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