FMO DATABASE

FMODB ID: QKL6Y

Calculation Name: 1C41-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 5-nitroso-6-ribityl-amino-2,4(1h,3h)-pyrimidinedione

Ligand 3-letter code: LMZ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1C41

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UVT8

Base Structure: X-ray

Registration Date: 2025-09-02

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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1541187.133432
FMO2-HF: Nuclear repulsion	1479568.420582
FMO2-HF: Total energy	-61618.712849
FMO2-MP2: Total energy	-61799.926236

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.
-76.519	-75.905	-0.004	-0.254	-0.355	-0.001

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 : 0.844 / q_NPA : 0.911

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	THR	0	0.015	0.007	3.850	-0.783	-0.169	-0.004	-0.254	-0.355	-0.001
4	A	8	PRO	0	-0.015	-0.001	6.563	2.273	2.273	0.000	0.000	0.000	0.000
5	A	9	GLN	0	0.025	0.006	8.825	2.976	2.976	0.000	0.000	0.000	0.000
6	A	10	GLN	0	-0.015	-0.004	12.501	-1.035	-1.035	0.000	0.000	0.000	0.000
7	A	11	HIS	0	-0.027	-0.018	15.116	1.584	1.584	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.797	-0.884	18.545	-12.396	-12.396	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.027	0.008	21.595	-0.330	-0.330	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.028	-0.036	23.113	0.306	0.306	0.000	0.000	0.000	0.000
11	A	15	ALA	0	-0.086	-0.054	25.983	0.459	0.459	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.041	-0.007	21.468	0.167	0.167	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.783	0.879	25.576	10.322	10.322	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.004	-0.002	20.518	-0.265	-0.265	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.025	0.025	23.475	0.468	0.468	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.031	-0.020	19.988	-0.568	-0.568	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.017	-0.010	22.171	0.710	0.710	0.000	0.000	0.000	0.000
18	A	22	HIS	0	-0.003	-0.008	21.745	-0.476	-0.476	0.000	0.000	0.000	0.000
19	A	23	ALA	0	-0.001	0.002	22.254	0.631	0.631	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.938	0.962	23.823	10.254	10.254	0.000	0.000	0.000	0.000
21	A	25	TRP	0	-0.024	-0.007	24.611	0.215	0.215	0.000	0.000	0.000	0.000
22	A	26	ASN	0	-0.025	-0.022	21.787	-0.153	-0.153	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.788	-0.909	22.166	-12.152	-12.152	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.040	-0.022	22.950	-0.378	-0.378	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.032	-0.015	17.122	-0.453	-0.453	0.000	0.000	0.000	0.000
26	A	30	ILE	0	-0.029	-0.006	18.153	-0.887	-0.887	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.893	-0.950	19.568	-13.691	-13.691	0.000	0.000	0.000	0.000
28	A	32	PRO	0	0.032	0.021	17.558	-0.268	-0.268	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.006	0.023	13.350	-0.839	-0.839	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.034	-0.023	16.277	-0.531	-0.531	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.015	0.007	19.123	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	36	GLY	0	0.039	0.020	15.337	0.059	0.059	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.063	-0.022	15.331	-0.063	-0.063	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.983	0.985	16.262	12.548	12.548	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.015	0.010	17.961	0.402	0.402	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.869	0.925	12.730	21.596	21.596	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.024	0.000	16.828	0.117	0.117	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.022	-0.010	19.331	0.342	0.342	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.043	-0.015	17.887	0.407	0.407	0.000	0.000	0.000	0.000
40	A	44	CYS	0	-0.084	-0.034	17.454	-0.509	-0.509	0.000	0.000	0.000	0.000
41	A	45	GLY	0	0.027	0.023	19.918	0.432	0.432	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.054	-0.012	20.995	0.619	0.619	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.958	0.971	23.928	10.222	10.222	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.802	-0.917	26.353	-11.648	-11.648	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.040	-0.022	27.596	0.003	0.003	0.000	0.000	0.000	0.000
46	A	50	ASN	0	-0.048	-0.024	27.273	0.633	0.633	0.000	0.000	0.000	0.000
47	A	51	ILE	0	0.023	0.027	22.584	-0.350	-0.350	0.000	0.000	0.000	0.000
48	A	52	VAL	0	-0.013	0.004	25.484	0.324	0.324	0.000	0.000	0.000	0.000
49	A	53	VAL	0	0.003	0.000	24.021	-0.477	-0.477	0.000	0.000	0.000	0.000
50	A	54	GLN	0	-0.024	-0.012	25.973	0.438	0.438	0.000	0.000	0.000	0.000
51	A	55	SER	0	0.012	0.016	25.824	-0.375	-0.375	0.000	0.000	0.000	0.000
52	A	56	VAL	0	-0.031	-0.014	25.786	0.471	0.471	0.000	0.000	0.000	0.000
53	A	57	PRO	0	0.003	-0.001	27.395	-0.213	-0.213	0.000	0.000	0.000	0.000
54	A	58	GLY	0	0.046	0.026	26.295	-0.326	-0.326	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.017	-0.020	21.431	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	60	TRP	0	-0.014	0.006	23.773	-0.369	-0.369	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.820	-0.936	26.610	-10.552	-10.552	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.006	0.017	20.374	0.180	0.180	0.000	0.000	0.000	0.000
59	A	63	PRO	0	0.022	0.012	23.599	0.021	0.021	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.008	0.007	25.032	0.205	0.205	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.029	0.011	27.154	0.256	0.256	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.032	0.014	22.559	0.185	0.185	0.000	0.000	0.000	0.000
63	A	67	GLN	0	0.052	0.041	25.858	0.476	0.476	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.829	0.901	28.303	9.741	9.741	0.000	0.000	0.000	0.000
65	A	69	LEU	0	0.011	0.020	26.129	0.278	0.278	0.000	0.000	0.000	0.000
66	A	70	TYR	0	0.034	0.007	26.889	0.097	0.097	0.000	0.000	0.000	0.000
67	A	71	SER	0	-0.024	-0.009	28.908	0.344	0.344	0.000	0.000	0.000	0.000
68	A	72	ALA	0	-0.009	-0.006	32.383	0.298	0.298	0.000	0.000	0.000	0.000
69	A	73	SER	0	-0.051	-0.036	30.085	0.109	0.109	0.000	0.000	0.000	0.000
70	A	74	GLN	0	0.001	-0.008	31.876	-0.063	-0.063	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.086	-0.032	34.078	0.223	0.223	0.000	0.000	0.000	0.000
72	A	76	GLN	-1	-0.884	-0.921	34.110	-8.539	-8.539	0.000	0.000	0.000	0.000
73	A	107	SER	0	-0.052	-0.032	31.205	0.028	0.028	0.000	0.000	0.000	0.000
74	A	108	THR	0	-0.040	-0.018	33.062	0.183	0.183	0.000	0.000	0.000	0.000
75	A	109	GLY	0	0.085	0.054	32.628	-0.238	-0.238	0.000	0.000	0.000	0.000
76	A	110	PRO	0	0.008	0.011	29.808	-0.190	-0.190	0.000	0.000	0.000	0.000
77	A	111	PHE	0	-0.033	-0.024	25.165	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	112	ASP	-1	-0.799	-0.873	23.888	-11.875	-11.875	0.000	0.000	0.000	0.000
79	A	113	ALA	0	0.050	0.001	19.351	-0.403	-0.403	0.000	0.000	0.000	0.000
80	A	114	LEU	0	-0.029	-0.006	20.531	0.552	0.552	0.000	0.000	0.000	0.000
81	A	115	ILE	0	-0.011	-0.007	16.308	-0.940	-0.940	0.000	0.000	0.000	0.000
82	A	116	ALA	0	0.016	0.015	18.020	0.899	0.899	0.000	0.000	0.000	0.000
83	A	117	ILE	0	-0.010	-0.005	17.043	-0.865	-0.865	0.000	0.000	0.000	0.000
84	A	118	GLY	0	0.038	0.002	17.622	1.116	1.116	0.000	0.000	0.000	0.000
85	A	119	VAL	0	-0.010	0.000	17.161	-1.084	-1.084	0.000	0.000	0.000	0.000
86	A	120	LEU	0	-0.007	0.008	18.742	0.962	0.962	0.000	0.000	0.000	0.000
87	A	121	ILE	0	0.040	0.005	18.934	-0.954	-0.954	0.000	0.000	0.000	0.000
88	A	122	LYS	1	0.819	0.905	21.036	13.051	13.051	0.000	0.000	0.000	0.000
89	A	123	GLY	0	0.028	0.022	22.896	0.227	0.227	0.000	0.000	0.000	0.000
90	A	124	GLU	-1	-0.932	-0.970	26.656	-9.836	-9.836	0.000	0.000	0.000	0.000
91	A	125	THR	0	-0.015	-0.010	29.323	0.040	0.040	0.000	0.000	0.000	0.000
92	A	126	MET	0	-0.012	-0.014	26.642	-0.368	-0.368	0.000	0.000	0.000	0.000
93	A	127	HIS	0	0.016	0.007	27.443	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	128	PHE	0	-0.019	0.006	18.646	-0.135	-0.135	0.000	0.000	0.000	0.000
95	A	129	GLU	-1	-0.753	-0.889	22.476	-13.210	-13.210	0.000	0.000	0.000	0.000
96	A	130	TYR	0	0.009	0.005	23.512	-0.176	-0.176	0.000	0.000	0.000	0.000
97	A	131	ILE	0	0.001	0.016	23.646	0.038	0.038	0.000	0.000	0.000	0.000
98	A	132	ALA	0	0.018	0.007	19.475	-0.242	-0.242	0.000	0.000	0.000	0.000
99	A	133	ASP	-1	-0.872	-0.917	20.449	-14.295	-14.295	0.000	0.000	0.000	0.000
100	A	134	SER	0	0.000	-0.015	22.169	0.020	0.020	0.000	0.000	0.000	0.000
101	A	135	VAL	0	-0.043	-0.019	20.381	0.154	0.154	0.000	0.000	0.000	0.000
102	A	136	SER	0	-0.021	-0.019	18.400	-0.607	-0.607	0.000	0.000	0.000	0.000
103	A	137	HIS	0	-0.053	-0.027	19.782	-0.390	-0.390	0.000	0.000	0.000	0.000
104	A	138	GLY	0	-0.007	0.001	22.644	0.287	0.287	0.000	0.000	0.000	0.000
105	A	139	LEU	0	-0.023	-0.023	18.889	0.308	0.308	0.000	0.000	0.000	0.000
106	A	140	MET	0	0.001	0.012	17.009	0.084	0.084	0.000	0.000	0.000	0.000
107	A	141	ARG	1	0.857	0.910	20.824	10.879	10.879	0.000	0.000	0.000	0.000
108	A	142	VAL	0	-0.041	-0.017	24.010	0.312	0.312	0.000	0.000	0.000	0.000
109	A	143	GLN	0	0.034	0.015	17.651	-0.083	-0.083	0.000	0.000	0.000	0.000
110	A	144	LEU	0	-0.047	-0.022	22.159	0.135	0.135	0.000	0.000	0.000	0.000
111	A	145	ASP	-1	-0.865	-0.922	24.820	-10.486	-10.486	0.000	0.000	0.000	0.000
112	A	146	THR	0	-0.055	-0.026	25.178	0.474	0.474	0.000	0.000	0.000	0.000
113	A	147	GLY	0	0.010	0.023	25.726	0.211	0.211	0.000	0.000	0.000	0.000
114	A	148	VAL	0	-0.048	-0.027	22.870	-0.150	-0.150	0.000	0.000	0.000	0.000
115	A	149	PRO	0	-0.007	-0.005	18.133	-0.132	-0.132	0.000	0.000	0.000	0.000
116	A	150	VAL	0	-0.008	-0.010	18.984	0.478	0.478	0.000	0.000	0.000	0.000
117	A	151	ILE	0	-0.025	-0.007	13.190	-0.829	-0.829	0.000	0.000	0.000	0.000
118	A	152	PHE	0	0.026	0.002	12.966	0.987	0.987	0.000	0.000	0.000	0.000
119	A	153	GLY	0	0.036	0.006	13.027	-1.653	-1.653	0.000	0.000	0.000	0.000
120	A	154	VAL	0	-0.041	-0.023	14.583	1.007	1.007	0.000	0.000	0.000	0.000
121	A	155	LEU	0	-0.015	-0.001	12.028	-1.177	-1.177	0.000	0.000	0.000	0.000
122	A	156	THR	0	0.002	-0.001	14.495	1.294	1.294	0.000	0.000	0.000	0.000
123	A	157	VAL	0	-0.033	-0.018	14.297	-1.108	-1.108	0.000	0.000	0.000	0.000
124	A	158	LEU	0	0.014	-0.004	16.648	1.096	1.096	0.000	0.000	0.000	0.000
125	A	159	THR	0	0.026	0.008	18.207	0.449	0.449	0.000	0.000	0.000	0.000
126	A	160	ASP	-1	-0.819	-0.914	18.346	-14.403	-14.403	0.000	0.000	0.000	0.000
127	A	161	ASP	-1	-0.849	-0.916	18.364	-15.389	-15.389	0.000	0.000	0.000	0.000
128	A	162	GLN	0	-0.019	-0.010	14.593	-1.229	-1.229	0.000	0.000	0.000	0.000
129	A	163	ALA	0	0.049	0.020	13.725	-1.719	-1.719	0.000	0.000	0.000	0.000
130	A	164	LYS	1	0.895	0.926	14.800	13.591	13.591	0.000	0.000	0.000	0.000
131	A	165	ALA	0	-0.016	-0.004	12.264	-0.393	-0.393	0.000	0.000	0.000	0.000
132	A	166	ARG	1	0.899	0.950	9.331	25.683	25.683	0.000	0.000	0.000	0.000
133	A	167	ALA	0	-0.001	0.005	11.308	-0.681	-0.681	0.000	0.000	0.000	0.000
134	A	168	GLY	0	-0.001	0.012	13.011	0.761	0.761	0.000	0.000	0.000	0.000
135	A	169	VAL	0	-0.045	-0.015	14.008	0.951	0.951	0.000	0.000	0.000	0.000
136	A	170	ILE	0	-0.048	-0.014	15.694	0.927	0.927	0.000	0.000	0.000	0.000
137	A	171	GLU	-1	-0.865	-0.929	15.859	-16.192	-16.192	0.000	0.000	0.000	0.000
138	A	172	GLY	0	-0.022	-0.008	14.163	-0.491	-0.491	0.000	0.000	0.000	0.000
139	A	173	SER	0	-0.106	-0.052	11.555	-1.988	-1.988	0.000	0.000	0.000	0.000
140	A	174	HIS	0	-0.015	-0.032	6.125	2.059	2.059	0.000	0.000	0.000	0.000
141	A	175	ASN	0	0.069	0.021	9.717	-0.692	-0.692	0.000	0.000	0.000	0.000
142	A	176	HIS	0	-0.056	-0.041	6.889	-3.568	-3.568	0.000	0.000	0.000	0.000
143	A	177	GLY	0	0.030	0.017	9.425	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	178	GLU	-1	-0.869	-0.937	10.807	-21.682	-21.682	0.000	0.000	0.000	0.000
145	A	179	ASP	-1	-0.857	-0.923	6.454	-38.229	-38.229	0.000	0.000	0.000	0.000
146	A	180	TRP	0	-0.029	0.002	9.495	1.964	1.964	0.000	0.000	0.000	0.000
147	A	181	GLY	0	0.054	0.029	12.279	1.288	1.288	0.000	0.000	0.000	0.000
148	A	182	LEU	0	0.003	-0.009	10.885	0.889	0.889	0.000	0.000	0.000	0.000
149	A	183	ALA	0	0.000	0.003	11.188	0.932	0.932	0.000	0.000	0.000	0.000
150	A	184	ALA	0	-0.006	-0.005	13.158	1.067	1.067	0.000	0.000	0.000	0.000
151	A	185	VAL	0	0.011	0.003	16.551	1.047	1.047	0.000	0.000	0.000	0.000
152	A	186	GLU	-1	-0.799	-0.879	13.519	-22.011	-22.011	0.000	0.000	0.000	0.000
153	A	187	MET	0	-0.013	-0.019	15.147	0.725	0.725	0.000	0.000	0.000	0.000
154	A	188	GLY	0	0.013	0.011	17.850	0.823	0.823	0.000	0.000	0.000	0.000
155	A	189	VAL	0	-0.004	-0.011	20.387	0.855	0.855	0.000	0.000	0.000	0.000
156	A	190	ARG	1	0.850	0.901	15.334	19.566	19.566	0.000	0.000	0.000	0.000
157	A	191	ARG	1	0.876	0.949	21.352	12.707	12.707	0.000	0.000	0.000	0.000
158	A	192	ARG	1	0.841	0.915	23.432	12.144	12.144	0.000	0.000	0.000	0.000
159	A	193	ASP	-1	-0.834	-0.908	24.372	-12.064	-12.064	0.000	0.000	0.000	0.000
160	A	194	TRP	0	-0.007	-0.013	18.901	0.048	0.048	0.000	0.000	0.000	0.000
161	A	195	ALA	0	-0.038	-0.014	26.449	0.422	0.422	0.000	0.000	0.000	0.000
162	A	196	ALA	0	-0.073	-0.028	28.999	0.450	0.450	0.000	0.000	0.000	0.000
163	A	197	GLY	0	-0.023	-0.012	30.090	0.259	0.259	0.000	0.000	0.000	0.000
164	A	198	LYS	1	0.795	0.893	27.350	11.404	11.404	0.000	0.000	0.000	0.000
165	A	199	THR	-1	-0.941	-0.964	25.798	-12.673	-12.673	0.000	0.000	0.000	0.000

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