FMO DATABASE

FMODB ID: VYJG1

Calculation Name: 3N3A-C-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | manganese (ii) ion

Ligand 3-letter code: FMN | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3N3A

Chain ID: C

ChEMBL ID:

UniProt ID: P0A772

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1181081.434517
FMO2-HF: Nuclear repulsion	1129828.369296
FMO2-HF: Total energy	-51253.065221
FMO2-MP2: Total energy	-51405.094931

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:3:GLN)

Summations of interaction energy for fragment #1(A:3:GLN)

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.
-93.073	-78.735	12.794	-12.452	-14.678	-0.129

Interaction energy analysis for fragmet #1(A:3:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.917

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	5	VAL	0	0.046	0.037	3.725	4.595	6.628	-0.007	-0.927	-1.099	-0.002
22	A	24	PRO	0	-0.005	-0.009	3.040	-0.198	0.883	0.291	-0.545	-0.827	0.004
23	A	25	ALA	0	0.011	0.005	3.336	-3.496	-2.177	0.229	-0.528	-1.020	0.001
24	A	26	VAL	0	0.024	0.023	4.314	1.777	1.984	-0.001	-0.005	-0.201	0.000
36	A	38	VAL	0	-0.017	-0.005	4.563	-0.202	-0.096	-0.001	-0.007	-0.098	0.000
38	A	40	GLU	-1	-0.908	-0.963	2.368	-75.213	-72.531	6.148	-3.767	-5.063	-0.048
39	A	41	PRO	0	0.034	0.005	4.136	-2.046	-1.376	0.000	-0.274	-0.396	-0.001
40	A	42	TYR	0	-0.047	-0.041	1.949	-42.991	-39.234	5.731	-5.264	-4.224	-0.070
41	A	43	ILE	0	0.009	0.010	3.534	12.120	12.575	0.006	-0.108	-0.352	-0.001
127	A	129	TRP	0	-0.008	-0.023	3.002	-9.186	-7.158	0.398	-1.027	-1.398	-0.012
4	A	6	TYR	0	-0.018	-0.034	5.986	1.288	1.288	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.013	0.011	9.583	1.011	1.011	0.000	0.000	0.000	0.000
6	A	8	SER	0	0.019	-0.008	13.075	0.259	0.259	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.008	0.011	15.910	0.163	0.163	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.067	0.019	19.081	-0.410	-0.410	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.016	-0.005	21.448	0.234	0.234	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.861	-0.922	17.975	-14.644	-14.644	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.020	-0.003	17.782	-0.358	-0.358	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.065	0.009	12.999	0.126	0.126	0.000	0.000	0.000	0.000
13	A	15	GLN	0	0.021	0.038	12.444	-1.620	-1.620	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.962	0.975	13.744	13.355	13.355	0.000	0.000	0.000	0.000
15	A	17	PHE	0	-0.019	0.004	12.006	0.020	0.020	0.000	0.000	0.000	0.000
16	A	18	ILE	0	0.015	0.005	8.677	-0.431	-0.431	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.865	-0.934	10.950	-17.007	-17.007	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.813	0.904	13.044	15.530	15.530	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.020	-0.008	8.765	0.128	0.128	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.010	0.015	11.094	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	23	LEU	0	-0.026	-0.004	5.795	-0.813	-0.813	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.759	0.869	6.180	16.949	16.949	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.005	-0.009	9.888	0.538	0.538	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.007	0.005	11.778	0.862	0.862	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.016	-0.001	15.122	0.289	0.289	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.023	-0.014	18.093	1.069	1.069	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.836	-0.925	19.421	-12.907	-12.907	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.919	0.965	20.853	11.719	11.719	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.914	-0.941	17.112	-14.745	-14.745	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.930	0.952	15.108	15.254	15.254	0.000	0.000	0.000	0.000
34	A	36	ILE	0	0.009	0.011	9.617	0.633	0.633	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.001	-0.003	10.686	1.237	1.237	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.856	-0.921	5.857	-28.017	-28.017	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.015	-0.004	6.271	-1.039	-1.039	0.000	0.000	0.000	0.000
43	A	45	ILE	0	0.010	-0.002	8.579	2.403	2.403	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.020	-0.010	11.155	0.777	0.777	0.000	0.000	0.000	0.000
45	A	47	PRO	0	-0.019	0.018	14.364	0.555	0.555	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.028	-0.035	17.976	0.046	0.046	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.012	0.007	20.201	0.245	0.245	0.000	0.000	0.000	0.000
48	A	50	GLY	0	-0.019	0.013	23.312	0.373	0.373	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.036	-0.003	26.160	0.076	0.076	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.056	-0.004	27.226	0.350	0.350	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.014	0.002	26.887	0.259	0.259	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.019	-0.021	23.422	-0.092	-0.092	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.015	0.035	26.800	-0.055	-0.055	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.013	-0.002	25.334	0.023	0.023	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.021	-0.012	22.858	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.004	0.012	17.448	-0.424	-0.424	0.000	0.000	0.000	0.000
57	A	59	PRO	0	0.029	0.020	17.735	0.572	0.572	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.949	0.961	18.644	11.697	11.697	0.000	0.000	0.000	0.000
59	A	61	GLN	0	0.025	0.010	16.309	-0.332	-0.332	0.000	0.000	0.000	0.000
60	A	62	VAL	0	0.012	0.010	13.555	-0.830	-0.830	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.032	-0.012	15.204	-0.597	-0.597	0.000	0.000	0.000	0.000
62	A	64	ARG	1	0.856	0.915	17.766	14.148	14.148	0.000	0.000	0.000	0.000
63	A	65	PHE	0	0.020	0.024	8.025	0.660	0.660	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.048	0.010	12.007	-0.459	-0.459	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.080	-0.049	14.523	0.093	0.093	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.858	-0.914	14.631	-18.136	-18.136	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.944	-0.998	14.811	-16.962	-16.962	0.000	0.000	0.000	0.000
68	A	70	HIS	0	0.018	0.024	10.265	0.887	0.887	0.000	0.000	0.000	0.000
69	A	71	ASN	0	0.002	-0.013	10.133	-3.504	-3.504	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.900	0.974	10.221	15.384	15.384	0.000	0.000	0.000	0.000
71	A	73	ALA	0	0.022	0.018	12.136	-0.811	-0.811	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.012	0.024	6.750	-0.457	-0.457	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.053	-0.006	6.921	-5.518	-5.518	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.860	0.917	6.331	35.259	35.259	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.051	0.020	8.254	2.640	2.640	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.049	-0.008	9.347	-2.071	-2.071	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.002	0.005	9.728	1.371	1.371	0.000	0.000	0.000	0.000
78	A	80	ALA	0	-0.026	-0.004	12.908	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.015	0.017	16.320	0.302	0.302	0.000	0.000	0.000	0.000
80	A	82	GLY	0	0.023	-0.010	18.359	0.324	0.324	0.000	0.000	0.000	0.000
81	A	83	ASN	0	0.015	0.008	22.133	0.199	0.199	0.000	0.000	0.000	0.000
82	A	84	ARG	1	1.013	0.990	25.194	11.773	11.773	0.000	0.000	0.000	0.000
83	A	85	ASN	0	0.000	0.007	27.294	0.274	0.274	0.000	0.000	0.000	0.000
84	A	86	PHE	0	-0.025	0.001	26.817	0.232	0.232	0.000	0.000	0.000	0.000
85	A	87	GLY	0	0.035	0.022	29.363	0.060	0.060	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.927	-0.970	27.910	-10.467	-10.467	0.000	0.000	0.000	0.000
87	A	89	ALA	0	-0.021	-0.020	26.734	-0.420	-0.420	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.036	-0.007	21.744	-0.628	-0.628	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.049	0.020	20.470	-0.180	-0.180	0.000	0.000	0.000	0.000
90	A	92	ARG	1	0.857	0.913	20.100	11.717	11.717	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.004	0.004	17.788	-0.058	-0.058	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.021	0.014	16.316	-0.645	-0.645	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.806	-0.894	17.243	-14.135	-14.135	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.025	-0.016	20.038	0.030	0.030	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.015	-0.007	13.934	0.156	0.156	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.023	0.016	15.870	-0.221	-0.221	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.911	0.945	16.834	13.383	13.383	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.920	0.971	19.235	14.918	14.918	0.000	0.000	0.000	0.000
99	A	101	CYS	0	-0.055	-0.034	14.771	0.267	0.267	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.029	0.035	15.649	-0.648	-0.648	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.018	0.009	11.468	-0.448	-0.448	0.000	0.000	0.000	0.000
102	A	104	PRO	0	0.023	0.006	11.933	1.344	1.344	0.000	0.000	0.000	0.000
103	A	105	TRP	0	-0.044	-0.037	13.064	-0.984	-0.984	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.020	-0.007	9.411	0.983	0.983	0.000	0.000	0.000	0.000
105	A	107	TYR	0	-0.007	-0.028	13.387	0.644	0.644	0.000	0.000	0.000	0.000
106	A	108	ARG	1	0.866	0.926	14.975	13.294	13.294	0.000	0.000	0.000	0.000
107	A	109	PHE	0	0.004	0.016	14.136	0.617	0.617	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.801	-0.911	19.011	-11.900	-11.900	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.005	-0.014	21.055	-0.186	-0.186	0.000	0.000	0.000	0.000
110	A	112	MET	0	0.017	0.013	18.226	-0.667	-0.667	0.000	0.000	0.000	0.000
111	A	113	GLY	0	-0.009	0.010	17.851	-0.703	-0.703	0.000	0.000	0.000	0.000
112	A	114	THR	0	0.011	-0.031	18.913	0.341	0.341	0.000	0.000	0.000	0.000
113	A	115	GLN	0	-0.019	-0.028	19.002	-0.749	-0.749	0.000	0.000	0.000	0.000
114	A	116	SER	0	0.070	0.029	18.901	-0.465	-0.465	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.792	-0.846	17.051	-15.889	-15.889	0.000	0.000	0.000	0.000
116	A	118	ILE	0	0.006	0.009	14.256	-1.426	-1.426	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.898	-0.937	14.182	-16.156	-16.156	0.000	0.000	0.000	0.000
118	A	120	ASN	0	-0.019	-0.022	15.005	-0.776	-0.776	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.010	0.001	10.070	-1.121	-1.121	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.885	0.942	10.250	17.646	17.646	0.000	0.000	0.000	0.000
121	A	123	LYS	1	0.938	0.998	10.635	15.663	15.663	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.029	0.014	11.612	-0.788	-0.788	0.000	0.000	0.000	0.000
123	A	125	VAL	0	-0.024	-0.021	5.150	-1.663	-1.663	0.000	0.000	0.000	0.000
124	A	126	THR	0	-0.054	-0.048	6.985	-2.798	-2.798	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.870	-0.937	8.757	-19.362	-19.362	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.013	-0.010	6.403	1.167	1.167	0.000	0.000	0.000	0.000
128	A	130	GLN	0	0.009	0.010	7.241	2.081	2.081	0.000	0.000	0.000	0.000
129	A	131	ARG	1	0.773	0.892	10.646	22.976	22.976	0.000	0.000	0.000	0.000
130	A	132	GLN	0	-0.029	-0.019	7.423	0.882	0.882	0.000	0.000	0.000	0.000
131	A	133	PRO	-1	-0.919	-0.938	9.197	-32.063	-32.063	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLN)