FMO DATABASE

FMODB ID: MRL7Z

Calculation Name: 1CZN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CZN

Chain ID: A

ChEMBL ID:

UniProt ID: P10340

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	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1756985.503438
FMO2-HF: Nuclear repulsion	1691981.132199
FMO2-HF: Total energy	-65004.371239
FMO2-MP2: Total energy	-65196.607913

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:1:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-441.713	-432.634	26.381	-18.175	-17.282	-0.21

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.725 / q_NPA : 0.869

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	3	ILE	0	0.008	0.011	2.661	7.310	10.210	0.232	-1.527	-1.604	-0.004
4	A	4	GLY	0	0.058	0.039	3.096	-11.340	-10.143	0.099	-0.662	-0.633	-0.006
28	A	28	GLU	-1	-0.917	-0.965	4.471	-38.211	-38.115	-0.001	-0.023	-0.072	0.000
29	A	29	SER	0	-0.053	-0.022	2.562	-17.261	-15.237	0.727	-1.169	-1.583	-0.015
30	A	30	ILE	0	-0.066	-0.029	2.651	-11.335	-9.348	1.791	-1.320	-2.458	-0.019
31	A	31	VAL	0	0.006	-0.009	2.463	-3.572	-3.367	3.433	-1.636	-2.001	-0.024
32	A	32	ASP	-1	-0.741	-0.835	1.782	-145.667	-145.956	20.080	-11.426	-8.365	-0.140
33	A	33	LEU	0	-0.026	-0.012	3.749	6.363	6.384	0.011	0.004	-0.036	0.000
47	A	47	TYR	0	-0.036	-0.035	3.167	4.257	5.195	0.009	-0.416	-0.530	-0.002
5	A	5	LEU	0	-0.078	-0.034	5.617	5.496	5.496	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.061	0.027	7.902	-1.006	-1.006	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.011	-0.019	11.014	1.176	1.176	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.125	0.082	14.049	-0.149	-0.149	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.060	-0.054	17.634	0.568	0.568	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.053	0.050	20.209	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.001	-0.012	23.598	0.122	0.122	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.039	0.027	20.539	0.191	0.191	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.024	0.016	19.712	-0.821	-0.821	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.049	0.010	16.538	-0.213	-0.213	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.010	0.005	15.007	-0.242	-0.242	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.002	-0.001	14.982	-0.929	-0.929	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.026	-0.004	15.769	-0.476	-0.476	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.035	0.024	11.672	-0.718	-0.718	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.853	-0.926	11.167	-21.534	-21.534	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.066	-0.044	11.894	-0.537	-0.537	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.010	-0.008	9.869	-0.196	-0.196	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.010	-0.011	5.394	2.858	2.858	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.038	-0.024	8.433	-0.511	-0.511	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.827	-0.895	10.990	-17.760	-17.760	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.001	-0.015	6.693	0.370	0.370	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.037	-0.015	8.381	-0.210	-0.210	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.025	-0.006	7.286	0.417	0.417	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.036	-0.019	6.572	1.814	1.814	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.852	-0.924	9.967	-17.525	-17.525	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.014	-0.009	13.726	-0.630	-0.630	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.013	0.013	15.346	0.491	0.491	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.147	-0.077	14.526	1.404	1.404	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.023	0.003	12.728	-0.784	-0.784	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.828	-0.883	14.208	-16.016	-16.016	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.055	0.022	14.598	-1.288	-1.288	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.123	-0.093	15.279	-1.167	-1.167	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.806	-0.907	10.413	-25.849	-25.849	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.024	-0.010	10.157	-3.047	-3.047	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.037	-0.033	11.868	0.390	0.390	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.057	-0.016	7.787	0.465	0.465	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.897	-0.935	8.404	-23.567	-23.567	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.050	-0.024	7.295	2.850	2.850	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.018	0.016	7.313	-4.522	-4.522	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.041	-0.028	8.302	2.076	2.076	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.003	0.016	10.560	-1.074	-1.074	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.041	0.014	13.592	0.951	0.951	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.018	-0.010	15.378	0.084	0.084	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.053	-0.011	19.029	0.424	0.424	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.019	0.009	22.190	0.029	0.029	0.000	0.000	0.000	0.000
57	A	57	TRP	0	-0.017	-0.017	24.662	0.385	0.385	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.051	-0.039	28.147	0.119	0.119	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.004	0.004	31.789	0.206	0.206	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.041	0.026	29.725	0.168	0.168	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.966	-0.967	28.681	-10.214	-10.214	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.025	0.007	22.616	-0.343	-0.343	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.086	-0.072	20.679	0.011	0.011	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.025	-0.031	23.296	-0.168	-0.168	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.818	-0.894	19.867	-14.444	-14.444	0.000	0.000	0.000	0.000
66	A	66	TRP	0	-0.019	-0.038	14.501	-0.327	-0.327	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.942	-0.974	20.659	-11.593	-11.593	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.045	-0.025	23.957	0.167	0.167	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.017	0.019	17.442	0.024	0.024	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.012	0.002	21.394	-0.256	-0.256	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.916	-0.977	22.990	-11.622	-11.622	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.907	-0.945	20.883	-13.841	-13.841	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.047	-0.010	17.751	-0.751	-0.751	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.836	-0.923	20.220	-13.214	-13.214	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.134	-0.073	20.149	0.065	0.065	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.029	-0.004	15.284	-0.516	-0.516	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.027	-0.019	17.406	1.285	1.285	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.050	-0.002	14.402	-1.414	-1.414	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.014	-0.004	17.277	-0.287	-0.287	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.065	-0.018	17.514	-0.689	-0.689	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.803	0.918	11.896	23.975	23.975	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.785	0.887	12.698	20.306	20.306	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.012	0.005	12.074	-2.206	-2.206	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.005	0.011	12.359	1.417	1.417	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.049	0.017	13.707	-0.926	-0.926	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.027	-0.016	12.416	0.366	0.366	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.058	0.038	17.179	-0.251	-0.251	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.052	-0.027	20.175	0.016	0.016	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.032	0.005	22.398	0.089	0.089	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.787	-0.874	26.186	-9.549	-9.549	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.046	-0.064	29.305	0.292	0.292	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.002	0.002	31.424	0.286	0.286	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.041	-0.026	34.011	0.264	0.264	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.060	-0.038	31.329	0.200	0.200	0.000	0.000	0.000	0.000
95	A	95	SER	0	0.054	0.040	32.464	-0.282	-0.282	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.879	-0.937	34.086	-8.286	-8.286	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.044	-0.035	30.987	0.179	0.179	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.041	0.045	26.885	-0.499	-0.499	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.044	-0.021	23.390	-0.522	-0.522	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.730	-0.846	24.716	-10.635	-10.635	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.007	-0.009	23.131	-0.114	-0.114	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.042	0.005	19.505	-0.691	-0.691	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.027	0.003	21.322	-0.406	-0.406	0.000	0.000	0.000	0.000
104	A	104	ILE	0	-0.016	0.009	24.002	-0.056	-0.056	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.023	0.006	18.217	-0.102	-0.102	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.734	-0.802	19.782	-13.768	-13.768	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.949	-0.953	20.767	-11.113	-11.113	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.817	0.919	22.059	12.946	12.946	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.029	0.010	16.266	-0.098	-0.098	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.046	-0.016	19.618	-0.123	-0.123	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.082	-0.046	21.072	0.263	0.263	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.028	-0.005	20.547	0.343	0.343	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.038	-0.029	21.087	-0.359	-0.359	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.030	-0.009	16.491	-0.462	-0.462	0.000	0.000	0.000	0.000
115	A	115	GLN	0	-0.059	-0.040	17.332	0.345	0.345	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.011	-0.027	16.745	-1.264	-1.264	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.071	-0.033	14.263	0.658	0.658	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.036	0.006	16.622	-0.501	-0.501	0.000	0.000	0.000	0.000
119	A	119	TYR	0	0.026	0.028	17.541	0.263	0.263	0.000	0.000	0.000	0.000
120	A	120	TRP	0	-0.041	-0.024	20.711	-0.359	-0.359	0.000	0.000	0.000	0.000
121	A	121	PRO	0	-0.008	-0.005	22.798	0.323	0.323	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.054	0.029	26.318	-0.233	-0.233	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.929	-0.973	29.014	-9.682	-9.682	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.058	-0.030	29.377	-0.279	-0.279	0.000	0.000	0.000	0.000
125	A	125	TYR	0	-0.084	-0.059	24.043	-0.226	-0.226	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.971	-0.984	31.053	-8.192	-8.192	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.025	-0.021	30.266	-0.237	-0.237	0.000	0.000	0.000	0.000
128	A	128	ASN	0	-0.106	-0.049	34.101	0.154	0.154	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.947	-0.972	34.048	-8.628	-8.628	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.021	-0.041	28.008	-0.311	-0.311	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.876	0.920	28.008	10.151	10.151	0.000	0.000	0.000	0.000
132	A	132	ALA	0	-0.011	0.010	23.960	-0.308	-0.308	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.012	0.002	25.172	-0.361	-0.361	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.827	0.857	23.363	12.588	12.588	0.000	0.000	0.000	0.000
135	A	135	ASN	0	-0.071	-0.041	27.891	0.170	0.170	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.006	-0.005	30.091	0.149	0.149	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.019	0.000	25.191	0.046	0.046	0.000	0.000	0.000	0.000
138	A	138	PHE	0	0.052	0.027	23.423	0.089	0.089	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.051	-0.035	21.204	-0.265	-0.265	0.000	0.000	0.000	0.000
140	A	140	GLY	0	0.055	0.012	18.757	-0.801	-0.801	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.065	-0.032	17.307	0.776	0.776	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.046	0.036	19.518	-0.273	-0.273	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.040	-0.011	19.546	0.230	0.230	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.693	-0.837	22.697	-10.382	-10.382	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.860	-0.925	23.578	-12.502	-12.502	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.936	-0.953	26.383	-10.482	-10.482	0.000	0.000	0.000	0.000
147	A	147	ASN	0	-0.096	-0.076	29.687	0.654	0.654	0.000	0.000	0.000	0.000
148	A	148	GLN	0	-0.039	-0.008	28.079	-0.131	-0.131	0.000	0.000	0.000	0.000
149	A	149	PRO	0	0.087	0.058	26.166	-0.319	-0.319	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.977	-0.990	25.800	-10.545	-10.545	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.071	-0.037	26.153	-0.171	-0.171	0.000	0.000	0.000	0.000
152	A	152	THR	0	0.003	-0.017	20.828	-0.411	-0.411	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.958	0.975	20.542	11.757	11.757	0.000	0.000	0.000	0.000
154	A	154	ASN	0	-0.025	-0.022	20.241	-0.512	-0.512	0.000	0.000	0.000	0.000
155	A	155	ARG	1	0.891	0.957	20.935	11.325	11.325	0.000	0.000	0.000	0.000
156	A	156	ILE	0	0.064	0.032	15.108	-0.408	-0.408	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.823	0.898	16.161	15.156	15.156	0.000	0.000	0.000	0.000
158	A	158	THR	0	-0.060	-0.023	16.953	-0.272	-0.272	0.000	0.000	0.000	0.000
159	A	159	TRP	0	0.014	-0.001	13.136	-0.612	-0.612	0.000	0.000	0.000	0.000
160	A	160	VAL	0	0.022	0.006	11.180	-0.499	-0.499	0.000	0.000	0.000	0.000
161	A	161	SER	0	-0.076	-0.050	13.161	-0.795	-0.795	0.000	0.000	0.000	0.000
162	A	162	GLN	0	-0.032	-0.022	15.553	0.353	0.353	0.000	0.000	0.000	0.000
163	A	163	LEU	0	0.027	0.020	11.865	0.065	0.065	0.000	0.000	0.000	0.000
164	A	164	LYS	1	0.841	0.949	9.978	21.557	21.557	0.000	0.000	0.000	0.000
165	A	165	SER	0	0.024	0.008	11.860	-0.499	-0.499	0.000	0.000	0.000	0.000
166	A	166	GLU	-1	-0.891	-0.931	14.024	-16.807	-16.807	0.000	0.000	0.000	0.000
167	A	167	PHE	0	0.010	-0.003	8.593	-0.347	-0.347	0.000	0.000	0.000	0.000
168	A	168	GLY	0	-0.020	0.003	9.591	-2.119	-2.119	0.000	0.000	0.000	0.000
169	A	169	LEU	-1	-0.945	-0.966	6.240	-23.936	-23.936	0.000	0.000	0.000	0.000

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