FMO DATABASE

FMODB ID: 742JK

Calculation Name: 7ARC-U-Other547

Preferred Name:

Target Type:

Ligand Name: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | flavin mononucleotide | s-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate | iron/sulfur cluster | fe2/s2 (inorganic) cluster | zinc ion

Ligand 3-letter code: NDP | FMN | 8Q1 | SF4 | FES | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7ARC

Chain ID: U

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-550423.487487
FMO2-HF: Nuclear repulsion	518353.575727
FMO2-HF: Total energy	-32069.911759
FMO2-MP2: Total energy	-32165.690572

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:39:SER)

Summations of interaction energy for fragment #1(A:39:SER)

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.
-206.83	-204.191	0.102	-0.994	-1.746	-0.003

Interaction energy analysis for fragmet #1(A:39:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.822 / q_NPA : 0.887

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

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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	41	PHE	0	-0.005	0.017	3.861	-1.912	-0.309	-0.007	-0.610	-0.985	-0.001
79	A	117	ILE	0	-0.069	-0.019	4.327	-2.798	-2.636	-0.001	-0.020	-0.140	0.000
80	A	118	SER	0	-0.102	-0.066	2.592	-11.673	-11.013	0.111	-0.325	-0.447	-0.002
81	A	119	ASN	0	0.051	0.023	3.638	-1.403	-1.189	-0.001	-0.039	-0.174	0.000
4	A	42	LEU	0	0.048	0.042	6.097	5.547	5.547	0.000	0.000	0.000	0.000
5	A	43	PRO	0	-0.022	-0.016	8.010	-4.711	-4.711	0.000	0.000	0.000	0.000
6	A	44	LYS	1	0.951	0.988	8.066	32.234	32.234	0.000	0.000	0.000	0.000
7	A	45	GLU	-1	-0.881	-0.957	9.924	-22.965	-22.965	0.000	0.000	0.000	0.000
8	A	46	GLU	-1	-0.906	-0.952	13.431	-18.380	-18.380	0.000	0.000	0.000	0.000
9	A	47	VAL	0	-0.006	-0.010	9.801	1.096	1.096	0.000	0.000	0.000	0.000
10	A	48	GLU	-1	-0.883	-0.931	12.710	-18.105	-18.105	0.000	0.000	0.000	0.000
11	A	49	SER	0	-0.019	-0.024	14.137	1.574	1.574	0.000	0.000	0.000	0.000
12	A	50	ARG	1	0.831	0.929	15.109	19.797	19.797	0.000	0.000	0.000	0.000
13	A	51	ILE	0	0.022	0.016	13.927	0.911	0.911	0.000	0.000	0.000	0.000
14	A	52	ILE	0	-0.048	-0.029	16.923	1.202	1.202	0.000	0.000	0.000	0.000
15	A	53	ALA	0	-0.066	-0.018	19.437	0.957	0.957	0.000	0.000	0.000	0.000
16	A	54	GLN	0	0.054	0.016	19.331	0.544	0.544	0.000	0.000	0.000	0.000
17	A	55	VAL	0	-0.020	-0.015	19.605	0.582	0.582	0.000	0.000	0.000	0.000
18	A	56	LYS	1	0.794	0.895	22.359	14.216	14.216	0.000	0.000	0.000	0.000
19	A	57	GLU	-1	-0.959	-0.963	25.099	-11.656	-11.656	0.000	0.000	0.000	0.000
20	A	58	GLN	0	-0.070	-0.046	24.666	0.283	0.283	0.000	0.000	0.000	0.000
21	A	59	ASN	0	-0.056	-0.028	27.616	0.375	0.375	0.000	0.000	0.000	0.000
22	A	60	LEU	0	-0.074	-0.032	29.792	0.264	0.264	0.000	0.000	0.000	0.000
23	A	61	ALA	0	0.040	0.015	24.536	-0.216	-0.216	0.000	0.000	0.000	0.000
24	A	62	ALA	0	0.071	0.035	25.647	-0.360	-0.360	0.000	0.000	0.000	0.000
25	A	63	GLY	0	-0.048	-0.022	28.185	0.182	0.182	0.000	0.000	0.000	0.000
26	A	64	ILE	0	-0.075	-0.047	29.269	0.102	0.102	0.000	0.000	0.000	0.000
27	A	65	LYS	1	0.824	0.910	22.713	12.831	12.831	0.000	0.000	0.000	0.000
28	A	66	VAL	0	-0.001	0.004	22.054	0.012	0.012	0.000	0.000	0.000	0.000
29	A	67	GLU	-1	-0.918	-0.946	19.711	-14.069	-14.069	0.000	0.000	0.000	0.000
30	A	68	LEU	0	0.037	0.009	13.284	-0.323	-0.323	0.000	0.000	0.000	0.000
31	A	69	SER	0	-0.044	-0.033	16.759	1.143	1.143	0.000	0.000	0.000	0.000
32	A	70	SER	0	-0.061	-0.027	18.531	1.329	1.329	0.000	0.000	0.000	0.000
33	A	71	ARG	1	0.839	0.907	19.496	12.682	12.682	0.000	0.000	0.000	0.000
34	A	72	PHE	0	0.100	0.049	17.365	0.711	0.711	0.000	0.000	0.000	0.000
35	A	73	ASP	-1	-0.809	-0.905	22.771	-11.800	-11.800	0.000	0.000	0.000	0.000
36	A	74	LYS	1	0.789	0.879	24.707	10.984	10.984	0.000	0.000	0.000	0.000
37	A	75	ASP	-1	-0.818	-0.889	23.416	-12.347	-12.347	0.000	0.000	0.000	0.000
38	A	76	LEU	0	0.015	0.006	22.138	0.299	0.299	0.000	0.000	0.000	0.000
39	A	77	GLY	0	-0.030	-0.007	26.131	0.264	0.264	0.000	0.000	0.000	0.000
40	A	78	LEU	0	-0.015	0.008	23.755	0.294	0.294	0.000	0.000	0.000	0.000
41	A	79	ASP	-1	-0.828	-0.910	27.704	-9.817	-9.817	0.000	0.000	0.000	0.000
42	A	80	SER	0	-0.023	-0.031	25.717	-0.306	-0.306	0.000	0.000	0.000	0.000
43	A	81	LEU	0	-0.015	-0.019	25.606	-0.290	-0.290	0.000	0.000	0.000	0.000
44	A	82	ASP	-1	-0.886	-0.920	26.096	-11.432	-11.432	0.000	0.000	0.000	0.000
45	A	83	LYS	1	0.911	0.947	20.043	13.598	13.598	0.000	0.000	0.000	0.000
46	A	84	VAL	0	-0.014	-0.012	21.562	-0.565	-0.565	0.000	0.000	0.000	0.000
47	A	85	GLU	-1	-0.882	-0.919	22.580	-12.074	-12.074	0.000	0.000	0.000	0.000
48	A	86	LEU	0	0.046	0.026	19.518	-0.391	-0.391	0.000	0.000	0.000	0.000
49	A	87	LEU	0	-0.063	-0.036	16.422	-0.779	-0.779	0.000	0.000	0.000	0.000
50	A	88	ILE	0	-0.009	-0.011	18.892	-0.415	-0.415	0.000	0.000	0.000	0.000
51	A	89	SER	0	-0.007	-0.016	21.398	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	90	LEU	0	-0.039	-0.032	15.829	-0.475	-0.475	0.000	0.000	0.000	0.000
53	A	91	GLU	-1	-0.850	-0.918	16.970	-17.200	-17.200	0.000	0.000	0.000	0.000
54	A	92	GLU	-1	-0.995	-0.982	18.417	-12.553	-12.553	0.000	0.000	0.000	0.000
55	A	93	ASP	-1	-0.940	-0.953	17.736	-15.210	-15.210	0.000	0.000	0.000	0.000
56	A	94	PHE	0	-0.087	-0.052	12.717	-1.074	-1.074	0.000	0.000	0.000	0.000
57	A	95	GLY	0	0.042	0.050	15.070	0.632	0.632	0.000	0.000	0.000	0.000
58	A	96	VAL	0	-0.140	-0.100	10.875	-0.463	-0.463	0.000	0.000	0.000	0.000
59	A	97	GLU	-1	-0.908	-0.934	14.205	-14.881	-14.881	0.000	0.000	0.000	0.000
60	A	98	VAL	0	-0.058	-0.035	13.806	-1.431	-1.431	0.000	0.000	0.000	0.000
61	A	99	PRO	0	-0.040	-0.023	13.812	0.966	0.966	0.000	0.000	0.000	0.000
62	A	100	ASP	-1	-0.800	-0.898	16.679	-13.483	-13.483	0.000	0.000	0.000	0.000
63	A	101	ALA	0	-0.045	-0.036	18.347	-0.079	-0.079	0.000	0.000	0.000	0.000
64	A	102	GLU	-1	-0.981	-0.999	12.147	-20.983	-20.983	0.000	0.000	0.000	0.000
65	A	103	ILE	0	0.005	0.003	15.727	-0.320	-0.320	0.000	0.000	0.000	0.000
66	A	104	ASP	-1	-0.954	-0.970	18.253	-12.709	-12.709	0.000	0.000	0.000	0.000
67	A	105	LYS	1	0.792	0.902	14.986	16.835	16.835	0.000	0.000	0.000	0.000
68	A	106	ILE	0	0.021	0.023	12.982	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	107	HIS	0	-0.025	-0.017	15.925	1.353	1.353	0.000	0.000	0.000	0.000
70	A	108	THR	0	-0.108	-0.074	15.283	0.512	0.512	0.000	0.000	0.000	0.000
71	A	109	VAL	0	0.059	0.031	15.269	-0.622	-0.622	0.000	0.000	0.000	0.000
72	A	110	GLU	-1	-0.834	-0.920	11.861	-19.910	-19.910	0.000	0.000	0.000	0.000
73	A	111	ASP	-1	-0.824	-0.894	10.903	-21.575	-21.575	0.000	0.000	0.000	0.000
74	A	112	ALA	0	0.060	0.039	11.011	-1.462	-1.462	0.000	0.000	0.000	0.000
75	A	113	VAL	0	0.015	0.006	9.557	-1.506	-1.506	0.000	0.000	0.000	0.000
76	A	114	ASN	0	-0.069	-0.055	6.886	-5.749	-5.749	0.000	0.000	0.000	0.000
77	A	115	PHE	0	0.030	0.024	6.148	-4.918	-4.918	0.000	0.000	0.000	0.000
78	A	116	PHE	0	0.084	0.040	7.194	-3.039	-3.039	0.000	0.000	0.000	0.000
82	A	120	PRO	0	-0.044	-0.029	6.363	0.346	0.346	0.000	0.000	0.000	0.000
83	A	121	SER	0	-0.060	-0.025	7.811	0.724	0.724	0.000	0.000	0.000	0.000
84	A	122	SER	-1	-0.874	-0.940	8.162	-23.506	-23.506	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:SER)