FMO DATABASE

FMODB ID: 8789Y

Calculation Name: 2MJD-A-Other547

Preferred Name:

Target Type:

Ligand Name: fe2/s2 (inorganic) cluster

Ligand 3-letter code: FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2MJD

Chain ID: A

ChEMBL ID:

UniProt ID: Q12184

Base Structure: SolutionNMR

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-877793.787608
FMO2-HF: Nuclear repulsion	831140.637893
FMO2-HF: Total energy	-46653.149715
FMO2-MP2: Total energy	-46781.225468

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-180.106	-178.396	0.002	-0.682	-1.031	-0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.891

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	GLU	-1	-0.903	-0.938	3.828	-29.086	-27.936	-0.014	-0.448	-0.689	-0.003
93	A	93	LYS	1	0.832	0.883	3.091	57.030	57.590	0.016	-0.234	-0.342	-0.002
4	A	4	LEU	0	0.014	0.019	5.614	-4.644	-4.644	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.949	0.971	8.144	26.331	26.331	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.053	0.030	11.668	-0.439	-0.439	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.062	-0.022	14.798	0.949	0.949	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.050	0.018	18.200	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.036	-0.020	21.564	0.243	0.243	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.009	-0.006	25.008	-0.078	-0.078	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.926	0.963	27.536	9.940	9.940	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.906	-0.949	30.950	-9.187	-9.187	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.024	-0.007	30.189	0.195	0.195	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.008	0.003	28.093	-0.196	-0.196	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.001	-0.004	23.291	0.024	0.024	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.889	0.949	22.277	13.016	13.016	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.005	-0.007	16.442	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.049	-0.038	16.661	0.689	0.689	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.905	-0.950	11.844	-24.148	-24.148	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.029	-0.020	11.174	1.815	1.815	0.000	0.000	0.000	0.000
21	A	21	CYS	0	0.036	0.019	9.386	-3.166	-3.166	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.828	-0.928	7.048	-42.878	-42.878	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.084	-0.048	9.613	1.276	1.276	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.908	-0.953	12.714	-17.745	-17.745	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.010	-0.022	15.065	-0.757	-0.757	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.024	0.001	17.136	0.085	0.085	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.020	0.001	19.543	0.377	0.377	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.804	-0.882	19.500	-14.557	-14.557	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.006	0.005	15.328	0.170	0.170	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.038	-0.019	19.331	0.352	0.352	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.006	-0.001	22.661	0.531	0.531	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.021	0.016	21.487	0.356	0.356	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.801	0.894	18.447	15.469	15.469	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.037	-0.014	22.085	0.432	0.432	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.025	-0.011	22.186	0.211	0.211	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.939	-0.959	26.084	-9.701	-9.701	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.099	-0.047	26.241	-0.089	-0.089	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.880	-0.950	29.608	-9.095	-9.095	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.024	-0.032	31.418	-0.040	-0.040	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.003	0.021	32.178	0.174	0.174	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.006	0.001	30.387	0.174	0.174	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.022	0.001	32.031	-0.085	-0.085	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.023	0.002	33.047	0.061	0.061	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.013	-0.013	31.210	-0.044	-0.044	0.000	0.000	0.000	0.000
45	A	45	CYS	0	0.005	0.027	30.822	-0.203	-0.203	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.005	-0.035	27.309	-0.378	-0.378	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.007	0.012	26.766	-0.517	-0.517	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.046	0.017	26.789	0.296	0.296	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.040	0.005	26.460	0.263	0.263	0.000	0.000	0.000	0.000
50	A	50	CYS	0	0.009	0.029	26.674	0.213	0.213	0.000	0.000	0.000	0.000
51	A	51	HIS	0	0.041	0.010	26.167	-0.179	-0.179	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.017	-0.017	22.220	-0.155	-0.155	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.012	0.023	25.130	0.320	0.320	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.021	-0.010	18.807	-0.432	-0.432	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.810	-0.915	18.542	-14.976	-14.976	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.017	-0.004	20.134	-0.425	-0.425	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.924	-0.940	16.973	-16.086	-16.086	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.071	-0.061	11.878	-0.077	-0.077	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.021	-0.003	16.797	-0.688	-0.688	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.923	-0.957	19.315	-14.582	-14.582	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.031	-0.005	15.543	0.106	0.106	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.093	-0.041	15.417	-0.671	-0.671	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.062	-0.027	18.445	0.555	0.555	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.902	-0.946	21.454	-11.939	-11.939	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.063	-0.021	24.829	-0.121	-0.121	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.877	-0.944	26.789	-9.548	-9.548	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.978	-0.996	30.356	-8.977	-8.977	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.957	-0.974	33.567	-9.209	-9.209	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.885	-0.966	27.423	-11.817	-11.817	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.082	-0.045	29.822	-0.048	-0.048	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.833	-0.908	31.071	-8.642	-8.642	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.007	-0.008	29.238	0.104	0.104	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.106	-0.044	27.783	-0.237	-0.237	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.902	-0.941	31.723	-8.675	-8.675	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.066	-0.029	35.125	0.387	0.387	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.033	-0.026	33.312	0.187	0.187	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.038	-0.025	35.342	0.165	0.165	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.043	-0.025	35.301	-0.174	-0.174	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.012	0.022	30.609	-0.178	-0.178	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.021	-0.006	29.040	0.102	0.102	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.910	-0.960	29.164	-10.392	-10.392	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.024	-0.010	23.764	-0.053	-0.053	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.105	-0.052	24.683	-0.421	-0.421	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.908	0.941	17.872	16.108	16.108	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.079	0.045	23.532	-0.065	-0.065	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.066	-0.039	21.692	-0.739	-0.739	0.000	0.000	0.000	0.000
87	A	87	CYS	0	0.005	-0.025	20.835	-0.684	-0.684	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.051	0.020	21.052	-0.516	-0.516	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.029	-0.009	15.210	-0.818	-0.818	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.966	0.998	12.743	21.739	21.739	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.000	0.020	11.088	-0.584	-0.584	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.019	-0.043	9.551	-0.659	-0.659	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.868	-0.891	6.538	-30.661	-30.661	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.036	-0.008	9.259	2.012	2.012	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.898	-0.956	6.731	-33.387	-33.387	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.066	-0.025	8.767	1.732	1.732	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.004	0.033	12.177	1.998	1.998	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.827	0.899	14.533	15.336	15.336	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.021	0.003	18.262	0.073	0.073	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.036	-0.021	21.036	0.148	0.148	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.021	0.015	24.661	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	103	PRO	0	-0.011	0.009	26.717	0.322	0.322	0.000	0.000	0.000	0.000
104	A	104	GLN	0	-0.054	-0.039	30.252	0.224	0.224	0.000	0.000	0.000	0.000
105	A	105	MET	0	0.014	0.024	33.753	0.095	0.095	0.000	0.000	0.000	0.000
106	A	106	THR	0	-0.010	-0.030	36.076	0.158	0.158	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.954	1.000	39.624	7.949	7.949	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.017	-0.007	41.498	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.043	-0.015	44.291	0.201	0.201	0.000	0.000	0.000	0.000
110	A	110	ASN	0	-0.012	-0.018	41.589	-0.334	-0.334	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.016	-0.009	39.644	0.120	0.120	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.044	-0.032	39.849	0.009	0.009	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.851	-0.917	37.032	-8.400	-8.400	0.000	0.000	0.000	0.000
114	A	114	PHE	0	-0.103	-0.051	38.367	-0.094	-0.094	0.000	0.000	0.000	0.000
115	A	115	SER	-1	-0.939	-0.955	36.454	-8.222	-8.222	0.000	0.000	0.000	0.000

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