FMO DATABASE

FMODB ID: RQRM8

Calculation Name: 2CKF-B-Xray547

Preferred Name:

Target Type:

Ligand Name: fe2/s2 (inorganic) cluster | fe (iii) ion

Ligand 3-letter code: FES | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CKF

Chain ID: B

ChEMBL ID:

UniProt ID: Q65AT1

Base Structure: X-ray

Registration Date: 2025-10-03

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1893136.577132
FMO2-HF: Nuclear repulsion	1822222.364767
FMO2-HF: Total energy	-70914.212366
FMO2-MP2: Total energy	-71123.126711

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:GLN)

Summations of interaction energy for fragment #1(A:5: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.
-203.46	-201.893	23.98	-12.827	-12.719	-0.129

Interaction energy analysis for fragmet #1(A:5:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.744 / q_NPA : 0.840

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	PRO	0	0.028	0.014	3.359	-2.767	-0.844	0.028	-0.824	-1.127	-0.003
105	A	109	PHE	0	-0.033	-0.029	2.234	-5.474	-4.409	1.969	-1.055	-1.979	-0.004
106	A	110	GLU	-1	-0.907	-0.958	3.352	-37.103	-35.637	0.029	-0.615	-0.880	-0.003
107	A	111	ALA	0	-0.019	0.000	1.868	-28.911	-28.978	8.496	-4.289	-4.139	-0.053
108	A	112	GLU	-1	-0.934	-0.964	3.594	-24.042	-23.943	0.010	-0.039	-0.070	0.000
113	A	117	ASP	-1	-0.809	-0.890	1.763	-57.983	-60.974	13.449	-5.983	-4.475	-0.066
114	A	118	VAL	0	-0.049	-0.041	4.163	-1.510	-1.438	-0.001	-0.022	-0.049	0.000
4	A	8	VAL	0	0.004	0.016	5.719	2.680	2.680	0.000	0.000	0.000	0.000
5	A	9	THR	0	0.024	0.009	7.969	1.516	1.516	0.000	0.000	0.000	0.000
6	A	10	PRO	0	0.034	-0.002	11.583	0.184	0.184	0.000	0.000	0.000	0.000
7	A	11	ASP	-1	-0.901	-0.941	14.273	-16.985	-16.985	0.000	0.000	0.000	0.000
8	A	12	VAL	0	0.002	-0.002	10.424	0.937	0.937	0.000	0.000	0.000	0.000
9	A	13	HIS	0	-0.037	-0.020	11.619	-1.284	-1.284	0.000	0.000	0.000	0.000
10	A	14	TYR	0	-0.007	-0.007	12.818	1.190	1.190	0.000	0.000	0.000	0.000
11	A	15	ALA	0	-0.010	-0.007	15.089	0.957	0.957	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.032	0.025	10.727	0.844	0.844	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.825	-0.897	14.049	-16.439	-16.439	0.000	0.000	0.000	0.000
14	A	18	ALA	0	-0.081	-0.040	16.737	1.059	1.059	0.000	0.000	0.000	0.000
15	A	19	HIS	0	0.020	0.021	15.485	0.975	0.975	0.000	0.000	0.000	0.000
16	A	20	TYR	0	0.011	-0.035	11.766	0.589	0.589	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.854	0.911	17.826	15.678	15.678	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.065	-0.026	20.960	0.796	0.796	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.713	-0.834	17.115	-14.939	-14.939	0.000	0.000	0.000	0.000
20	A	24	VAL	0	0.007	0.007	20.714	0.606	0.606	0.000	0.000	0.000	0.000
21	A	25	ARG	1	0.907	0.955	23.025	11.733	11.733	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.021	0.006	23.610	0.519	0.519	0.000	0.000	0.000	0.000
23	A	27	LEU	0	0.032	0.023	21.478	0.504	0.504	0.000	0.000	0.000	0.000
24	A	28	GLN	0	-0.036	-0.028	25.872	0.316	0.316	0.000	0.000	0.000	0.000
25	A	29	THR	0	-0.104	-0.064	28.557	0.383	0.383	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.041	0.027	30.110	0.242	0.242	0.000	0.000	0.000	0.000
27	A	31	GLN	0	-0.074	-0.024	28.253	0.104	0.104	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.057	0.015	26.429	-0.287	-0.287	0.000	0.000	0.000	0.000
29	A	33	ARG	1	0.855	0.897	25.964	8.356	8.356	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.877	-0.940	26.416	-9.810	-9.810	0.000	0.000	0.000	0.000
31	A	35	TRP	0	-0.042	-0.043	19.354	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	36	LEU	0	-0.001	0.010	21.797	-0.466	-0.466	0.000	0.000	0.000	0.000
33	A	37	HIS	0	0.006	-0.022	21.767	-0.277	-0.277	0.000	0.000	0.000	0.000
34	A	38	GLY	0	-0.020	0.006	22.663	-0.152	-0.152	0.000	0.000	0.000	0.000
35	A	39	MET	0	-0.041	-0.026	18.430	-0.438	-0.438	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.010	0.013	17.161	-0.966	-0.966	0.000	0.000	0.000	0.000
37	A	41	ALA	0	0.014	0.009	15.766	0.467	0.467	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.915	-0.968	17.670	-11.506	-11.506	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.846	-0.900	14.510	-16.382	-16.382	0.000	0.000	0.000	0.000
40	A	44	ILE	0	-0.090	-0.027	14.831	-0.692	-0.692	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.047	-0.016	14.889	-0.195	-0.195	0.000	0.000	0.000	0.000
42	A	46	TYR	0	0.029	0.007	15.072	-0.976	-0.976	0.000	0.000	0.000	0.000
43	A	47	TRP	0	0.011	-0.002	13.641	0.275	0.275	0.000	0.000	0.000	0.000
44	A	48	MET	0	-0.003	0.003	17.145	-0.345	-0.345	0.000	0.000	0.000	0.000
45	A	49	PRO	0	0.019	0.019	16.831	0.754	0.754	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.062	-0.028	20.107	0.068	0.068	0.000	0.000	0.000	0.000
47	A	51	TYR	0	0.033	0.028	15.496	0.108	0.108	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.852	-0.930	22.161	-10.238	-10.238	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.011	-0.016	24.353	-0.453	-0.453	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.811	0.901	21.784	12.644	12.644	0.000	0.000	0.000	0.000
51	A	55	PHE	0	0.003	-0.005	26.093	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.060	0.015	23.358	-0.134	-0.134	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.936	0.971	24.688	9.497	9.497	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.849	-0.911	25.162	-10.841	-10.841	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.939	0.961	22.509	12.189	12.189	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.804	0.896	23.133	10.564	10.564	0.000	0.000	0.000	0.000
57	A	61	PRO	0	0.016	0.012	19.233	-0.277	-0.277	0.000	0.000	0.000	0.000
58	A	62	ASP	-1	-0.847	-0.930	15.686	-15.477	-15.477	0.000	0.000	0.000	0.000
59	A	63	PRO	0	-0.071	-0.025	17.930	0.009	0.009	0.000	0.000	0.000	0.000
60	A	64	THR	0	-0.009	-0.031	16.903	-0.820	-0.820	0.000	0.000	0.000	0.000
61	A	65	PRO	0	-0.003	-0.020	16.146	0.341	0.341	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.898	-0.922	18.891	-12.140	-12.140	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.898	-0.910	21.341	-11.885	-11.885	0.000	0.000	0.000	0.000
64	A	68	ALA	0	-0.038	-0.025	23.181	0.040	0.040	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.001	-0.007	21.681	-0.419	-0.419	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.059	-0.029	23.223	0.509	0.509	0.000	0.000	0.000	0.000
67	A	71	TYR	0	-0.076	-0.068	21.169	0.449	0.449	0.000	0.000	0.000	0.000
68	A	72	ASN	0	-0.032	-0.044	20.257	-0.958	-0.958	0.000	0.000	0.000	0.000
69	A	73	ASP	-1	-0.734	-0.825	20.572	-11.133	-11.133	0.000	0.000	0.000	0.000
70	A	74	ASP	-1	-0.796	-0.903	19.804	-11.849	-11.849	0.000	0.000	0.000	0.000
71	A	75	PHE	0	0.010	-0.006	20.560	0.186	0.186	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.805	-0.912	22.303	-9.619	-9.619	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.891	-0.929	24.241	-10.475	-10.475	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.005	-0.013	19.665	0.261	0.261	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.842	0.920	24.270	10.087	10.087	0.000	0.000	0.000	0.000
76	A	80	GLN	0	-0.049	-0.020	26.971	0.496	0.496	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.796	0.894	25.106	11.037	11.037	0.000	0.000	0.000	0.000
78	A	82	VAL	0	0.015	0.016	25.532	0.186	0.186	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.781	-0.867	28.544	-8.611	-8.611	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.884	0.953	31.590	8.882	8.882	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.055	-0.031	29.377	0.237	0.237	0.000	0.000	0.000	0.000
82	A	86	TYR	0	0.010	0.012	30.429	0.068	0.068	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.025	0.008	35.469	0.299	0.299	0.000	0.000	0.000	0.000
84	A	88	GLY	0	0.041	0.011	38.303	-0.049	-0.049	0.000	0.000	0.000	0.000
85	A	89	GLN	0	-0.030	-0.030	40.339	0.286	0.286	0.000	0.000	0.000	0.000
86	A	90	VAL	0	-0.021	0.010	35.554	0.002	0.002	0.000	0.000	0.000	0.000
87	A	91	TRP	0	0.061	0.022	38.868	-0.073	-0.073	0.000	0.000	0.000	0.000
88	A	92	MET	0	-0.087	-0.040	36.406	0.065	0.065	0.000	0.000	0.000	0.000
89	A	93	GLU	-1	-0.812	-0.878	34.514	-8.507	-8.507	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.878	-0.905	37.861	-6.915	-6.915	0.000	0.000	0.000	0.000
91	A	95	PRO	0	-0.021	-0.030	41.422	0.098	0.098	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.013	0.000	36.494	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	97	SER	0	-0.093	-0.063	33.809	0.010	0.010	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.896	0.940	33.585	8.386	8.386	0.000	0.000	0.000	0.000
95	A	99	ILE	0	0.046	0.034	26.417	0.045	0.045	0.000	0.000	0.000	0.000
96	A	100	ARG	1	0.867	0.929	28.171	10.005	10.005	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.017	-0.013	22.214	0.177	0.177	0.000	0.000	0.000	0.000
98	A	102	PHE	0	-0.070	-0.042	23.532	0.285	0.285	0.000	0.000	0.000	0.000
99	A	103	VAL	0	0.035	0.029	17.067	-0.132	-0.132	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.052	-0.032	18.257	0.018	0.018	0.000	0.000	0.000	0.000
101	A	105	ASN	0	-0.010	-0.014	12.901	0.636	0.636	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.016	0.018	12.213	-0.750	-0.750	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.924	-0.959	8.025	-29.404	-29.404	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.019	0.015	7.566	-0.553	-0.553	0.000	0.000	0.000	0.000
109	A	113	ASN	0	-0.043	-0.036	7.252	1.189	1.189	0.000	0.000	0.000	0.000
110	A	114	GLY	0	0.011	0.019	8.899	1.690	1.690	0.000	0.000	0.000	0.000
111	A	115	GLU	-1	-0.910	-0.956	7.172	-22.283	-22.283	0.000	0.000	0.000	0.000
112	A	116	LEU	0	-0.024	-0.022	5.153	-3.900	-3.900	0.000	0.000	0.000	0.000
115	A	119	LEU	0	0.043	0.038	6.963	2.179	2.179	0.000	0.000	0.000	0.000
116	A	120	SER	0	0.004	-0.007	9.666	0.876	0.876	0.000	0.000	0.000	0.000
117	A	121	ASN	0	0.030	0.029	13.494	-0.093	-0.093	0.000	0.000	0.000	0.000
118	A	122	ILE	0	0.000	-0.011	16.660	0.318	0.318	0.000	0.000	0.000	0.000
119	A	123	LEU	0	-0.010	0.010	19.746	0.337	0.337	0.000	0.000	0.000	0.000
120	A	124	VAL	0	0.000	-0.001	23.070	0.042	0.042	0.000	0.000	0.000	0.000
121	A	125	TYR	0	0.004	0.001	25.628	0.368	0.368	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.849	0.907	28.738	9.561	9.561	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.029	-0.017	31.677	0.323	0.323	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.866	0.902	35.399	7.821	7.821	0.000	0.000	0.000	0.000
125	A	129	ARG	1	0.858	0.921	38.006	7.294	7.294	0.000	0.000	0.000	0.000
126	A	130	GLN	0	0.009	0.008	41.800	-0.067	-0.067	0.000	0.000	0.000	0.000
127	A	131	THR	0	0.011	-0.005	41.867	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	132	GLU	-1	-0.841	-0.876	38.098	-7.730	-7.730	0.000	0.000	0.000	0.000
129	A	133	VAL	0	0.002	-0.006	34.394	-0.112	-0.112	0.000	0.000	0.000	0.000
130	A	134	THR	0	-0.057	-0.042	31.878	0.070	0.070	0.000	0.000	0.000	0.000
131	A	135	VAL	0	-0.014	-0.019	27.940	-0.077	-0.077	0.000	0.000	0.000	0.000
132	A	136	HIS	0	-0.034	-0.022	24.960	-0.109	-0.109	0.000	0.000	0.000	0.000
133	A	137	THR	0	-0.073	-0.071	22.151	0.169	0.169	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.014	0.000	18.578	0.308	0.308	0.000	0.000	0.000	0.000
135	A	139	GLY	0	0.055	0.048	15.200	-0.351	-0.351	0.000	0.000	0.000	0.000
136	A	140	ARG	1	0.750	0.858	12.861	18.165	18.165	0.000	0.000	0.000	0.000
137	A	141	GLU	-1	-0.837	-0.919	8.968	-22.699	-22.699	0.000	0.000	0.000	0.000
138	A	142	ASP	-1	-0.692	-0.810	9.330	-17.924	-17.924	0.000	0.000	0.000	0.000
139	A	143	LYS	1	0.895	0.964	4.998	26.228	26.228	0.000	0.000	0.000	0.000
140	A	144	LEU	0	0.003	0.007	7.921	2.622	2.622	0.000	0.000	0.000	0.000
141	A	145	ARG	1	0.812	0.880	8.819	16.524	16.524	0.000	0.000	0.000	0.000
142	A	146	GLN	0	0.000	-0.006	11.412	1.522	1.522	0.000	0.000	0.000	0.000
143	A	147	ASP	-1	-0.874	-0.931	14.182	-13.591	-13.591	0.000	0.000	0.000	0.000
144	A	148	GLY	0	-0.018	0.010	17.683	0.304	0.304	0.000	0.000	0.000	0.000
145	A	149	ASN	0	-0.095	-0.052	20.198	0.082	0.082	0.000	0.000	0.000	0.000
146	A	150	GLY	0	0.070	0.024	18.666	0.499	0.499	0.000	0.000	0.000	0.000
147	A	151	PHE	0	0.014	0.000	11.484	-0.710	-0.710	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.816	0.910	14.580	14.367	14.367	0.000	0.000	0.000	0.000
149	A	153	VAL	0	-0.023	-0.004	11.906	-1.333	-1.333	0.000	0.000	0.000	0.000
150	A	154	PHE	0	0.024	0.002	8.337	1.345	1.345	0.000	0.000	0.000	0.000
151	A	155	ARG	1	0.836	0.920	9.857	18.050	18.050	0.000	0.000	0.000	0.000
152	A	156	ARG	1	0.727	0.806	11.179	15.562	15.562	0.000	0.000	0.000	0.000
153	A	157	LYS	1	0.857	0.946	11.830	20.246	20.246	0.000	0.000	0.000	0.000
154	A	158	LEU	0	-0.021	-0.013	13.773	-0.605	-0.605	0.000	0.000	0.000	0.000
155	A	159	ILE	0	0.001	-0.006	13.264	0.661	0.661	0.000	0.000	0.000	0.000
156	A	160	LEU	0	-0.004	-0.011	17.428	0.051	0.051	0.000	0.000	0.000	0.000
157	A	161	ASP	-1	-0.807	-0.871	19.910	-14.113	-14.113	0.000	0.000	0.000	0.000
158	A	162	ALA	0	-0.057	-0.024	22.101	0.379	0.379	0.000	0.000	0.000	0.000
159	A	163	ARG	1	0.920	0.966	25.576	10.530	10.530	0.000	0.000	0.000	0.000
160	A	164	VAL	0	-0.027	-0.020	26.780	0.208	0.208	0.000	0.000	0.000	0.000
161	A	165	THR	0	0.040	0.020	28.294	-0.118	-0.118	0.000	0.000	0.000	0.000
162	A	166	GLN	0	-0.009	-0.001	29.778	0.467	0.467	0.000	0.000	0.000	0.000
163	A	167	ASP	-1	-0.734	-0.838	31.130	-9.247	-9.247	0.000	0.000	0.000	0.000
164	A	168	LYS	1	0.838	0.911	33.002	7.924	7.924	0.000	0.000	0.000	0.000
165	A	169	ASN	0	-0.013	-0.003	31.506	-0.132	-0.132	0.000	0.000	0.000	0.000
166	A	170	LEU	0	0.069	0.042	25.345	0.023	0.023	0.000	0.000	0.000	0.000
167	A	171	TYR	0	-0.059	-0.029	26.638	-0.216	-0.216	0.000	0.000	0.000	0.000
168	A	172	PHE	0	-0.016	-0.025	23.683	0.373	0.373	0.000	0.000	0.000	0.000
169	A	173	PHE	0	0.032	0.033	21.938	-0.132	-0.132	0.000	0.000	0.000	0.000
170	A	174	CYS	-1	-0.751	-0.835	17.580	-14.544	-14.544	0.000	0.000	0.000	0.000

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