FMO DATABASE

FMODB ID: N6G2Q

Calculation Name: 1FFK-F-Xray549

Preferred Name:

Target Type:

Ligand Name: cadmium ion | magnesium ion | potassium ion

Ligand 3-letter code: CD | MG | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FFK

Chain ID: F

ChEMBL ID:

UniProt ID: P60617

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	177
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1633126.897665
FMO2-HF: Nuclear repulsion	1564296.969744
FMO2-HF: Total energy	-68829.927921
FMO2-MP2: Total energy	-69029.927437

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(F:1:MET)

Summations of interaction energy for fragment #1(F:1:MET)

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.
-123.201	-121.913	-0.008	-0.453	-0.827	0

Interaction energy analysis for fragmet #1(F:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.903

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].
3	F	3	SER	0	-0.005	0.003	3.837	-0.475	0.813	-0.008	-0.453	-0.827
4	F	4	GLU	-1	-0.927	-0.963	5.676	-31.877	-31.877	0.000	0.000	0.000
5	F	5	SER	0	-0.052	-0.016	7.809	1.196	1.196	0.000	0.000	0.000
6	F	6	GLU	-1	-0.909	-0.966	11.130	-20.917	-20.917	0.000	0.000	0.000
7	F	7	SER	0	-0.034	-0.007	13.211	0.951	0.951	0.000	0.000	0.000
8	F	8	GLY	0	-0.007	-0.016	16.083	0.510	0.510	0.000	0.000	0.000
9	F	9	GLY	0	-0.032	0.001	17.636	0.362	0.362	0.000	0.000	0.000
10	F	10	ASP	-1	-0.920	-0.962	19.932	-12.337	-12.337	0.000	0.000	0.000
11	F	11	PHE	0	-0.019	-0.010	23.509	-0.366	-0.366	0.000	0.000	0.000
12	F	12	HIS	0	-0.017	-0.009	24.814	0.461	0.461	0.000	0.000	0.000
13	F	13	GLU	-1	-0.823	-0.906	27.206	-9.258	-9.258	0.000	0.000	0.000
14	F	14	MET	0	-0.047	-0.033	29.710	0.176	0.176	0.000	0.000	0.000
15	F	15	ARG	1	0.879	0.917	20.546	13.810	13.810	0.000	0.000	0.000
16	F	16	GLU	-1	-0.872	-0.918	27.811	-10.131	-10.131	0.000	0.000	0.000
17	F	17	PRO	0	-0.066	-0.035	28.939	0.149	0.149	0.000	0.000	0.000
18	F	18	ARG	1	0.978	1.001	31.745	8.773	8.773	0.000	0.000	0.000
19	F	19	ILE	0	0.107	0.058	35.535	-0.189	-0.189	0.000	0.000	0.000
20	F	20	GLU	-1	-0.951	-0.959	38.162	-8.274	-8.274	0.000	0.000	0.000
21	F	21	LYS	1	0.876	0.921	39.663	8.170	8.170	0.000	0.000	0.000
22	F	22	VAL	0	0.078	0.051	41.142	-0.223	-0.223	0.000	0.000	0.000
23	F	23	VAL	0	-0.128	-0.056	43.491	0.195	0.195	0.000	0.000	0.000
24	F	24	VAL	0	0.091	0.055	45.353	-0.098	-0.098	0.000	0.000	0.000
25	F	25	HIS	0	-0.142	-0.092	48.041	0.204	0.204	0.000	0.000	0.000
26	F	26	MET	0	0.078	0.062	49.924	0.023	0.023	0.000	0.000	0.000
27	F	27	GLY	0	0.014	0.003	51.866	0.084	0.084	0.000	0.000	0.000
28	F	28	ILE	0	0.027	0.020	52.859	0.018	0.018	0.000	0.000	0.000
29	F	29	GLY	0	-0.015	-0.006	55.647	0.082	0.082	0.000	0.000	0.000
30	F	30	HIS	1	0.792	0.865	56.715	5.398	5.398	0.000	0.000	0.000
31	F	31	GLY	0	0.061	0.043	60.136	-0.026	-0.026	0.000	0.000	0.000
32	F	32	GLY	0	-0.030	-0.021	62.066	0.054	0.054	0.000	0.000	0.000
33	F	33	ARG	1	0.952	0.963	64.537	4.665	4.665	0.000	0.000	0.000
34	F	34	ASP	-1	-0.781	-0.875	62.166	-5.102	-5.102	0.000	0.000	0.000
35	F	35	LEU	0	-0.028	0.002	58.253	-0.074	-0.074	0.000	0.000	0.000
36	F	36	ALA	0	-0.032	-0.019	60.649	-0.055	-0.055	0.000	0.000	0.000
37	F	37	ASN	0	0.045	0.014	62.620	0.032	0.032	0.000	0.000	0.000
38	F	38	ALA	0	0.059	0.033	57.545	-0.031	-0.031	0.000	0.000	0.000
39	F	39	GLU	-1	-0.814	-0.879	58.031	-5.533	-5.533	0.000	0.000	0.000
40	F	40	ASP	-1	-0.906	-0.951	59.175	-5.168	-5.168	0.000	0.000	0.000
41	F	41	ILE	0	0.022	0.022	56.780	-0.048	-0.048	0.000	0.000	0.000
42	F	42	LEU	0	-0.011	-0.018	52.915	-0.090	-0.090	0.000	0.000	0.000
43	F	43	GLY	0	-0.012	0.009	55.583	-0.093	-0.093	0.000	0.000	0.000
44	F	44	GLU	-1	-0.942	-0.958	57.713	-5.286	-5.286	0.000	0.000	0.000
45	F	45	ILE	0	-0.051	-0.011	52.597	-0.041	-0.041	0.000	0.000	0.000
46	F	46	THR	0	-0.058	-0.051	51.485	-0.114	-0.114	0.000	0.000	0.000
47	F	47	GLY	0	0.025	0.028	53.374	-0.065	-0.065	0.000	0.000	0.000
48	F	48	GLN	0	-0.108	-0.073	51.081	0.026	0.026	0.000	0.000	0.000
49	F	49	MET	0	-0.012	-0.006	55.712	0.076	0.076	0.000	0.000	0.000
50	F	50	PRO	0	0.014	0.025	54.835	-0.103	-0.103	0.000	0.000	0.000
51	F	51	VAL	0	-0.064	-0.039	53.338	0.095	0.095	0.000	0.000	0.000
52	F	52	ARG	1	0.782	0.847	54.511	5.240	5.240	0.000	0.000	0.000
53	F	53	THR	0	-0.041	-0.024	50.720	-0.104	-0.104	0.000	0.000	0.000
54	F	54	LYS	1	0.933	0.960	53.868	5.607	5.607	0.000	0.000	0.000
55	F	55	ALA	0	0.027	0.025	53.562	-0.157	-0.157	0.000	0.000	0.000
56	F	56	LYS	1	0.935	0.953	47.216	6.831	6.831	0.000	0.000	0.000
57	F	57	ARG	1	0.964	0.977	48.351	6.472	6.472	0.000	0.000	0.000
58	F	58	THR	0	0.025	0.017	54.787	0.007	0.007	0.000	0.000	0.000
59	F	59	VAL	0	-0.056	-0.025	53.109	-0.083	-0.083	0.000	0.000	0.000
60	F	60	GLY	0	0.017	0.003	56.420	0.032	0.032	0.000	0.000	0.000
61	F	61	GLU	-1	-0.963	-0.969	53.969	-5.986	-5.986	0.000	0.000	0.000
62	F	62	PHE	0	-0.006	-0.013	52.053	-0.021	-0.021	0.000	0.000	0.000
63	F	63	ASP	-1	-0.924	-0.954	57.944	-5.144	-5.144	0.000	0.000	0.000
64	F	64	ILE	0	-0.027	0.009	55.594	0.048	0.048	0.000	0.000	0.000
65	F	65	ARG	1	0.927	0.945	59.126	4.964	4.964	0.000	0.000	0.000
66	F	66	GLU	-1	-0.944	-0.985	56.513	-5.778	-5.778	0.000	0.000	0.000
67	F	67	GLY	0	-0.039	-0.021	57.612	0.102	0.102	0.000	0.000	0.000
68	F	68	ASP	-1	-0.842	-0.914	59.237	-5.268	-5.268	0.000	0.000	0.000
69	F	69	PRO	0	-0.087	-0.053	57.893	-0.126	-0.126	0.000	0.000	0.000
70	F	70	ILE	0	0.010	0.012	54.000	0.055	0.055	0.000	0.000	0.000
71	F	71	GLY	0	0.062	0.028	54.398	0.003	0.003	0.000	0.000	0.000
72	F	72	ALA	0	-0.019	0.010	54.651	0.028	0.028	0.000	0.000	0.000
73	F	73	LYS	1	0.954	0.976	48.309	6.525	6.525	0.000	0.000	0.000
74	F	74	VAL	0	0.074	0.048	50.560	0.107	0.107	0.000	0.000	0.000
75	F	75	THR	0	-0.119	-0.080	45.485	-0.208	-0.208	0.000	0.000	0.000
76	F	76	LEU	0	0.062	0.062	47.022	0.055	0.055	0.000	0.000	0.000
77	F	77	ARG	1	0.907	0.926	43.656	7.023	7.023	0.000	0.000	0.000
78	F	78	ASP	-1	-0.899	-0.952	43.713	-7.123	-7.123	0.000	0.000	0.000
79	F	79	GLU	-1	-0.869	-0.930	44.713	-6.646	-6.646	0.000	0.000	0.000
80	F	80	MET	0	0.066	0.046	46.753	0.041	0.041	0.000	0.000	0.000
81	F	81	ALA	0	-0.065	-0.033	43.764	0.026	0.026	0.000	0.000	0.000
82	F	82	GLU	-1	-0.926	-0.958	41.262	-7.780	-7.780	0.000	0.000	0.000
83	F	83	GLU	-1	-0.923	-0.963	44.186	-6.386	-6.386	0.000	0.000	0.000
84	F	84	PHE	0	-0.005	-0.008	45.940	0.026	0.026	0.000	0.000	0.000
85	F	85	LEU	0	-0.011	-0.018	40.598	-0.003	-0.003	0.000	0.000	0.000
86	F	86	GLN	0	-0.007	-0.005	44.253	0.046	0.046	0.000	0.000	0.000
87	F	87	THR	0	-0.070	-0.032	45.513	0.105	0.105	0.000	0.000	0.000
88	F	88	ALA	0	-0.016	-0.017	45.902	0.051	0.051	0.000	0.000	0.000
89	F	89	LEU	0	-0.030	-0.015	39.969	-0.051	-0.051	0.000	0.000	0.000
90	F	90	PRO	0	-0.019	-0.012	43.578	-0.070	-0.070	0.000	0.000	0.000
91	F	91	LEU	0	-0.033	-0.001	45.539	0.083	0.083	0.000	0.000	0.000
92	F	92	ALA	0	-0.018	-0.008	43.488	0.056	0.056	0.000	0.000	0.000
93	F	93	GLU	-1	-0.950	-0.959	40.978	-7.613	-7.613	0.000	0.000	0.000
94	F	94	LEU	0	0.006	0.001	36.731	-0.091	-0.091	0.000	0.000	0.000
95	F	95	ALA	0	0.034	0.035	35.143	-0.083	-0.083	0.000	0.000	0.000
96	F	96	THR	0	0.011	-0.013	28.500	-0.161	-0.161	0.000	0.000	0.000
97	F	97	SER	0	-0.077	-0.044	31.722	-0.086	-0.086	0.000	0.000	0.000
98	F	98	GLN	0	0.009	0.019	33.293	0.023	0.023	0.000	0.000	0.000
99	F	99	PHE	0	-0.005	-0.006	31.230	0.093	0.093	0.000	0.000	0.000
100	F	100	ASP	-1	-0.765	-0.847	31.363	-10.107	-10.107	0.000	0.000	0.000
101	F	101	ASP	-1	-0.934	-0.981	26.650	-11.890	-11.890	0.000	0.000	0.000
102	F	102	THR	0	-0.241	-0.146	26.930	-0.354	-0.354	0.000	0.000	0.000
103	F	103	GLY	0	0.014	0.003	29.411	0.031	0.031	0.000	0.000	0.000
104	F	104	ASN	0	-0.076	-0.060	30.594	0.397	0.397	0.000	0.000	0.000
105	F	105	PHE	0	0.085	0.040	33.743	-0.228	-0.228	0.000	0.000	0.000
106	F	106	SER	0	-0.078	-0.035	36.274	0.261	0.261	0.000	0.000	0.000
107	F	107	PHE	0	0.053	0.021	39.576	-0.157	-0.157	0.000	0.000	0.000
108	F	108	GLY	0	0.018	0.013	42.202	0.110	0.110	0.000	0.000	0.000
109	F	109	VAL	0	0.003	0.004	45.845	-0.093	-0.093	0.000	0.000	0.000
110	F	110	GLU	-1	-0.926	-0.967	48.613	-6.484	-6.484	0.000	0.000	0.000
111	F	111	GLU	-1	-0.928	-0.968	51.107	-5.613	-5.613	0.000	0.000	0.000
112	F	112	HIS	0	0.004	-0.002	53.714	-0.116	-0.116	0.000	0.000	0.000
113	F	113	THR	0	-0.042	-0.038	55.215	0.029	0.029	0.000	0.000	0.000
114	F	114	GLU	-1	-0.892	-0.942	51.454	-6.312	-6.312	0.000	0.000	0.000
115	F	115	PHE	0	0.008	-0.002	49.306	-0.089	-0.089	0.000	0.000	0.000
116	F	116	PRO	0	0.002	-0.006	53.344	0.120	0.120	0.000	0.000	0.000
117	F	117	SER	0	-0.067	-0.026	56.270	0.074	0.074	0.000	0.000	0.000
118	F	118	GLN	0	-0.038	-0.038	57.502	0.073	0.073	0.000	0.000	0.000
119	F	119	GLU	-1	-0.923	-0.953	59.799	-4.962	-4.962	0.000	0.000	0.000
120	F	120	TYR	0	-0.016	-0.018	62.441	0.021	0.021	0.000	0.000	0.000
121	F	121	ASP	-1	-0.783	-0.860	63.740	-4.703	-4.703	0.000	0.000	0.000
122	F	122	PRO	0	-0.032	-0.034	65.712	-0.036	-0.036	0.000	0.000	0.000
123	F	123	SER	0	-0.168	-0.100	67.638	0.016	0.016	0.000	0.000	0.000
124	F	124	ILE	0	-0.023	-0.004	62.836	0.008	0.008	0.000	0.000	0.000
125	F	125	GLY	0	-0.017	0.005	63.270	-0.054	-0.054	0.000	0.000	0.000
126	F	126	ILE	0	0.011	-0.007	57.150	0.009	0.009	0.000	0.000	0.000
127	F	127	TYR	0	-0.082	-0.049	56.183	0.008	0.008	0.000	0.000	0.000
128	F	128	GLY	0	0.089	0.067	52.448	-0.026	-0.026	0.000	0.000	0.000
129	F	129	LEU	0	-0.099	-0.061	48.844	0.072	0.072	0.000	0.000	0.000
130	F	130	ASP	-1	-0.843	-0.904	45.686	-6.987	-6.987	0.000	0.000	0.000
131	F	131	VAL	0	0.007	0.003	43.105	0.109	0.109	0.000	0.000	0.000
132	F	132	THR	0	-0.040	-0.028	39.723	-0.216	-0.216	0.000	0.000	0.000
133	F	133	VAL	0	0.001	0.019	38.001	0.169	0.169	0.000	0.000	0.000
134	F	134	ASN	0	-0.088	-0.055	36.200	-0.185	-0.185	0.000	0.000	0.000
135	F	135	LEU	0	0.068	0.048	32.920	0.165	0.165	0.000	0.000	0.000
136	F	136	VAL	0	-0.085	-0.049	32.807	-0.182	-0.182	0.000	0.000	0.000
137	F	137	ARG	1	0.881	0.929	25.011	12.261	12.261	0.000	0.000	0.000
138	F	138	PRO	0	0.062	0.025	31.644	0.281	0.281	0.000	0.000	0.000
139	F	139	GLY	0	-0.004	0.001	31.748	-0.334	-0.334	0.000	0.000	0.000
140	F	140	TYR	0	0.060	0.025	29.594	0.001	0.001	0.000	0.000	0.000
141	F	141	ARG	1	0.964	0.981	33.710	7.798	7.798	0.000	0.000	0.000
142	F	142	VAL	0	-0.042	-0.021	32.804	0.215	0.215	0.000	0.000	0.000
143	F	143	ALA	0	-0.001	0.001	33.153	0.061	0.061	0.000	0.000	0.000
144	F	144	LYS	1	0.800	0.895	35.145	8.801	8.801	0.000	0.000	0.000
145	F	145	ARG	1	0.849	0.936	36.046	8.868	8.868	0.000	0.000	0.000
146	F	146	ASP	-1	-0.846	-0.924	40.072	-7.384	-7.384	0.000	0.000	0.000
147	F	147	LYS	1	0.936	0.958	41.490	7.174	7.174	0.000	0.000	0.000
148	F	148	ALA	0	0.000	-0.011	37.224	-0.100	-0.100	0.000	0.000	0.000
149	F	149	SER	0	0.060	0.056	36.659	-0.234	-0.234	0.000	0.000	0.000
150	F	150	ARG	1	0.912	0.935	27.927	10.513	10.513	0.000	0.000	0.000
151	F	151	SER	0	0.027	0.027	28.924	0.095	0.095	0.000	0.000	0.000
152	F	152	ILE	0	0.023	0.019	27.544	-0.254	-0.254	0.000	0.000	0.000
153	F	153	PRO	0	0.002	-0.003	23.640	-0.207	-0.207	0.000	0.000	0.000
154	F	154	THR	0	0.070	0.017	21.043	0.335	0.335	0.000	0.000	0.000
155	F	155	LYS	1	0.959	0.977	16.139	18.300	18.300	0.000	0.000	0.000
156	F	156	HIS	0	-0.047	-0.017	21.458	-0.452	-0.452	0.000	0.000	0.000
157	F	157	ARG	1	0.860	0.934	24.737	12.517	12.517	0.000	0.000	0.000
158	F	158	LEU	0	0.038	0.034	25.200	-0.490	-0.490	0.000	0.000	0.000
159	F	159	ASN	0	-0.090	-0.038	22.097	-0.307	-0.307	0.000	0.000	0.000
160	F	160	PRO	0	0.048	0.013	24.817	0.238	0.238	0.000	0.000	0.000
161	F	161	ALA	0	0.041	0.026	23.714	0.282	0.282	0.000	0.000	0.000
162	F	162	ASP	-1	-0.816	-0.908	23.986	-13.100	-13.100	0.000	0.000	0.000
163	F	163	ALA	0	-0.024	-0.006	26.692	0.332	0.332	0.000	0.000	0.000
164	F	164	VAL	0	0.045	0.037	28.853	0.319	0.319	0.000	0.000	0.000
165	F	165	ALA	0	0.052	0.028	27.300	0.275	0.275	0.000	0.000	0.000
166	F	166	PHE	0	-0.025	-0.006	29.405	0.271	0.271	0.000	0.000	0.000
167	F	167	ILE	0	0.011	0.012	31.760	0.296	0.296	0.000	0.000	0.000
168	F	168	GLU	-1	-0.856	-0.932	30.910	-9.888	-9.888	0.000	0.000	0.000
169	F	169	SER	0	-0.105	-0.076	31.861	0.245	0.245	0.000	0.000	0.000
170	F	170	THR	0	-0.086	-0.047	34.057	0.164	0.164	0.000	0.000	0.000
171	F	171	TYR	0	-0.043	-0.041	36.925	0.318	0.318	0.000	0.000	0.000
172	F	172	ASP	-1	-0.941	-0.950	37.708	-7.967	-7.967	0.000	0.000	0.000
173	F	173	VAL	0	-0.057	-0.020	38.081	0.134	0.134	0.000	0.000	0.000
174	F	174	GLU	-1	-0.946	-0.978	35.510	-8.687	-8.687	0.000	0.000	0.000
175	F	175	VAL	0	-0.072	-0.033	32.683	0.180	0.180	0.000	0.000	0.000
176	F	176	SER	0	-0.030	-0.023	33.263	-0.188	-0.188	0.000	0.000	0.000
177	F	177	GLU	-2	-1.893	-1.953	28.469	-20.978	-20.978	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:1:MET)