FMO DATABASE

FMODB ID: M23LZ

Calculation Name: 5AN6-A-Xray549

Preferred Name:

Target Type:

Ligand Name: cadmium ion

Ligand 3-letter code: CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5AN6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2D0

Base Structure: X-ray

Registration Date: 2025-10-12

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-928880.738543
FMO2-HF: Nuclear repulsion	878419.682019
FMO2-HF: Total energy	-50461.056524
FMO2-MP2: Total energy	-50612.011465

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:6:GLY)

Summations of interaction energy for fragment #1(A:6: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.
22.79	23.747	-0.012	-0.296	-0.651	-0.001

Interaction energy analysis for fragmet #1(A:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	8	SER	0	-0.002	0.001	3.828	4.276	5.029	-0.013	-0.237	-0.504	-0.001
14	A	19	LYS	1	0.922	0.957	3.507	56.718	56.922	0.001	-0.059	-0.147	0.000
4	A	9	LEU	0	0.012	0.008	6.612	1.780	1.780	0.000	0.000	0.000	0.000
5	A	10	LYS	1	0.943	0.963	9.584	26.503	26.503	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.876	-0.927	6.153	-48.079	-48.079	0.000	0.000	0.000	0.000
7	A	12	ASP	-1	-0.820	-0.918	10.316	-18.033	-18.033	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.017	-0.006	12.636	-1.574	-1.574	0.000	0.000	0.000	0.000
9	A	14	LYS	1	0.966	0.976	14.382	15.772	15.772	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.808	-0.882	10.020	-26.520	-26.520	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.029	-0.019	8.425	-3.038	-3.038	0.000	0.000	0.000	0.000
12	A	17	VAL	0	-0.010	0.004	10.668	-1.010	-1.010	0.000	0.000	0.000	0.000
13	A	18	ARG	1	0.907	0.938	7.736	31.761	31.761	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.007	-0.001	8.336	-2.306	-2.306	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.883	-0.951	10.474	-20.178	-20.178	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.945	-0.956	8.167	-26.746	-26.746	0.000	0.000	0.000	0.000
18	A	23	ILE	0	0.008	0.005	5.719	0.676	0.676	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.008	0.004	9.676	1.908	1.908	0.000	0.000	0.000	0.000
20	A	25	ARG	1	0.855	0.921	12.658	24.810	24.810	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.948	-0.961	9.131	-31.787	-31.787	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.037	-0.028	11.401	1.320	1.320	0.000	0.000	0.000	0.000
23	A	28	SER	0	-0.045	-0.020	14.236	1.642	1.642	0.000	0.000	0.000	0.000
24	A	29	GLY	0	0.026	0.020	17.498	0.987	0.987	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.869	0.936	14.118	20.575	20.575	0.000	0.000	0.000	0.000
26	A	31	LEU	0	-0.006	-0.001	15.672	0.755	0.755	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.968	0.987	18.397	13.695	13.695	0.000	0.000	0.000	0.000
28	A	33	THR	0	0.014	-0.011	20.771	-0.424	-0.424	0.000	0.000	0.000	0.000
29	A	34	ASN	0	-0.025	-0.008	17.586	0.648	0.648	0.000	0.000	0.000	0.000
30	A	35	GLN	0	0.036	0.020	20.471	0.545	0.545	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.039	0.032	16.013	0.180	0.180	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.977	0.975	20.586	12.118	12.118	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.989	0.989	23.907	11.162	11.162	0.000	0.000	0.000	0.000
34	A	39	PHE	0	0.042	0.034	15.967	0.198	0.198	0.000	0.000	0.000	0.000
35	A	40	HIS	0	0.057	0.018	20.709	-0.341	-0.341	0.000	0.000	0.000	0.000
36	A	41	GLY	0	0.016	0.025	21.695	0.246	0.246	0.000	0.000	0.000	0.000
37	A	42	HIS	0	0.013	0.007	22.825	0.341	0.341	0.000	0.000	0.000	0.000
38	A	43	LEU	0	0.037	0.017	17.788	0.156	0.156	0.000	0.000	0.000	0.000
39	A	44	THR	0	-0.082	-0.056	21.672	0.328	0.328	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.917	0.975	24.349	10.748	10.748	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.053	0.034	22.504	0.304	0.304	0.000	0.000	0.000	0.000
42	A	47	TRP	0	0.015	0.005	21.067	0.013	0.013	0.000	0.000	0.000	0.000
43	A	48	SER	0	-0.077	-0.059	24.179	0.451	0.451	0.000	0.000	0.000	0.000
44	A	49	ASN	0	-0.016	-0.023	27.268	0.679	0.679	0.000	0.000	0.000	0.000
45	A	50	TYR	0	0.034	0.011	23.509	0.294	0.294	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.052	-0.041	25.461	0.302	0.302	0.000	0.000	0.000	0.000
47	A	52	TYR	0	-0.033	-0.010	28.290	0.293	0.293	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.869	0.930	30.309	10.210	10.210	0.000	0.000	0.000	0.000
49	A	54	LYS	1	0.933	0.982	26.812	11.367	11.367	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.831	0.882	28.460	9.132	9.132	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.805	-0.896	30.632	-9.684	-9.684	0.000	0.000	0.000	0.000
52	A	57	TYR	0	-0.015	-0.046	26.247	-0.148	-0.148	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.867	0.933	22.797	12.460	12.460	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.837	-0.880	27.356	-9.922	-9.922	0.000	0.000	0.000	0.000
55	A	60	ASN	0	-0.052	-0.028	30.024	0.191	0.191	0.000	0.000	0.000	0.000
56	A	61	PRO	0	0.019	-0.001	25.428	-0.169	-0.169	0.000	0.000	0.000	0.000
57	A	62	GLU	-1	-0.887	-0.936	25.899	-10.998	-10.998	0.000	0.000	0.000	0.000
58	A	63	LYS	1	0.918	0.951	27.630	9.409	9.409	0.000	0.000	0.000	0.000
59	A	64	PHE	0	-0.039	-0.026	20.426	-0.200	-0.200	0.000	0.000	0.000	0.000
60	A	65	ASN	0	-0.020	-0.017	23.062	-0.951	-0.951	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.904	-0.956	24.362	-10.496	-10.496	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.807	-0.840	27.215	-9.971	-9.971	0.000	0.000	0.000	0.000
63	A	68	ILE	0	0.014	0.008	22.001	-0.364	-0.364	0.000	0.000	0.000	0.000
64	A	69	LEU	0	-0.032	-0.020	18.804	-0.698	-0.698	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.022	0.029	20.985	-0.785	-0.785	0.000	0.000	0.000	0.000
66	A	71	GLU	-1	-0.842	-0.921	23.465	-11.879	-11.879	0.000	0.000	0.000	0.000
67	A	72	LEU	0	-0.031	-0.029	18.010	-0.374	-0.374	0.000	0.000	0.000	0.000
68	A	73	HIS	0	0.005	0.010	18.965	-1.456	-1.456	0.000	0.000	0.000	0.000
69	A	74	PHE	0	0.036	0.017	20.128	-0.204	-0.204	0.000	0.000	0.000	0.000
70	A	75	MET	0	-0.024	-0.004	17.468	0.014	0.014	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.931	0.966	13.376	20.294	20.294	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.006	-0.001	17.859	-0.514	-0.514	0.000	0.000	0.000	0.000
73	A	78	PHE	0	0.000	-0.012	20.518	0.122	0.122	0.000	0.000	0.000	0.000
74	A	79	LEU	0	-0.023	-0.010	14.287	0.155	0.155	0.000	0.000	0.000	0.000
75	A	80	ALA	0	-0.001	0.001	17.837	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	81	TYR	0	0.005	0.007	18.914	0.366	0.366	0.000	0.000	0.000	0.000
77	A	82	GLN	0	-0.021	-0.020	21.133	0.771	0.771	0.000	0.000	0.000	0.000
78	A	83	VAL	0	0.023	0.010	16.422	0.169	0.169	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.009	0.004	19.699	0.076	0.076	0.000	0.000	0.000	0.000
80	A	85	ARG	1	0.931	0.967	21.754	11.632	11.632	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.893	-0.944	21.555	-13.639	-13.639	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.045	-0.026	18.274	0.170	0.170	0.000	0.000	0.000	0.000
83	A	88	GLU	-1	-0.896	-0.927	22.904	-11.286	-11.286	0.000	0.000	0.000	0.000
84	A	89	GLY	0	0.070	0.035	26.343	0.355	0.355	0.000	0.000	0.000	0.000
85	A	90	ILE	0	-0.072	-0.042	23.665	0.327	0.327	0.000	0.000	0.000	0.000
86	A	91	SER	0	-0.040	-0.034	25.333	0.111	0.111	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.939	-0.965	27.745	-9.789	-9.789	0.000	0.000	0.000	0.000
88	A	93	LEU	0	-0.027	-0.014	30.346	0.318	0.318	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.872	0.928	27.598	11.269	11.269	0.000	0.000	0.000	0.000
90	A	95	GLU	-1	-0.869	-0.935	30.644	-10.027	-10.027	0.000	0.000	0.000	0.000
91	A	96	ILE	0	-0.045	-0.014	33.166	0.343	0.343	0.000	0.000	0.000	0.000
92	A	97	LEU	0	-0.048	-0.032	33.192	0.285	0.285	0.000	0.000	0.000	0.000
93	A	98	GLU	-1	-0.938	-0.972	31.923	-9.762	-9.762	0.000	0.000	0.000	0.000
94	A	99	PRO	0	-0.005	0.002	35.128	0.169	0.169	0.000	0.000	0.000	0.000
95	A	100	LEU	0	0.021	0.011	38.518	0.205	0.205	0.000	0.000	0.000	0.000
96	A	101	ILE	0	-0.042	-0.028	35.517	0.192	0.192	0.000	0.000	0.000	0.000
97	A	102	ASP	-1	-0.914	-0.948	39.200	-7.839	-7.839	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.967	-0.995	40.994	-7.196	-7.196	0.000	0.000	0.000	0.000
99	A	104	ILE	0	-0.098	-0.032	41.803	0.239	0.239	0.000	0.000	0.000	0.000
100	A	105	LYS	1	0.848	0.930	44.504	7.132	7.132	0.000	0.000	0.000	0.000
101	A	106	THR	0	-0.059	-0.042	48.330	0.134	0.134	0.000	0.000	0.000	0.000
102	A	107	PRO	0	0.019	-0.012	48.749	-0.129	-0.129	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.861	-0.927	49.193	-6.130	-6.130	0.000	0.000	0.000	0.000
104	A	109	GLU	-1	-0.847	-0.910	47.093	-6.602	-6.602	0.000	0.000	0.000	0.000
105	A	110	PHE	0	0.024	0.027	41.677	-0.172	-0.172	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.871	-0.936	44.970	-6.502	-6.502	0.000	0.000	0.000	0.000
107	A	112	LYS	1	0.913	0.949	46.591	6.258	6.258	0.000	0.000	0.000	0.000
108	A	113	PHE	0	0.049	0.033	37.444	-0.079	-0.079	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.833	0.896	40.147	7.668	7.668	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.873	0.922	42.321	6.335	6.335	0.000	0.000	0.000	0.000
111	A	116	PHE	0	0.011	0.011	39.094	-0.024	-0.024	0.000	0.000	0.000	0.000
112	A	117	TYR	0	0.025	0.016	33.819	-0.233	-0.233	0.000	0.000	0.000	0.000
113	A	118	ASP	-1	-0.824	-0.905	38.620	-8.047	-8.047	0.000	0.000	0.000	0.000
114	A	119	ALA	0	-0.023	-0.006	40.674	-0.046	-0.046	0.000	0.000	0.000	0.000
115	A	120	ILE	0	0.026	0.017	35.901	-0.060	-0.060	0.000	0.000	0.000	0.000
116	A	121	LEU	0	-0.050	-0.020	34.490	-0.211	-0.211	0.000	0.000	0.000	0.000
117	A	122	ALA	0	0.003	-0.005	36.982	-0.168	-0.168	0.000	0.000	0.000	0.000
118	A	123	TYR	0	0.008	-0.015	39.133	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	124	HIS	0	-0.010	0.014	30.508	0.103	0.103	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.866	0.920	33.186	8.980	8.980	0.000	0.000	0.000	0.000
121	A	126	PHE	0	-0.063	-0.016	36.508	0.036	0.036	0.000	0.000	0.000	0.000
122	A	127	HIS	0	-0.061	-0.031	36.604	0.264	0.264	0.000	0.000	0.000	0.000
123	A	128	SER	-1	-0.977	-0.967	31.830	-9.758	-9.758	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)