FMO DATABASE

FMODB ID: JVQ29

Calculation Name: 1X3E-B-Xray547

Preferred Name:

Target Type:

Ligand Name: cadmium ion

Ligand 3-letter code: CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X3E

Chain ID: B

ChEMBL ID:

UniProt ID: Q9AFI5

Base Structure: X-ray

Registration Date: 2025-10-05

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-847831.176707
FMO2-HF: Nuclear repulsion	802240.0214
FMO2-HF: Total energy	-45591.155307
FMO2-MP2: Total energy	-45725.032043

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-43.609	-41.238	0.03	-1.239	-1.163	-0.006

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.911

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	4	ASP	-1	-0.832	-0.905	3.211	-60.706	-58.335	0.030	-1.239	-1.163	-0.006
4	A	5	THR	0	-0.011	-0.015	5.531	2.350	2.350	0.000	0.000	0.000	0.000
5	A	6	THR	0	-0.006	0.003	8.772	3.122	3.122	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.005	0.006	10.989	1.056	1.056	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.008	-0.008	14.795	0.189	0.189	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.011	-0.002	18.118	0.340	0.340	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.001	-0.004	21.209	0.262	0.262	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.001	0.008	24.840	0.115	0.115	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.071	-0.039	27.610	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.035	0.037	26.475	-0.289	-0.289	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.035	-0.036	29.403	0.493	0.493	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.017	-0.018	30.964	0.429	0.429	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.834	-0.911	31.353	-9.289	-9.289	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.046	-0.019	27.928	-0.124	-0.124	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.827	-0.886	28.391	-10.713	-10.713	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.015	-0.003	27.646	-0.505	-0.505	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.874	0.927	24.499	12.441	12.441	0.000	0.000	0.000	0.000
20	A	21	PHE	0	0.043	0.024	27.931	-0.314	-0.314	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.038	-0.016	23.995	0.117	0.117	0.000	0.000	0.000	0.000
22	A	23	PRO	0	0.021	-0.005	27.229	0.208	0.208	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.054	-0.030	25.748	0.121	0.121	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.032	0.021	27.993	0.054	0.054	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.013	0.000	23.871	0.018	0.018	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.073	0.050	26.011	0.011	0.011	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.047	-0.027	21.913	-0.737	-0.737	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.026	0.026	23.578	0.620	0.620	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.082	-0.038	22.224	-0.378	-0.378	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.096	0.038	22.385	0.542	0.542	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.008	0.002	24.553	-0.432	-0.432	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.015	0.020	23.455	0.434	0.434	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.032	0.019	25.812	-0.200	-0.200	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.045	-0.043	25.075	0.151	0.151	0.000	0.000	0.000	0.000
35	A	36	THR	0	0.010	0.004	27.152	0.015	0.015	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.021	0.026	27.598	0.056	0.056	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.853	0.907	29.407	9.510	9.510	0.000	0.000	0.000	0.000
38	A	39	MET	0	-0.007	0.008	31.769	-0.341	-0.341	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.026	-0.019	34.160	0.203	0.203	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.905	-0.951	37.151	-8.003	-8.003	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.910	0.954	39.402	8.030	8.030	0.000	0.000	0.000	0.000
42	A	43	GLN	0	0.021	0.008	41.232	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.054	-0.029	44.699	0.208	0.208	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.073	0.040	43.702	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.925	-0.952	42.484	-7.335	-7.335	0.000	0.000	0.000	0.000
46	A	47	TRP	0	-0.036	-0.034	36.678	-0.159	-0.159	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.929	0.965	37.307	8.727	8.727	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.864	-0.915	34.562	-9.263	-9.263	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.029	-0.023	32.030	0.220	0.220	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.885	-0.936	31.017	-9.602	-9.602	0.000	0.000	0.000	0.000
51	A	52	ALA	0	-0.058	-0.038	29.595	-0.355	-0.355	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.014	0.000	21.603	-0.097	-0.097	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.002	-0.005	25.980	-0.049	-0.049	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.012	0.006	19.562	-0.388	-0.388	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.839	0.898	21.917	12.435	12.435	0.000	0.000	0.000	0.000
56	A	57	CYS	0	-0.022	0.004	19.777	-1.013	-1.013	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.001	0.009	17.403	1.832	1.832	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.037	0.025	18.537	-0.898	-0.898	0.000	0.000	0.000	0.000
59	A	60	TRP	0	0.009	-0.012	17.669	1.095	1.095	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.889	0.942	18.444	15.545	15.545	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.751	-0.887	23.755	-12.122	-12.122	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.044	-0.006	21.364	0.277	0.277	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.039	-0.029	23.398	0.159	0.159	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.874	-0.942	24.794	-10.909	-10.909	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.040	0.011	25.745	0.643	0.643	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.041	-0.015	24.066	0.256	0.256	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.024	-0.029	27.322	0.299	0.299	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.973	-0.965	30.190	-9.246	-9.246	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.058	-0.031	29.808	0.331	0.331	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.106	-0.049	26.940	0.060	0.060	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.045	0.015	31.204	0.118	0.118	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.955	0.972	32.549	8.166	8.166	0.000	0.000	0.000	0.000
73	A	74	GLY	0	-0.010	-0.006	33.231	0.278	0.278	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.012	0.007	31.123	0.030	0.030	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.931	0.969	29.771	10.229	10.229	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.018	0.008	25.547	0.086	0.086	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.039	-0.027	22.197	0.063	0.063	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.027	0.011	19.032	0.082	0.082	0.000	0.000	0.000	0.000
79	A	80	THR	0	0.003	-0.002	15.899	-0.473	-0.473	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.067	0.029	14.100	0.808	0.808	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.821	0.906	8.521	25.467	25.467	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.003	0.001	11.293	1.753	1.753	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.840	0.914	8.350	29.488	29.488	0.000	0.000	0.000	0.000
84	A	85	GLN	0	0.007	0.000	13.158	2.039	2.039	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.820	0.908	15.712	15.047	15.047	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.019	-0.013	18.422	0.225	0.225	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.036	-0.014	21.153	0.084	0.084	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.937	-0.966	24.877	-10.269	-10.269	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.039	-0.009	28.267	0.233	0.233	0.000	0.000	0.000	0.000
90	A	91	ARG	1	1.013	0.994	31.232	8.404	8.404	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.933	-0.964	34.409	-8.468	-8.468	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.020	-0.005	32.415	0.052	0.052	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.959	-0.980	27.823	-11.304	-11.304	0.000	0.000	0.000	0.000
94	A	95	LYS	0	0.004	-0.001	21.101	-0.314	-0.314	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.913	0.973	23.277	12.332	12.332	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.016	-0.013	19.151	0.050	0.050	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.009	-0.007	20.521	0.539	0.539	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.006	-0.008	15.813	-0.781	-0.781	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.809	-0.885	16.755	-14.599	-14.599	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.011	-0.007	15.664	-1.532	-1.532	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.881	-0.943	12.985	-18.344	-18.344	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.024	-0.027	14.115	-1.456	-1.456	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.886	-0.927	12.625	-25.876	-25.876	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.924	-0.952	15.789	-15.651	-15.651	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.023	-0.026	18.994	-0.161	-0.161	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.026	0.025	22.172	0.329	0.329	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.038	0.022	25.787	-0.110	-0.110	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.056	-0.035	28.604	0.036	0.036	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.015	-0.004	29.736	0.307	0.307	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.887	0.954	30.240	10.419	10.419	0.000	0.000	0.000	0.000
111	A	112	TYR	0	-0.016	-0.023	33.572	0.095	0.095	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.031	0.030	34.802	0.223	0.223	0.000	0.000	0.000	0.000
113	A	114	THR	0	0.006	0.004	35.744	-0.168	-0.168	0.000	0.000	0.000	0.000
114	A	115	ALA	0	0.058	0.017	33.368	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.846	0.926	35.437	8.699	8.699	0.000	0.000	0.000	0.000
116	A	117	VAL	0	0.030	0.011	30.602	-0.087	-0.087	0.000	0.000	0.000	0.000
117	A	118	ASN	0	0.015	0.005	32.366	0.546	0.546	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.921	0.965	28.395	10.661	10.661	0.000	0.000	0.000	0.000
119	A	120	ALA	-1	-0.845	-0.906	28.254	-10.292	-10.292	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)