FMO DATABASE

FMODB ID: JVNM9

Calculation Name: 3PMC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: iodide ion

Ligand 3-letter code: IOD

Ligand of Interest (LOI):

PDB ID: 3PMC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RMX2

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1308340.179609
FMO2-HF: Nuclear repulsion	1253089.30394
FMO2-HF: Total energy	-55250.875668
FMO2-MP2: Total energy	-55413.607518

3D Structure

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:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
23.048	24.909	-0.018	-0.805	-1.039	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.875 / q_NPA : 1.921

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	LEU	0	0.066	0.032	3.887	-0.290	1.281	-0.017	-0.730	-0.825	-0.002
104	A	108	GLN	0	0.017	-0.005	3.809	-3.422	-3.132	-0.001	-0.075	-0.214	0.000
4	A	8	LEU	0	0.075	0.038	5.976	4.442	4.442	0.000	0.000	0.000	0.000
5	A	9	CYS	0	0.009	-0.004	6.042	3.519	3.519	0.000	0.000	0.000	0.000
6	A	10	ARG	1	0.934	0.968	5.410	64.310	64.310	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.045	0.021	8.460	4.229	4.229	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.034	0.010	11.203	3.134	3.134	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.928	0.964	10.682	44.972	44.972	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.911	-0.955	11.774	-35.814	-35.814	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.872	0.938	14.327	34.981	34.981	0.000	0.000	0.000	0.000
12	A	16	GLN	0	0.031	0.033	16.311	2.206	2.206	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.847	-0.918	17.880	-24.225	-24.225	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.870	0.934	20.098	26.143	26.143	0.000	0.000	0.000	0.000
15	A	19	PHE	0	-0.011	-0.009	18.200	0.755	0.755	0.000	0.000	0.000	0.000
16	A	20	ILE	0	0.051	0.025	20.485	0.884	0.884	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.001	0.000	22.893	1.441	1.441	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.872	-0.923	23.060	-23.341	-23.341	0.000	0.000	0.000	0.000
19	A	23	TRP	0	0.008	0.005	23.200	0.794	0.794	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.967	0.976	25.216	20.184	20.184	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.783	0.880	28.097	21.403	21.403	0.000	0.000	0.000	0.000
22	A	26	LYS	1	0.856	0.925	24.523	24.544	24.544	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.013	0.011	27.721	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.026	-0.014	30.645	0.620	0.620	0.000	0.000	0.000	0.000
25	A	29	ILE	0	0.016	0.013	29.958	-0.183	-0.183	0.000	0.000	0.000	0.000
26	A	30	ARG	1	0.796	0.853	34.479	16.544	16.544	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.826	-0.933	38.085	-16.222	-16.222	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.923	0.960	39.757	14.775	14.775	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.807	-0.870	36.366	-17.058	-17.058	0.000	0.000	0.000	0.000
30	A	34	PRO	0	-0.003	-0.006	38.231	-0.175	-0.175	0.000	0.000	0.000	0.000
31	A	35	TYR	0	0.055	0.028	34.087	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.841	0.930	33.348	15.485	15.485	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.834	-0.919	32.032	-17.534	-17.534	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.823	-0.911	30.245	-20.597	-20.597	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.066	-0.017	28.860	-0.875	-0.875	0.000	0.000	0.000	0.000
36	A	40	ILE	0	-0.035	-0.019	26.560	-0.854	-0.854	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.987	1.011	25.343	19.572	19.572	0.000	0.000	0.000	0.000
38	A	42	ASN	0	-0.022	-0.012	24.461	-1.212	-1.212	0.000	0.000	0.000	0.000
39	A	43	GLY	0	0.022	0.015	22.894	-1.072	-1.072	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.913	-0.974	20.971	-24.910	-24.910	0.000	0.000	0.000	0.000
41	A	45	HIS	0	0.009	0.017	19.607	-2.093	-2.093	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.020	0.000	18.977	-1.766	-1.766	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.018	0.000	15.885	-1.935	-1.935	0.000	0.000	0.000	0.000
44	A	48	SER	0	-0.029	-0.028	15.037	-2.996	-2.996	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.019	0.004	14.283	-2.510	-2.510	0.000	0.000	0.000	0.000
46	A	50	PHE	0	0.005	0.008	12.765	-2.726	-2.726	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.033	-0.028	9.324	-4.180	-4.180	0.000	0.000	0.000	0.000
48	A	52	MET	0	-0.003	0.000	9.700	-4.888	-4.888	0.000	0.000	0.000	0.000
49	A	53	TYR	0	-0.008	0.003	10.483	-2.976	-2.976	0.000	0.000	0.000	0.000
50	A	54	LEU	0	-0.026	-0.035	7.686	-4.141	-4.141	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.687	0.815	5.820	47.422	47.422	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.907	-0.926	6.114	-80.579	-80.579	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.814	-0.893	9.321	-51.099	-51.099	0.000	0.000	0.000	0.000
54	A	58	ILE	0	-0.008	0.012	11.616	2.850	2.850	0.000	0.000	0.000	0.000
55	A	59	SER	0	-0.055	-0.055	13.814	-1.701	-1.701	0.000	0.000	0.000	0.000
56	A	60	LEU	0	-0.007	-0.018	16.432	0.611	0.611	0.000	0.000	0.000	0.000
57	A	61	GLN	0	-0.007	0.002	18.502	0.780	0.780	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.790	-0.872	18.167	-31.888	-31.888	0.000	0.000	0.000	0.000
59	A	63	ILE	0	-0.021	-0.006	19.027	0.713	0.713	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.844	-0.910	21.805	-23.832	-23.832	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.004	-0.007	24.719	1.040	1.040	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.009	0.002	23.714	0.562	0.562	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.004	-0.015	24.695	0.488	0.488	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.947	0.971	27.067	20.697	20.697	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.752	0.852	28.419	21.265	21.265	0.000	0.000	0.000	0.000
66	A	70	ILE	0	0.010	0.003	25.897	0.618	0.618	0.000	0.000	0.000	0.000
67	A	71	ALA	0	0.013	0.002	30.336	0.599	0.599	0.000	0.000	0.000	0.000
68	A	72	ARG	1	0.871	0.942	32.765	16.724	16.724	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.747	-0.855	31.471	-19.177	-19.177	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.732	0.825	32.417	18.323	18.323	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.010	0.007	35.532	0.425	0.425	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.868	-0.931	38.412	-15.353	-15.353	0.000	0.000	0.000	0.000
73	A	77	ALA	0	-0.044	-0.028	37.620	0.438	0.438	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.886	0.948	39.630	14.406	14.406	0.000	0.000	0.000	0.000
75	A	79	VAL	0	-0.012	0.015	35.923	0.232	0.232	0.000	0.000	0.000	0.000
76	A	80	ASN	0	0.031	0.008	37.323	-0.334	-0.334	0.000	0.000	0.000	0.000
77	A	81	ILE	0	0.065	0.039	31.820	-0.330	-0.330	0.000	0.000	0.000	0.000
78	A	82	ALA	0	0.035	0.004	32.531	-0.685	-0.685	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.805	-0.868	32.375	-17.169	-17.169	0.000	0.000	0.000	0.000
80	A	84	PHE	0	0.023	0.015	26.172	-0.317	-0.317	0.000	0.000	0.000	0.000
81	A	85	ILE	0	0.007	0.019	28.087	-0.888	-0.888	0.000	0.000	0.000	0.000
82	A	86	HIS	0	-0.027	-0.016	27.575	-0.740	-0.740	0.000	0.000	0.000	0.000
83	A	87	ASN	0	0.041	0.011	27.717	-0.583	-0.583	0.000	0.000	0.000	0.000
84	A	88	THR	0	0.005	0.007	23.028	-1.068	-1.068	0.000	0.000	0.000	0.000
85	A	89	ASN	0	0.002	-0.008	23.086	-2.011	-2.011	0.000	0.000	0.000	0.000
86	A	90	VAL	0	-0.008	0.006	23.711	-0.912	-0.912	0.000	0.000	0.000	0.000
87	A	91	ALA	0	-0.013	-0.002	20.767	-0.754	-0.754	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.864	0.940	19.002	28.154	28.154	0.000	0.000	0.000	0.000
89	A	93	ILE	0	0.010	0.000	19.276	-1.392	-1.392	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.853	-0.928	19.747	-28.338	-28.338	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.012	-0.015	14.463	-1.598	-1.598	0.000	0.000	0.000	0.000
92	A	96	MET	0	-0.006	0.004	15.595	-3.210	-3.210	0.000	0.000	0.000	0.000
93	A	97	ASN	0	-0.017	0.011	17.281	-0.864	-0.864	0.000	0.000	0.000	0.000
94	A	98	ILE	0	-0.012	-0.007	13.170	-1.114	-1.114	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.056	-0.028	10.675	-2.436	-2.436	0.000	0.000	0.000	0.000
96	A	100	THR	0	-0.015	-0.027	13.277	-1.899	-1.899	0.000	0.000	0.000	0.000
97	A	101	LEU	0	-0.005	-0.003	15.978	0.082	0.082	0.000	0.000	0.000	0.000
98	A	102	LEU	0	-0.096	-0.043	9.668	-0.842	-0.842	0.000	0.000	0.000	0.000
99	A	103	ASN	0	-0.048	-0.004	11.407	-1.290	-1.290	0.000	0.000	0.000	0.000
100	A	104	PRO	0	-0.017	-0.001	9.252	-2.241	-2.241	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.804	-0.898	9.080	-55.249	-55.249	0.000	0.000	0.000	0.000
102	A	106	LEU	0	0.043	-0.001	10.907	-1.568	-1.568	0.000	0.000	0.000	0.000
103	A	107	GLN	0	-0.007	0.008	6.866	-5.289	-5.289	0.000	0.000	0.000	0.000
105	A	109	TYR	0	-0.003	-0.001	7.653	-0.055	-0.055	0.000	0.000	0.000	0.000
106	A	110	GLN	0	-0.001	-0.008	11.070	0.061	0.061	0.000	0.000	0.000	0.000
107	A	111	ALA	0	-0.032	-0.009	7.496	1.769	1.769	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.003	-0.015	6.473	0.670	0.670	0.000	0.000	0.000	0.000
109	A	113	VAL	0	0.053	0.020	10.134	2.820	2.820	0.000	0.000	0.000	0.000
110	A	114	LYS	1	0.914	0.968	11.870	43.198	43.198	0.000	0.000	0.000	0.000
111	A	115	LYS	1	0.826	0.907	6.384	73.358	73.358	0.000	0.000	0.000	0.000
112	A	116	ILE	0	0.024	0.007	12.705	2.262	2.262	0.000	0.000	0.000	0.000
113	A	117	ASN	0	0.000	-0.005	14.926	2.451	2.451	0.000	0.000	0.000	0.000
114	A	118	GLN	0	0.035	0.028	13.781	-0.719	-0.719	0.000	0.000	0.000	0.000
115	A	119	PHE	0	0.035	0.018	15.101	1.286	1.286	0.000	0.000	0.000	0.000
116	A	120	PHE	0	0.005	-0.016	16.684	1.642	1.642	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.857	-0.933	20.024	-27.207	-27.207	0.000	0.000	0.000	0.000
118	A	122	HIS	0	-0.020	-0.007	20.457	1.087	1.087	0.000	0.000	0.000	0.000
119	A	123	LEU	0	0.023	0.017	21.199	1.208	1.208	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.020	-0.009	22.999	1.374	1.374	0.000	0.000	0.000	0.000
121	A	125	TYR	0	0.008	0.010	25.362	1.195	1.195	0.000	0.000	0.000	0.000
122	A	126	TYR	0	0.063	0.016	25.224	1.003	1.003	0.000	0.000	0.000	0.000
123	A	127	THR	0	-0.064	-0.031	26.361	0.810	0.810	0.000	0.000	0.000	0.000
124	A	128	VAL	0	-0.029	-0.025	28.918	0.856	0.856	0.000	0.000	0.000	0.000
125	A	129	HIS	0	-0.022	0.002	30.520	0.207	0.207	0.000	0.000	0.000	0.000
126	A	130	SER	0	0.010	-0.014	31.159	0.574	0.574	0.000	0.000	0.000	0.000
127	A	131	TYR	0	-0.020	-0.008	32.826	0.697	0.697	0.000	0.000	0.000	0.000
128	A	132	TYR	0	-0.001	0.004	34.903	0.441	0.441	0.000	0.000	0.000	0.000
129	A	133	GLU	-1	-0.883	-0.953	35.060	-16.590	-16.590	0.000	0.000	0.000	0.000
130	A	134	GLN	0	-0.116	-0.055	33.649	0.702	0.702	0.000	0.000	0.000	0.000
131	A	135	LYS	1	0.821	0.905	38.162	15.695	15.695	0.000	0.000	0.000	0.000
132	A	136	ALA	-1	-0.911	-0.928	40.756	-14.269	-14.269	0.000	0.000	0.000	0.000

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