FMO DATABASE

FMODB ID: 153MZ

Calculation Name: 1ID3-D-Xray547

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion

Ligand 3-letter code: MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ID3

Chain ID: D

ChEMBL ID:

UniProt ID: P04911

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-569134.814903
FMO2-HF: Nuclear repulsion	533411.843085
FMO2-HF: Total energy	-35722.971818
FMO2-MP2: Total energy	-35828.81385

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:36:ARG)

Summations of interaction energy for fragment #1(A:36:ARG)

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.
45.397	47.132	-0.013	-0.665	-1.057	-0.001

Interaction energy analysis for fragmet #1(A:36:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.821 / q_NPA : 1.895

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	38	GLU	-1	-0.845	-0.909	3.860	-71.151	-69.416	-0.013	-0.665	-1.057	-0.001
4	A	39	THR	0	-0.046	-0.028	6.286	5.277	5.277	0.000	0.000	0.000	0.000
5	A	40	TYR	0	0.093	0.046	9.601	-1.020	-1.020	0.000	0.000	0.000	0.000
6	A	41	SER	0	0.011	-0.033	11.622	3.205	3.205	0.000	0.000	0.000	0.000
7	A	42	SER	0	-0.013	-0.008	11.086	1.217	1.217	0.000	0.000	0.000	0.000
8	A	43	TYR	0	-0.039	-0.021	10.550	2.785	2.785	0.000	0.000	0.000	0.000
9	A	44	ILE	0	0.042	0.018	15.603	2.006	2.006	0.000	0.000	0.000	0.000
10	A	45	TYR	0	0.014	0.002	16.438	1.902	1.902	0.000	0.000	0.000	0.000
11	A	46	LYS	1	0.932	0.981	13.106	39.859	39.859	0.000	0.000	0.000	0.000
12	A	47	VAL	0	0.052	0.024	18.951	1.298	1.298	0.000	0.000	0.000	0.000
13	A	48	LEU	0	0.001	0.003	21.240	1.113	1.113	0.000	0.000	0.000	0.000
14	A	49	LYS	1	0.796	0.893	20.801	26.565	26.565	0.000	0.000	0.000	0.000
15	A	50	GLN	0	-0.039	-0.033	21.159	-0.314	-0.314	0.000	0.000	0.000	0.000
16	A	51	THR	0	-0.061	-0.017	24.466	0.916	0.916	0.000	0.000	0.000	0.000
17	A	52	HIS	0	0.042	0.022	26.659	0.991	0.991	0.000	0.000	0.000	0.000
18	A	53	PRO	0	0.025	0.009	25.218	-0.808	-0.808	0.000	0.000	0.000	0.000
19	A	54	ASP	-1	-0.819	-0.889	25.420	-21.650	-21.650	0.000	0.000	0.000	0.000
20	A	55	THR	0	-0.027	-0.021	25.751	-0.626	-0.626	0.000	0.000	0.000	0.000
21	A	56	GLY	0	-0.032	-0.001	23.490	-1.101	-1.101	0.000	0.000	0.000	0.000
22	A	57	ILE	0	0.020	-0.002	19.247	0.489	0.489	0.000	0.000	0.000	0.000
23	A	58	SER	0	0.028	0.027	20.369	-1.365	-1.365	0.000	0.000	0.000	0.000
24	A	59	GLN	0	0.074	0.017	13.718	-1.062	-1.062	0.000	0.000	0.000	0.000
25	A	60	LYS	1	0.987	0.989	16.911	28.820	28.820	0.000	0.000	0.000	0.000
26	A	61	SER	0	0.037	0.013	19.007	0.398	0.398	0.000	0.000	0.000	0.000
27	A	62	MET	0	0.022	0.038	15.129	0.083	0.083	0.000	0.000	0.000	0.000
28	A	63	SER	0	-0.064	-0.020	15.190	-0.613	-0.613	0.000	0.000	0.000	0.000
29	A	64	ILE	0	0.036	0.024	16.184	-0.614	-0.614	0.000	0.000	0.000	0.000
30	A	65	LEU	0	0.044	0.018	18.889	0.007	0.007	0.000	0.000	0.000	0.000
31	A	66	ASN	0	0.046	0.023	12.333	-1.690	-1.690	0.000	0.000	0.000	0.000
32	A	67	SER	0	-0.035	-0.017	16.036	-1.083	-1.083	0.000	0.000	0.000	0.000
33	A	68	PHE	0	0.009	0.006	17.335	0.345	0.345	0.000	0.000	0.000	0.000
34	A	69	VAL	0	0.007	0.004	17.080	0.698	0.698	0.000	0.000	0.000	0.000
35	A	70	ASN	0	-0.037	-0.035	13.661	-0.760	-0.760	0.000	0.000	0.000	0.000
36	A	71	ASP	-1	-0.797	-0.853	17.471	-24.909	-24.909	0.000	0.000	0.000	0.000
37	A	72	ILE	0	-0.012	-0.010	20.638	0.994	0.994	0.000	0.000	0.000	0.000
38	A	73	PHE	0	-0.007	-0.003	18.096	0.698	0.698	0.000	0.000	0.000	0.000
39	A	74	GLU	-1	-0.850	-0.938	18.747	-28.667	-28.667	0.000	0.000	0.000	0.000
40	A	75	ARG	1	0.790	0.869	21.232	24.726	24.726	0.000	0.000	0.000	0.000
41	A	76	ILE	0	-0.012	-0.002	23.935	1.035	1.035	0.000	0.000	0.000	0.000
42	A	77	ALA	0	0.025	0.011	21.770	0.870	0.870	0.000	0.000	0.000	0.000
43	A	78	THR	0	0.021	0.004	22.950	1.015	1.015	0.000	0.000	0.000	0.000
44	A	79	GLU	-1	-0.881	-0.925	25.300	-18.828	-18.828	0.000	0.000	0.000	0.000
45	A	80	ALA	0	-0.016	-0.009	26.522	0.655	0.655	0.000	0.000	0.000	0.000
46	A	81	SER	0	-0.009	-0.005	25.533	0.788	0.788	0.000	0.000	0.000	0.000
47	A	82	LYS	1	0.865	0.924	27.639	21.296	21.296	0.000	0.000	0.000	0.000
48	A	83	LEU	0	-0.038	-0.010	30.876	0.684	0.684	0.000	0.000	0.000	0.000
49	A	84	ALA	0	0.028	0.014	29.891	0.635	0.635	0.000	0.000	0.000	0.000
50	A	85	ALA	0	0.032	0.018	30.749	0.584	0.584	0.000	0.000	0.000	0.000
51	A	86	TYR	0	-0.023	-0.022	32.654	0.526	0.526	0.000	0.000	0.000	0.000
52	A	87	ASN	0	-0.120	-0.067	35.508	0.996	0.996	0.000	0.000	0.000	0.000
53	A	88	LYS	1	0.930	0.968	35.921	16.272	16.272	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.867	0.937	32.514	18.567	18.567	0.000	0.000	0.000	0.000
55	A	90	SER	0	0.014	0.011	30.272	-0.300	-0.300	0.000	0.000	0.000	0.000
56	A	91	THR	0	-0.014	-0.020	27.832	-0.512	-0.512	0.000	0.000	0.000	0.000
57	A	92	ILE	0	0.011	0.018	24.478	0.765	0.765	0.000	0.000	0.000	0.000
58	A	93	SER	0	-0.008	-0.023	26.762	-0.542	-0.542	0.000	0.000	0.000	0.000
59	A	94	ALA	0	0.085	0.023	28.005	-0.126	-0.126	0.000	0.000	0.000	0.000
60	A	95	ARG	1	0.974	0.993	28.912	17.374	17.374	0.000	0.000	0.000	0.000
61	A	96	GLU	-1	-0.778	-0.851	29.552	-18.725	-18.725	0.000	0.000	0.000	0.000
62	A	97	ILE	0	0.047	0.021	24.597	0.117	0.117	0.000	0.000	0.000	0.000
63	A	98	GLN	0	0.020	0.021	28.317	0.657	0.657	0.000	0.000	0.000	0.000
64	A	99	THR	0	-0.048	-0.037	31.138	0.567	0.567	0.000	0.000	0.000	0.000
65	A	100	ALA	0	0.048	0.019	28.727	0.312	0.312	0.000	0.000	0.000	0.000
66	A	101	VAL	0	-0.023	-0.012	27.959	0.045	0.045	0.000	0.000	0.000	0.000
67	A	102	ARG	1	0.863	0.906	30.224	17.650	17.650	0.000	0.000	0.000	0.000
68	A	103	LEU	0	-0.023	0.012	32.747	0.484	0.484	0.000	0.000	0.000	0.000
69	A	104	ILE	0	-0.024	-0.006	27.133	0.122	0.122	0.000	0.000	0.000	0.000
70	A	105	LEU	0	-0.032	-0.006	27.737	-0.365	-0.365	0.000	0.000	0.000	0.000
71	A	106	PRO	0	0.043	0.016	31.763	0.593	0.593	0.000	0.000	0.000	0.000
72	A	107	GLY	0	0.048	0.019	34.420	-0.249	-0.249	0.000	0.000	0.000	0.000
73	A	108	GLU	-1	-0.786	-0.864	35.568	-16.657	-16.657	0.000	0.000	0.000	0.000
74	A	109	LEU	0	0.014	-0.002	30.073	-0.262	-0.262	0.000	0.000	0.000	0.000
75	A	110	ALA	0	0.020	0.013	31.439	-0.496	-0.496	0.000	0.000	0.000	0.000
76	A	111	LYS	1	0.844	0.911	33.080	15.885	15.885	0.000	0.000	0.000	0.000
77	A	112	HIS	0	-0.024	-0.027	31.803	-0.343	-0.343	0.000	0.000	0.000	0.000
78	A	113	ALA	0	0.022	0.021	28.598	-0.398	-0.398	0.000	0.000	0.000	0.000
79	A	114	VAL	0	-0.011	-0.014	29.655	-0.370	-0.370	0.000	0.000	0.000	0.000
80	A	115	SER	0	-0.038	0.004	32.156	0.064	0.064	0.000	0.000	0.000	0.000
81	A	116	GLU	-1	-0.863	-0.950	27.493	-21.657	-21.657	0.000	0.000	0.000	0.000
82	A	117	GLY	0	-0.013	-0.004	27.303	-0.555	-0.555	0.000	0.000	0.000	0.000
83	A	118	THR	0	-0.034	-0.034	28.345	-0.125	-0.125	0.000	0.000	0.000	0.000
84	A	119	ARG	1	0.929	0.979	30.193	18.857	18.857	0.000	0.000	0.000	0.000
85	A	120	ALA	0	0.002	0.010	25.350	0.032	0.032	0.000	0.000	0.000	0.000
86	A	121	VAL	0	0.013	0.005	27.227	-0.245	-0.245	0.000	0.000	0.000	0.000
87	A	122	THR	0	-0.010	-0.006	28.685	0.370	0.370	0.000	0.000	0.000	0.000
88	A	123	LYS	1	0.957	0.974	27.147	21.929	21.929	0.000	0.000	0.000	0.000
89	A	124	TYR	0	-0.026	-0.002	22.429	-0.420	-0.420	0.000	0.000	0.000	0.000
90	A	125	SER	0	0.018	-0.007	27.281	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	126	SER	0	-0.106	-0.057	30.212	0.587	0.587	0.000	0.000	0.000	0.000
92	A	127	SER	0	-0.115	-0.058	26.908	0.210	0.210	0.000	0.000	0.000	0.000
93	A	128	THR	-1	-0.930	-0.946	28.343	-20.924	-20.924	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:36:ARG)