FMO DATABASE

FMODB ID: 4YRVN

Calculation Name: 1ID3-A-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: A

ChEMBL ID:

UniProt ID: P04911

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-642334.954145
FMO2-HF: Nuclear repulsion	603718.289338
FMO2-HF: Total energy	-38616.664807
FMO2-MP2: Total energy	-38732.950839

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:38:PRO)

Summations of interaction energy for fragment #1(A:38:PRO)

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.
138.149	139.641	-0.019	-0.615	-0.858	0

Interaction energy analysis for fragmet #1(A:38:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.917 / q_NPA : 0.934

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	A	40	ARG	1	0.980	0.980	3.851	34.797	36.289	-0.019	-0.615	-0.858
4	A	41	TYR	0	0.018	0.022	6.341	1.145	1.145	0.000	0.000	0.000
5	A	42	LYS	1	1.006	0.998	10.093	23.807	23.807	0.000	0.000	0.000
6	A	43	PRO	0	0.064	0.016	12.125	0.579	0.579	0.000	0.000	0.000
7	A	44	GLY	0	0.048	0.031	14.721	0.411	0.411	0.000	0.000	0.000
8	A	45	THR	0	-0.031	-0.021	14.102	0.276	0.276	0.000	0.000	0.000
9	A	46	VAL	0	-0.042	-0.026	13.585	0.123	0.123	0.000	0.000	0.000
10	A	47	ALA	0	0.078	0.048	16.412	0.653	0.653	0.000	0.000	0.000
11	A	48	LEU	0	0.059	0.026	19.789	0.572	0.572	0.000	0.000	0.000
12	A	49	ARG	1	0.880	0.950	13.597	20.464	20.464	0.000	0.000	0.000
13	A	50	GLU	-1	-0.900	-0.957	19.258	-15.057	-15.057	0.000	0.000	0.000
14	A	51	ILE	0	0.014	0.014	21.932	0.471	0.471	0.000	0.000	0.000
15	A	52	ARG	1	0.963	0.969	21.445	14.022	14.022	0.000	0.000	0.000
16	A	53	ARG	1	0.885	0.958	21.461	13.418	13.418	0.000	0.000	0.000
17	A	54	PHE	0	-0.008	-0.024	23.276	0.225	0.225	0.000	0.000	0.000
18	A	55	GLN	0	0.017	0.018	27.404	0.117	0.117	0.000	0.000	0.000
19	A	56	LYS	1	0.892	0.961	25.388	12.255	12.255	0.000	0.000	0.000
20	A	57	SER	0	-0.078	-0.053	28.313	0.255	0.255	0.000	0.000	0.000
21	A	58	THR	0	0.044	0.017	30.570	0.060	0.060	0.000	0.000	0.000
22	A	59	GLU	-1	-0.909	-0.927	27.699	-11.108	-11.108	0.000	0.000	0.000
23	A	60	LEU	0	0.000	0.005	32.326	-0.058	-0.058	0.000	0.000	0.000
24	A	61	LEU	0	-0.051	-0.035	28.198	-0.311	-0.311	0.000	0.000	0.000
25	A	62	ILE	0	-0.046	-0.012	29.973	-0.310	-0.310	0.000	0.000	0.000
26	A	63	ARG	1	0.923	0.953	27.823	10.653	10.653	0.000	0.000	0.000
27	A	64	LYS	1	1.028	1.005	32.665	8.527	8.527	0.000	0.000	0.000
28	A	65	LEU	0	0.002	0.016	35.775	0.191	0.191	0.000	0.000	0.000
29	A	66	PRO	0	-0.006	-0.025	33.162	0.184	0.184	0.000	0.000	0.000
30	A	67	PHE	0	0.063	0.046	36.454	0.117	0.117	0.000	0.000	0.000
31	A	68	GLN	0	0.049	0.033	38.143	0.389	0.389	0.000	0.000	0.000
32	A	69	ARG	1	0.916	0.953	35.365	8.578	8.578	0.000	0.000	0.000
33	A	70	LEU	0	0.071	0.044	38.520	0.141	0.141	0.000	0.000	0.000
34	A	71	VAL	0	-0.004	0.000	41.547	0.156	0.156	0.000	0.000	0.000
35	A	72	ARG	1	0.863	0.911	44.116	7.011	7.011	0.000	0.000	0.000
36	A	73	GLU	-1	-0.968	-0.973	42.265	-7.341	-7.341	0.000	0.000	0.000
37	A	74	ILE	0	0.017	-0.001	42.830	0.121	0.121	0.000	0.000	0.000
38	A	75	ALA	0	-0.029	-0.022	46.790	0.134	0.134	0.000	0.000	0.000
39	A	76	GLN	0	-0.004	-0.003	49.199	0.257	0.257	0.000	0.000	0.000
40	A	77	ASP	-1	-0.891	-0.938	49.802	-6.217	-6.217	0.000	0.000	0.000
41	A	78	PHE	0	-0.104	-0.037	49.921	0.119	0.119	0.000	0.000	0.000
42	A	79	LYS	1	0.907	0.944	54.037	5.565	5.565	0.000	0.000	0.000
43	A	80	THR	0	0.063	0.046	54.005	-0.090	-0.090	0.000	0.000	0.000
44	A	81	ASP	-1	-0.936	-0.971	54.162	-5.643	-5.643	0.000	0.000	0.000
45	A	82	LEU	0	-0.021	0.003	52.179	0.061	0.061	0.000	0.000	0.000
46	A	83	ARG	1	0.909	0.949	51.361	5.718	5.718	0.000	0.000	0.000
47	A	84	PHE	0	0.048	0.017	48.070	0.023	0.023	0.000	0.000	0.000
48	A	85	GLN	0	0.000	0.003	49.293	0.021	0.021	0.000	0.000	0.000
49	A	86	SER	0	0.016	0.001	44.309	-0.132	-0.132	0.000	0.000	0.000
50	A	87	SER	0	0.049	0.012	44.952	-0.121	-0.121	0.000	0.000	0.000
51	A	88	ALA	0	0.023	0.021	46.317	-0.051	-0.051	0.000	0.000	0.000
52	A	89	ILE	0	0.016	0.006	41.903	-0.065	-0.065	0.000	0.000	0.000
53	A	90	GLY	0	-0.008	-0.007	41.638	-0.169	-0.169	0.000	0.000	0.000
54	A	91	ALA	0	0.044	0.023	42.105	-0.136	-0.136	0.000	0.000	0.000
55	A	92	LEU	0	0.021	0.027	43.769	-0.049	-0.049	0.000	0.000	0.000
56	A	93	GLN	0	-0.074	-0.049	35.211	0.058	0.058	0.000	0.000	0.000
57	A	94	GLU	-1	-0.882	-0.957	38.984	-8.276	-8.276	0.000	0.000	0.000
58	A	95	SER	0	-0.046	-0.034	40.085	-0.084	-0.084	0.000	0.000	0.000
59	A	96	VAL	0	0.001	0.002	38.424	-0.050	-0.050	0.000	0.000	0.000
60	A	97	GLU	-1	-0.733	-0.864	34.029	-9.394	-9.394	0.000	0.000	0.000
61	A	98	ALA	0	0.020	0.017	36.544	-0.174	-0.174	0.000	0.000	0.000
62	A	99	TYR	0	-0.067	-0.061	38.629	-0.110	-0.110	0.000	0.000	0.000
63	A	100	LEU	0	-0.017	-0.015	34.995	-0.068	-0.068	0.000	0.000	0.000
64	A	101	VAL	0	-0.015	-0.006	32.770	-0.197	-0.197	0.000	0.000	0.000
65	A	102	SER	0	0.053	0.038	34.806	-0.036	-0.036	0.000	0.000	0.000
66	A	103	LEU	0	0.001	0.000	37.016	0.016	0.016	0.000	0.000	0.000
67	A	104	PHE	0	-0.050	-0.023	31.764	-0.093	-0.093	0.000	0.000	0.000
68	A	105	GLU	-1	-0.913	-0.949	33.197	-9.156	-9.156	0.000	0.000	0.000
69	A	106	ASP	-1	-0.783	-0.878	34.731	-7.968	-7.968	0.000	0.000	0.000
70	A	107	THR	0	-0.095	-0.086	33.185	0.033	0.033	0.000	0.000	0.000
71	A	108	ASN	0	-0.028	-0.030	29.604	-0.364	-0.364	0.000	0.000	0.000
72	A	109	LEU	0	0.020	0.019	32.570	-0.129	-0.129	0.000	0.000	0.000
73	A	110	ALA	0	-0.022	-0.006	35.502	0.079	0.079	0.000	0.000	0.000
74	A	111	ALA	0	-0.004	-0.005	30.832	0.035	0.035	0.000	0.000	0.000
75	A	112	ILE	0	0.014	0.009	30.890	-0.051	-0.051	0.000	0.000	0.000
76	A	113	HIS	0	-0.001	0.012	33.203	0.012	0.012	0.000	0.000	0.000
77	A	114	ALA	0	-0.076	-0.044	34.649	0.136	0.136	0.000	0.000	0.000
78	A	115	LYS	1	0.922	0.960	32.973	8.345	8.345	0.000	0.000	0.000
79	A	116	ARG	1	0.774	0.880	29.434	9.218	9.218	0.000	0.000	0.000
80	A	117	VAL	0	0.029	0.011	24.363	0.096	0.096	0.000	0.000	0.000
81	A	118	THR	0	-0.017	-0.013	24.997	-0.409	-0.409	0.000	0.000	0.000
82	A	119	ILE	0	0.042	0.040	27.335	0.382	0.382	0.000	0.000	0.000
83	A	120	GLN	0	0.029	-0.006	29.164	-0.238	-0.238	0.000	0.000	0.000
84	A	121	LYS	1	0.992	0.985	31.696	8.781	8.781	0.000	0.000	0.000
85	A	122	LYS	1	0.942	0.964	34.665	8.704	8.704	0.000	0.000	0.000
86	A	123	GLU	-1	-0.769	-0.847	32.959	-8.742	-8.742	0.000	0.000	0.000
87	A	124	ILE	0	0.066	0.042	33.320	0.178	0.178	0.000	0.000	0.000
88	A	125	LYS	1	0.912	0.954	37.177	7.902	7.902	0.000	0.000	0.000
89	A	126	LEU	0	0.009	0.012	39.395	0.197	0.197	0.000	0.000	0.000
90	A	127	ALA	0	0.057	0.026	38.407	0.186	0.186	0.000	0.000	0.000
91	A	128	ARG	1	0.886	0.929	40.231	7.467	7.467	0.000	0.000	0.000
92	A	129	ARG	1	0.961	0.984	42.768	6.628	6.628	0.000	0.000	0.000
93	A	130	LEU	0	-0.088	-0.056	42.845	0.211	0.211	0.000	0.000	0.000
94	A	131	ARG	1	0.838	0.917	40.420	7.683	7.683	0.000	0.000	0.000
95	A	132	GLY	0	-0.057	-0.015	45.913	0.108	0.108	0.000	0.000	0.000
96	A	133	GLU	-1	-0.769	-0.852	43.521	-7.264	-7.264	0.000	0.000	0.000
97	A	134	ARG	0	-0.017	0.010	46.324	-0.261	-0.261	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:PRO)