FMO DATABASE

FMODB ID: 6529Z

Calculation Name: 1M0D-A-Xray549

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion

Ligand 3-letter code: MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1M0D

Chain ID: A

ChEMBL ID:

UniProt ID: P00641

Base Structure: X-ray

Registration Date: 2025-10-11

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1004308.029011
FMO2-HF: Nuclear repulsion	952448.405653
FMO2-HF: Total energy	-51859.623358
FMO2-MP2: Total energy	-52014.819623

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:17:SER)

Summations of interaction energy for fragment #1(A:17:SER)

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.
-138.026	-132.558	31.08	-21.127	-15.422	-0.151

Interaction energy analysis for fragmet #1(A:17:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.876

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	19	LEU	0	-0.004	0.005	2.884	5.226	8.340	0.149	-1.587	-1.676	0.010
4	A	20	GLU	-1	-0.722	-0.827	1.611	-141.287	-144.669	30.666	-16.375	-10.910	-0.128
5	A	21	ASP	-1	-0.847	-0.918	2.750	-83.780	-78.394	0.267	-3.094	-2.559	-0.033
6	A	22	LYS	1	0.829	0.911	4.795	45.092	45.222	-0.001	-0.013	-0.116	0.000
20	A	36	TYR	0	-0.074	-0.060	3.648	3.307	3.527	-0.001	-0.058	-0.161	0.000
7	A	23	VAL	0	0.033	0.014	7.236	4.088	4.088	0.000	0.000	0.000	0.000
8	A	24	SER	0	0.017	0.002	6.280	4.180	4.180	0.000	0.000	0.000	0.000
9	A	25	LYS	1	1.013	1.010	8.780	27.339	27.339	0.000	0.000	0.000	0.000
10	A	26	GLN	0	-0.047	-0.017	10.814	1.667	1.667	0.000	0.000	0.000	0.000
11	A	27	LEU	0	0.010	0.013	11.212	2.499	2.499	0.000	0.000	0.000	0.000
12	A	28	GLU	-1	-0.870	-0.937	11.262	-25.368	-25.368	0.000	0.000	0.000	0.000
13	A	29	SER	0	-0.122	-0.072	14.669	1.890	1.890	0.000	0.000	0.000	0.000
14	A	30	LYS	1	0.890	0.941	16.699	17.232	17.232	0.000	0.000	0.000	0.000
15	A	31	GLY	0	0.033	0.029	18.163	0.773	0.773	0.000	0.000	0.000	0.000
16	A	32	ILE	0	-0.039	-0.018	16.322	0.750	0.750	0.000	0.000	0.000	0.000
17	A	33	LYS	1	0.879	0.931	16.142	14.857	14.857	0.000	0.000	0.000	0.000
18	A	34	PHE	0	-0.012	-0.012	9.594	0.454	0.454	0.000	0.000	0.000	0.000
19	A	35	GLU	-1	-0.838	-0.902	13.636	-18.023	-18.023	0.000	0.000	0.000	0.000
21	A	37	GLU	-1	-0.971	-0.996	7.972	-39.014	-39.014	0.000	0.000	0.000	0.000
22	A	38	GLU	-1	-0.937	-0.941	10.970	-18.658	-18.658	0.000	0.000	0.000	0.000
23	A	39	TRP	0	-0.070	-0.043	14.608	1.829	1.829	0.000	0.000	0.000	0.000
24	A	40	LYS	1	0.939	0.964	15.126	16.661	16.661	0.000	0.000	0.000	0.000
25	A	41	VAL	0	0.035	0.012	16.665	1.048	1.048	0.000	0.000	0.000	0.000
26	A	42	PRO	0	-0.035	-0.021	18.559	-0.277	-0.277	0.000	0.000	0.000	0.000
27	A	43	TYR	0	-0.017	-0.004	17.208	0.074	0.074	0.000	0.000	0.000	0.000
28	A	44	VAL	0	0.011	0.001	22.085	0.001	0.001	0.000	0.000	0.000	0.000
29	A	45	ILE	0	-0.003	0.003	20.439	-0.085	-0.085	0.000	0.000	0.000	0.000
30	A	46	PRO	0	-0.007	-0.007	24.386	0.317	0.317	0.000	0.000	0.000	0.000
31	A	47	ALA	0	0.027	0.021	27.999	-0.127	-0.127	0.000	0.000	0.000	0.000
32	A	48	SER	0	0.014	0.004	29.294	0.070	0.070	0.000	0.000	0.000	0.000
33	A	49	ASN	0	-0.029	-0.011	31.761	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	50	HIS	0	0.010	0.004	30.227	0.077	0.077	0.000	0.000	0.000	0.000
35	A	51	THR	0	-0.027	-0.018	35.408	0.268	0.268	0.000	0.000	0.000	0.000
36	A	52	TYR	0	-0.033	-0.070	37.023	-0.242	-0.242	0.000	0.000	0.000	0.000
37	A	53	THR	0	-0.022	-0.002	39.082	0.224	0.224	0.000	0.000	0.000	0.000
38	A	54	PRO	0	-0.015	-0.006	41.120	-0.119	-0.119	0.000	0.000	0.000	0.000
39	A	55	ASP	-1	-0.816	-0.877	42.162	-7.372	-7.372	0.000	0.000	0.000	0.000
40	A	56	PHE	0	-0.032	-0.018	44.450	0.179	0.179	0.000	0.000	0.000	0.000
41	A	57	LEU	0	-0.005	-0.002	47.507	-0.097	-0.097	0.000	0.000	0.000	0.000
42	A	58	LEU	0	-0.013	0.001	50.262	0.102	0.102	0.000	0.000	0.000	0.000
43	A	59	PRO	0	0.011	-0.011	53.367	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	60	ASN	0	-0.038	-0.037	54.508	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	61	GLY	0	0.060	0.022	53.271	0.004	0.004	0.000	0.000	0.000	0.000
46	A	62	ILE	0	-0.078	-0.019	49.178	-0.129	-0.129	0.000	0.000	0.000	0.000
47	A	63	PHE	0	0.050	0.012	45.725	0.034	0.034	0.000	0.000	0.000	0.000
48	A	64	VAL	0	-0.033	-0.027	45.402	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	65	GLU	-1	-0.786	-0.839	38.414	-8.030	-8.030	0.000	0.000	0.000	0.000
50	A	66	THR	0	-0.057	-0.043	42.063	0.088	0.088	0.000	0.000	0.000	0.000
51	A	67	LYS	1	0.822	0.885	35.126	8.326	8.326	0.000	0.000	0.000	0.000
52	A	68	GLY	0	0.046	0.024	36.964	0.146	0.146	0.000	0.000	0.000	0.000
53	A	69	LEU	0	0.002	-0.001	28.961	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	70	TRP	0	-0.013	-0.018	32.600	0.091	0.091	0.000	0.000	0.000	0.000
55	A	71	GLU	-1	-0.869	-0.930	27.341	-11.064	-11.064	0.000	0.000	0.000	0.000
56	A	72	SER	0	-0.022	-0.021	24.931	0.350	0.350	0.000	0.000	0.000	0.000
57	A	73	ASP	-1	-0.763	-0.884	25.608	-11.782	-11.782	0.000	0.000	0.000	0.000
58	A	74	ASP	-1	-0.779	-0.894	28.608	-8.606	-8.606	0.000	0.000	0.000	0.000
59	A	75	ARG	1	0.859	0.923	28.027	10.713	10.713	0.000	0.000	0.000	0.000
60	A	76	LYS	1	0.886	0.936	24.406	12.351	12.351	0.000	0.000	0.000	0.000
61	A	77	LYS	1	0.900	0.977	31.442	9.080	9.080	0.000	0.000	0.000	0.000
62	A	78	HIS	1	0.823	0.903	33.917	8.636	8.636	0.000	0.000	0.000	0.000
63	A	79	LEU	0	-0.036	-0.008	32.869	0.227	0.227	0.000	0.000	0.000	0.000
64	A	80	LEU	0	0.029	0.014	31.561	0.151	0.151	0.000	0.000	0.000	0.000
65	A	81	ILE	0	-0.002	-0.005	35.955	0.203	0.203	0.000	0.000	0.000	0.000
66	A	82	ARG	1	0.851	0.927	39.078	7.780	7.780	0.000	0.000	0.000	0.000
67	A	83	GLU	-1	-0.940	-0.955	38.342	-7.936	-7.936	0.000	0.000	0.000	0.000
68	A	84	GLN	0	0.040	0.014	36.609	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	85	HIS	0	-0.041	-0.025	41.057	0.331	0.331	0.000	0.000	0.000	0.000
70	A	86	PRO	0	0.013	0.016	44.042	0.047	0.047	0.000	0.000	0.000	0.000
71	A	87	GLU	-1	-0.925	-0.959	45.529	-6.338	-6.338	0.000	0.000	0.000	0.000
72	A	88	LEU	0	-0.048	-0.011	44.004	0.111	0.111	0.000	0.000	0.000	0.000
73	A	89	ASP	-1	-0.752	-0.829	45.765	-6.607	-6.607	0.000	0.000	0.000	0.000
74	A	90	ILE	0	-0.019	-0.007	41.553	0.028	0.028	0.000	0.000	0.000	0.000
75	A	91	ARG	1	0.681	0.784	43.566	6.284	6.284	0.000	0.000	0.000	0.000
76	A	92	ILE	0	-0.023	-0.014	38.169	-0.087	-0.087	0.000	0.000	0.000	0.000
77	A	93	VAL	0	0.002	0.015	42.345	0.066	0.066	0.000	0.000	0.000	0.000
78	A	94	PHE	0	0.020	-0.003	36.780	-0.158	-0.158	0.000	0.000	0.000	0.000
79	A	95	SER	0	0.019	0.005	39.272	0.210	0.210	0.000	0.000	0.000	0.000
80	A	96	SER	0	-0.032	-0.030	38.826	0.200	0.200	0.000	0.000	0.000	0.000
81	A	97	SER	0	-0.011	-0.018	38.292	-0.324	-0.324	0.000	0.000	0.000	0.000
82	A	98	ARG	1	0.965	0.974	38.043	7.331	7.331	0.000	0.000	0.000	0.000
83	A	99	THR	0	-0.036	-0.015	32.924	-0.170	-0.170	0.000	0.000	0.000	0.000
84	A	100	LYS	1	0.883	0.939	30.807	9.371	9.371	0.000	0.000	0.000	0.000
85	A	101	LEU	0	-0.026	-0.009	28.818	-0.146	-0.146	0.000	0.000	0.000	0.000
86	A	102	TYR	0	0.046	0.011	24.451	-0.326	-0.326	0.000	0.000	0.000	0.000
87	A	103	LYS	1	0.983	0.981	23.339	12.859	12.859	0.000	0.000	0.000	0.000
88	A	104	GLY	0	0.024	0.021	25.619	0.183	0.183	0.000	0.000	0.000	0.000
89	A	105	SER	0	-0.077	-0.027	26.536	-0.035	-0.035	0.000	0.000	0.000	0.000
90	A	106	PRO	0	0.030	0.006	28.588	0.318	0.318	0.000	0.000	0.000	0.000
91	A	107	THR	0	0.025	0.037	31.529	0.188	0.188	0.000	0.000	0.000	0.000
92	A	108	SER	0	-0.044	-0.055	32.301	-0.245	-0.245	0.000	0.000	0.000	0.000
93	A	109	TYR	0	0.022	0.000	31.207	0.005	0.005	0.000	0.000	0.000	0.000
94	A	110	GLY	0	0.076	0.040	35.842	0.074	0.074	0.000	0.000	0.000	0.000
95	A	111	GLU	-1	-0.759	-0.836	36.512	-8.703	-8.703	0.000	0.000	0.000	0.000
96	A	112	PHE	0	-0.027	-0.023	31.487	-0.077	-0.077	0.000	0.000	0.000	0.000
97	A	113	CYS	0	-0.073	-0.025	36.020	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.898	-0.951	39.207	-7.421	-7.421	0.000	0.000	0.000	0.000
99	A	115	LYS	1	0.916	0.967	32.793	9.538	9.538	0.000	0.000	0.000	0.000
100	A	116	HIS	0	-0.041	-0.032	34.026	-0.197	-0.197	0.000	0.000	0.000	0.000
101	A	117	GLY	0	0.042	0.032	39.321	0.084	0.084	0.000	0.000	0.000	0.000
102	A	118	ILE	0	-0.062	-0.029	37.891	0.131	0.131	0.000	0.000	0.000	0.000
103	A	119	LYS	1	0.931	0.971	42.267	6.368	6.368	0.000	0.000	0.000	0.000
104	A	120	PHE	0	0.016	-0.007	42.052	-0.097	-0.097	0.000	0.000	0.000	0.000
105	A	121	ALA	0	0.035	0.019	44.075	0.158	0.158	0.000	0.000	0.000	0.000
106	A	122	ASP	-1	-0.760	-0.858	42.771	-7.573	-7.573	0.000	0.000	0.000	0.000
107	A	123	LYS	1	0.894	0.936	43.877	7.257	7.257	0.000	0.000	0.000	0.000
108	A	124	LEU	0	-0.018	-0.010	46.203	0.044	0.044	0.000	0.000	0.000	0.000
109	A	125	ILE	0	0.024	0.014	48.540	-0.092	-0.092	0.000	0.000	0.000	0.000
110	A	126	PRO	0	0.012	0.013	49.182	0.114	0.114	0.000	0.000	0.000	0.000
111	A	127	ALA	0	0.035	0.008	52.369	0.043	0.043	0.000	0.000	0.000	0.000
112	A	128	GLU	-1	-0.889	-0.967	53.575	-5.813	-5.813	0.000	0.000	0.000	0.000
113	A	129	TRP	0	-0.001	-0.001	45.896	0.016	0.016	0.000	0.000	0.000	0.000
114	A	130	ILE	0	-0.002	-0.002	53.600	0.016	0.016	0.000	0.000	0.000	0.000
115	A	131	LYS	1	0.917	0.968	56.105	5.419	5.419	0.000	0.000	0.000	0.000
116	A	132	GLU	-1	-0.815	-0.862	52.977	-6.013	-6.013	0.000	0.000	0.000	0.000
117	A	133	PRO	0	0.019	0.015	57.297	0.014	0.014	0.000	0.000	0.000	0.000
118	A	134	LYS	1	0.798	0.899	57.540	5.346	5.346	0.000	0.000	0.000	0.000
119	A	135	LYS	1	0.866	0.943	51.793	6.141	6.141	0.000	0.000	0.000	0.000
120	A	136	GLU	-1	-0.822	-0.918	56.126	-5.515	-5.515	0.000	0.000	0.000	0.000
121	A	137	VAL	0	0.006	0.011	50.168	-0.096	-0.096	0.000	0.000	0.000	0.000
122	A	138	PRO	0	0.028	0.026	49.355	0.084	0.084	0.000	0.000	0.000	0.000
123	A	139	PHE	0	-0.012	-0.034	50.216	-0.151	-0.151	0.000	0.000	0.000	0.000
124	A	140	ASP	-1	-0.888	-0.936	50.892	-6.190	-6.190	0.000	0.000	0.000	0.000
125	A	141	ARG	1	0.855	0.921	44.707	6.788	6.788	0.000	0.000	0.000	0.000
126	A	142	LEU	0	-0.054	-0.019	46.065	-0.203	-0.203	0.000	0.000	0.000	0.000
127	A	143	LYS	1	0.881	0.944	44.601	6.889	6.889	0.000	0.000	0.000	0.000
128	A	144	ARG	1	0.906	0.944	46.450	5.954	5.954	0.000	0.000	0.000	0.000
129	A	145	LYS	0	0.163	0.096	45.885	0.265	0.265	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:SER)