FMO DATABASE

FMODB ID: Y7LN2

Calculation Name: 1VJ2-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: 1VJ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1H0

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-950991.668569
FMO2-HF: Nuclear repulsion	905393.785652
FMO2-HF: Total energy	-45597.882917
FMO2-MP2: Total energy	-45732.044118

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:1:MET)

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

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.
-8.4660000000001	-5.323	2.342	-1.822	-3.662	-0.008

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.925

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	3	LEU	0	0.037	0.014	2.717	-0.514	2.605	2.343	-1.817	-3.645	-0.008
4	A	4	LYS	1	0.947	0.967	4.922	27.208	27.232	-0.001	-0.005	-0.017	0.000
5	A	5	ARG	1	0.924	0.972	8.659	17.242	17.242	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.049	0.013	11.958	0.142	0.142	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.015	-0.050	13.301	0.361	0.361	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.848	-0.901	14.015	-18.040	-18.040	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.081	-0.030	13.356	-0.594	-0.594	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.043	0.012	15.915	0.706	0.706	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.020	0.000	19.567	-0.235	-0.235	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.017	0.008	20.089	0.331	0.331	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.935	0.968	23.914	9.844	9.844	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.012	0.008	24.767	0.095	0.095	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.083	-0.068	28.511	0.364	0.364	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.025	0.020	31.260	0.067	0.067	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.861	-0.915	34.105	-8.368	-8.368	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.925	0.950	33.782	8.956	8.956	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.002	0.018	29.014	-0.121	-0.121	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.884	0.924	32.458	8.800	8.800	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.037	0.032	31.688	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.028	0.024	26.118	-0.170	-0.170	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.897	0.947	23.599	11.341	11.341	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.914	0.958	20.098	14.544	14.544	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.849	0.932	16.564	15.601	15.601	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.036	0.027	14.126	0.039	0.039	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.072	-0.042	11.248	-0.556	-0.556	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.023	-0.013	7.826	-2.891	-2.891	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.082	0.037	10.697	1.910	1.910	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.001	-0.015	12.161	-1.756	-1.756	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.826	0.906	10.389	27.696	27.696	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.892	-0.920	7.967	-31.797	-31.797	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.000	-0.001	8.152	-3.555	-3.555	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.001	0.014	9.947	1.910	1.910	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.025	-0.019	12.916	2.295	2.295	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.045	0.027	11.985	1.145	1.145	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.002	0.020	13.130	-1.786	-1.786	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.003	0.001	10.622	0.742	0.742	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.838	0.881	14.154	14.829	14.829	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.018	0.002	16.216	0.014	0.014	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.010	-0.015	17.797	0.190	0.190	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.001	0.007	21.604	-0.223	-0.223	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.041	-0.014	23.904	0.157	0.157	0.000	0.000	0.000	0.000
44	A	44	GLU	0	-0.083	-0.095	27.609	0.144	0.144	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.071	0.035	30.418	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.012	0.020	33.692	0.100	0.100	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.083	-0.029	31.713	0.078	0.078	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.001	-0.014	32.439	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.026	-0.029	26.717	-0.218	-0.218	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.801	-0.898	31.148	-8.468	-8.468	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.834	0.908	33.292	7.913	7.913	0.000	0.000	0.000	0.000
52	A	52	HIS	0	-0.079	-0.036	29.264	-0.150	-0.150	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.037	0.037	31.839	-0.100	-0.100	0.000	0.000	0.000	0.000
54	A	54	HIS	1	0.830	0.899	26.241	11.487	11.487	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.038	0.032	28.800	-0.089	-0.089	0.000	0.000	0.000	0.000
56	A	56	TRP	0	0.012	0.031	23.621	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.788	-0.901	22.032	-12.936	-12.936	0.000	0.000	0.000	0.000
58	A	58	HIS	0	-0.069	-0.047	22.339	0.065	0.065	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.892	-0.925	18.514	-14.789	-14.789	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.033	-0.032	19.689	-0.643	-0.643	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.014	0.011	18.523	0.132	0.132	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.006	0.007	20.378	-0.398	-0.398	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.072	-0.040	17.242	-0.184	-0.184	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.865	0.929	21.106	11.982	11.982	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.055	0.023	24.209	0.065	0.065	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.885	0.923	27.759	9.103	9.103	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.026	-0.003	25.711	0.077	0.077	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.011	-0.020	29.468	0.051	0.051	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.011	-0.005	29.226	-0.183	-0.183	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.069	-0.025	31.847	0.335	0.335	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.916	0.931	33.052	8.677	8.677	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.875	-0.940	35.776	-7.683	-7.683	0.000	0.000	0.000	0.000
73	A	73	GLN	0	-0.045	-0.021	38.473	0.253	0.253	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.024	0.013	39.575	0.174	0.174	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.849	-0.905	36.422	-8.272	-8.272	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.863	-0.918	33.611	-8.833	-8.833	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.049	-0.017	33.000	-0.179	-0.179	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.016	0.026	28.299	0.093	0.093	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.881	-0.948	28.241	-9.432	-9.432	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.894	-0.942	24.092	-11.361	-11.361	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.002	-0.001	22.808	0.262	0.262	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.002	0.001	23.817	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.027	-0.008	21.910	-0.493	-0.493	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.031	-0.026	23.117	0.553	0.553	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.001	0.002	23.287	-0.634	-0.634	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.032	-0.014	25.200	0.411	0.411	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.845	-0.925	26.426	-10.421	-10.421	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.034	-0.023	27.039	0.111	0.111	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.091	-0.059	29.300	0.309	0.309	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.814	-0.886	30.822	-9.420	-9.420	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.036	-0.012	32.090	-0.263	-0.263	0.000	0.000	0.000	0.000
92	A	92	HIS	1	0.829	0.897	28.724	10.459	10.459	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.010	0.000	30.822	0.009	0.009	0.000	0.000	0.000	0.000
94	A	94	PHE	0	-0.008	-0.007	26.638	-0.102	-0.102	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.785	0.829	30.565	8.443	8.443	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.006	-0.004	30.203	0.055	0.055	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.770	-0.828	32.206	-8.291	-8.291	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.003	-0.012	32.308	0.149	0.149	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.895	-0.951	34.199	-8.175	-8.175	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.066	-0.034	30.555	-0.104	-0.104	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.865	-0.901	25.898	-11.461	-11.461	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.009	0.014	26.501	-0.130	-0.130	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.839	-0.899	20.684	-13.729	-13.729	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.014	0.003	21.079	0.180	0.180	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.020	0.010	13.986	-0.450	-0.450	0.000	0.000	0.000	0.000
106	A	106	CYS	0	0.001	0.007	17.963	0.717	0.717	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.006	0.005	13.683	-0.850	-0.850	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.010	0.002	17.813	1.046	1.046	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.056	0.036	17.745	-1.285	-1.285	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.900	0.913	16.864	17.732	17.732	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.971	-0.972	18.781	-11.866	-11.866	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.019	-0.015	21.849	0.451	0.451	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.046	-0.014	21.097	0.292	0.292	0.000	0.000	0.000	0.000
114	A	114	GLU	-2	-1.681	-1.828	16.119	-34.686	-34.686	0.000	0.000	0.000	0.000

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