FMO DATABASE

FMODB ID: 2465R

Calculation Name: 2CV5-D-Xray547

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion | chloride ion

Ligand 3-letter code: MN | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CV5

Chain ID: D

ChEMBL ID:

UniProt ID: P04908

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-595220.414987
FMO2-HF: Nuclear repulsion	557987.894073
FMO2-HF: Total energy	-37232.520914
FMO2-MP2: Total energy	-37342.071297

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:27:LYS)

Summations of interaction energy for fragment #1(A:27: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.
148.165	153.395	-0.041	-2.781	-2.409	-0.015

Interaction energy analysis for fragmet #1(A:27:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.865 / q_NPA : 1.913

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	29	SER	0	0.071	0.051	3.874	0.436	5.666	-0.041	-2.781	-2.409	-0.015
4	A	30	ARG	1	0.883	0.939	5.954	49.850	49.850	0.000	0.000	0.000	0.000
5	A	31	LYS	1	0.984	0.986	8.601	41.146	41.146	0.000	0.000	0.000	0.000
6	A	32	GLU	-1	-0.827	-0.885	11.911	-36.664	-36.664	0.000	0.000	0.000	0.000
7	A	33	SER	0	-0.007	-0.024	14.991	0.819	0.819	0.000	0.000	0.000	0.000
8	A	34	TYR	0	0.080	0.032	18.528	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	35	SER	0	0.032	-0.026	20.649	0.699	0.699	0.000	0.000	0.000	0.000
10	A	36	VAL	0	-0.008	-0.004	20.113	0.885	0.885	0.000	0.000	0.000	0.000
11	A	37	TYR	0	-0.022	-0.003	20.694	0.609	0.609	0.000	0.000	0.000	0.000
12	A	38	VAL	0	0.035	0.013	25.297	0.833	0.833	0.000	0.000	0.000	0.000
13	A	39	TYR	0	0.013	0.003	25.799	0.773	0.773	0.000	0.000	0.000	0.000
14	A	40	LYS	1	0.951	0.975	25.316	23.308	23.308	0.000	0.000	0.000	0.000
15	A	41	VAL	0	0.045	0.025	29.047	0.550	0.550	0.000	0.000	0.000	0.000
16	A	42	LEU	0	-0.012	-0.007	30.341	0.494	0.494	0.000	0.000	0.000	0.000
17	A	43	LYS	1	0.780	0.866	30.600	19.110	19.110	0.000	0.000	0.000	0.000
18	A	44	GLN	0	-0.027	-0.012	33.143	0.216	0.216	0.000	0.000	0.000	0.000
19	A	45	VAL	0	-0.040	-0.011	35.019	0.442	0.442	0.000	0.000	0.000	0.000
20	A	46	HIS	0	0.015	0.011	36.062	0.154	0.154	0.000	0.000	0.000	0.000
21	A	47	PRO	0	0.022	0.010	35.584	-0.499	-0.499	0.000	0.000	0.000	0.000
22	A	48	ASP	-1	-0.831	-0.902	35.556	-16.376	-16.376	0.000	0.000	0.000	0.000
23	A	49	THR	0	-0.019	0.005	34.573	-0.223	-0.223	0.000	0.000	0.000	0.000
24	A	50	GLY	0	-0.005	0.010	31.619	-0.535	-0.535	0.000	0.000	0.000	0.000
25	A	51	ILE	0	-0.003	-0.016	27.642	0.322	0.322	0.000	0.000	0.000	0.000
26	A	52	SER	0	0.040	0.025	28.383	-0.774	-0.774	0.000	0.000	0.000	0.000
27	A	53	SER	0	0.037	0.001	23.038	0.177	0.177	0.000	0.000	0.000	0.000
28	A	54	LYS	1	0.996	0.990	24.589	22.536	22.536	0.000	0.000	0.000	0.000
29	A	55	ALA	0	0.045	0.034	26.651	0.002	0.002	0.000	0.000	0.000	0.000
30	A	56	MET	0	0.011	0.049	23.462	0.025	0.025	0.000	0.000	0.000	0.000
31	A	57	GLY	0	0.038	0.026	23.704	-0.595	-0.595	0.000	0.000	0.000	0.000
32	A	58	ILE	0	0.019	0.022	24.673	-0.112	-0.112	0.000	0.000	0.000	0.000
33	A	59	MET	0	0.019	0.009	26.948	0.213	0.213	0.000	0.000	0.000	0.000
34	A	60	ASN	0	-0.036	-0.029	21.460	-0.769	-0.769	0.000	0.000	0.000	0.000
35	A	61	SER	0	-0.002	0.000	24.274	-0.427	-0.427	0.000	0.000	0.000	0.000
36	A	62	PHE	0	0.012	0.007	25.890	0.191	0.191	0.000	0.000	0.000	0.000
37	A	63	VAL	0	-0.004	-0.002	25.625	0.319	0.319	0.000	0.000	0.000	0.000
38	A	64	ASN	0	-0.032	-0.033	21.596	-0.216	-0.216	0.000	0.000	0.000	0.000
39	A	65	ASP	-1	-0.798	-0.849	25.442	-18.517	-18.517	0.000	0.000	0.000	0.000
40	A	66	ILE	0	-0.014	-0.009	28.738	0.454	0.454	0.000	0.000	0.000	0.000
41	A	67	PHE	0	-0.014	-0.004	24.964	0.352	0.352	0.000	0.000	0.000	0.000
42	A	68	GLU	-1	-0.924	-0.966	26.637	-19.793	-19.793	0.000	0.000	0.000	0.000
43	A	69	ARG	1	0.820	0.877	28.623	18.098	18.098	0.000	0.000	0.000	0.000
44	A	70	ILE	0	-0.018	-0.005	31.824	0.564	0.564	0.000	0.000	0.000	0.000
45	A	71	ALA	0	0.013	0.006	28.880	0.413	0.413	0.000	0.000	0.000	0.000
46	A	72	GLY	0	0.061	0.023	30.808	0.253	0.253	0.000	0.000	0.000	0.000
47	A	73	GLU	-1	-0.914	-0.945	31.980	-15.118	-15.118	0.000	0.000	0.000	0.000
48	A	74	ALA	0	0.004	-0.009	33.454	0.375	0.375	0.000	0.000	0.000	0.000
49	A	75	SER	0	-0.010	-0.009	31.793	0.408	0.408	0.000	0.000	0.000	0.000
50	A	76	ARG	1	0.908	0.958	33.717	16.928	16.928	0.000	0.000	0.000	0.000
51	A	77	LEU	0	-0.016	-0.003	37.188	0.383	0.383	0.000	0.000	0.000	0.000
52	A	78	ALA	0	0.001	0.005	35.964	0.404	0.404	0.000	0.000	0.000	0.000
53	A	79	HIS	0	0.013	0.013	36.516	0.508	0.508	0.000	0.000	0.000	0.000
54	A	80	TYR	0	0.001	-0.010	38.562	0.277	0.277	0.000	0.000	0.000	0.000
55	A	81	ASN	0	-0.104	-0.058	41.553	0.629	0.629	0.000	0.000	0.000	0.000
56	A	82	LYS	1	0.929	0.965	41.349	13.902	13.902	0.000	0.000	0.000	0.000
57	A	83	ARG	1	0.854	0.930	38.848	14.772	14.772	0.000	0.000	0.000	0.000
58	A	84	SER	0	0.009	0.004	35.256	-0.168	-0.168	0.000	0.000	0.000	0.000
59	A	85	THR	0	-0.023	-0.018	33.686	-0.621	-0.621	0.000	0.000	0.000	0.000
60	A	86	ILE	0	0.019	0.027	31.035	0.473	0.473	0.000	0.000	0.000	0.000
61	A	87	THR	0	-0.033	-0.045	33.347	-0.188	-0.188	0.000	0.000	0.000	0.000
62	A	88	SER	0	0.040	-0.001	35.762	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	89	ARG	1	0.959	0.985	36.611	13.781	13.781	0.000	0.000	0.000	0.000
64	A	90	GLU	-1	-0.707	-0.818	36.533	-15.169	-15.169	0.000	0.000	0.000	0.000
65	A	91	ILE	0	0.052	0.029	32.031	0.088	0.088	0.000	0.000	0.000	0.000
66	A	92	GLN	0	-0.006	-0.002	35.966	0.139	0.139	0.000	0.000	0.000	0.000
67	A	93	THR	0	-0.068	-0.049	39.216	0.329	0.329	0.000	0.000	0.000	0.000
68	A	94	ALA	0	0.065	0.035	36.067	0.184	0.184	0.000	0.000	0.000	0.000
69	A	95	VAL	0	-0.022	-0.020	36.242	0.050	0.050	0.000	0.000	0.000	0.000
70	A	96	ARG	1	0.904	0.939	38.361	13.707	13.707	0.000	0.000	0.000	0.000
71	A	97	LEU	0	-0.009	0.017	40.127	0.294	0.294	0.000	0.000	0.000	0.000
72	A	98	LEU	0	-0.018	-0.003	35.804	0.046	0.046	0.000	0.000	0.000	0.000
73	A	99	LEU	0	-0.044	-0.009	36.397	-0.090	-0.090	0.000	0.000	0.000	0.000
74	A	100	PRO	0	0.038	0.025	40.354	0.330	0.330	0.000	0.000	0.000	0.000
75	A	101	GLY	0	0.042	0.002	43.822	-0.046	-0.046	0.000	0.000	0.000	0.000
76	A	102	GLU	-1	-0.802	-0.895	45.915	-12.604	-12.604	0.000	0.000	0.000	0.000
77	A	103	LEU	0	0.008	0.012	38.851	-0.163	-0.163	0.000	0.000	0.000	0.000
78	A	104	ALA	0	0.028	0.021	40.717	-0.329	-0.329	0.000	0.000	0.000	0.000
79	A	105	LYS	1	0.809	0.887	42.005	12.503	12.503	0.000	0.000	0.000	0.000
80	A	106	HIS	0	0.060	0.038	41.446	-0.136	-0.136	0.000	0.000	0.000	0.000
81	A	107	ALA	0	0.028	0.018	37.479	-0.199	-0.199	0.000	0.000	0.000	0.000
82	A	108	VAL	0	-0.016	-0.012	38.480	-0.238	-0.238	0.000	0.000	0.000	0.000
83	A	109	SER	0	-0.028	-0.008	40.967	0.075	0.075	0.000	0.000	0.000	0.000
84	A	110	GLU	-1	-0.825	-0.902	36.988	-15.540	-15.540	0.000	0.000	0.000	0.000
85	A	111	GLY	0	0.011	0.006	36.292	-0.282	-0.282	0.000	0.000	0.000	0.000
86	A	112	THR	0	-0.014	-0.024	37.310	-0.109	-0.109	0.000	0.000	0.000	0.000
87	A	113	LYS	1	0.835	0.921	38.507	15.423	15.423	0.000	0.000	0.000	0.000
88	A	114	ALA	0	-0.011	-0.001	34.467	-0.073	-0.073	0.000	0.000	0.000	0.000
89	A	115	VAL	0	0.003	-0.003	35.627	-0.166	-0.166	0.000	0.000	0.000	0.000
90	A	116	THR	0	-0.009	-0.005	37.231	0.023	0.023	0.000	0.000	0.000	0.000
91	A	117	LYS	1	0.839	0.911	35.826	16.550	16.550	0.000	0.000	0.000	0.000
92	A	118	TYR	0	0.015	0.004	31.018	-0.103	-0.103	0.000	0.000	0.000	0.000
93	A	119	THR	0	-0.034	-0.045	35.895	0.056	0.056	0.000	0.000	0.000	0.000
94	A	120	SER	0	-0.084	-0.038	38.070	0.318	0.318	0.000	0.000	0.000	0.000
95	A	121	ALA	0	-0.027	-0.012	36.557	0.200	0.200	0.000	0.000	0.000	0.000
96	A	122	LYS	0	0.084	0.082	36.692	-2.320	-2.320	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:LYS)