FMO DATABASE

FMODB ID: Z73GN

Calculation Name: 2CV5-A-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: A

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

Total energy (hartree)

FMO2-HF: Electronic energy	-649895.462581
FMO2-HF: Nuclear repulsion	609922.408043
FMO2-HF: Total energy	-39973.054538
FMO2-MP2: Total energy	-40089.147028

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.
127.061	128.305	-0.007	-0.488	-0.749	0.001

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 : 0.911 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	40	ARG	1	0.992	0.988	3.849	35.834	37.078	-0.007	-0.488	-0.749	0.001
4	A	41	TYR	0	0.043	0.028	6.018	2.027	2.027	0.000	0.000	0.000	0.000
5	A	42	ARG	1	1.024	1.011	9.820	20.817	20.817	0.000	0.000	0.000	0.000
6	A	43	PRO	0	0.062	0.031	12.199	0.730	0.730	0.000	0.000	0.000	0.000
7	A	44	GLY	0	0.064	0.038	14.627	0.489	0.489	0.000	0.000	0.000	0.000
8	A	45	THR	0	-0.041	-0.036	14.167	0.692	0.692	0.000	0.000	0.000	0.000
9	A	46	VAL	0	-0.014	-0.015	12.413	0.275	0.275	0.000	0.000	0.000	0.000
10	A	47	ALA	0	0.081	0.047	15.583	0.612	0.612	0.000	0.000	0.000	0.000
11	A	48	LEU	0	0.043	0.016	19.000	0.674	0.674	0.000	0.000	0.000	0.000
12	A	49	ARG	1	0.850	0.931	12.584	21.305	21.305	0.000	0.000	0.000	0.000
13	A	50	GLU	-1	-0.895	-0.935	18.504	-15.360	-15.360	0.000	0.000	0.000	0.000
14	A	51	ILE	0	0.038	0.023	21.044	0.479	0.479	0.000	0.000	0.000	0.000
15	A	52	ARG	1	0.919	0.945	21.553	14.066	14.066	0.000	0.000	0.000	0.000
16	A	53	ARG	1	0.808	0.915	17.825	15.305	15.305	0.000	0.000	0.000	0.000
17	A	54	TYR	0	0.097	0.018	21.500	0.174	0.174	0.000	0.000	0.000	0.000
18	A	55	GLN	0	-0.004	0.014	26.800	0.155	0.155	0.000	0.000	0.000	0.000
19	A	56	LYS	1	0.876	0.952	25.546	12.087	12.087	0.000	0.000	0.000	0.000
20	A	57	SER	0	-0.085	-0.056	28.027	0.179	0.179	0.000	0.000	0.000	0.000
21	A	58	THR	0	0.030	0.001	29.873	0.088	0.088	0.000	0.000	0.000	0.000
22	A	59	GLU	-1	-0.905	-0.922	28.012	-10.676	-10.676	0.000	0.000	0.000	0.000
23	A	60	LEU	0	-0.028	-0.001	31.661	-0.060	-0.060	0.000	0.000	0.000	0.000
24	A	61	LEU	0	-0.002	-0.006	26.960	-0.293	-0.293	0.000	0.000	0.000	0.000
25	A	62	ILE	0	-0.065	-0.020	28.722	-0.296	-0.296	0.000	0.000	0.000	0.000
26	A	63	ARG	1	0.928	0.958	25.781	11.143	11.143	0.000	0.000	0.000	0.000
27	A	64	LYS	1	0.950	0.952	31.476	8.737	8.737	0.000	0.000	0.000	0.000
28	A	65	LEU	0	0.022	0.013	34.830	0.187	0.187	0.000	0.000	0.000	0.000
29	A	66	PRO	0	-0.034	-0.034	31.845	0.173	0.173	0.000	0.000	0.000	0.000
30	A	67	PHE	0	0.075	0.052	35.086	0.120	0.120	0.000	0.000	0.000	0.000
31	A	68	GLN	0	0.036	0.019	36.891	0.356	0.356	0.000	0.000	0.000	0.000
32	A	69	ARG	1	0.920	0.956	34.780	8.605	8.605	0.000	0.000	0.000	0.000
33	A	70	LEU	0	0.056	0.035	37.039	0.135	0.135	0.000	0.000	0.000	0.000
34	A	71	VAL	0	-0.010	-0.001	40.115	0.160	0.160	0.000	0.000	0.000	0.000
35	A	72	ARG	1	0.875	0.922	42.770	7.100	7.100	0.000	0.000	0.000	0.000
36	A	73	GLU	-1	-0.951	-0.966	41.413	-7.393	-7.393	0.000	0.000	0.000	0.000
37	A	74	ILE	0	0.046	0.013	41.445	0.137	0.137	0.000	0.000	0.000	0.000
38	A	75	ALA	0	-0.031	-0.016	45.497	0.140	0.140	0.000	0.000	0.000	0.000
39	A	76	GLN	0	0.031	0.016	48.076	0.174	0.174	0.000	0.000	0.000	0.000
40	A	77	ASP	-1	-0.918	-0.950	47.570	-6.375	-6.375	0.000	0.000	0.000	0.000
41	A	78	PHE	0	-0.093	-0.033	48.132	0.100	0.100	0.000	0.000	0.000	0.000
42	A	79	LYS	1	0.897	0.939	52.526	5.666	5.666	0.000	0.000	0.000	0.000
43	A	80	THR	0	0.019	0.011	52.861	-0.084	-0.084	0.000	0.000	0.000	0.000
44	A	81	ASP	-1	-0.946	-0.975	53.085	-5.722	-5.722	0.000	0.000	0.000	0.000
45	A	82	LEU	0	-0.011	0.011	51.017	0.064	0.064	0.000	0.000	0.000	0.000
46	A	83	ARG	1	0.935	0.966	50.636	5.705	5.705	0.000	0.000	0.000	0.000
47	A	84	PHE	0	0.035	0.008	46.765	0.013	0.013	0.000	0.000	0.000	0.000
48	A	85	GLN	0	-0.005	-0.003	48.288	0.052	0.052	0.000	0.000	0.000	0.000
49	A	86	SER	0	0.015	0.005	44.023	-0.134	-0.134	0.000	0.000	0.000	0.000
50	A	87	SER	0	0.065	0.018	44.057	-0.112	-0.112	0.000	0.000	0.000	0.000
51	A	88	ALA	0	0.037	0.028	45.384	-0.055	-0.055	0.000	0.000	0.000	0.000
52	A	89	VAL	0	0.010	-0.002	40.903	-0.081	-0.081	0.000	0.000	0.000	0.000
53	A	90	MET	0	-0.017	0.006	38.900	-0.299	-0.299	0.000	0.000	0.000	0.000
54	A	91	ALA	0	0.052	0.033	40.991	-0.129	-0.129	0.000	0.000	0.000	0.000
55	A	92	LEU	0	0.024	0.010	42.616	-0.046	-0.046	0.000	0.000	0.000	0.000
56	A	93	GLN	0	-0.047	-0.033	34.031	0.068	0.068	0.000	0.000	0.000	0.000
57	A	94	GLU	-1	-0.872	-0.953	37.905	-8.370	-8.370	0.000	0.000	0.000	0.000
58	A	95	ALA	0	-0.013	-0.001	39.031	-0.091	-0.091	0.000	0.000	0.000	0.000
59	A	96	CYS	0	-0.052	-0.027	37.715	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	97	GLU	-1	-0.734	-0.869	32.759	-9.563	-9.563	0.000	0.000	0.000	0.000
61	A	98	ALA	0	0.022	0.014	35.332	-0.174	-0.174	0.000	0.000	0.000	0.000
62	A	99	TYR	0	-0.061	-0.046	37.714	-0.114	-0.114	0.000	0.000	0.000	0.000
63	A	100	LEU	0	-0.028	-0.025	33.664	-0.083	-0.083	0.000	0.000	0.000	0.000
64	A	101	VAL	0	-0.026	-0.004	31.616	-0.211	-0.211	0.000	0.000	0.000	0.000
65	A	102	GLY	0	0.120	0.064	33.715	-0.122	-0.122	0.000	0.000	0.000	0.000
66	A	103	LEU	0	-0.044	-0.016	35.803	0.070	0.070	0.000	0.000	0.000	0.000
67	A	104	PHE	0	-0.044	-0.023	30.733	-0.108	-0.108	0.000	0.000	0.000	0.000
68	A	105	GLU	-1	-0.910	-0.953	32.395	-9.147	-9.147	0.000	0.000	0.000	0.000
69	A	106	ASP	-1	-0.770	-0.877	33.992	-8.092	-8.092	0.000	0.000	0.000	0.000
70	A	107	THR	0	-0.053	-0.054	32.285	0.041	0.041	0.000	0.000	0.000	0.000
71	A	108	ASN	0	-0.031	-0.027	29.250	-0.325	-0.325	0.000	0.000	0.000	0.000
72	A	109	LEU	0	0.015	0.018	31.951	-0.119	-0.119	0.000	0.000	0.000	0.000
73	A	110	CYS	0	-0.047	-0.022	35.002	0.138	0.138	0.000	0.000	0.000	0.000
74	A	111	ALA	0	-0.034	-0.019	30.630	0.043	0.043	0.000	0.000	0.000	0.000
75	A	112	ILE	0	0.012	0.010	29.892	-0.061	-0.061	0.000	0.000	0.000	0.000
76	A	113	HIS	0	0.004	0.014	32.602	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	114	ALA	0	-0.071	-0.034	34.509	0.122	0.122	0.000	0.000	0.000	0.000
78	A	115	LYS	1	0.923	0.953	32.616	8.710	8.710	0.000	0.000	0.000	0.000
79	A	116	ARG	1	0.721	0.826	29.006	9.489	9.489	0.000	0.000	0.000	0.000
80	A	117	VAL	0	0.049	0.017	24.089	0.060	0.060	0.000	0.000	0.000	0.000
81	A	118	THR	0	-0.044	-0.014	24.146	-0.162	-0.162	0.000	0.000	0.000	0.000
82	A	119	ILE	0	0.054	0.037	26.511	0.376	0.376	0.000	0.000	0.000	0.000
83	A	120	MET	0	-0.040	-0.029	28.481	-0.111	-0.111	0.000	0.000	0.000	0.000
84	A	121	PRO	0	0.059	0.020	30.943	0.211	0.211	0.000	0.000	0.000	0.000
85	A	122	LYS	1	0.961	0.981	33.854	9.268	9.268	0.000	0.000	0.000	0.000
86	A	123	ASP	-1	-0.716	-0.815	32.550	-9.269	-9.269	0.000	0.000	0.000	0.000
87	A	124	ILE	0	0.048	0.033	32.244	0.181	0.181	0.000	0.000	0.000	0.000
88	A	125	GLN	0	-0.079	-0.048	36.308	0.318	0.318	0.000	0.000	0.000	0.000
89	A	126	LEU	0	-0.009	0.005	38.800	0.220	0.220	0.000	0.000	0.000	0.000
90	A	127	ALA	0	0.069	0.025	37.875	0.194	0.194	0.000	0.000	0.000	0.000
91	A	128	ARG	1	0.864	0.914	39.237	7.663	7.663	0.000	0.000	0.000	0.000
92	A	129	ARG	1	0.898	0.963	42.040	6.910	6.910	0.000	0.000	0.000	0.000
93	A	130	ILE	0	-0.001	-0.005	42.275	0.159	0.159	0.000	0.000	0.000	0.000
94	A	131	ARG	1	0.772	0.890	39.045	7.903	7.903	0.000	0.000	0.000	0.000
95	A	132	GLY	0	0.024	0.029	45.468	0.107	0.107	0.000	0.000	0.000	0.000
96	A	133	GLU	-1	-0.810	-0.881	42.687	-7.386	-7.386	0.000	0.000	0.000	0.000
97	A	134	ARG	0	0.012	0.010	41.100	0.717	0.717	0.000	0.000	0.000	0.000

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