FMO DATABASE

FMODB ID: 6R34Z

Calculation Name: 2PVB-A-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion | formic acid | ammonium ion | acetyl group

Ligand 3-letter code: CA | FMT | NH4 | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PVB

Chain ID: A

ChEMBL ID:

UniProt ID: P02619

Base Structure: X-ray

Registration Date: 2025-10-12

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-784634.795577
FMO2-HF: Nuclear repulsion	744627.847616
FMO2-HF: Total energy	-40006.947962
FMO2-MP2: Total energy	-40123.749648

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-200.176	-198.44	24.213	-14.201	-11.749	-0.146

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.733 / q_NPA : 0.857

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	ALA	0	0.038	0.030	3.847	2.934	4.567	-0.019	-0.739	-0.874	0.000
7	A	8	ASP	-1	-0.793	-0.892	1.728	-105.997	-108.948	19.670	-9.788	-6.931	-0.100
8	A	9	ALA	0	-0.020	-0.015	3.641	-0.955	-0.846	0.001	-0.013	-0.097	0.000
10	A	11	VAL	0	0.034	0.008	2.324	-0.179	0.760	0.616	-0.495	-1.061	-0.006
11	A	12	ALA	0	-0.011	-0.003	5.034	2.079	2.126	-0.001	-0.004	-0.042	0.000
14	A	15	LEU	0	0.012	0.004	4.257	2.242	2.299	-0.001	-0.010	-0.046	0.000
69	A	70	PHE	0	-0.027	-0.012	3.889	-6.883	-6.608	0.000	-0.121	-0.154	-0.001
70	A	71	SER	0	-0.030	-0.042	2.311	-42.120	-40.580	3.948	-3.010	-2.479	-0.039
71	A	72	PRO	0	0.041	0.044	4.314	7.126	7.213	-0.001	-0.021	-0.065	0.000
4	A	4	GLY	0	0.011	0.009	5.835	2.177	2.177	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.018	-0.003	5.427	3.791	3.791	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.893	0.934	5.293	26.179	26.179	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.863	-0.914	6.806	-27.213	-27.213	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.017	-0.016	5.794	5.001	5.001	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.007	0.006	7.804	3.325	3.325	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.014	-0.008	8.279	2.920	2.920	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.035	-0.011	11.011	2.253	2.253	0.000	0.000	0.000	0.000
17	A	18	CYS	0	-0.058	0.001	10.814	1.121	1.121	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.007	-0.002	12.743	0.932	0.932	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.021	-0.006	13.758	0.558	0.558	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.032	0.022	17.094	-0.579	-0.579	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.843	-0.903	19.098	-13.663	-13.663	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.049	-0.032	16.898	0.198	0.198	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.014	-0.018	11.984	-0.453	-0.453	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.851	0.921	15.864	17.545	17.545	0.000	0.000	0.000	0.000
25	A	26	HIS	0	0.004	-0.001	14.679	-1.517	-1.517	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.905	0.949	14.805	13.748	13.748	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.851	-0.909	16.016	-17.090	-17.090	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.002	-0.006	7.055	-0.895	-0.895	0.000	0.000	0.000	0.000
29	A	30	PHE	0	0.042	0.000	11.256	-2.260	-2.260	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.008	0.008	13.053	-0.432	-0.432	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.895	0.960	10.647	23.923	23.923	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.016	-0.014	7.201	-1.783	-1.783	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.004	-0.002	8.704	-1.640	-1.640	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.017	0.001	10.257	1.362	1.362	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.065	0.040	12.504	1.344	1.344	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.058	-0.022	14.519	1.727	1.727	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.761	0.901	10.946	24.930	24.930	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.038	0.023	15.379	0.854	0.854	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.081	0.024	17.289	-0.713	-0.713	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.844	-0.915	18.008	-16.711	-16.711	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.803	-0.892	13.390	-21.140	-21.140	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.012	0.001	13.853	-1.452	-1.452	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.973	0.990	15.569	13.391	13.391	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.782	0.874	13.170	18.455	18.455	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.017	-0.015	11.638	-0.821	-0.821	0.000	0.000	0.000	0.000
46	A	47	PHE	0	0.018	0.022	12.579	-1.135	-1.135	0.000	0.000	0.000	0.000
47	A	48	TYR	0	0.039	0.014	15.601	-0.058	-0.058	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.113	-0.046	9.160	-0.163	-0.163	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.043	-0.033	10.019	-0.877	-0.877	0.000	0.000	0.000	0.000
50	A	51	ASP	-1	-0.746	-0.848	13.259	-15.891	-15.891	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.050	-0.018	12.373	-1.035	-1.035	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.883	-0.933	15.683	-14.598	-14.598	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.700	0.839	14.216	20.555	20.555	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.007	0.005	20.265	0.805	0.805	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.046	-0.025	21.535	0.665	0.665	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.057	-0.035	21.882	0.241	0.241	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.044	-0.009	16.208	-0.698	-0.698	0.000	0.000	0.000	0.000
58	A	59	GLU	0	0.052	0.006	19.372	0.530	0.530	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.778	-0.888	19.527	-13.730	-13.730	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.895	-0.959	19.665	-15.885	-15.885	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.754	-0.880	15.906	-18.782	-18.782	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.033	-0.013	14.881	-1.734	-1.734	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.802	0.884	15.545	14.476	14.476	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.010	-0.006	13.385	-0.545	-0.545	0.000	0.000	0.000	0.000
65	A	66	PHE	0	0.051	0.046	11.052	-3.185	-3.185	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.001	-0.013	8.557	-3.426	-3.426	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.021	-0.019	7.143	-4.988	-4.988	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.030	-0.015	6.856	-3.100	-3.100	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.045	-0.022	7.430	2.558	2.558	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.028	-0.006	7.549	2.129	2.129	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.710	0.825	9.434	21.747	21.747	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.053	0.028	12.492	-1.115	-1.115	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.041	-0.007	13.880	0.203	0.203	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.028	-0.050	16.624	0.669	0.669	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.826	-0.896	20.317	-13.961	-13.961	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.014	0.004	22.910	0.218	0.218	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.712	-0.827	17.615	-18.172	-18.172	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.023	-0.025	19.177	-0.544	-0.544	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.847	0.895	20.115	12.364	12.364	0.000	0.000	0.000	0.000
83	A	84	ALA	0	-0.031	-0.007	21.787	0.346	0.346	0.000	0.000	0.000	0.000
84	A	85	PHE	0	-0.038	-0.033	14.493	-0.059	-0.059	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.049	0.021	20.016	-0.068	-0.068	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.016	-0.006	22.398	0.302	0.302	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.891	-0.938	22.086	-13.566	-13.566	0.000	0.000	0.000	0.000
88	A	89	GLY	0	-0.024	-0.049	21.915	0.092	0.092	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.837	-0.915	22.816	-11.502	-11.502	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.780	0.883	25.638	12.686	12.686	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.967	-0.978	28.370	-10.592	-10.592	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.029	-0.006	29.288	0.438	0.438	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.902	-0.955	27.329	-11.466	-11.466	0.000	0.000	0.000	0.000
94	A	95	GLY	0	-0.038	-0.015	27.448	0.111	0.111	0.000	0.000	0.000	0.000
95	A	96	MET	0	-0.123	-0.058	23.737	-0.572	-0.572	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.001	0.013	19.541	-0.136	-0.136	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.101	0.043	21.703	-0.370	-0.370	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.042	-0.032	19.885	-0.513	-0.513	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.919	-0.981	20.976	-13.312	-13.312	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.778	-0.865	22.925	-12.745	-12.745	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.021	0.007	13.044	-0.600	-0.600	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.038	-0.033	18.517	-0.629	-0.629	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.001	0.001	20.113	-0.144	-0.144	0.000	0.000	0.000	0.000
104	A	105	MET	0	-0.029	0.013	18.271	0.017	0.017	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.056	-0.017	14.587	-0.382	-0.382	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.736	0.844	17.973	16.155	16.155	0.000	0.000	0.000	0.000
107	A	108	ALA	-1	-0.916	-0.931	20.856	-12.824	-12.824	0.000	0.000	0.000	0.000

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