FMO DATABASE

FMODB ID: 9RRK2

Calculation Name: 2Q2H-B-Xray547

Preferred Name:

Target Type:

Ligand Name: citric acid | acetate ion

Ligand 3-letter code: CIT | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2Q2H

Chain ID: B

ChEMBL ID:

UniProt ID: A9CI62

Base Structure: X-ray

Registration Date: 2025-10-05

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-796145.636987
FMO2-HF: Nuclear repulsion	754648.805907
FMO2-HF: Total energy	-41496.83108
FMO2-MP2: Total energy	-41619.604057

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:3:GLY)

Summations of interaction energy for fragment #1(A:3:GLY)

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.
-42.712	-40.456	0.06	-1.404	-0.912	-0.009

Interaction energy analysis for fragmet #1(A:3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.893

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	5	ILE	0	-0.027	-0.012	3.124	-15.539	-13.283	0.060	-1.404	-0.912	-0.009
4	A	6	SER	0	-0.024	-0.029	6.043	4.620	4.620	0.000	0.000	0.000	0.000
5	A	7	TYR	0	0.046	0.012	9.472	-0.227	-0.227	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.098	0.056	12.835	0.693	0.693	0.000	0.000	0.000	0.000
7	A	9	ASP	-1	-0.874	-0.924	8.761	-32.186	-32.186	0.000	0.000	0.000	0.000
8	A	10	PHE	0	-0.010	0.002	11.221	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.905	-0.960	12.910	-17.760	-17.760	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.842	0.914	11.461	26.614	26.614	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.023	0.008	13.359	0.772	0.772	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.801	-0.877	16.341	-13.583	-13.583	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.010	-0.005	16.396	0.503	0.503	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.793	0.860	20.442	12.882	12.882	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.040	0.019	24.198	-0.210	-0.210	0.000	0.000	0.000	0.000
16	A	18	GLY	0	0.037	0.013	26.948	0.245	0.245	0.000	0.000	0.000	0.000
17	A	19	THR	0	-0.043	-0.037	29.925	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	20	ILE	0	-0.026	-0.004	30.548	0.070	0.070	0.000	0.000	0.000	0.000
19	A	21	VAL	0	0.006	-0.008	33.876	0.264	0.264	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.855	-0.912	36.261	-7.941	-7.941	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.025	0.012	35.567	-0.337	-0.337	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.010	0.002	36.254	0.297	0.297	0.000	0.000	0.000	0.000
23	A	25	PRO	0	0.047	0.021	36.025	-0.279	-0.279	0.000	0.000	0.000	0.000
24	A	26	PHE	0	-0.027	-0.033	34.656	0.272	0.272	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.018	0.015	34.117	-0.213	-0.213	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.817	-0.884	27.362	-11.555	-11.555	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.011	0.008	27.020	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.852	0.911	27.914	10.702	10.702	0.000	0.000	0.000	0.000
29	A	31	LYS	0	0.051	0.043	27.610	0.110	0.110	0.000	0.000	0.000	0.000
30	A	32	PRO	0	-0.014	-0.013	31.325	0.035	0.035	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.013	0.021	30.248	-0.277	-0.277	0.000	0.000	0.000	0.000
32	A	34	ILE	0	0.013	-0.005	31.166	0.444	0.444	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.840	0.960	31.341	8.545	8.545	0.000	0.000	0.000	0.000
34	A	36	VAL	0	0.034	0.002	30.329	0.318	0.318	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.799	0.884	32.443	8.150	8.150	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.007	-0.002	28.281	0.147	0.147	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.833	-0.906	32.147	-9.290	-9.290	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.005	-0.021	26.367	-0.195	-0.195	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.080	0.048	30.862	-0.196	-0.196	0.000	0.000	0.000	0.000
40	A	42	PRO	0	-0.030	-0.025	33.602	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.902	-0.951	31.120	-9.558	-9.558	0.000	0.000	0.000	0.000
42	A	44	ILE	0	-0.082	-0.031	27.197	-0.247	-0.247	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.014	0.010	30.955	0.046	0.046	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.037	-0.024	32.599	-0.217	-0.217	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.925	0.980	28.396	10.881	10.881	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.834	0.924	31.196	9.678	9.678	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.002	-0.010	26.244	-0.465	-0.465	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.089	-0.078	27.683	0.708	0.708	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.080	0.044	26.664	-0.542	-0.542	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.015	-0.008	25.687	0.388	0.388	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.027	0.002	26.744	-0.145	-0.145	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.039	-0.033	29.090	0.176	0.176	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.025	0.015	30.324	0.333	0.333	0.000	0.000	0.000	0.000
54	A	56	HIS	0	-0.014	-0.013	27.958	0.532	0.532	0.000	0.000	0.000	0.000
55	A	57	TYR	0	-0.022	-0.006	28.347	-0.051	-0.051	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.010	-0.010	33.561	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	59	PRO	0	0.013	-0.003	36.255	-0.140	-0.140	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.810	-0.897	37.523	-8.047	-8.047	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.059	-0.020	35.475	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.001	-0.006	31.635	-0.302	-0.302	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.001	-0.005	34.924	-0.158	-0.158	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.006	0.007	36.920	0.159	0.159	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.835	0.919	30.654	9.703	9.703	0.000	0.000	0.000	0.000
64	A	66	GLN	0	-0.007	-0.016	30.421	-0.101	-0.101	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.020	-0.011	26.877	-0.082	-0.082	0.000	0.000	0.000	0.000
66	A	68	LEU	0	0.034	0.021	21.796	0.008	0.008	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.021	-0.001	22.701	0.055	0.055	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.045	-0.005	18.005	-0.152	-0.152	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.010	-0.013	21.069	0.438	0.438	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.025	-0.008	18.320	0.348	0.348	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.016	0.013	16.433	-0.485	-0.485	0.000	0.000	0.000	0.000
72	A	74	PRO	0	-0.013	-0.013	20.857	0.663	0.663	0.000	0.000	0.000	0.000
73	A	75	PRO	0	0.005	0.015	24.024	-0.067	-0.067	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.913	0.948	21.714	13.535	13.535	0.000	0.000	0.000	0.000
75	A	77	GLN	0	0.016	0.006	27.602	0.092	0.092	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.024	0.013	28.025	-0.168	-0.168	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.049	0.026	31.728	0.276	0.276	0.000	0.000	0.000	0.000
78	A	80	PRO	0	0.013	-0.001	35.282	-0.063	-0.063	0.000	0.000	0.000	0.000
79	A	81	PHE	0	-0.007	0.000	30.517	0.159	0.159	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.875	0.937	30.344	10.038	10.038	0.000	0.000	0.000	0.000
81	A	83	SER	0	0.020	0.012	26.964	0.146	0.146	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.867	-0.959	27.387	-10.206	-10.206	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.046	0.038	24.256	-0.262	-0.262	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.033	0.018	18.687	0.292	0.292	0.000	0.000	0.000	0.000
85	A	87	THR	0	0.040	0.001	22.625	-0.077	-0.077	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.030	-0.017	18.375	-0.393	-0.393	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.028	0.003	20.476	0.801	0.801	0.000	0.000	0.000	0.000
88	A	90	PHE	0	-0.047	-0.015	16.562	-0.993	-0.993	0.000	0.000	0.000	0.000
89	A	91	ALA	0	0.008	0.015	19.774	0.697	0.697	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.763	-0.876	21.389	-11.922	-11.922	0.000	0.000	0.000	0.000
91	A	93	ALA	0	-0.043	-0.036	23.231	-0.331	-0.331	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.068	-0.029	24.908	0.202	0.202	0.000	0.000	0.000	0.000
93	A	95	GLY	0	-0.013	0.000	22.988	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.923	-0.959	23.980	-11.174	-11.174	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.057	-0.037	22.101	-0.275	-0.275	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.023	0.014	24.304	0.592	0.592	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.038	-0.026	23.912	-0.602	-0.602	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.021	-0.006	21.644	0.017	0.017	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.006	-0.020	23.730	0.385	0.385	0.000	0.000	0.000	0.000
100	A	102	VAL	0	0.007	0.011	25.374	-0.504	-0.504	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.812	-0.864	27.787	-9.917	-9.917	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.795	0.856	29.607	10.090	10.090	0.000	0.000	0.000	0.000
103	A	105	PRO	0	-0.006	-0.016	31.511	-0.267	-0.267	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.015	0.018	28.890	0.041	0.041	0.000	0.000	0.000	0.000
105	A	107	PRO	0	0.013	0.013	32.003	0.114	0.114	0.000	0.000	0.000	0.000
106	A	108	ASN	0	0.002	0.015	30.974	-0.553	-0.553	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.040	0.019	28.782	0.222	0.222	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.924	-0.952	27.560	-11.470	-11.470	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.817	0.918	18.865	16.254	16.254	0.000	0.000	0.000	0.000
110	A	112	MET	0	-0.021	-0.016	17.380	0.238	0.238	0.000	0.000	0.000	0.000
111	A	113	CYS	-1	-0.968	-0.977	19.220	-16.700	-16.700	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLY)