FMO DATABASE

FMODB ID: ZZQQN

Calculation Name: 6BYF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: citric acid | 1,2-ethanediol | chloride ion

Ligand 3-letter code: CIT | EDO | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6BYF

Chain ID: A

ChEMBL ID:

UniProt ID: P53965

Base Structure: X-ray

Registration Date: 2025-10-06

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	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1890461.452582
FMO2-HF: Nuclear repulsion	1821714.510799
FMO2-HF: Total energy	-68746.941783
FMO2-MP2: Total energy	-68948.528182

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:113:SER)

Summations of interaction energy for fragment #1(A:113: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.
22.492	27.298	0.519	-2.326	-3	-0.002

Interaction energy analysis for fragmet #1(A:113:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.907

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	115	SER	0	0.025	0.015	2.890	0.265	4.901	0.520	-2.306	-2.850	-0.002
4	A	116	VAL	0	-0.033	-0.003	4.673	4.181	4.351	-0.001	-0.020	-0.150	0.000
5	A	117	ILE	0	0.033	0.026	7.637	-1.244	-1.244	0.000	0.000	0.000	0.000
6	A	118	PRO	0	0.013	0.024	10.320	1.829	1.829	0.000	0.000	0.000	0.000
7	A	119	PRO	0	0.003	0.007	13.814	-0.355	-0.355	0.000	0.000	0.000	0.000
8	A	120	GLU	-1	-0.869	-0.948	16.874	-15.307	-15.307	0.000	0.000	0.000	0.000
9	A	121	ASN	0	-0.081	-0.065	18.448	0.619	0.619	0.000	0.000	0.000	0.000
10	A	122	PHE	0	0.007	0.007	16.865	0.623	0.623	0.000	0.000	0.000	0.000
11	A	123	SER	0	-0.032	-0.032	19.426	-0.434	-0.434	0.000	0.000	0.000	0.000
12	A	124	HIS	0	-0.023	-0.013	20.899	0.092	0.092	0.000	0.000	0.000	0.000
13	A	125	VAL	0	-0.031	0.005	22.550	0.104	0.104	0.000	0.000	0.000	0.000
14	A	126	VAL	0	0.067	0.025	26.388	0.235	0.235	0.000	0.000	0.000	0.000
15	A	127	GLY	0	0.078	0.062	27.907	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	128	GLU	-1	-0.909	-0.944	25.095	-11.996	-11.996	0.000	0.000	0.000	0.000
17	A	129	ILE	0	-0.015	-0.008	25.713	-0.122	-0.122	0.000	0.000	0.000	0.000
18	A	130	TYR	0	0.002	-0.006	20.262	-0.360	-0.360	0.000	0.000	0.000	0.000
19	A	131	ARG	1	0.904	0.955	22.964	12.567	12.567	0.000	0.000	0.000	0.000
20	A	132	SER	0	-0.007	-0.030	20.524	-0.784	-0.784	0.000	0.000	0.000	0.000
21	A	133	SER	0	-0.058	-0.034	20.429	0.707	0.707	0.000	0.000	0.000	0.000
22	A	134	PHE	0	0.003	0.006	22.199	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	135	PRO	0	-0.020	0.000	19.098	-0.586	-0.586	0.000	0.000	0.000	0.000
24	A	136	ARG	1	0.860	0.913	16.423	18.128	18.128	0.000	0.000	0.000	0.000
25	A	137	GLN	0	0.075	0.043	13.625	-1.296	-1.296	0.000	0.000	0.000	0.000
26	A	138	GLU	-1	-0.796	-0.887	11.322	-19.937	-19.937	0.000	0.000	0.000	0.000
27	A	139	ASN	0	-0.029	-0.031	11.578	-0.312	-0.312	0.000	0.000	0.000	0.000
28	A	140	PHE	0	0.006	0.010	14.101	0.334	0.334	0.000	0.000	0.000	0.000
29	A	141	SER	0	0.071	0.041	9.759	0.905	0.905	0.000	0.000	0.000	0.000
30	A	142	PHE	0	-0.028	-0.015	11.853	0.188	0.188	0.000	0.000	0.000	0.000
31	A	143	LEU	0	0.009	-0.009	13.096	0.717	0.717	0.000	0.000	0.000	0.000
32	A	144	HIS	0	0.054	0.031	15.968	0.790	0.790	0.000	0.000	0.000	0.000
33	A	145	GLU	-1	-0.908	-0.961	11.068	-21.996	-21.996	0.000	0.000	0.000	0.000
34	A	146	ARG	1	0.837	0.923	7.950	27.201	27.201	0.000	0.000	0.000	0.000
35	A	147	LEU	0	-0.015	-0.014	14.771	0.609	0.609	0.000	0.000	0.000	0.000
36	A	148	LYS	1	0.863	0.952	16.979	17.022	17.022	0.000	0.000	0.000	0.000
37	A	149	LEU	0	-0.013	-0.002	19.863	0.592	0.592	0.000	0.000	0.000	0.000
38	A	150	LYS	1	0.857	0.948	22.304	10.299	10.299	0.000	0.000	0.000	0.000
39	A	151	SER	0	-0.034	-0.047	25.769	0.448	0.448	0.000	0.000	0.000	0.000
40	A	152	ILE	0	-0.007	-0.004	22.326	-0.485	-0.485	0.000	0.000	0.000	0.000
41	A	153	LEU	0	-0.018	-0.009	26.480	0.483	0.483	0.000	0.000	0.000	0.000
42	A	154	VAL	0	-0.003	0.013	28.266	-0.257	-0.257	0.000	0.000	0.000	0.000
43	A	155	LEU	0	-0.004	-0.023	29.608	0.414	0.414	0.000	0.000	0.000	0.000
44	A	156	ILE	0	-0.036	-0.011	29.656	0.208	0.208	0.000	0.000	0.000	0.000
45	A	157	PRO	0	-0.011	-0.008	33.084	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	158	GLU	-1	-0.894	-0.945	32.590	-9.188	-9.188	0.000	0.000	0.000	0.000
47	A	159	GLU	-1	-0.921	-0.956	32.949	-8.955	-8.955	0.000	0.000	0.000	0.000
48	A	160	TYR	0	-0.026	-0.036	25.003	-0.390	-0.390	0.000	0.000	0.000	0.000
49	A	161	PRO	0	0.049	0.020	25.336	0.148	0.148	0.000	0.000	0.000	0.000
50	A	162	GLN	0	0.031	0.004	26.481	-0.274	-0.274	0.000	0.000	0.000	0.000
51	A	163	GLU	-1	-0.888	-0.945	19.550	-14.793	-14.793	0.000	0.000	0.000	0.000
52	A	164	ASN	0	0.000	-0.014	21.687	-0.152	-0.152	0.000	0.000	0.000	0.000
53	A	165	LEU	0	0.008	-0.001	23.493	0.019	0.019	0.000	0.000	0.000	0.000
54	A	166	ASN	0	-0.039	-0.013	22.074	0.516	0.516	0.000	0.000	0.000	0.000
55	A	167	PHE	0	0.031	0.015	17.628	-0.077	-0.077	0.000	0.000	0.000	0.000
56	A	168	LEU	0	-0.008	0.012	21.617	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	169	LYS	1	0.891	0.944	24.600	10.430	10.430	0.000	0.000	0.000	0.000
58	A	170	LEU	0	-0.041	-0.013	20.507	0.178	0.178	0.000	0.000	0.000	0.000
59	A	171	THR	0	-0.043	-0.033	19.683	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	172	GLY	0	-0.012	0.003	22.424	0.092	0.092	0.000	0.000	0.000	0.000
61	A	173	ILE	0	-0.049	-0.006	20.745	0.311	0.311	0.000	0.000	0.000	0.000
62	A	174	LYS	1	0.907	0.953	25.283	9.265	9.265	0.000	0.000	0.000	0.000
63	A	175	LEU	0	-0.007	-0.002	27.556	-0.244	-0.244	0.000	0.000	0.000	0.000
64	A	176	TYR	0	-0.036	-0.037	29.459	0.569	0.569	0.000	0.000	0.000	0.000
65	A	177	GLN	0	-0.015	-0.022	31.178	-0.260	-0.260	0.000	0.000	0.000	0.000
66	A	178	VAL	0	-0.061	-0.032	33.622	0.345	0.345	0.000	0.000	0.000	0.000
67	A	179	GLY	0	0.030	0.015	35.371	-0.146	-0.146	0.000	0.000	0.000	0.000
68	A	180	MET	0	-0.031	0.007	35.541	0.218	0.218	0.000	0.000	0.000	0.000
69	A	181	SER	0	0.007	-0.004	36.429	-0.220	-0.220	0.000	0.000	0.000	0.000
70	A	182	GLY	0	0.053	0.024	35.767	-0.194	-0.194	0.000	0.000	0.000	0.000
71	A	183	ASN	0	-0.058	-0.039	36.725	-0.200	-0.200	0.000	0.000	0.000	0.000
72	A	184	LYS	1	0.915	0.942	35.350	8.730	8.730	0.000	0.000	0.000	0.000
73	A	185	GLU	-1	-0.801	-0.916	36.791	-8.600	-8.600	0.000	0.000	0.000	0.000
74	A	186	PRO	0	0.002	0.010	40.720	0.092	0.092	0.000	0.000	0.000	0.000
75	A	187	PHE	0	-0.003	0.006	42.397	0.150	0.150	0.000	0.000	0.000	0.000
76	A	188	VAL	0	-0.066	-0.016	38.753	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	189	ASN	0	0.058	0.019	42.078	0.022	0.022	0.000	0.000	0.000	0.000
78	A	190	ILE	0	-0.008	-0.005	36.614	-0.166	-0.166	0.000	0.000	0.000	0.000
79	A	191	PRO	0	0.028	0.016	40.811	0.029	0.029	0.000	0.000	0.000	0.000
80	A	192	SER	0	0.108	0.042	42.114	-0.198	-0.198	0.000	0.000	0.000	0.000
81	A	193	HIS	0	0.066	0.051	42.997	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	194	LEU	0	-0.035	-0.010	39.059	-0.104	-0.104	0.000	0.000	0.000	0.000
83	A	195	LEU	0	0.032	0.000	37.254	-0.222	-0.222	0.000	0.000	0.000	0.000
84	A	196	THR	0	0.029	0.017	38.508	-0.155	-0.155	0.000	0.000	0.000	0.000
85	A	197	LYS	1	0.997	1.004	38.621	7.782	7.782	0.000	0.000	0.000	0.000
86	A	198	ALA	0	-0.012	-0.015	34.746	-0.156	-0.156	0.000	0.000	0.000	0.000
87	A	199	LEU	0	0.006	-0.001	34.904	-0.290	-0.290	0.000	0.000	0.000	0.000
88	A	200	GLU	-1	-0.910	-0.963	36.180	-7.673	-7.673	0.000	0.000	0.000	0.000
89	A	201	ILE	0	-0.105	-0.035	32.496	-0.076	-0.076	0.000	0.000	0.000	0.000
90	A	202	VAL	0	0.030	0.004	30.684	-0.173	-0.173	0.000	0.000	0.000	0.000
91	A	203	LEU	0	0.017	0.012	31.862	-0.235	-0.235	0.000	0.000	0.000	0.000
92	A	204	ASN	0	0.025	0.034	34.455	0.041	0.041	0.000	0.000	0.000	0.000
93	A	205	PRO	0	0.093	0.042	32.289	-0.250	-0.250	0.000	0.000	0.000	0.000
94	A	206	ALA	0	-0.009	-0.005	31.948	-0.249	-0.249	0.000	0.000	0.000	0.000
95	A	207	ASN	0	-0.063	-0.026	31.244	-0.043	-0.043	0.000	0.000	0.000	0.000
96	A	208	GLN	0	-0.037	0.009	28.236	-0.373	-0.373	0.000	0.000	0.000	0.000
97	A	209	PRO	0	0.091	0.042	23.580	0.235	0.235	0.000	0.000	0.000	0.000
98	A	210	ILE	0	-0.050	-0.019	25.740	0.065	0.065	0.000	0.000	0.000	0.000
99	A	211	LEU	0	-0.005	0.009	20.850	-0.174	-0.174	0.000	0.000	0.000	0.000
100	A	212	ILE	0	0.004	0.001	24.609	0.404	0.404	0.000	0.000	0.000	0.000
101	A	213	HIS	0	0.021	0.013	24.381	-0.502	-0.502	0.000	0.000	0.000	0.000
102	A	214	CYS	-1	-0.823	-0.809	26.472	-10.838	-10.838	0.000	0.000	0.000	0.000
103	A	215	ASN	0	0.043	0.005	26.705	-0.286	-0.286	0.000	0.000	0.000	0.000
104	A	216	ARG	0	0.042	0.007	24.553	-0.132	-0.132	0.000	0.000	0.000	0.000
105	A	217	GLY	0	0.113	0.044	24.613	-0.459	-0.459	0.000	0.000	0.000	0.000
106	A	218	LYS	1	0.817	0.932	23.365	13.434	13.434	0.000	0.000	0.000	0.000
107	A	219	HIS	0	-0.025	-0.023	28.331	0.235	0.235	0.000	0.000	0.000	0.000
108	A	220	ARG	1	0.906	0.956	31.990	9.655	9.655	0.000	0.000	0.000	0.000
109	A	221	THR	0	0.036	-0.038	26.665	0.147	0.147	0.000	0.000	0.000	0.000
110	A	222	GLY	0	0.018	0.003	30.124	-0.073	-0.073	0.000	0.000	0.000	0.000
111	A	223	CYS	0	-0.049	-0.009	31.305	0.209	0.209	0.000	0.000	0.000	0.000
112	A	224	LEU	0	0.066	0.030	31.818	0.174	0.174	0.000	0.000	0.000	0.000
113	A	225	ILE	0	0.016	0.006	27.722	0.102	0.102	0.000	0.000	0.000	0.000
114	A	226	GLY	0	0.045	0.012	32.017	0.061	0.061	0.000	0.000	0.000	0.000
115	A	227	CYS	0	-0.048	-0.019	34.726	0.292	0.292	0.000	0.000	0.000	0.000
116	A	228	ILE	0	0.001	0.006	31.114	0.160	0.160	0.000	0.000	0.000	0.000
117	A	229	ARG	1	0.734	0.819	27.953	10.816	10.816	0.000	0.000	0.000	0.000
118	A	230	LYS	1	0.838	0.905	35.022	7.677	7.677	0.000	0.000	0.000	0.000
119	A	231	LEU	0	0.017	0.013	37.521	0.184	0.184	0.000	0.000	0.000	0.000
120	A	232	GLN	0	-0.049	-0.003	31.956	-0.097	-0.097	0.000	0.000	0.000	0.000
121	A	233	ASN	0	-0.026	-0.011	37.208	0.054	0.054	0.000	0.000	0.000	0.000
122	A	234	TRP	0	-0.010	0.000	30.138	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	235	SER	0	0.013	0.006	38.013	0.137	0.137	0.000	0.000	0.000	0.000
124	A	236	LEU	0	0.084	0.023	37.965	-0.269	-0.269	0.000	0.000	0.000	0.000
125	A	237	THR	0	0.011	0.007	36.925	-0.156	-0.156	0.000	0.000	0.000	0.000
126	A	238	MET	0	0.032	0.017	33.718	-0.289	-0.289	0.000	0.000	0.000	0.000
127	A	239	ILE	0	-0.011	0.024	32.959	-0.385	-0.385	0.000	0.000	0.000	0.000
128	A	240	PHE	0	0.006	-0.016	33.485	-0.301	-0.301	0.000	0.000	0.000	0.000
129	A	241	ASP	-1	-0.915	-0.950	30.591	-10.557	-10.557	0.000	0.000	0.000	0.000
130	A	242	GLU	-1	-0.840	-0.896	28.015	-11.437	-11.437	0.000	0.000	0.000	0.000
131	A	243	TYR	0	-0.081	-0.050	28.795	-0.383	-0.383	0.000	0.000	0.000	0.000
132	A	244	ARG	1	0.891	0.923	29.949	8.729	8.729	0.000	0.000	0.000	0.000
133	A	245	ARG	1	0.928	0.972	24.990	11.658	11.658	0.000	0.000	0.000	0.000
134	A	246	PHE	0	0.010	0.012	22.351	-0.419	-0.419	0.000	0.000	0.000	0.000
135	A	247	ALA	0	-0.016	-0.005	26.081	-0.258	-0.258	0.000	0.000	0.000	0.000
136	A	248	PHE	0	0.016	0.037	25.905	0.240	0.240	0.000	0.000	0.000	0.000
137	A	249	PRO	0	-0.013	-0.023	26.505	-0.441	-0.441	0.000	0.000	0.000	0.000
138	A	250	LYS	1	0.840	0.907	28.531	11.211	11.211	0.000	0.000	0.000	0.000
139	A	251	ALA	0	0.051	0.025	31.752	0.078	0.078	0.000	0.000	0.000	0.000
140	A	252	ARG	1	0.796	0.863	33.022	9.246	9.246	0.000	0.000	0.000	0.000
141	A	253	ALA	0	0.023	0.015	36.387	-0.033	-0.033	0.000	0.000	0.000	0.000
142	A	254	LEU	0	0.034	0.019	39.573	0.039	0.039	0.000	0.000	0.000	0.000
143	A	255	ASP	-1	-0.704	-0.808	34.909	-9.137	-9.137	0.000	0.000	0.000	0.000
144	A	256	GLN	0	-0.003	-0.008	36.323	0.040	0.040	0.000	0.000	0.000	0.000
145	A	257	GLN	0	0.072	0.037	38.562	0.118	0.118	0.000	0.000	0.000	0.000
146	A	258	PHE	0	0.002	-0.011	39.258	0.116	0.116	0.000	0.000	0.000	0.000
147	A	259	ILE	0	-0.011	0.000	35.226	0.063	0.063	0.000	0.000	0.000	0.000
148	A	260	GLU	-1	-0.979	-0.983	39.787	-7.229	-7.229	0.000	0.000	0.000	0.000
149	A	261	MET	0	-0.049	-0.035	42.834	0.173	0.173	0.000	0.000	0.000	0.000
150	A	262	TYR	0	-0.050	-0.029	40.971	0.067	0.067	0.000	0.000	0.000	0.000
151	A	263	ASP	-1	-0.846	-0.910	43.924	-6.693	-6.693	0.000	0.000	0.000	0.000
152	A	264	ASP	-1	-0.847	-0.934	42.342	-7.437	-7.437	0.000	0.000	0.000	0.000
153	A	265	ASP	-1	-0.865	-0.934	44.143	-6.623	-6.623	0.000	0.000	0.000	0.000
154	A	266	GLU	-1	-1.028	-1.018	45.937	-6.665	-6.665	0.000	0.000	0.000	0.000
155	A	267	ILE	0	0.019	0.007	39.345	-0.021	-0.021	0.000	0.000	0.000	0.000
156	A	268	LYS	1	0.921	0.959	42.582	7.101	7.101	0.000	0.000	0.000	0.000
157	A	269	ARG	1	0.952	1.000	43.828	6.482	6.482	0.000	0.000	0.000	0.000
158	A	270	ILE	0	-0.023	-0.011	42.300	0.041	0.041	0.000	0.000	0.000	0.000
159	A	271	ALA	0	-0.005	-0.010	40.059	-0.028	-0.028	0.000	0.000	0.000	0.000
160	A	272	SER	0	-0.011	-0.020	41.787	-0.069	-0.069	0.000	0.000	0.000	0.000
161	A	273	LYS	1	0.877	0.951	44.364	6.981	6.981	0.000	0.000	0.000	0.000
162	A	274	ASN	0	-0.039	-0.025	41.150	0.227	0.227	0.000	0.000	0.000	0.000
163	A	275	ASN	0	-0.037	-0.013	41.411	-0.099	-0.099	0.000	0.000	0.000	0.000
164	A	276	TRP	0	0.009	-0.006	37.259	-0.150	-0.150	0.000	0.000	0.000	0.000
165	A	277	LEU	0	-0.037	0.006	37.268	-0.232	-0.232	0.000	0.000	0.000	0.000
166	A	278	PRO	0	0.026	0.007	37.538	0.195	0.195	0.000	0.000	0.000	0.000
167	A	279	LEU	0	-0.012	-0.013	33.145	-0.099	-0.099	0.000	0.000	0.000	0.000
168	A	280	GLN	0	-0.026	-0.012	32.194	0.119	0.119	0.000	0.000	0.000	0.000
169	A	281	TRP	-1	-0.883	-0.948	27.101	-11.294	-11.294	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:113:SER)