FMO DATABASE

FMODB ID: 5GV4Z

Calculation Name: 1H0R-A-Xray549

Preferred Name: 3-dehydroquinate dehydratase

Target Type: SINGLE PROTEIN

Ligand Name: 2,3-anhydro-quinic acid | phosphate ion

Ligand 3-letter code: FA1 | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H0R

Chain ID: A

ChEMBL ID: CHEMBL3345

UniProt ID: P9WPX7

Base Structure: X-ray

Registration Date: 2025-10-11

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1263105.77503
FMO2-HF: Nuclear repulsion	1210035.393051
FMO2-HF: Total energy	-53070.381979
FMO2-MP2: Total energy	-53228.932505

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:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
-65.856	-61.067	8.933	-5.967	-7.757	0.036

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.015

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	4	ILE	0	-0.025	0.000	1.916	-24.412	-21.386	7.046	-4.676	-5.396	0.048
4	A	5	VAL	0	0.019	0.015	3.882	-7.611	-7.205	0.009	-0.192	-0.223	0.001
69	A	70	GLU	-1	-0.883	-0.926	4.395	9.314	9.516	-0.001	-0.013	-0.189	0.000
70	A	71	PRO	0	0.001	0.000	4.320	-0.791	-0.691	-0.001	-0.010	-0.089	0.000
143	A	144	VAL	-1	-0.930	-0.940	2.243	-31.430	-30.375	1.880	-1.076	-1.860	-0.013
5	A	6	ASN	0	0.002	0.005	6.771	0.724	0.724	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.023	-0.019	9.897	-1.100	-1.100	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.015	0.011	13.211	0.301	0.301	0.000	0.000	0.000	0.000
8	A	9	ASN	0	0.005	0.007	16.195	-0.461	-0.461	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.067	0.022	19.855	0.120	0.120	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.010	0.002	22.704	0.014	0.014	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.082	-0.052	26.432	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.026	0.001	22.264	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.082	0.046	25.236	0.025	0.025	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.889	0.935	26.272	-0.336	-0.336	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.011	0.018	23.902	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.038	0.035	28.258	0.041	0.041	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.818	0.887	30.734	-0.275	-0.275	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.830	0.895	32.893	-0.084	-0.084	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.791	-0.870	31.994	0.018	0.018	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.010	0.010	32.075	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.004	-0.007	33.158	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.040	-0.013	31.418	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.024	-0.024	26.770	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.059	0.044	28.079	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.011	-0.020	30.310	0.043	0.043	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.018	0.011	24.767	0.010	0.010	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.036	-0.053	26.874	0.018	0.018	0.000	0.000	0.000	0.000
28	A	29	HIS	0	0.054	0.022	19.631	-0.083	-0.083	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.856	-0.921	21.869	0.949	0.949	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.862	-0.909	22.003	0.354	0.354	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.036	-0.018	19.674	-0.055	-0.055	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.009	0.009	16.833	-0.071	-0.071	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.046	0.024	17.382	0.067	0.067	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.085	-0.047	18.820	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	36	ILE	0	0.005	-0.006	13.959	-0.185	-0.185	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.910	-0.960	13.541	2.146	2.146	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.921	0.964	14.136	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.858	-0.916	14.207	-1.370	-1.370	0.000	0.000	0.000	0.000
39	A	40	ALA	0	-0.016	-0.015	10.372	-0.452	-0.452	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.002	0.001	11.179	-0.277	-0.277	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.937	-0.946	13.101	-1.488	-1.488	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.036	-0.021	9.735	-0.334	-0.334	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.012	0.012	8.595	-1.628	-1.628	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.046	-0.018	5.355	0.702	0.702	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.917	0.948	6.003	-7.833	-7.833	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.024	0.014	7.170	0.865	0.865	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.019	-0.009	8.150	0.415	0.415	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.002	0.002	10.844	-0.545	-0.545	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.874	0.938	11.124	-3.437	-3.437	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.071	-0.065	16.921	-0.198	-0.198	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.006	-0.001	20.516	0.100	0.100	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.814	-0.904	23.094	0.410	0.410	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.046	-0.010	25.536	-0.086	-0.086	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.750	-0.868	24.210	0.331	0.331	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.010	0.002	23.024	0.040	0.040	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.038	-0.014	19.353	0.044	0.044	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.022	0.000	19.200	0.151	0.151	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.013	-0.008	18.197	0.048	0.048	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.876	-0.925	18.051	1.855	1.855	0.000	0.000	0.000	0.000
60	A	61	TRP	0	0.001	-0.014	14.813	0.090	0.090	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.005	0.003	13.472	0.254	0.254	0.000	0.000	0.000	0.000
62	A	63	HIS	1	0.885	0.941	13.606	-0.904	-0.904	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.020	-0.015	12.177	0.459	0.459	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.008	0.003	9.207	0.600	0.600	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.010	0.001	8.831	-0.153	-0.153	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.934	-0.970	10.230	1.566	1.566	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.074	-0.037	6.545	0.154	0.154	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.034	-0.012	5.406	0.837	0.837	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.014	-0.014	7.203	1.733	1.733	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.014	0.005	10.532	-0.604	-0.604	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.009	0.003	13.131	0.473	0.473	0.000	0.000	0.000	0.000
74	A	75	ASN	0	0.010	0.002	16.435	-0.228	-0.228	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.068	0.026	20.009	0.154	0.154	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.033	0.024	21.994	0.057	0.057	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.024	-0.017	25.241	-0.075	-0.075	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.023	0.015	24.360	-0.042	-0.042	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.005	-0.014	24.184	-0.040	-0.040	0.000	0.000	0.000	0.000
80	A	81	HIS	0	-0.064	-0.036	25.268	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.051	-0.025	28.192	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.023	-0.037	25.226	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.017	0.005	25.353	-0.048	-0.048	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.035	0.028	24.946	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.017	-0.006	19.651	0.036	0.036	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.896	0.945	20.398	0.483	0.483	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.896	-0.960	20.617	-0.262	-0.262	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.021	-0.009	18.740	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	90	CYS	0	-0.052	-0.037	16.387	0.052	0.052	0.000	0.000	0.000	0.000
90	A	91	ALA	0	-0.036	-0.015	16.147	-0.205	-0.205	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.894	-0.938	15.389	0.337	0.337	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.082	-0.032	11.039	0.042	0.042	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.016	0.011	9.921	-0.410	-0.410	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.003	0.019	6.688	-1.025	-1.025	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.031	-0.029	7.522	0.899	0.899	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.046	0.037	9.961	0.362	0.362	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.029	-0.020	12.236	-0.093	-0.093	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.685	-0.785	14.691	-0.355	-0.355	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.003	-0.008	16.911	-0.121	-0.121	0.000	0.000	0.000	0.000
100	A	101	HIS	1	0.755	0.857	19.666	0.622	0.622	0.000	0.000	0.000	0.000
101	A	102	ILE	0	0.023	0.032	23.103	-0.068	-0.068	0.000	0.000	0.000	0.000
102	A	103	SER	0	0.017	0.017	24.925	-0.021	-0.021	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.062	0.014	27.433	-0.048	-0.048	0.000	0.000	0.000	0.000
104	A	105	VAL	0	0.000	-0.009	27.330	0.046	0.046	0.000	0.000	0.000	0.000
105	A	106	HIS	0	0.043	0.029	28.135	0.066	0.066	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.053	-0.008	32.277	0.004	0.004	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.871	0.932	30.645	0.213	0.213	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.744	-0.847	35.216	-0.158	-0.158	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.813	-0.904	34.830	-0.370	-0.370	0.000	0.000	0.000	0.000
110	A	111	PHE	0	-0.013	-0.012	33.558	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.784	0.854	30.624	0.141	0.141	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.825	0.901	29.729	0.403	0.403	0.000	0.000	0.000	0.000
113	A	114	HIS	0	0.017	0.025	28.886	-0.088	-0.088	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.016	-0.030	23.685	0.064	0.064	0.000	0.000	0.000	0.000
115	A	116	TYR	0	-0.006	-0.005	25.558	-0.053	-0.053	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.033	0.022	20.062	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.006	-0.036	20.942	-0.086	-0.086	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.099	-0.054	21.604	-0.118	-0.118	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.016	0.003	18.516	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.013	0.018	16.832	-0.074	-0.074	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.011	-0.008	12.715	-0.193	-0.193	0.000	0.000	0.000	0.000
122	A	123	GLY	0	0.024	0.008	15.737	-0.097	-0.097	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.019	-0.007	17.514	0.125	0.125	0.000	0.000	0.000	0.000
124	A	125	ILE	0	0.002	0.015	16.825	-0.022	-0.022	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.006	-0.023	20.988	0.158	0.158	0.000	0.000	0.000	0.000
126	A	127	GLY	0	-0.039	-0.016	24.530	-0.045	-0.045	0.000	0.000	0.000	0.000
127	A	128	LEU	0	0.003	0.013	21.592	0.041	0.041	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.013	0.003	23.984	0.013	0.013	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.021	-0.009	21.578	-0.051	-0.051	0.000	0.000	0.000	0.000
130	A	131	GLN	0	0.035	0.017	20.462	-0.101	-0.101	0.000	0.000	0.000	0.000
131	A	132	GLY	0	0.020	0.017	19.226	-0.175	-0.175	0.000	0.000	0.000	0.000
132	A	133	TYR	0	-0.001	-0.031	16.302	-0.235	-0.235	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.008	0.016	14.957	-0.139	-0.139	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.013	0.001	14.726	-0.356	-0.356	0.000	0.000	0.000	0.000
135	A	136	ALA	0	-0.009	0.001	13.848	-0.425	-0.425	0.000	0.000	0.000	0.000
136	A	137	LEU	0	0.013	0.002	10.018	-0.612	-0.612	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.827	0.886	9.892	1.018	1.018	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.048	-0.023	11.141	-0.660	-0.660	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.015	-0.025	7.023	-0.611	-0.611	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.016	0.015	6.303	-3.139	-3.139	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.960	-0.971	7.040	-7.211	-7.211	0.000	0.000	0.000	0.000
142	A	143	HIS	1	0.778	0.885	7.204	8.308	8.308	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)