FMO DATABASE

FMODB ID: JQNN9

Calculation Name: 1IDP-A-Xray372

Preferred Name: Scytalone dehydratase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1IDP

Chain ID: A

ChEMBL ID: CHEMBL2578

UniProt ID: P56221

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1480886.532819
FMO2-HF: Nuclear repulsion	1419952.532002
FMO2-HF: Total energy	-60934.000817
FMO2-MP2: Total energy	-61111.557896

3D Structure

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:9:ASP)

Summations of interaction energy for fragment #1(A:9:ASP)

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.
-60.514	-58.858	11.457	-6.867	-6.245	0.082

Interaction energy analysis for fragmet #1(A:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.883 / q_NPA : -0.949

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	11	ILE	0	-0.046	-0.021	3.797	6.457	8.233	-0.017	-0.813	-0.946	0.002
4	A	12	THR	0	0.043	0.020	6.546	-2.588	-2.588	0.000	0.000	0.000	0.000
5	A	13	PHE	0	0.032	-0.007	8.431	-2.421	-2.421	0.000	0.000	0.000	0.000
6	A	14	SER	0	0.021	-0.006	11.785	-1.935	-1.935	0.000	0.000	0.000	0.000
7	A	15	ASP	-1	-0.781	-0.882	7.856	33.610	33.610	0.000	0.000	0.000	0.000
8	A	16	TYR	0	-0.005	0.000	11.360	-2.269	-2.269	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.005	0.007	13.342	-1.590	-1.590	0.000	0.000	0.000	0.000
10	A	18	GLY	0	0.020	0.021	15.060	-1.335	-1.335	0.000	0.000	0.000	0.000
11	A	19	LEU	0	-0.011	-0.008	10.984	-1.166	-1.166	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.023	-0.011	15.664	-0.940	-0.940	0.000	0.000	0.000	0.000
13	A	21	THR	0	-0.026	-0.009	18.520	-1.162	-1.162	0.000	0.000	0.000	0.000
14	A	22	CYS	0	-0.035	0.000	17.949	-1.057	-1.057	0.000	0.000	0.000	0.000
15	A	23	VAL	0	0.018	0.002	18.890	-0.847	-0.847	0.000	0.000	0.000	0.000
16	A	24	TYR	0	-0.009	-0.007	20.765	-0.705	-0.705	0.000	0.000	0.000	0.000
17	A	25	GLU	-1	-0.824	-0.919	23.443	11.079	11.079	0.000	0.000	0.000	0.000
18	A	26	TRP	0	-0.056	-0.005	23.014	-0.542	-0.542	0.000	0.000	0.000	0.000
19	A	27	ALA	0	-0.030	-0.018	24.841	-0.514	-0.514	0.000	0.000	0.000	0.000
20	A	28	ASP	-1	-0.804	-0.894	26.717	9.815	9.815	0.000	0.000	0.000	0.000
21	A	29	SER	0	-0.019	0.007	28.018	-0.557	-0.557	0.000	0.000	0.000	0.000
22	A	30	TYR	0	-0.015	-0.030	26.917	-0.342	-0.342	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.777	-0.855	30.784	9.697	9.697	0.000	0.000	0.000	0.000
24	A	32	SER	0	-0.086	-0.057	32.541	-0.354	-0.354	0.000	0.000	0.000	0.000
25	A	33	LYS	1	0.812	0.900	34.004	-8.662	-8.662	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.859	-0.912	32.533	9.221	9.221	0.000	0.000	0.000	0.000
27	A	35	TRP	0	0.048	-0.004	31.379	0.435	0.435	0.000	0.000	0.000	0.000
28	A	36	ASP	-1	-0.837	-0.919	31.475	9.350	9.350	0.000	0.000	0.000	0.000
29	A	37	ARG	1	0.762	0.873	28.941	-10.142	-10.142	0.000	0.000	0.000	0.000
30	A	38	LEU	0	0.008	0.007	26.191	0.461	0.461	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.774	0.857	26.512	-8.919	-8.919	0.000	0.000	0.000	0.000
32	A	40	LYS	1	0.890	0.960	26.442	-9.987	-9.987	0.000	0.000	0.000	0.000
33	A	41	VAL	0	-0.005	-0.003	22.307	0.538	0.538	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.038	0.005	21.559	0.724	0.724	0.000	0.000	0.000	0.000
35	A	43	ALA	0	-0.003	0.000	19.387	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.023	-0.005	21.221	-0.548	-0.548	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.038	-0.004	22.297	-0.519	-0.519	0.000	0.000	0.000	0.000
38	A	46	LEU	0	-0.012	-0.008	21.564	0.656	0.656	0.000	0.000	0.000	0.000
39	A	47	ARG	1	0.956	1.006	18.725	-14.731	-14.731	0.000	0.000	0.000	0.000
40	A	48	ILE	0	-0.040	-0.019	21.747	0.278	0.278	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.815	-0.931	22.256	11.992	11.992	0.000	0.000	0.000	0.000
42	A	50	TYR	0	0.034	-0.006	24.200	0.030	0.030	0.000	0.000	0.000	0.000
43	A	51	ARG	1	0.888	0.943	22.209	-12.210	-12.210	0.000	0.000	0.000	0.000
44	A	52	SER	0	-0.033	-0.007	25.932	-0.390	-0.390	0.000	0.000	0.000	0.000
45	A	53	PHE	0	0.022	0.000	27.304	-0.289	-0.289	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.073	-0.044	30.430	-0.330	-0.330	0.000	0.000	0.000	0.000
47	A	55	ASP	-1	-0.935	-0.950	30.558	9.020	9.020	0.000	0.000	0.000	0.000
48	A	56	LYS	1	0.954	0.983	29.875	-8.775	-8.775	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.039	-0.020	23.142	0.410	0.410	0.000	0.000	0.000	0.000
50	A	58	TRP	0	0.020	0.024	26.339	-0.264	-0.264	0.000	0.000	0.000	0.000
51	A	59	GLU	-1	-0.942	-0.995	22.916	12.283	12.283	0.000	0.000	0.000	0.000
52	A	60	ALA	0	0.032	0.005	22.258	0.611	0.611	0.000	0.000	0.000	0.000
53	A	61	MET	0	-0.037	0.003	24.382	-0.351	-0.351	0.000	0.000	0.000	0.000
54	A	62	PRO	0	0.049	0.028	25.951	0.483	0.483	0.000	0.000	0.000	0.000
55	A	63	ALA	0	0.058	0.019	26.109	-0.228	-0.228	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.810	-0.900	27.520	9.477	9.477	0.000	0.000	0.000	0.000
57	A	65	GLU	-1	-0.913	-0.953	30.693	9.368	9.368	0.000	0.000	0.000	0.000
58	A	66	PHE	0	0.043	0.006	25.959	-0.121	-0.121	0.000	0.000	0.000	0.000
59	A	67	VAL	0	-0.002	-0.007	29.405	-0.131	-0.131	0.000	0.000	0.000	0.000
60	A	68	GLY	0	-0.001	0.020	31.242	-0.269	-0.269	0.000	0.000	0.000	0.000
61	A	69	MET	0	-0.023	-0.003	28.566	-0.271	-0.271	0.000	0.000	0.000	0.000
62	A	70	VAL	0	-0.007	-0.007	28.997	-0.229	-0.229	0.000	0.000	0.000	0.000
63	A	71	SER	0	-0.021	-0.030	32.399	-0.279	-0.279	0.000	0.000	0.000	0.000
64	A	72	SER	0	0.038	0.032	35.353	-0.364	-0.364	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.916	0.937	37.857	-6.971	-6.971	0.000	0.000	0.000	0.000
66	A	74	GLN	0	0.013	0.001	38.765	0.062	0.062	0.000	0.000	0.000	0.000
67	A	75	VAL	0	-0.021	0.007	32.823	0.079	0.079	0.000	0.000	0.000	0.000
68	A	76	LEU	0	-0.031	-0.020	31.303	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	77	GLY	0	0.047	0.032	35.674	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.895	-0.936	38.230	7.042	7.042	0.000	0.000	0.000	0.000
71	A	79	PRO	0	0.023	0.010	40.697	0.093	0.093	0.000	0.000	0.000	0.000
72	A	80	THR	0	-0.039	-0.024	42.747	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	81	LEU	0	-0.018	0.005	36.440	-0.055	-0.055	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.864	0.913	38.373	-7.518	-7.518	0.000	0.000	0.000	0.000
75	A	83	THR	0	-0.019	-0.031	33.163	-0.089	-0.089	0.000	0.000	0.000	0.000
76	A	84	GLN	0	0.039	0.028	30.759	-0.104	-0.104	0.000	0.000	0.000	0.000
77	A	85	HIS	1	0.798	0.879	27.149	-10.311	-10.311	0.000	0.000	0.000	0.000
78	A	86	PHE	0	0.018	0.012	27.128	0.365	0.365	0.000	0.000	0.000	0.000
79	A	87	ILE	0	0.034	0.018	21.071	0.021	0.021	0.000	0.000	0.000	0.000
80	A	88	GLY	0	-0.018	0.004	23.116	-0.166	-0.166	0.000	0.000	0.000	0.000
81	A	89	GLY	0	0.006	-0.012	20.056	0.529	0.529	0.000	0.000	0.000	0.000
82	A	90	THR	0	0.005	-0.001	14.906	-0.314	-0.314	0.000	0.000	0.000	0.000
83	A	91	ARG	1	0.811	0.906	10.581	-19.621	-19.621	0.000	0.000	0.000	0.000
84	A	92	TRP	0	0.036	-0.013	9.508	-0.780	-0.780	0.000	0.000	0.000	0.000
85	A	93	GLU	-1	-0.835	-0.896	6.564	23.750	23.750	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.859	0.920	1.783	-111.562	-111.943	11.475	-6.034	-5.060	0.080
87	A	95	VAL	0	-0.035	-0.003	5.047	0.235	0.265	-0.001	-0.004	-0.024	0.000
88	A	96	SER	0	0.002	-0.015	6.055	0.893	0.893	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.861	-0.933	4.312	65.115	65.346	0.000	-0.016	-0.215	0.000
90	A	98	ASP	-1	-0.920	-0.951	7.159	22.748	22.748	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.882	-0.945	8.932	18.340	18.340	0.000	0.000	0.000	0.000
92	A	100	VAL	0	0.004	0.017	7.765	3.256	3.256	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.033	-0.006	9.745	-2.766	-2.766	0.000	0.000	0.000	0.000
94	A	102	GLY	0	0.012	0.002	11.146	1.328	1.328	0.000	0.000	0.000	0.000
95	A	103	TYR	0	-0.028	-0.009	11.721	-1.776	-1.776	0.000	0.000	0.000	0.000
96	A	104	HIS	0	0.059	0.036	15.583	0.525	0.525	0.000	0.000	0.000	0.000
97	A	105	GLN	0	-0.015	-0.002	18.839	-0.590	-0.590	0.000	0.000	0.000	0.000
98	A	106	LEU	0	0.004	0.013	21.884	0.013	0.013	0.000	0.000	0.000	0.000
99	A	107	ARG	1	0.844	0.920	24.780	-9.499	-9.499	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.016	-0.001	28.470	0.072	0.072	0.000	0.000	0.000	0.000
101	A	109	PRO	0	-0.069	-0.024	30.974	-0.320	-0.320	0.000	0.000	0.000	0.000
102	A	110	HIS	0	0.008	-0.008	34.422	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	111	GLN	0	0.041	0.021	36.908	-0.159	-0.159	0.000	0.000	0.000	0.000
104	A	112	ARG	1	0.934	0.977	39.413	-7.477	-7.477	0.000	0.000	0.000	0.000
105	A	113	TYR	0	-0.007	-0.005	43.034	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	114	LYS	1	0.911	0.945	46.427	-5.802	-5.802	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.785	-0.869	49.320	6.062	6.062	0.000	0.000	0.000	0.000
108	A	116	THR	0	0.016	-0.023	46.728	0.068	0.068	0.000	0.000	0.000	0.000
109	A	117	THR	0	-0.079	-0.051	48.928	0.019	0.019	0.000	0.000	0.000	0.000
110	A	118	MET	0	-0.105	-0.041	45.035	0.052	0.052	0.000	0.000	0.000	0.000
111	A	119	LYS	1	0.972	0.991	48.723	-5.748	-5.748	0.000	0.000	0.000	0.000
112	A	120	GLU	-1	-0.870	-0.931	50.572	5.756	5.756	0.000	0.000	0.000	0.000
113	A	121	VAL	0	-0.056	-0.022	44.844	0.103	0.103	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.004	-0.001	46.424	-0.056	-0.056	0.000	0.000	0.000	0.000
115	A	123	MET	0	-0.012	0.024	39.485	0.006	0.006	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.910	0.927	41.019	-7.000	-7.000	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.020	0.017	38.287	-0.106	-0.106	0.000	0.000	0.000	0.000
118	A	126	HIS	1	0.863	0.926	33.299	-8.436	-8.436	0.000	0.000	0.000	0.000
119	A	127	ALA	0	0.057	0.048	30.930	-0.129	-0.129	0.000	0.000	0.000	0.000
120	A	128	HIS	0	0.035	0.022	28.462	0.190	0.190	0.000	0.000	0.000	0.000
121	A	129	SER	0	-0.015	-0.015	24.487	-0.179	-0.179	0.000	0.000	0.000	0.000
122	A	130	ALA	0	-0.009	0.009	20.248	0.184	0.184	0.000	0.000	0.000	0.000
123	A	131	ASN	0	0.004	-0.021	20.854	-0.574	-0.574	0.000	0.000	0.000	0.000
124	A	132	LEU	0	-0.019	0.019	14.031	0.493	0.493	0.000	0.000	0.000	0.000
125	A	133	HIS	0	0.008	0.008	16.568	-1.374	-1.374	0.000	0.000	0.000	0.000
126	A	134	TRP	0	0.044	0.017	14.008	0.369	0.369	0.000	0.000	0.000	0.000
127	A	135	TYR	0	-0.022	-0.044	13.104	-1.429	-1.429	0.000	0.000	0.000	0.000
128	A	136	LYS	1	0.902	0.944	12.711	-20.262	-20.262	0.000	0.000	0.000	0.000
129	A	137	LYS	1	0.895	0.952	10.505	-26.273	-26.273	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.021	-0.011	14.076	-0.091	-0.091	0.000	0.000	0.000	0.000
131	A	139	ASP	-1	-0.875	-0.935	17.391	14.810	14.810	0.000	0.000	0.000	0.000
132	A	140	GLY	0	-0.036	-0.024	14.826	-0.304	-0.304	0.000	0.000	0.000	0.000
133	A	141	VAL	0	-0.022	-0.012	15.771	0.475	0.475	0.000	0.000	0.000	0.000
134	A	142	TRP	0	-0.050	-0.024	9.237	-1.092	-1.092	0.000	0.000	0.000	0.000
135	A	143	LYS	1	0.906	0.962	15.720	-15.442	-15.442	0.000	0.000	0.000	0.000
136	A	144	PHE	0	0.027	-0.012	17.154	0.862	0.862	0.000	0.000	0.000	0.000
137	A	145	ALA	0	0.014	-0.001	16.886	-0.671	-0.671	0.000	0.000	0.000	0.000
138	A	146	GLY	0	0.048	0.025	18.951	-0.313	-0.313	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.051	-0.026	19.511	0.516	0.516	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.960	0.991	17.778	-14.863	-14.863	0.000	0.000	0.000	0.000
141	A	149	PRO	0	-0.046	-0.016	20.993	0.305	0.305	0.000	0.000	0.000	0.000
142	A	150	ASP	-1	-0.839	-0.904	22.380	11.435	11.435	0.000	0.000	0.000	0.000
143	A	151	ILE	0	-0.005	-0.017	24.183	0.005	0.005	0.000	0.000	0.000	0.000
144	A	152	ARG	1	0.845	0.916	21.809	-12.043	-12.043	0.000	0.000	0.000	0.000
145	A	153	TRP	0	0.060	0.020	28.556	-0.326	-0.326	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.012	0.002	31.766	0.234	0.234	0.000	0.000	0.000	0.000
147	A	155	GLU	-1	-0.897	-0.940	34.463	8.199	8.199	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASP)