FMO DATABASE

FMODB ID: LNYY9

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	OptAll
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	-1479262.409432
FMO2-HF: Nuclear repulsion	1418327.624519
FMO2-HF: Total energy	-60934.784914
FMO2-MP2: Total energy	-61112.308964

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.
-66.475	-68.985	17.451	-8.271	-6.671	0.085

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 : -0.823 / q_NPA : -0.900

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	-0.027	-0.014	3.865	4.575	7.529	-0.011	-1.566	-1.378	0.007
4	A	12	THR	0	0.006	-0.023	6.793	-3.173	-3.173	0.000	0.000	0.000	0.000
5	A	13	PHE	0	0.038	-0.001	8.675	-2.210	-2.210	0.000	0.000	0.000	0.000
6	A	14	SER	0	0.034	0.003	12.221	-1.732	-1.732	0.000	0.000	0.000	0.000
7	A	15	ASP	-1	-0.753	-0.829	9.031	31.513	31.513	0.000	0.000	0.000	0.000
8	A	16	TYR	0	0.006	0.009	11.871	-1.902	-1.902	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.020	0.012	13.415	-1.535	-1.535	0.000	0.000	0.000	0.000
10	A	18	GLY	0	0.016	0.026	15.599	-1.297	-1.297	0.000	0.000	0.000	0.000
11	A	19	LEU	0	0.000	-0.005	11.375	-1.270	-1.270	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.027	-0.010	15.984	-1.008	-1.008	0.000	0.000	0.000	0.000
13	A	21	THR	0	-0.033	-0.025	18.800	-1.204	-1.204	0.000	0.000	0.000	0.000
14	A	22	CYS	0	-0.065	-0.005	18.509	-0.773	-0.773	0.000	0.000	0.000	0.000
15	A	23	VAL	0	0.019	-0.006	19.240	-0.818	-0.818	0.000	0.000	0.000	0.000
16	A	24	TYR	0	-0.061	-0.044	21.277	-0.623	-0.623	0.000	0.000	0.000	0.000
17	A	25	GLU	-1	-0.794	-0.900	23.955	11.017	11.017	0.000	0.000	0.000	0.000
18	A	26	TRP	0	-0.048	0.000	23.543	-0.579	-0.579	0.000	0.000	0.000	0.000
19	A	27	ALA	0	-0.008	-0.004	25.443	-0.521	-0.521	0.000	0.000	0.000	0.000
20	A	28	ASP	-1	-0.784	-0.860	27.242	9.919	9.919	0.000	0.000	0.000	0.000
21	A	29	SER	0	-0.010	0.003	28.458	-0.565	-0.565	0.000	0.000	0.000	0.000
22	A	30	TYR	0	-0.013	-0.028	27.220	-0.313	-0.313	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.800	-0.861	31.008	9.728	9.728	0.000	0.000	0.000	0.000
24	A	32	SER	0	-0.065	-0.061	32.894	-0.365	-0.365	0.000	0.000	0.000	0.000
25	A	33	LYS	1	0.818	0.901	34.504	-8.753	-8.753	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.794	-0.858	32.656	9.476	9.476	0.000	0.000	0.000	0.000
27	A	35	TRP	0	0.020	-0.017	31.712	0.429	0.429	0.000	0.000	0.000	0.000
28	A	36	ASP	-1	-0.818	-0.885	31.973	9.773	9.773	0.000	0.000	0.000	0.000
29	A	37	ARG	1	0.738	0.839	29.008	-10.257	-10.257	0.000	0.000	0.000	0.000
30	A	38	LEU	0	0.014	0.011	26.574	0.462	0.462	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.781	0.840	26.617	-9.087	-9.087	0.000	0.000	0.000	0.000
32	A	40	LYS	1	0.819	0.911	26.421	-9.953	-9.953	0.000	0.000	0.000	0.000
33	A	41	VAL	0	0.004	0.004	22.688	0.595	0.595	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.012	0.015	21.786	0.723	0.723	0.000	0.000	0.000	0.000
35	A	43	ALA	0	0.015	0.010	19.728	0.094	0.094	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.022	-0.006	21.471	-0.566	-0.566	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.017	-0.003	22.168	-0.645	-0.645	0.000	0.000	0.000	0.000
38	A	46	LEU	0	-0.044	-0.018	21.677	0.757	0.757	0.000	0.000	0.000	0.000
39	A	47	ARG	1	0.817	0.900	18.370	-15.385	-15.385	0.000	0.000	0.000	0.000
40	A	48	ILE	0	-0.020	-0.013	21.706	0.255	0.255	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.801	-0.904	22.127	12.176	12.176	0.000	0.000	0.000	0.000
42	A	50	TYR	0	0.043	-0.011	24.065	0.181	0.181	0.000	0.000	0.000	0.000
43	A	51	ARG	1	0.872	0.923	22.573	-12.376	-12.376	0.000	0.000	0.000	0.000
44	A	52	SER	0	-0.046	-0.022	25.389	-0.335	-0.335	0.000	0.000	0.000	0.000
45	A	53	PHE	0	-0.033	-0.025	27.138	-0.253	-0.253	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.070	-0.035	30.491	-0.343	-0.343	0.000	0.000	0.000	0.000
47	A	55	ASP	-1	-0.920	-0.952	30.334	9.433	9.433	0.000	0.000	0.000	0.000
48	A	56	LYS	1	0.945	0.981	29.775	-8.878	-8.878	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.021	-0.013	23.187	0.350	0.350	0.000	0.000	0.000	0.000
50	A	58	TRP	0	0.002	0.014	26.253	-0.280	-0.280	0.000	0.000	0.000	0.000
51	A	59	GLU	-1	-0.834	-0.910	22.379	13.632	13.632	0.000	0.000	0.000	0.000
52	A	60	ALA	0	0.020	0.002	22.181	0.688	0.688	0.000	0.000	0.000	0.000
53	A	61	MET	0	-0.024	0.025	24.315	-0.319	-0.319	0.000	0.000	0.000	0.000
54	A	62	PRO	0	0.028	0.018	26.217	0.444	0.444	0.000	0.000	0.000	0.000
55	A	63	ALA	0	0.045	0.022	26.446	-0.211	-0.211	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.788	-0.876	27.879	9.754	9.754	0.000	0.000	0.000	0.000
57	A	65	GLU	-1	-0.898	-0.946	30.592	9.684	9.684	0.000	0.000	0.000	0.000
58	A	66	PHE	0	0.031	-0.006	25.995	-0.144	-0.144	0.000	0.000	0.000	0.000
59	A	67	VAL	0	0.040	0.010	29.545	-0.150	-0.150	0.000	0.000	0.000	0.000
60	A	68	GLY	0	0.002	0.030	31.544	-0.265	-0.265	0.000	0.000	0.000	0.000
61	A	69	MET	0	-0.023	-0.004	28.412	-0.281	-0.281	0.000	0.000	0.000	0.000
62	A	70	VAL	0	-0.024	-0.006	29.337	-0.267	-0.267	0.000	0.000	0.000	0.000
63	A	71	SER	0	-0.016	-0.034	32.767	-0.306	-0.306	0.000	0.000	0.000	0.000
64	A	72	SER	0	0.009	0.002	35.782	-0.397	-0.397	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.909	0.939	37.846	-7.116	-7.116	0.000	0.000	0.000	0.000
66	A	74	GLN	0	0.017	-0.005	38.652	0.027	0.027	0.000	0.000	0.000	0.000
67	A	75	VAL	0	-0.043	0.010	32.589	0.070	0.070	0.000	0.000	0.000	0.000
68	A	76	LEU	0	0.016	0.001	31.503	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	77	GLY	0	0.024	0.028	35.899	-0.068	-0.068	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.843	-0.883	38.554	7.160	7.160	0.000	0.000	0.000	0.000
71	A	79	PRO	0	0.025	0.009	40.951	0.094	0.094	0.000	0.000	0.000	0.000
72	A	80	THR	0	-0.021	-0.024	43.374	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	81	LEU	0	-0.024	0.005	36.844	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.830	0.894	38.574	-7.526	-7.526	0.000	0.000	0.000	0.000
75	A	83	THR	0	-0.035	-0.061	33.392	-0.121	-0.121	0.000	0.000	0.000	0.000
76	A	84	GLN	0	0.048	0.030	31.057	-0.125	-0.125	0.000	0.000	0.000	0.000
77	A	85	HIS	1	0.821	0.891	27.303	-10.368	-10.368	0.000	0.000	0.000	0.000
78	A	86	PHE	0	0.011	0.011	27.079	0.369	0.369	0.000	0.000	0.000	0.000
79	A	87	ILE	0	0.033	0.020	21.299	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	88	GLY	0	-0.007	0.006	22.954	-0.294	-0.294	0.000	0.000	0.000	0.000
81	A	89	GLY	0	-0.002	-0.008	19.868	0.573	0.573	0.000	0.000	0.000	0.000
82	A	90	THR	0	-0.013	-0.011	15.517	-0.221	-0.221	0.000	0.000	0.000	0.000
83	A	91	ARG	1	0.791	0.894	9.666	-20.897	-20.897	0.000	0.000	0.000	0.000
84	A	92	TRP	0	0.045	-0.004	9.767	-0.966	-0.966	0.000	0.000	0.000	0.000
85	A	93	GLU	-1	-0.765	-0.838	6.664	23.779	23.779	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.828	0.899	1.669	-117.071	-122.754	17.463	-6.694	-5.086	0.078
87	A	95	VAL	0	-0.056	-0.018	5.250	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	96	SER	0	-0.008	-0.044	6.316	0.675	0.675	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.837	-0.914	4.489	67.754	67.973	-0.001	-0.011	-0.207	0.000
90	A	98	ASP	-1	-0.852	-0.881	7.120	22.919	22.919	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.854	-0.919	9.246	19.092	19.092	0.000	0.000	0.000	0.000
92	A	100	VAL	0	0.003	0.014	8.220	3.942	3.942	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.005	0.008	9.879	-2.868	-2.868	0.000	0.000	0.000	0.000
94	A	102	GLY	0	0.002	-0.003	11.131	1.520	1.520	0.000	0.000	0.000	0.000
95	A	103	TYR	0	-0.066	-0.058	11.009	-2.092	-2.092	0.000	0.000	0.000	0.000
96	A	104	HIS	0	0.038	0.021	15.670	0.569	0.569	0.000	0.000	0.000	0.000
97	A	105	GLN	0	-0.005	0.000	18.981	-0.760	-0.760	0.000	0.000	0.000	0.000
98	A	106	LEU	0	0.000	0.007	21.936	0.058	0.058	0.000	0.000	0.000	0.000
99	A	107	ARG	1	0.828	0.898	24.870	-9.620	-9.620	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.020	-0.001	28.515	0.069	0.069	0.000	0.000	0.000	0.000
101	A	109	PRO	0	-0.061	-0.017	30.996	-0.341	-0.341	0.000	0.000	0.000	0.000
102	A	110	HIS	0	0.008	-0.013	34.459	-0.070	-0.070	0.000	0.000	0.000	0.000
103	A	111	GLN	0	0.020	0.020	36.963	-0.211	-0.211	0.000	0.000	0.000	0.000
104	A	112	ARG	1	0.907	0.946	39.191	-7.602	-7.602	0.000	0.000	0.000	0.000
105	A	113	TYR	0	-0.007	-0.002	43.277	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	114	LYS	1	0.817	0.892	46.797	-5.784	-5.784	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.780	-0.869	49.759	6.102	6.102	0.000	0.000	0.000	0.000
108	A	116	THR	0	0.032	-0.015	47.382	0.089	0.089	0.000	0.000	0.000	0.000
109	A	117	THR	0	-0.084	-0.064	49.450	0.011	0.011	0.000	0.000	0.000	0.000
110	A	118	MET	0	-0.092	-0.031	46.009	0.046	0.046	0.000	0.000	0.000	0.000
111	A	119	LYS	1	0.959	0.989	49.042	-5.745	-5.745	0.000	0.000	0.000	0.000
112	A	120	GLU	-1	-0.801	-0.878	50.973	5.773	5.773	0.000	0.000	0.000	0.000
113	A	121	VAL	0	-0.066	-0.030	45.270	0.093	0.093	0.000	0.000	0.000	0.000
114	A	122	THR	0	0.021	0.018	46.903	-0.046	-0.046	0.000	0.000	0.000	0.000
115	A	123	MET	0	-0.020	0.001	39.660	0.004	0.004	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.927	0.938	41.417	-7.009	-7.009	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.058	0.035	38.459	-0.108	-0.108	0.000	0.000	0.000	0.000
118	A	126	HIS	1	0.779	0.890	33.858	-8.339	-8.339	0.000	0.000	0.000	0.000
119	A	127	ALA	0	0.069	0.052	31.242	-0.172	-0.172	0.000	0.000	0.000	0.000
120	A	128	HIS	0	0.015	0.013	28.113	0.195	0.195	0.000	0.000	0.000	0.000
121	A	129	SER	0	-0.024	-0.031	24.324	-0.170	-0.170	0.000	0.000	0.000	0.000
122	A	130	ALA	0	-0.009	0.005	20.198	0.189	0.189	0.000	0.000	0.000	0.000
123	A	131	ASN	0	-0.008	-0.012	20.848	-0.348	-0.348	0.000	0.000	0.000	0.000
124	A	132	LEU	0	0.014	0.035	14.141	0.528	0.528	0.000	0.000	0.000	0.000
125	A	133	HIS	0	-0.016	-0.012	16.505	-1.537	-1.537	0.000	0.000	0.000	0.000
126	A	134	TRP	0	0.033	0.013	14.282	0.387	0.387	0.000	0.000	0.000	0.000
127	A	135	TYR	0	-0.021	-0.028	13.713	-1.595	-1.595	0.000	0.000	0.000	0.000
128	A	136	LYS	1	0.855	0.890	13.335	-20.632	-20.632	0.000	0.000	0.000	0.000
129	A	137	LYS	1	0.845	0.934	10.151	-28.183	-28.183	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.011	-0.006	14.075	-0.065	-0.065	0.000	0.000	0.000	0.000
131	A	139	ASP	-1	-0.881	-0.938	17.544	15.177	15.177	0.000	0.000	0.000	0.000
132	A	140	GLY	0	-0.011	-0.002	14.812	-0.370	-0.370	0.000	0.000	0.000	0.000
133	A	141	VAL	0	-0.069	-0.047	15.113	0.954	0.954	0.000	0.000	0.000	0.000
134	A	142	TRP	0	-0.068	-0.046	9.443	-0.823	-0.823	0.000	0.000	0.000	0.000
135	A	143	LYS	1	0.882	0.942	15.975	-15.864	-15.864	0.000	0.000	0.000	0.000
136	A	144	PHE	0	0.023	-0.002	17.548	0.927	0.927	0.000	0.000	0.000	0.000
137	A	145	ALA	0	0.018	-0.006	17.112	-0.682	-0.682	0.000	0.000	0.000	0.000
138	A	146	GLY	0	0.042	0.019	19.235	-0.235	-0.235	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.048	-0.014	19.699	0.470	0.470	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.979	0.998	18.998	-14.445	-14.445	0.000	0.000	0.000	0.000
141	A	149	PRO	0	-0.013	0.003	21.182	0.229	0.229	0.000	0.000	0.000	0.000
142	A	150	ASP	-1	-0.800	-0.867	22.413	11.882	11.882	0.000	0.000	0.000	0.000
143	A	151	ILE	0	0.008	-0.004	24.304	0.076	0.076	0.000	0.000	0.000	0.000
144	A	152	ARG	1	0.816	0.892	21.550	-12.328	-12.328	0.000	0.000	0.000	0.000
145	A	153	TRP	0	0.054	0.014	28.552	-0.399	-0.399	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.014	-0.011	31.612	0.263	0.263	0.000	0.000	0.000	0.000
147	A	155	GLU	-1	-0.814	-0.876	34.352	8.483	8.483	0.000	0.000	0.000	0.000

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