FMO DATABASE

FMODB ID: 3JLLL

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1480886.837358
FMO2-HF: Nuclear repulsion	1419952.2936
FMO2-HF: Total energy	-60934.543758
FMO2-MP2: Total energy	-61112.141527

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.
-61.491	-63.551	17.367	-8.52	-6.786	0.089

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 : -0.840 / q_NPA : -0.914

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	-0.049	-0.024	3.797	6.156	9.192	-0.014	-1.525	-1.497	0.007
4	A	12	THR	0	0.025	-0.013	6.403	-2.862	-2.862	0.000	0.000	0.000	0.000
5	A	13	PHE	0	0.029	-0.008	8.428	-2.616	-2.616	0.000	0.000	0.000	0.000
6	A	14	SER	0	0.026	0.000	11.766	-1.985	-1.985	0.000	0.000	0.000	0.000
7	A	15	ASP	-1	-0.767	-0.849	8.015	34.307	34.307	0.000	0.000	0.000	0.000
8	A	16	TYR	0	0.008	0.008	11.224	-2.271	-2.271	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.020	0.015	13.201	-1.648	-1.648	0.000	0.000	0.000	0.000
10	A	18	GLY	0	0.014	0.024	14.924	-1.396	-1.396	0.000	0.000	0.000	0.000
11	A	19	LEU	0	-0.006	-0.007	10.877	-1.204	-1.204	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.027	-0.013	15.449	-1.020	-1.020	0.000	0.000	0.000	0.000
13	A	21	THR	0	-0.039	-0.027	18.366	-1.198	-1.198	0.000	0.000	0.000	0.000
14	A	22	CYS	0	-0.056	-0.001	17.966	-0.858	-0.858	0.000	0.000	0.000	0.000
15	A	23	VAL	0	0.035	0.005	19.188	-0.868	-0.868	0.000	0.000	0.000	0.000
16	A	24	TYR	0	-0.065	-0.046	20.964	-0.674	-0.674	0.000	0.000	0.000	0.000
17	A	25	GLU	-1	-0.787	-0.898	23.318	11.083	11.083	0.000	0.000	0.000	0.000
18	A	26	TRP	0	-0.046	0.004	23.232	-0.602	-0.602	0.000	0.000	0.000	0.000
19	A	27	ALA	0	-0.030	-0.017	25.049	-0.540	-0.540	0.000	0.000	0.000	0.000
20	A	28	ASP	-1	-0.781	-0.862	27.013	9.970	9.970	0.000	0.000	0.000	0.000
21	A	29	SER	0	0.010	0.015	27.931	-0.549	-0.549	0.000	0.000	0.000	0.000
22	A	30	TYR	0	0.001	-0.026	27.186	-0.338	-0.338	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.783	-0.832	31.018	9.773	9.773	0.000	0.000	0.000	0.000
24	A	32	SER	0	-0.077	-0.053	32.536	-0.367	-0.367	0.000	0.000	0.000	0.000
25	A	33	LYS	1	0.804	0.893	34.233	-8.748	-8.748	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.832	-0.889	32.575	9.429	9.429	0.000	0.000	0.000	0.000
27	A	35	TRP	0	0.051	-0.003	31.603	0.430	0.430	0.000	0.000	0.000	0.000
28	A	36	ASP	-1	-0.795	-0.886	31.412	9.823	9.823	0.000	0.000	0.000	0.000
29	A	37	ARG	1	0.724	0.842	28.704	-10.239	-10.239	0.000	0.000	0.000	0.000
30	A	38	LEU	0	0.005	0.007	26.338	0.464	0.464	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.769	0.839	26.425	-9.043	-9.043	0.000	0.000	0.000	0.000
32	A	40	LYS	1	0.820	0.911	26.351	-9.973	-9.973	0.000	0.000	0.000	0.000
33	A	41	VAL	0	0.019	0.006	22.126	0.603	0.603	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.036	0.005	21.438	0.754	0.754	0.000	0.000	0.000	0.000
35	A	43	ALA	0	0.001	0.003	19.456	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.027	0.000	21.191	-0.583	-0.583	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.005	0.005	22.067	-0.656	-0.656	0.000	0.000	0.000	0.000
38	A	46	LEU	0	-0.046	-0.020	21.726	0.704	0.704	0.000	0.000	0.000	0.000
39	A	47	ARG	1	0.843	0.922	18.740	-15.001	-15.001	0.000	0.000	0.000	0.000
40	A	48	ILE	0	-0.034	-0.019	21.879	0.269	0.269	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.787	-0.908	22.185	12.155	12.155	0.000	0.000	0.000	0.000
42	A	50	TYR	0	0.026	-0.013	24.189	0.203	0.203	0.000	0.000	0.000	0.000
43	A	51	ARG	1	0.867	0.928	22.360	-12.400	-12.400	0.000	0.000	0.000	0.000
44	A	52	SER	0	-0.024	-0.004	26.003	-0.353	-0.353	0.000	0.000	0.000	0.000
45	A	53	PHE	0	0.005	-0.011	27.435	-0.299	-0.299	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.068	-0.039	30.489	-0.337	-0.337	0.000	0.000	0.000	0.000
47	A	55	ASP	-1	-0.931	-0.945	30.470	9.220	9.220	0.000	0.000	0.000	0.000
48	A	56	LYS	1	0.933	0.970	29.850	-8.837	-8.837	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.032	-0.009	23.009	0.357	0.357	0.000	0.000	0.000	0.000
50	A	58	TRP	0	0.010	0.017	26.364	-0.289	-0.289	0.000	0.000	0.000	0.000
51	A	59	GLU	-1	-0.825	-0.914	22.699	13.363	13.363	0.000	0.000	0.000	0.000
52	A	60	ALA	0	0.024	-0.003	22.337	0.635	0.635	0.000	0.000	0.000	0.000
53	A	61	MET	0	-0.049	0.009	24.476	-0.321	-0.321	0.000	0.000	0.000	0.000
54	A	62	PRO	0	0.055	0.032	26.102	0.503	0.503	0.000	0.000	0.000	0.000
55	A	63	ALA	0	0.055	0.020	26.167	-0.241	-0.241	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.801	-0.877	27.716	9.663	9.663	0.000	0.000	0.000	0.000
57	A	65	GLU	-1	-0.902	-0.951	30.799	9.579	9.579	0.000	0.000	0.000	0.000
58	A	66	PHE	0	0.042	-0.001	26.119	-0.150	-0.150	0.000	0.000	0.000	0.000
59	A	67	VAL	0	0.012	-0.002	29.470	-0.148	-0.148	0.000	0.000	0.000	0.000
60	A	68	GLY	0	0.001	0.027	31.468	-0.281	-0.281	0.000	0.000	0.000	0.000
61	A	69	MET	0	-0.032	-0.007	28.678	-0.282	-0.282	0.000	0.000	0.000	0.000
62	A	70	VAL	0	-0.018	-0.011	29.183	-0.267	-0.267	0.000	0.000	0.000	0.000
63	A	71	SER	0	-0.015	-0.027	32.619	-0.290	-0.290	0.000	0.000	0.000	0.000
64	A	72	SER	0	0.031	0.023	35.590	-0.380	-0.380	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.926	0.945	38.078	-7.063	-7.063	0.000	0.000	0.000	0.000
66	A	74	GLN	0	0.007	-0.003	39.000	0.042	0.042	0.000	0.000	0.000	0.000
67	A	75	VAL	0	-0.030	0.002	32.998	0.080	0.080	0.000	0.000	0.000	0.000
68	A	76	LEU	0	-0.016	-0.013	31.603	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	77	GLY	0	0.054	0.038	35.915	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.869	-0.894	38.478	7.116	7.116	0.000	0.000	0.000	0.000
71	A	79	PRO	0	0.025	0.009	40.955	0.094	0.094	0.000	0.000	0.000	0.000
72	A	80	THR	0	-0.030	-0.021	43.015	0.001	0.001	0.000	0.000	0.000	0.000
73	A	81	LEU	0	-0.022	0.004	36.729	-0.053	-0.053	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.835	0.895	38.628	-7.571	-7.571	0.000	0.000	0.000	0.000
75	A	83	THR	0	-0.026	-0.043	33.430	-0.096	-0.096	0.000	0.000	0.000	0.000
76	A	84	GLN	0	0.034	0.021	31.125	-0.123	-0.123	0.000	0.000	0.000	0.000
77	A	85	HIS	1	0.796	0.864	27.475	-10.372	-10.372	0.000	0.000	0.000	0.000
78	A	86	PHE	0	0.016	0.012	27.416	0.368	0.368	0.000	0.000	0.000	0.000
79	A	87	ILE	0	0.036	0.016	21.458	0.018	0.018	0.000	0.000	0.000	0.000
80	A	88	GLY	0	-0.020	0.005	23.471	-0.175	-0.175	0.000	0.000	0.000	0.000
81	A	89	GLY	0	0.008	-0.007	20.184	0.537	0.537	0.000	0.000	0.000	0.000
82	A	90	THR	0	-0.005	-0.008	15.351	-0.268	-0.268	0.000	0.000	0.000	0.000
83	A	91	ARG	1	0.788	0.893	10.344	-20.141	-20.141	0.000	0.000	0.000	0.000
84	A	92	TRP	0	0.036	-0.009	9.885	-0.767	-0.767	0.000	0.000	0.000	0.000
85	A	93	GLU	-1	-0.771	-0.852	6.884	22.951	22.951	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.844	0.903	1.659	-116.772	-122.150	17.382	-6.968	-5.035	0.082
87	A	95	VAL	0	-0.045	-0.010	4.941	0.022	0.040	-0.001	-0.006	-0.011	0.000
88	A	96	SER	0	-0.008	-0.031	6.071	0.704	0.704	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.850	-0.922	4.303	68.977	69.241	0.000	-0.021	-0.243	0.000
90	A	98	ASP	-1	-0.856	-0.890	6.905	24.192	24.192	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.863	-0.928	9.032	18.636	18.636	0.000	0.000	0.000	0.000
92	A	100	VAL	0	0.002	0.013	7.981	3.604	3.604	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.013	0.000	9.980	-2.852	-2.852	0.000	0.000	0.000	0.000
94	A	102	GLY	0	0.010	0.003	11.357	1.361	1.361	0.000	0.000	0.000	0.000
95	A	103	TYR	0	-0.079	-0.047	11.511	-2.090	-2.090	0.000	0.000	0.000	0.000
96	A	104	HIS	0	0.059	0.032	15.892	0.606	0.606	0.000	0.000	0.000	0.000
97	A	105	GLN	0	-0.010	-0.004	19.175	-0.619	-0.619	0.000	0.000	0.000	0.000
98	A	106	LEU	0	0.006	0.010	22.261	0.016	0.016	0.000	0.000	0.000	0.000
99	A	107	ARG	1	0.820	0.888	25.113	-9.576	-9.576	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.021	0.002	28.816	0.072	0.072	0.000	0.000	0.000	0.000
101	A	109	PRO	0	-0.069	-0.022	31.276	-0.343	-0.343	0.000	0.000	0.000	0.000
102	A	110	HIS	0	0.006	-0.008	34.725	-0.050	-0.050	0.000	0.000	0.000	0.000
103	A	111	GLN	0	0.022	0.018	37.191	-0.185	-0.185	0.000	0.000	0.000	0.000
104	A	112	ARG	1	0.921	0.945	39.222	-7.593	-7.593	0.000	0.000	0.000	0.000
105	A	113	TYR	0	-0.014	-0.006	43.273	-0.046	-0.046	0.000	0.000	0.000	0.000
106	A	114	LYS	1	0.841	0.903	46.663	-5.811	-5.811	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.784	-0.868	49.506	6.112	6.112	0.000	0.000	0.000	0.000
108	A	116	THR	0	0.025	-0.020	46.976	0.079	0.079	0.000	0.000	0.000	0.000
109	A	117	THR	0	-0.078	-0.059	49.199	0.020	0.020	0.000	0.000	0.000	0.000
110	A	118	MET	0	-0.114	-0.036	45.723	0.057	0.057	0.000	0.000	0.000	0.000
111	A	119	LYS	1	0.977	0.993	48.960	-5.792	-5.792	0.000	0.000	0.000	0.000
112	A	120	GLU	-1	-0.815	-0.892	50.840	5.791	5.791	0.000	0.000	0.000	0.000
113	A	121	VAL	0	-0.057	-0.021	45.161	0.098	0.098	0.000	0.000	0.000	0.000
114	A	122	THR	0	0.014	0.004	46.823	-0.058	-0.058	0.000	0.000	0.000	0.000
115	A	123	MET	0	-0.024	0.007	39.642	0.002	0.002	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.933	0.941	41.327	-7.034	-7.034	0.000	0.000	0.000	0.000
117	A	125	GLY	0	0.021	0.015	38.591	-0.113	-0.113	0.000	0.000	0.000	0.000
118	A	126	HIS	1	0.854	0.916	33.697	-8.449	-8.449	0.000	0.000	0.000	0.000
119	A	127	ALA	0	0.052	0.046	31.197	-0.126	-0.126	0.000	0.000	0.000	0.000
120	A	128	HIS	0	0.031	0.027	28.841	0.235	0.235	0.000	0.000	0.000	0.000
121	A	129	SER	0	-0.024	-0.027	24.715	-0.172	-0.172	0.000	0.000	0.000	0.000
122	A	130	ALA	0	-0.003	0.011	20.591	0.175	0.175	0.000	0.000	0.000	0.000
123	A	131	ASN	0	-0.005	-0.012	21.141	-0.576	-0.576	0.000	0.000	0.000	0.000
124	A	132	LEU	0	-0.006	0.024	14.181	0.483	0.483	0.000	0.000	0.000	0.000
125	A	133	HIS	0	-0.001	-0.004	16.742	-1.431	-1.431	0.000	0.000	0.000	0.000
126	A	134	TRP	0	0.043	0.017	14.223	0.391	0.391	0.000	0.000	0.000	0.000
127	A	135	TYR	0	-0.028	-0.034	13.416	-1.535	-1.535	0.000	0.000	0.000	0.000
128	A	136	LYS	1	0.864	0.903	12.801	-20.948	-20.948	0.000	0.000	0.000	0.000
129	A	137	LYS	1	0.872	0.937	10.471	-26.872	-26.872	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.035	-0.016	13.813	-0.079	-0.079	0.000	0.000	0.000	0.000
131	A	139	ASP	-1	-0.870	-0.935	17.146	15.289	15.289	0.000	0.000	0.000	0.000
132	A	140	GLY	0	-0.021	-0.011	14.675	-0.363	-0.363	0.000	0.000	0.000	0.000
133	A	141	VAL	0	-0.034	-0.020	15.620	0.478	0.478	0.000	0.000	0.000	0.000
134	A	142	TRP	0	-0.064	-0.037	8.895	-1.055	-1.055	0.000	0.000	0.000	0.000
135	A	143	LYS	1	0.886	0.948	15.471	-15.866	-15.866	0.000	0.000	0.000	0.000
136	A	144	PHE	0	0.040	0.000	17.224	0.890	0.890	0.000	0.000	0.000	0.000
137	A	145	ALA	0	0.015	-0.004	17.060	-0.707	-0.707	0.000	0.000	0.000	0.000
138	A	146	GLY	0	0.040	0.025	19.155	-0.326	-0.326	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.051	-0.023	19.706	0.561	0.561	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.977	0.996	18.443	-14.703	-14.703	0.000	0.000	0.000	0.000
141	A	149	PRO	0	-0.032	-0.010	21.140	0.296	0.296	0.000	0.000	0.000	0.000
142	A	150	ASP	-1	-0.837	-0.893	22.667	11.609	11.609	0.000	0.000	0.000	0.000
143	A	151	ILE	0	0.003	-0.017	24.397	0.002	0.002	0.000	0.000	0.000	0.000
144	A	152	ARG	1	0.826	0.897	22.045	-12.151	-12.151	0.000	0.000	0.000	0.000
145	A	153	TRP	0	0.043	0.016	28.853	-0.365	-0.365	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.007	-0.003	32.083	0.236	0.236	0.000	0.000	0.000	0.000
147	A	155	GLU	-1	-0.840	-0.888	34.774	8.392	8.392	0.000	0.000	0.000	0.000

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