FMO DATABASE

FMODB ID: P2N1R

Calculation Name: 1IDP-A-Xray25

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: 2018-07-25

Reference:

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1487182.849974
FMO2-HF: Nuclear repulsion	1426078.28941
FMO2-HF: Total energy	-61104.560564
FMO2-MP2: Total energy	-61282.669603

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:8:ACE)

Summations of interaction energy for fragment #1(A:8:ACE)

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.
1.151	2.01	-0.011	-0.368	-0.481	0

Interaction energy analysis for fragmet #1(A:8:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.031

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].
3	A	10	GLU	-1	-0.951	-0.963	3.847	0.397	1.256	-0.011	-0.368	-0.481
4	A	11	ILE	0	-0.043	-0.018	6.920	0.070	0.070	0.000	0.000	0.000
5	A	12	THR	0	0.041	0.019	10.440	0.022	0.022	0.000	0.000	0.000
6	A	13	PHE	0	0.030	-0.007	13.282	0.055	0.055	0.000	0.000	0.000
7	A	14	SER	0	0.019	-0.006	16.389	0.038	0.038	0.000	0.000	0.000
8	A	15	ASP	-1	-0.781	-0.882	13.165	-0.383	-0.383	0.000	0.000	0.000
9	A	16	TYR	0	-0.004	0.001	15.442	0.043	0.043	0.000	0.000	0.000
10	A	17	LEU	0	0.003	0.007	16.816	0.032	0.032	0.000	0.000	0.000
11	A	18	GLY	0	0.019	0.020	19.617	0.021	0.021	0.000	0.000	0.000
12	A	19	LEU	0	-0.012	-0.009	14.267	0.022	0.022	0.000	0.000	0.000
13	A	20	MET	0	-0.022	-0.011	18.865	0.026	0.026	0.000	0.000	0.000
14	A	21	THR	0	-0.028	-0.010	21.394	0.015	0.015	0.000	0.000	0.000
15	A	22	CYS	0	-0.037	-0.001	20.960	0.016	0.016	0.000	0.000	0.000
16	A	23	VAL	0	0.020	0.003	21.141	0.011	0.011	0.000	0.000	0.000
17	A	24	TYR	0	-0.010	-0.006	23.189	0.010	0.010	0.000	0.000	0.000
18	A	25	GLU	-1	-0.831	-0.923	26.257	-0.037	-0.037	0.000	0.000	0.000
19	A	26	TRP	0	-0.054	-0.007	25.311	0.007	0.007	0.000	0.000	0.000
20	A	27	ALA	0	-0.012	-0.008	27.077	0.005	0.005	0.000	0.000	0.000
21	A	28	ASP	-1	-0.804	-0.893	28.765	-0.018	-0.018	0.000	0.000	0.000
22	A	29	SER	0	-0.029	0.001	30.799	0.001	0.001	0.000	0.000	0.000
23	A	30	TYR	0	0.000	-0.020	28.495	0.004	0.004	0.000	0.000	0.000
24	A	31	ASP	-1	-0.785	-0.859	32.630	0.000	0.000	0.000	0.000	0.000
25	A	32	SER	0	-0.099	-0.065	34.906	0.001	0.001	0.000	0.000	0.000
26	A	33	LYS	1	0.813	0.900	36.228	0.000	0.000	0.000	0.000	0.000
27	A	34	ASP	-1	-0.866	-0.915	35.327	-0.023	-0.023	0.000	0.000	0.000
28	A	35	TRP	0	0.051	-0.002	33.488	-0.002	-0.002	0.000	0.000	0.000
29	A	36	ASP	-1	-0.844	-0.923	34.302	-0.023	-0.023	0.000	0.000	0.000
30	A	37	ARG	1	0.758	0.871	32.015	0.025	0.025	0.000	0.000	0.000
31	A	38	LEU	0	0.016	0.012	28.694	-0.003	-0.003	0.000	0.000	0.000
32	A	39	ARG	1	0.772	0.857	29.441	0.014	0.014	0.000	0.000	0.000
33	A	40	LYS	1	0.884	0.957	29.842	0.034	0.034	0.000	0.000	0.000
34	A	41	VAL	0	-0.004	-0.003	25.456	-0.008	-0.008	0.000	0.000	0.000
35	A	42	ILE	0	-0.035	0.008	24.631	-0.003	-0.003	0.000	0.000	0.000
36	A	43	ALA	0	-0.006	-0.002	22.206	-0.006	-0.006	0.000	0.000	0.000
37	A	44	PRO	0	0.020	-0.007	24.150	0.007	0.007	0.000	0.000	0.000
38	A	45	THR	0	-0.041	-0.005	24.463	0.007	0.007	0.000	0.000	0.000
39	A	46	LEU	0	-0.009	-0.006	23.361	-0.004	-0.004	0.000	0.000	0.000
40	A	47	ARG	1	0.952	1.004	19.149	-0.074	-0.074	0.000	0.000	0.000
41	A	48	ILE	0	-0.036	-0.017	22.670	0.001	0.001	0.000	0.000	0.000
42	A	49	ASP	-1	-0.819	-0.933	22.207	0.097	0.097	0.000	0.000	0.000
43	A	50	TYR	0	0.041	-0.002	24.473	0.001	0.001	0.000	0.000	0.000
44	A	51	ARG	1	0.884	0.941	21.952	-0.097	-0.097	0.000	0.000	0.000
45	A	52	SER	0	-0.034	-0.008	25.942	-0.003	-0.003	0.000	0.000	0.000
46	A	53	PHE	0	0.027	0.002	27.810	-0.002	-0.002	0.000	0.000	0.000
47	A	54	LEU	0	-0.072	-0.043	30.543	-0.005	-0.005	0.000	0.000	0.000
48	A	55	ASP	-1	-0.940	-0.953	30.349	0.056	0.056	0.000	0.000	0.000
49	A	56	LYS	1	0.952	0.982	29.884	-0.036	-0.036	0.000	0.000	0.000
50	A	57	LEU	0	-0.039	-0.019	23.148	0.006	0.006	0.000	0.000	0.000
51	A	58	TRP	0	0.020	0.024	26.677	-0.001	-0.001	0.000	0.000	0.000
52	A	59	GLU	-1	-0.944	-0.996	23.040	0.053	0.053	0.000	0.000	0.000
53	A	60	ALA	0	0.031	0.005	23.283	-0.003	-0.003	0.000	0.000	0.000
54	A	61	MET	0	-0.037	0.004	25.695	-0.004	-0.004	0.000	0.000	0.000
55	A	62	PRO	0	0.045	0.026	27.784	-0.005	-0.005	0.000	0.000	0.000
56	A	63	ALA	0	0.059	0.020	28.735	0.002	0.002	0.000	0.000	0.000
57	A	64	GLU	-1	-0.812	-0.901	29.909	-0.014	-0.014	0.000	0.000	0.000
58	A	65	GLU	-1	-0.917	-0.955	32.455	0.010	0.010	0.000	0.000	0.000
59	A	66	PHE	0	0.043	0.006	27.723	0.003	0.003	0.000	0.000	0.000
60	A	67	VAL	0	0.002	-0.005	31.268	0.002	0.002	0.000	0.000	0.000
61	A	68	GLY	0	-0.005	0.018	33.409	0.001	0.001	0.000	0.000	0.000
62	A	69	MET	0	-0.025	-0.005	29.664	0.002	0.002	0.000	0.000	0.000
63	A	70	VAL	0	0.001	-0.002	30.693	0.002	0.002	0.000	0.000	0.000
64	A	71	SER	0	-0.019	-0.027	34.010	0.001	0.001	0.000	0.000	0.000
65	A	72	SER	0	0.031	0.028	37.245	0.000	0.000	0.000	0.000	0.000
66	A	73	LYS	1	0.913	0.936	39.325	-0.001	-0.001	0.000	0.000	0.000
67	A	74	GLN	0	0.005	-0.004	39.767	0.000	0.000	0.000	0.000	0.000
68	A	75	VAL	0	-0.024	0.006	33.971	0.003	0.003	0.000	0.000	0.000
69	A	76	LEU	0	-0.003	-0.004	32.760	0.000	0.000	0.000	0.000	0.000
70	A	77	GLY	0	0.039	0.028	37.167	-0.002	-0.002	0.000	0.000	0.000
71	A	78	ASP	-1	-0.898	-0.939	40.000	0.005	0.005	0.000	0.000	0.000
72	A	79	PRO	0	0.022	0.009	42.293	0.000	0.000	0.000	0.000	0.000
73	A	80	THR	0	-0.046	-0.029	44.524	0.000	0.000	0.000	0.000	0.000
74	A	81	LEU	0	-0.013	0.007	37.730	0.001	0.001	0.000	0.000	0.000
75	A	82	ARG	1	0.853	0.907	39.972	-0.002	-0.002	0.000	0.000	0.000
76	A	83	THR	0	-0.001	-0.022	34.666	0.003	0.003	0.000	0.000	0.000
77	A	84	GLN	0	0.022	0.017	32.429	0.000	0.000	0.000	0.000	0.000
78	A	85	HIS	0	-0.069	-0.055	28.736	0.008	0.008	0.000	0.000	0.000
79	A	86	PHE	0	-0.014	-0.005	28.857	-0.004	-0.004	0.000	0.000	0.000
80	A	87	ILE	0	0.030	0.015	22.814	0.008	0.008	0.000	0.000	0.000
81	A	88	GLY	0	-0.022	0.001	24.439	-0.004	-0.004	0.000	0.000	0.000
82	A	89	GLY	0	0.000	-0.015	21.073	-0.007	-0.007	0.000	0.000	0.000
83	A	90	THR	0	0.007	0.001	16.499	0.010	0.010	0.000	0.000	0.000
84	A	91	ARG	1	0.806	0.904	10.937	-0.309	-0.309	0.000	0.000	0.000
85	A	92	TRP	0	0.037	-0.011	11.304	0.007	0.007	0.000	0.000	0.000
86	A	93	GLU	-1	-0.841	-0.900	7.818	0.575	0.575	0.000	0.000	0.000
87	A	94	LYS	1	0.860	0.921	6.081	1.245	1.245	0.000	0.000	0.000
88	A	95	VAL	0	-0.037	-0.004	6.030	0.103	0.103	0.000	0.000	0.000
89	A	96	SER	0	0.000	-0.015	7.641	-0.010	-0.010	0.000	0.000	0.000
90	A	97	GLU	-1	-0.861	-0.934	9.348	-0.881	-0.881	0.000	0.000	0.000
91	A	98	ASP	-1	-0.921	-0.952	11.547	-0.140	-0.140	0.000	0.000	0.000
92	A	99	GLU	-1	-0.881	-0.944	12.024	0.063	0.063	0.000	0.000	0.000
93	A	100	VAL	0	0.003	0.016	10.769	-0.050	-0.050	0.000	0.000	0.000
94	A	101	ILE	0	-0.033	-0.006	10.782	0.026	0.026	0.000	0.000	0.000
95	A	102	GLY	0	0.012	0.002	12.666	-0.015	-0.015	0.000	0.000	0.000
96	A	103	TYR	0	-0.031	-0.011	12.323	0.003	0.003	0.000	0.000	0.000
97	A	104	HIS	0	0.062	0.037	16.778	-0.015	-0.015	0.000	0.000	0.000
98	A	105	GLN	0	-0.021	-0.006	20.142	0.001	0.001	0.000	0.000	0.000
99	A	106	LEU	0	0.012	0.018	22.917	-0.010	-0.010	0.000	0.000	0.000
100	A	107	ARG	1	0.834	0.914	26.010	-0.020	-0.020	0.000	0.000	0.000
101	A	108	VAL	0	0.044	0.016	29.649	-0.004	-0.004	0.000	0.000	0.000
102	A	109	PRO	0	-0.085	-0.033	32.326	0.002	0.002	0.000	0.000	0.000
103	A	110	HIS	0	0.021	0.000	35.754	-0.002	-0.002	0.000	0.000	0.000
104	A	111	GLN	0	0.033	0.016	38.306	0.002	0.002	0.000	0.000	0.000
105	A	112	ARG	1	0.935	0.978	40.520	-0.013	-0.013	0.000	0.000	0.000
106	A	113	TYR	0	-0.009	-0.007	44.362	0.000	0.000	0.000	0.000	0.000
107	A	114	LYS	1	0.906	0.942	47.824	-0.006	-0.006	0.000	0.000	0.000
108	A	115	ASP	-1	-0.788	-0.870	50.678	0.004	0.004	0.000	0.000	0.000
109	A	116	THR	0	0.020	-0.021	48.445	0.000	0.000	0.000	0.000	0.000
110	A	117	THR	0	-0.084	-0.054	50.605	-0.001	-0.001	0.000	0.000	0.000
111	A	118	MET	0	-0.101	-0.039	46.901	0.000	0.000	0.000	0.000	0.000
112	A	119	LYS	1	0.969	0.989	50.332	0.000	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.873	-0.933	52.067	0.006	0.006	0.000	0.000	0.000
114	A	121	VAL	0	-0.053	-0.020	46.200	0.000	0.000	0.000	0.000	0.000
115	A	122	THR	0	-0.010	-0.004	47.617	0.001	0.001	0.000	0.000	0.000
116	A	123	MET	0	-0.015	0.023	40.532	0.001	0.001	0.000	0.000	0.000
117	A	124	LYS	1	0.903	0.922	42.287	-0.011	-0.011	0.000	0.000	0.000
118	A	125	GLY	0	0.034	0.021	39.366	0.002	0.002	0.000	0.000	0.000
119	A	126	HIS	1	0.842	0.920	34.308	-0.022	-0.022	0.000	0.000	0.000
120	A	127	ALA	0	0.063	0.050	31.882	0.003	0.003	0.000	0.000	0.000
121	A	128	HIS	0	0.032	0.020	29.156	-0.006	-0.006	0.000	0.000	0.000
122	A	129	SER	0	-0.012	-0.013	25.422	0.007	0.007	0.000	0.000	0.000
123	A	130	ALA	0	-0.016	0.005	20.918	-0.002	-0.002	0.000	0.000	0.000
124	A	131	ASN	0	0.016	-0.014	21.910	0.012	0.012	0.000	0.000	0.000
125	A	132	LEU	0	-0.027	0.015	14.697	0.000	0.000	0.000	0.000	0.000
126	A	133	HIS	0	0.008	0.010	17.734	0.001	0.001	0.000	0.000	0.000
127	A	134	TRP	0	0.039	0.014	14.979	0.008	0.008	0.000	0.000	0.000
128	A	135	TYR	0	-0.019	-0.042	15.692	-0.007	-0.007	0.000	0.000	0.000
129	A	136	LYS	1	0.900	0.942	14.825	0.068	0.068	0.000	0.000	0.000
130	A	137	LYS	1	0.894	0.951	15.968	0.252	0.252	0.000	0.000	0.000
131	A	138	ILE	0	-0.021	-0.010	18.202	0.002	0.002	0.000	0.000	0.000
132	A	139	ASP	-1	-0.877	-0.937	21.663	-0.095	-0.095	0.000	0.000	0.000
133	A	140	GLY	0	-0.038	-0.025	20.504	0.001	0.001	0.000	0.000	0.000
134	A	141	VAL	0	-0.022	-0.012	21.345	-0.010	-0.010	0.000	0.000	0.000
135	A	142	TRP	0	-0.051	-0.025	13.228	0.025	0.025	0.000	0.000	0.000
136	A	143	LYS	1	0.905	0.961	19.771	0.083	0.083	0.000	0.000	0.000
137	A	144	PHE	0	0.034	-0.008	20.051	-0.001	-0.001	0.000	0.000	0.000
138	A	145	ALA	0	0.011	-0.003	18.998	0.001	0.001	0.000	0.000	0.000
139	A	146	GLY	0	0.047	0.024	21.120	0.009	0.009	0.000	0.000	0.000
140	A	147	LEU	0	-0.045	-0.022	20.842	-0.001	-0.001	0.000	0.000	0.000
141	A	148	LYS	1	0.955	0.988	17.796	-0.157	-0.157	0.000	0.000	0.000
142	A	149	PRO	0	-0.038	-0.011	21.578	0.009	0.009	0.000	0.000	0.000
143	A	150	ASP	-1	-0.846	-0.908	22.712	0.112	0.112	0.000	0.000	0.000
144	A	151	ILE	0	0.002	-0.013	24.628	-0.003	-0.003	0.000	0.000	0.000
145	A	152	ARG	1	0.840	0.913	21.982	-0.101	-0.101	0.000	0.000	0.000
146	A	153	TRP	0	0.052	0.015	29.023	-0.001	-0.001	0.000	0.000	0.000
147	A	154	GLY	0	-0.011	0.003	32.449	-0.001	-0.001	0.000	0.000	0.000
148	A	155	GLU	-1	-0.927	-0.959	35.185	0.028	0.028	0.000	0.000	0.000
149	A	156	NME	0	0.039	0.028	37.880	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:ACE)