FMO DATABASE

FMODB ID: 721ZK

Calculation Name: 3DKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DKZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W9W5

Base Structure: X-ray

Registration Date: 2023-09-20

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-977575.042315
FMO2-HF: Nuclear repulsion	930429.761354
FMO2-HF: Total energy	-47145.280961
FMO2-MP2: Total energy	-47280.423806

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:39:THR)

Summations of interaction energy for fragment #1(A:39:THR)

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.
-13.921	-12.095	10.737	-4.98	-7.582	0.015

Interaction energy analysis for fragmet #1(A:39:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.013

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

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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	41	PHE	0	-0.019	-0.018	3.027	-2.529	0.041	0.384	-1.194	-1.759	-0.006
4	A	42	PHE	0	0.001	-0.007	5.633	0.767	0.767	0.000	0.000	0.000	0.000
5	A	43	GLY	0	0.058	0.037	7.473	0.442	0.442	0.000	0.000	0.000	0.000
6	A	44	LEU	0	-0.028	-0.014	6.132	0.489	0.489	0.000	0.000	0.000	0.000
7	A	45	THR	0	0.015	0.023	2.432	-2.706	-1.826	1.653	-0.872	-1.662	-0.006
8	A	46	ILE	0	0.039	0.015	3.774	0.785	0.961	0.007	0.036	-0.219	0.000
9	A	47	PRO	0	0.013	-0.008	5.323	0.092	0.092	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.040	0.028	6.131	0.197	0.197	0.000	0.000	0.000	0.000
11	A	49	MET	0	0.040	0.015	5.938	0.142	0.142	0.000	0.000	0.000	0.000
12	A	50	GLN	0	-0.047	-0.043	1.881	-11.010	-13.001	8.696	-2.934	-3.772	0.027
13	A	51	LEU	0	-0.010	0.009	4.575	0.024	0.078	-0.001	-0.010	-0.043	0.000
14	A	52	LEU	0	0.028	0.018	8.265	-0.050	-0.050	0.000	0.000	0.000	0.000
15	A	53	GLY	0	-0.039	0.001	6.730	0.015	0.015	0.000	0.000	0.000	0.000
16	A	54	VAL	0	-0.017	-0.008	6.369	0.077	0.077	0.000	0.000	0.000	0.000
17	A	55	VAL	0	0.016	-0.007	5.102	-0.971	-0.900	-0.001	-0.001	-0.068	0.000
18	A	56	PRO	0	-0.021	0.002	4.438	0.389	0.455	-0.001	-0.005	-0.059	0.000
19	A	57	GLU	-1	-0.872	-0.962	7.283	-0.352	-0.352	0.000	0.000	0.000	0.000
20	A	58	HIS	0	-0.050	-0.034	10.599	0.106	0.106	0.000	0.000	0.000	0.000
21	A	59	SER	0	-0.030	-0.010	12.309	-0.093	-0.093	0.000	0.000	0.000	0.000
22	A	60	GLY	0	0.045	0.028	14.059	0.010	0.010	0.000	0.000	0.000	0.000
23	A	61	ASN	0	-0.075	-0.042	17.480	0.034	0.034	0.000	0.000	0.000	0.000
24	A	62	GLY	0	0.028	0.021	20.338	0.025	0.025	0.000	0.000	0.000	0.000
25	A	63	THR	0	-0.025	-0.008	18.865	0.016	0.016	0.000	0.000	0.000	0.000
26	A	64	ALA	0	-0.008	-0.010	13.552	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	65	ARG	1	0.852	0.920	13.193	0.556	0.556	0.000	0.000	0.000	0.000
28	A	66	THR	0	0.003	-0.005	8.920	-0.235	-0.235	0.000	0.000	0.000	0.000
29	A	67	ARG	1	0.844	0.925	9.722	0.599	0.599	0.000	0.000	0.000	0.000
30	A	68	LEU	0	-0.002	-0.018	9.850	-0.164	-0.164	0.000	0.000	0.000	0.000
31	A	69	PRO	0	-0.017	0.008	9.917	0.095	0.095	0.000	0.000	0.000	0.000
32	A	70	ALA	0	0.000	0.004	12.876	0.018	0.018	0.000	0.000	0.000	0.000
33	A	71	ARG	1	0.781	0.863	10.416	-0.037	-0.037	0.000	0.000	0.000	0.000
34	A	72	ALA	0	0.020	0.005	15.726	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	73	ASP	-1	-0.849	-0.925	14.552	0.163	0.163	0.000	0.000	0.000	0.000
36	A	74	LEU	0	-0.042	-0.015	12.399	0.000	0.000	0.000	0.000	0.000	0.000
37	A	75	VAL	0	-0.007	0.007	16.691	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	76	ASN	0	-0.044	-0.006	20.397	0.019	0.019	0.000	0.000	0.000	0.000
39	A	77	SER	0	0.021	0.004	23.584	0.008	0.008	0.000	0.000	0.000	0.000
40	A	78	ARG	1	0.871	0.931	26.855	0.051	0.051	0.000	0.000	0.000	0.000
41	A	79	GLY	0	0.037	0.017	24.881	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	80	ASP	-1	-0.822	-0.895	23.448	-0.089	-0.089	0.000	0.000	0.000	0.000
43	A	81	ILE	0	0.048	0.015	17.013	0.013	0.013	0.000	0.000	0.000	0.000
44	A	82	HIS	0	0.029	0.017	19.386	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	83	GLY	0	0.069	0.030	19.273	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	84	GLY	0	0.034	0.012	19.081	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	85	THR	0	-0.016	-0.006	14.354	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	86	LEU	0	-0.013	-0.007	15.034	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	87	MET	0	0.016	0.008	16.465	-0.046	-0.046	0.000	0.000	0.000	0.000
50	A	88	SER	0	-0.019	-0.007	12.874	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	89	VAL	0	0.037	0.017	10.988	-0.108	-0.108	0.000	0.000	0.000	0.000
52	A	90	LEU	0	-0.013	-0.005	12.792	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	91	ASP	-1	-0.869	-0.928	14.585	-0.502	-0.502	0.000	0.000	0.000	0.000
54	A	92	PHE	0	-0.013	-0.012	7.379	-0.096	-0.096	0.000	0.000	0.000	0.000
55	A	93	THR	0	-0.005	-0.020	12.086	-0.101	-0.101	0.000	0.000	0.000	0.000
56	A	94	LEU	0	-0.002	0.023	13.283	0.047	0.047	0.000	0.000	0.000	0.000
57	A	95	GLY	0	0.056	0.028	15.316	0.040	0.040	0.000	0.000	0.000	0.000
58	A	96	ALA	0	-0.006	-0.003	11.943	0.027	0.027	0.000	0.000	0.000	0.000
59	A	97	ALA	0	-0.016	0.012	13.916	0.024	0.024	0.000	0.000	0.000	0.000
60	A	98	ILE	0	-0.025	-0.016	17.168	0.070	0.070	0.000	0.000	0.000	0.000
61	A	99	ARG	1	0.802	0.898	10.998	1.040	1.040	0.000	0.000	0.000	0.000
62	A	100	GLY	0	0.090	0.064	14.799	-0.096	-0.096	0.000	0.000	0.000	0.000
63	A	101	ASP	-1	-0.895	-0.945	15.958	-0.362	-0.362	0.000	0.000	0.000	0.000
64	A	102	THR	0	-0.102	-0.067	18.108	0.062	0.062	0.000	0.000	0.000	0.000
65	A	103	PRO	0	0.008	0.035	13.354	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	104	GLU	-1	-0.836	-0.946	14.551	-0.420	-0.420	0.000	0.000	0.000	0.000
67	A	105	VAL	0	-0.078	-0.022	17.304	0.043	0.043	0.000	0.000	0.000	0.000
68	A	106	GLY	0	0.029	0.017	16.022	-0.068	-0.068	0.000	0.000	0.000	0.000
69	A	107	VAL	0	-0.016	-0.014	15.624	0.047	0.047	0.000	0.000	0.000	0.000
70	A	108	ALA	0	-0.005	-0.001	16.608	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	109	THR	0	0.000	-0.011	17.273	0.013	0.013	0.000	0.000	0.000	0.000
72	A	110	ILE	0	-0.096	-0.036	19.778	0.026	0.026	0.000	0.000	0.000	0.000
73	A	111	ASP	-1	-0.858	-0.913	23.516	-0.176	-0.176	0.000	0.000	0.000	0.000
74	A	112	MET	0	-0.003	0.000	18.362	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	113	ASN	0	-0.056	-0.017	23.280	0.020	0.020	0.000	0.000	0.000	0.000
76	A	114	THR	0	0.018	-0.002	21.741	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	115	SER	0	-0.022	0.002	24.427	0.024	0.024	0.000	0.000	0.000	0.000
78	A	116	PHE	0	0.004	-0.024	21.899	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	117	MET	0	-0.061	-0.008	26.174	0.008	0.008	0.000	0.000	0.000	0.000
80	A	118	SER	0	0.019	-0.005	26.079	0.019	0.019	0.000	0.000	0.000	0.000
81	A	119	PRO	0	-0.050	-0.018	24.994	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	120	GLY	0	0.070	0.046	21.326	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	121	ARG	1	0.828	0.881	21.354	0.106	0.106	0.000	0.000	0.000	0.000
84	A	122	GLY	0	0.033	0.023	19.597	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	123	ASP	-1	-0.802	-0.899	14.955	-0.286	-0.286	0.000	0.000	0.000	0.000
86	A	124	LEU	0	-0.035	-0.002	15.364	0.023	0.023	0.000	0.000	0.000	0.000
87	A	125	VAL	0	-0.002	0.010	14.531	-0.076	-0.076	0.000	0.000	0.000	0.000
88	A	126	ILE	0	-0.026	-0.029	12.717	0.046	0.046	0.000	0.000	0.000	0.000
89	A	127	GLU	-1	-0.837	-0.916	14.800	-0.452	-0.452	0.000	0.000	0.000	0.000
90	A	128	THR	0	-0.064	-0.054	16.240	0.052	0.052	0.000	0.000	0.000	0.000
91	A	129	ARG	1	0.836	0.893	18.631	0.289	0.289	0.000	0.000	0.000	0.000
92	A	130	CYS	0	-0.034	-0.009	21.237	0.017	0.017	0.000	0.000	0.000	0.000
93	A	131	LEU	0	-0.025	-0.015	22.704	0.019	0.019	0.000	0.000	0.000	0.000
94	A	132	ARG	1	0.949	0.960	25.878	0.195	0.195	0.000	0.000	0.000	0.000
95	A	133	ARG	1	0.947	0.975	20.702	0.337	0.337	0.000	0.000	0.000	0.000
96	A	134	GLY	0	-0.032	-0.007	26.608	0.018	0.018	0.000	0.000	0.000	0.000
97	A	135	ALA	0	0.017	-0.001	26.983	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	136	SER	0	-0.029	-0.013	26.362	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	137	ILE	0	0.034	0.010	25.544	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	138	ALA	0	-0.003	0.011	22.622	0.006	0.006	0.000	0.000	0.000	0.000
101	A	139	PHE	0	0.030	0.019	24.195	0.002	0.002	0.000	0.000	0.000	0.000
102	A	140	CYS	0	-0.011	0.007	19.572	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	141	GLU	-1	-0.799	-0.887	22.221	-0.218	-0.218	0.000	0.000	0.000	0.000
104	A	142	GLY	0	0.049	0.011	19.829	-0.035	-0.035	0.000	0.000	0.000	0.000
105	A	143	GLU	-1	-0.873	-0.912	19.827	-0.218	-0.218	0.000	0.000	0.000	0.000
106	A	144	ILE	0	0.014	0.014	16.983	-0.040	-0.040	0.000	0.000	0.000	0.000
107	A	145	ARG	1	0.838	0.901	19.080	0.249	0.249	0.000	0.000	0.000	0.000
108	A	146	ASP	-1	-0.777	-0.897	19.362	-0.197	-0.197	0.000	0.000	0.000	0.000
109	A	147	SER	0	0.004	0.002	20.831	0.000	0.000	0.000	0.000	0.000	0.000
110	A	148	ALA	0	-0.076	-0.032	21.794	0.007	0.007	0.000	0.000	0.000	0.000
111	A	149	GLY	0	0.001	0.008	23.569	0.008	0.008	0.000	0.000	0.000	0.000
112	A	150	GLU	-1	-0.886	-0.937	24.594	-0.140	-0.140	0.000	0.000	0.000	0.000
113	A	151	LEU	0	-0.053	-0.029	23.714	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	152	VAL	0	-0.007	0.013	20.883	0.015	0.015	0.000	0.000	0.000	0.000
115	A	153	ALA	0	0.014	-0.013	21.327	0.018	0.018	0.000	0.000	0.000	0.000
116	A	154	LYS	1	0.875	0.942	22.251	0.212	0.212	0.000	0.000	0.000	0.000
117	A	155	ALA	0	-0.007	-0.003	20.859	0.017	0.017	0.000	0.000	0.000	0.000
118	A	156	THR	0	-0.004	-0.003	22.876	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	157	ALA	0	0.022	0.008	21.004	0.002	0.002	0.000	0.000	0.000	0.000
120	A	158	THR	0	-0.039	-0.025	22.940	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	159	PHE	0	0.037	0.007	17.067	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	160	LYS	1	0.870	0.927	21.659	0.236	0.236	0.000	0.000	0.000	0.000
123	A	161	ILE	0	0.008	-0.002	20.318	-0.032	-0.032	0.000	0.000	0.000	0.000
124	A	162	ILE	0	-0.101	-0.060	18.962	0.038	0.038	0.000	0.000	0.000	0.000
125	A	163	GLN	0	0.024	0.024	20.316	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:THR)