FMO DATABASE

FMODB ID: MVQ2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-977406.4277
FMO2-HF: Nuclear repulsion	930261.870516
FMO2-HF: Total energy	-47144.557184
FMO2-MP2: Total energy	-47279.763987

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.
-7.919	-3.145	2.737	-2.334	-5.176	0.01

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 : 0.007 / q_NPA : -0.021

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	-0.005	-0.012	3.150	-1.298	0.660	0.175	-0.636	-1.497	-0.003
4	A	42	PHE	0	-0.012	-0.017	5.692	0.557	0.557	0.000	0.000	0.000	0.000
5	A	43	GLY	0	0.063	0.041	7.068	0.275	0.275	0.000	0.000	0.000	0.000
6	A	44	LEU	0	-0.014	-0.013	6.206	0.317	0.317	0.000	0.000	0.000	0.000
7	A	45	THR	0	-0.009	0.017	2.127	-0.963	-0.815	1.790	-0.693	-1.244	0.002
8	A	46	ILE	0	0.033	0.016	3.467	0.389	0.483	0.010	0.142	-0.246	0.000
9	A	47	PRO	0	0.004	-0.012	5.324	0.412	0.412	0.000	0.000	0.000	0.000
10	A	48	PHE	0	0.048	0.030	6.848	0.079	0.079	0.000	0.000	0.000	0.000
11	A	49	MET	0	0.028	0.013	6.025	0.049	0.049	0.000	0.000	0.000	0.000
12	A	50	GLN	0	-0.032	-0.026	2.812	-6.700	-4.324	0.765	-1.131	-2.010	0.011
13	A	51	LEU	0	-0.008	0.008	4.591	-0.317	-0.258	-0.001	-0.010	-0.048	0.000
14	A	52	LEU	0	0.009	-0.009	8.284	-0.195	-0.195	0.000	0.000	0.000	0.000
15	A	53	GLY	0	-0.062	-0.007	6.827	-0.094	-0.094	0.000	0.000	0.000	0.000
16	A	54	VAL	0	-0.010	-0.002	6.303	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	55	VAL	0	-0.013	-0.020	5.041	-0.603	-0.530	-0.001	-0.001	-0.071	0.000
18	A	56	PRO	0	-0.038	-0.001	4.531	0.162	0.228	-0.001	-0.005	-0.060	0.000
19	A	57	GLU	-1	-0.878	-0.962	7.318	0.056	0.056	0.000	0.000	0.000	0.000
20	A	58	HIS	0	-0.029	-0.031	10.645	0.046	0.046	0.000	0.000	0.000	0.000
21	A	59	SER	0	-0.040	-0.008	12.477	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	60	GLY	0	0.046	0.028	14.127	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	61	ASN	0	-0.061	-0.042	17.557	0.021	0.021	0.000	0.000	0.000	0.000
24	A	62	GLY	0	0.029	0.026	20.535	0.014	0.014	0.000	0.000	0.000	0.000
25	A	63	THR	0	-0.052	-0.019	18.912	0.015	0.015	0.000	0.000	0.000	0.000
26	A	64	ALA	0	0.004	-0.011	13.655	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	65	ARG	1	0.856	0.939	13.236	0.196	0.196	0.000	0.000	0.000	0.000
28	A	66	THR	0	0.025	0.011	9.338	-0.134	-0.134	0.000	0.000	0.000	0.000
29	A	67	ARG	1	0.917	0.961	9.707	0.110	0.110	0.000	0.000	0.000	0.000
30	A	68	LEU	0	-0.015	-0.024	9.806	-0.054	-0.054	0.000	0.000	0.000	0.000
31	A	69	PRO	0	-0.015	0.008	9.764	0.025	0.025	0.000	0.000	0.000	0.000
32	A	70	ALA	0	0.001	0.010	12.810	0.020	0.020	0.000	0.000	0.000	0.000
33	A	71	ARG	1	0.890	0.945	10.412	-0.358	-0.358	0.000	0.000	0.000	0.000
34	A	72	ALA	0	0.014	-0.002	15.814	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	73	ASP	-1	-0.914	-0.961	14.931	0.293	0.293	0.000	0.000	0.000	0.000
36	A	74	LEU	0	-0.040	-0.022	12.433	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	75	VAL	0	-0.001	0.012	16.801	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	76	ASN	0	-0.015	0.011	20.508	0.011	0.011	0.000	0.000	0.000	0.000
39	A	77	SER	0	0.004	-0.005	23.622	0.004	0.004	0.000	0.000	0.000	0.000
40	A	78	ARG	1	0.874	0.926	26.966	-0.039	-0.039	0.000	0.000	0.000	0.000
41	A	79	GLY	0	0.035	0.016	24.987	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	80	ASP	-1	-0.883	-0.943	23.476	0.040	0.040	0.000	0.000	0.000	0.000
43	A	81	ILE	0	0.028	0.003	17.045	0.011	0.011	0.000	0.000	0.000	0.000
44	A	82	HIS	0	0.042	0.028	19.401	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	83	GLY	0	0.060	0.021	19.188	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	84	GLY	0	0.036	0.012	19.099	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	85	THR	0	-0.011	0.011	14.246	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	86	LEU	0	-0.027	-0.012	14.960	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	87	MET	0	0.017	0.012	16.410	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	88	SER	0	-0.024	-0.022	12.933	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	89	VAL	0	0.040	0.014	10.609	-0.054	-0.054	0.000	0.000	0.000	0.000
52	A	90	LEU	0	-0.006	-0.006	12.741	-0.066	-0.066	0.000	0.000	0.000	0.000
53	A	91	ASP	-1	-0.875	-0.938	14.439	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	92	PHE	0	-0.038	-0.021	7.262	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	93	THR	0	0.000	-0.025	12.097	-0.081	-0.081	0.000	0.000	0.000	0.000
56	A	94	LEU	0	-0.006	0.023	13.285	0.011	0.011	0.000	0.000	0.000	0.000
57	A	95	GLY	0	0.053	0.027	15.319	0.011	0.011	0.000	0.000	0.000	0.000
58	A	96	ALA	0	-0.004	-0.002	11.973	0.002	0.002	0.000	0.000	0.000	0.000
59	A	97	ALA	0	-0.012	0.014	13.954	0.006	0.006	0.000	0.000	0.000	0.000
60	A	98	ILE	0	-0.030	-0.017	17.214	0.033	0.033	0.000	0.000	0.000	0.000
61	A	99	ARG	1	0.833	0.914	10.904	0.610	0.610	0.000	0.000	0.000	0.000
62	A	100	GLY	0	0.089	0.063	14.654	-0.062	-0.062	0.000	0.000	0.000	0.000
63	A	101	ASP	-1	-0.904	-0.940	16.034	-0.177	-0.177	0.000	0.000	0.000	0.000
64	A	102	THR	0	-0.109	-0.077	17.860	0.034	0.034	0.000	0.000	0.000	0.000
65	A	103	PRO	0	-0.005	0.030	13.189	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	104	GLU	-1	-0.844	-0.944	14.473	-0.280	-0.280	0.000	0.000	0.000	0.000
67	A	105	VAL	0	-0.084	-0.021	17.213	0.027	0.027	0.000	0.000	0.000	0.000
68	A	106	GLY	0	0.030	0.013	15.903	-0.038	-0.038	0.000	0.000	0.000	0.000
69	A	107	VAL	0	-0.021	-0.017	15.425	0.023	0.023	0.000	0.000	0.000	0.000
70	A	108	ALA	0	0.005	0.004	16.321	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	109	THR	0	0.013	0.001	17.297	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	110	ILE	0	-0.105	-0.036	19.776	0.013	0.013	0.000	0.000	0.000	0.000
73	A	111	ASP	-1	-0.875	-0.936	23.513	-0.043	-0.043	0.000	0.000	0.000	0.000
74	A	112	MET	0	0.012	0.008	18.282	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	113	ASN	0	-0.062	-0.018	23.262	0.012	0.012	0.000	0.000	0.000	0.000
76	A	114	THR	0	0.018	0.000	21.412	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	115	SER	0	-0.014	0.002	24.383	0.009	0.009	0.000	0.000	0.000	0.000
78	A	116	PHE	0	0.006	-0.021	22.039	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	117	MET	0	-0.069	-0.012	26.122	0.001	0.001	0.000	0.000	0.000	0.000
80	A	118	SER	0	0.024	0.007	26.141	0.005	0.005	0.000	0.000	0.000	0.000
81	A	119	PRO	0	-0.055	-0.023	24.932	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	120	GLY	0	0.079	0.052	21.257	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	121	ARG	1	0.908	0.938	21.250	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	122	GLY	0	0.029	0.025	19.526	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	123	ASP	-1	-0.837	-0.921	14.680	0.045	0.045	0.000	0.000	0.000	0.000
86	A	124	LEU	0	-0.026	0.002	15.311	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	125	VAL	0	-0.001	0.012	14.494	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	126	ILE	0	-0.022	-0.032	12.941	0.015	0.015	0.000	0.000	0.000	0.000
89	A	127	GLU	-1	-0.854	-0.932	14.804	-0.159	-0.159	0.000	0.000	0.000	0.000
90	A	128	THR	0	-0.064	-0.058	16.218	0.023	0.023	0.000	0.000	0.000	0.000
91	A	129	ARG	1	0.883	0.920	18.647	0.094	0.094	0.000	0.000	0.000	0.000
92	A	130	CYS	0	-0.034	-0.009	21.267	0.009	0.009	0.000	0.000	0.000	0.000
93	A	131	LEU	0	-0.030	-0.016	22.739	0.008	0.008	0.000	0.000	0.000	0.000
94	A	132	ARG	1	0.966	0.970	25.909	0.083	0.083	0.000	0.000	0.000	0.000
95	A	133	ARG	1	0.961	0.972	20.283	0.177	0.177	0.000	0.000	0.000	0.000
96	A	134	GLY	0	-0.045	-0.011	26.652	0.008	0.008	0.000	0.000	0.000	0.000
97	A	135	ALA	0	0.025	0.005	26.881	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	136	SER	0	-0.022	-0.010	26.194	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	137	ILE	0	0.042	0.019	25.336	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	138	ALA	0	-0.005	0.008	22.625	0.000	0.000	0.000	0.000	0.000	0.000
101	A	139	PHE	0	0.024	0.018	24.198	0.003	0.003	0.000	0.000	0.000	0.000
102	A	140	CYS	0	-0.024	-0.006	19.590	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	141	GLU	-1	-0.826	-0.895	22.240	-0.066	-0.066	0.000	0.000	0.000	0.000
104	A	142	GLY	0	0.030	0.001	19.821	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	143	GLU	-1	-0.947	-0.977	19.814	-0.054	-0.054	0.000	0.000	0.000	0.000
106	A	144	ILE	0	0.005	0.021	17.291	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	145	ARG	1	0.867	0.934	19.054	0.061	0.061	0.000	0.000	0.000	0.000
108	A	146	ASP	-1	-0.762	-0.887	19.328	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	147	SER	0	-0.012	-0.009	20.830	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	148	ALA	0	-0.083	-0.040	21.761	0.000	0.000	0.000	0.000	0.000	0.000
111	A	149	GLY	0	0.008	0.012	23.550	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	150	GLU	-1	-0.907	-0.951	24.573	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	151	LEU	0	-0.077	-0.042	23.667	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	152	VAL	0	0.010	0.014	20.941	0.006	0.006	0.000	0.000	0.000	0.000
115	A	153	ALA	0	0.014	-0.016	21.353	0.007	0.007	0.000	0.000	0.000	0.000
116	A	154	LYS	1	0.948	0.980	22.218	0.054	0.054	0.000	0.000	0.000	0.000
117	A	155	ALA	0	-0.003	-0.002	20.835	0.009	0.009	0.000	0.000	0.000	0.000
118	A	156	THR	0	-0.010	-0.004	22.862	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	157	ALA	0	0.032	0.013	21.021	0.006	0.006	0.000	0.000	0.000	0.000
120	A	158	THR	0	-0.033	-0.009	22.948	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	159	PHE	0	0.040	0.005	17.113	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	160	LYS	1	0.864	0.928	21.579	0.099	0.099	0.000	0.000	0.000	0.000
123	A	161	ILE	0	-0.013	-0.004	20.349	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	162	ILE	0	-0.086	-0.055	19.003	0.018	0.018	0.000	0.000	0.000	0.000
125	A	163	GLN	0	0.036	0.025	20.608	0.007	0.007	0.000	0.000	0.000	0.000

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