FMO DATABASE

FMODB ID: N15LQ

Calculation Name: 3WTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BUH6

Base Structure: X-ray

Registration Date: 2023-06-20

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002271.318963
FMO2-HF: Nuclear repulsion	953369.223217
FMO2-HF: Total energy	-48902.095746
FMO2-MP2: Total energy	-49043.642594

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-4.904	-1.854	0.097	-1.167	-1.98	0.006

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.009

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	7	PRO	0	0.011	0.020	3.849	0.320	1.369	-0.012	-0.374	-0.663	0.002
4	A	8	LEU	0	0.027	-0.008	6.052	0.217	0.217	0.000	0.000	0.000	0.000
5	A	9	CYS	0	-0.005	0.010	9.057	-0.055	-0.055	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.033	0.004	11.886	0.036	0.036	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.004	0.023	15.239	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.024	0.007	18.754	0.012	0.012	0.000	0.000	0.000	0.000
9	A	13	PRO	0	0.044	0.018	18.080	0.007	0.007	0.000	0.000	0.000	0.000
10	A	14	GLY	0	-0.041	-0.006	19.093	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.019	0.000	20.800	0.004	0.004	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.859	-0.915	22.583	0.043	0.043	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.011	0.010	21.829	0.005	0.005	0.000	0.000	0.000	0.000
14	A	18	PRO	0	-0.004	0.010	17.705	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.790	0.850	19.876	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.032	0.013	19.110	0.003	0.003	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.023	0.002	12.613	0.004	0.004	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.015	0.007	13.919	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.043	-0.035	9.748	0.027	0.027	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.014	0.008	8.983	-0.054	-0.054	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.909	-0.979	9.010	0.184	0.184	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.020	-0.002	8.339	0.007	0.007	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.745	-0.761	9.102	0.039	0.039	0.000	0.000	0.000	0.000
24	A	36	GLY	0	0.009	-0.019	14.287	0.003	0.003	0.000	0.000	0.000	0.000
25	A	37	PHE	0	0.004	0.013	11.144	0.010	0.010	0.000	0.000	0.000	0.000
26	A	38	ASN	0	0.010	0.035	13.144	0.008	0.008	0.000	0.000	0.000	0.000
27	A	39	LEU	0	0.000	0.007	13.052	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	40	TYR	0	0.003	-0.018	13.654	0.003	0.003	0.000	0.000	0.000	0.000
29	A	41	VAL	0	0.044	0.008	15.408	0.004	0.004	0.000	0.000	0.000	0.000
30	A	42	THR	0	-0.037	-0.036	16.536	0.002	0.002	0.000	0.000	0.000	0.000
31	A	43	ASP	-1	-0.748	-0.871	18.912	0.105	0.105	0.000	0.000	0.000	0.000
32	A	44	ALA	0	-0.086	-0.045	19.328	0.002	0.002	0.000	0.000	0.000	0.000
33	A	45	ALA	0	-0.052	-0.015	20.406	0.001	0.001	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.884	-0.947	23.540	0.066	0.066	0.000	0.000	0.000	0.000
35	A	47	LEU	0	-0.039	0.001	17.192	0.013	0.013	0.000	0.000	0.000	0.000
36	A	48	TRP	0	0.034	0.016	20.298	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	49	SER	0	0.030	-0.003	18.862	0.007	0.007	0.000	0.000	0.000	0.000
38	A	50	THR	0	0.039	0.012	17.955	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	51	CYS	0	-0.107	-0.045	19.844	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	52	PHE	0	-0.005	-0.019	17.062	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	53	THR	0	-0.026	-0.033	20.436	0.002	0.002	0.000	0.000	0.000	0.000
42	A	54	PRO	0	0.007	-0.021	20.330	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.809	-0.875	21.370	0.012	0.012	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.008	-0.010	23.323	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	57	LEU	0	0.035	0.027	16.375	0.000	0.000	0.000	0.000	0.000	0.000
46	A	58	ALA	0	0.016	0.006	20.725	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.013	-0.012	22.449	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	60	LEU	0	-0.028	-0.002	19.745	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.930	0.959	16.095	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	62	ALA	0	-0.010	0.006	21.463	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.909	0.955	24.955	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	64	PHE	0	-0.022	-0.010	22.155	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	65	GLY	0	-0.020	0.010	24.076	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	66	LEU	0	-0.071	-0.043	16.812	0.000	0.000	0.000	0.000	0.000	0.000
55	A	67	SER	0	-0.051	-0.030	20.990	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	68	ALA	0	0.004	0.024	22.079	0.000	0.000	0.000	0.000	0.000	0.000
57	A	69	ALA	0	0.065	0.021	18.008	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-1.008	-0.980	14.894	0.034	0.034	0.000	0.000	0.000	0.000
59	A	71	ASP	-1	-0.819	-0.943	11.803	0.016	0.016	0.000	0.000	0.000	0.000
60	A	72	ILE	0	-0.042	-0.034	13.490	0.008	0.008	0.000	0.000	0.000	0.000
61	A	73	THR	0	-0.074	-0.121	6.781	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	74	PRO	0	-0.026	-0.012	9.695	0.020	0.020	0.000	0.000	0.000	0.000
63	A	75	ARG	1	0.982	0.999	10.609	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.025	0.012	9.877	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.881	0.923	3.050	-1.264	-0.289	0.032	-0.383	-0.624	0.001
66	A	78	ALA	0	0.025	0.022	8.941	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.026	0.010	11.570	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	80	CYS	0	-0.061	-0.024	9.306	0.010	0.010	0.000	0.000	0.000	0.000
69	A	81	GLU	-1	-0.978	-0.984	7.581	-0.291	-0.291	0.000	0.000	0.000	0.000
70	A	82	GLN	0	-0.055	-0.029	10.956	0.011	0.011	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.027	-0.005	13.755	0.028	0.028	0.000	0.000	0.000	0.000
72	A	84	ALA	0	-0.012	0.005	15.502	0.008	0.008	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.023	-0.024	14.285	0.004	0.004	0.000	0.000	0.000	0.000
74	A	86	ALA	0	-0.019	-0.005	17.546	0.002	0.002	0.000	0.000	0.000	0.000
75	A	87	LEU	0	0.011	-0.002	20.137	0.002	0.002	0.000	0.000	0.000	0.000
76	A	88	THR	0	-0.079	-0.022	22.247	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	89	LEU	0	0.048	-0.007	23.854	0.003	0.003	0.000	0.000	0.000	0.000
78	A	90	GLN	0	-0.041	-0.035	26.815	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.856	-0.898	30.104	0.031	0.031	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.908	-0.971	28.762	0.051	0.051	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.814	0.896	26.606	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.036	0.028	23.195	0.001	0.001	0.000	0.000	0.000	0.000
83	A	95	SER	0	0.026	0.024	23.587	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	96	LEU	0	-0.009	-0.002	16.181	0.002	0.002	0.000	0.000	0.000	0.000
85	A	97	THR	0	-0.019	-0.017	20.576	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.024	-0.011	15.036	0.000	0.000	0.000	0.000	0.000	0.000
87	A	99	SER	0	0.012	-0.004	18.361	0.000	0.000	0.000	0.000	0.000	0.000
88	A	100	GLY	0	0.057	0.023	17.946	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	101	GLY	0	-0.041	-0.026	19.069	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	102	PRO	0	-0.003	-0.004	20.101	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	103	SER	0	-0.014	-0.008	22.729	0.000	0.000	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.001	0.012	21.939	0.001	0.001	0.000	0.000	0.000	0.000
93	A	105	LEU	0	-0.041	-0.014	17.956	0.001	0.001	0.000	0.000	0.000	0.000
94	A	106	ALA	0	0.021	0.020	21.062	0.001	0.001	0.000	0.000	0.000	0.000
95	A	107	PHE	0	-0.036	-0.021	17.739	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	108	ASP	-1	-0.884	-0.940	21.834	0.027	0.027	0.000	0.000	0.000	0.000
97	A	109	LEU	0	-0.061	-0.039	18.495	0.001	0.001	0.000	0.000	0.000	0.000
98	A	110	SER	0	-0.009	-0.014	22.987	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	111	LYS	1	0.885	0.971	23.579	-0.053	-0.053	0.000	0.000	0.000	0.000
100	A	112	VAL	0	-0.019	-0.009	20.806	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	113	PRO	0	0.030	0.019	24.230	0.003	0.003	0.000	0.000	0.000	0.000
102	A	114	GLY	0	0.069	0.026	25.331	0.006	0.006	0.000	0.000	0.000	0.000
103	A	115	PRO	0	-0.033	-0.030	25.289	0.008	0.008	0.000	0.000	0.000	0.000
104	A	116	GLU	-1	-0.920	-0.953	21.899	0.076	0.076	0.000	0.000	0.000	0.000
105	A	117	ALA	0	0.015	0.000	20.980	0.011	0.011	0.000	0.000	0.000	0.000
106	A	118	ALA	0	0.021	0.014	20.312	0.019	0.019	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.023	-0.021	19.805	0.020	0.020	0.000	0.000	0.000	0.000
108	A	120	ARG	1	0.960	0.984	15.003	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	121	LEU	0	0.056	0.036	15.793	0.046	0.046	0.000	0.000	0.000	0.000
110	A	122	ARG	1	0.934	0.973	17.087	-0.122	-0.122	0.000	0.000	0.000	0.000
111	A	123	ALA	0	0.006	-0.011	13.903	0.028	0.028	0.000	0.000	0.000	0.000
112	A	124	LEU	0	0.015	0.026	11.459	0.102	0.102	0.000	0.000	0.000	0.000
113	A	125	THR	0	0.009	0.004	12.676	0.098	0.098	0.000	0.000	0.000	0.000
114	A	126	LEU	0	-0.028	-0.022	14.173	0.037	0.037	0.000	0.000	0.000	0.000
115	A	127	GLY	0	-0.005	-0.003	10.563	0.030	0.030	0.000	0.000	0.000	0.000
116	A	128	LEU	0	-0.002	-0.009	9.045	0.314	0.314	0.000	0.000	0.000	0.000
117	A	129	ALA	0	0.029	0.026	10.270	0.039	0.039	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.964	0.984	9.945	-0.553	-0.553	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.887	0.934	3.173	-4.511	-3.641	0.079	-0.392	-0.558	0.003
120	A	132	VAL	0	0.055	0.040	7.766	-0.173	-0.173	0.000	0.000	0.000	0.000
121	A	133	TRP	0	0.044	0.028	9.882	-0.122	-0.122	0.000	0.000	0.000	0.000
122	A	134	SER	0	-0.031	-0.025	7.469	-0.189	-0.189	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.041	-0.040	3.882	-0.404	-0.308	-0.001	-0.013	-0.081	0.000
124	A	136	GLU	-1	-0.880	-0.932	7.904	-0.035	-0.035	0.000	0.000	0.000	0.000
125	A	137	ARG	1	0.904	0.960	11.421	-0.103	-0.103	0.000	0.000	0.000	0.000
126	A	138	ARG	1	0.868	0.925	4.013	1.276	1.336	-0.001	-0.005	-0.054	0.000
127	A	139	LEU	0	0.002	0.009	10.525	-0.039	-0.039	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.017	0.012	11.810	0.010	0.010	0.000	0.000	0.000	0.000
129	A	141	ALA	0	-0.077	-0.022	14.018	0.017	0.017	0.000	0.000	0.000	0.000
130	A	142	ALA	0	-0.016	0.001	13.435	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)