FMO DATABASE

FMODB ID: J3JV9

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:

Apendix: None

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002917.006122
FMO2-HF: Nuclear repulsion	954014.521968
FMO2-HF: Total energy	-48902.484154
FMO2-MP2: Total energy	-49044.061864

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.
-11.65	-8.604	2.097	-1.974	-3.17	0.018

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 : 0.018 / q_NPA : -0.004

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	0.022	0.033	3.849	0.785	1.950	-0.012	-0.431	-0.722	0.001
4	A	8	LEU	0	0.022	-0.008	6.259	0.172	0.172	0.000	0.000	0.000	0.000
5	A	9	CYS	0	-0.012	0.008	8.951	-0.094	-0.094	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.026	0.005	11.681	0.047	0.047	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.001	0.027	14.751	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.025	0.008	18.379	0.014	0.014	0.000	0.000	0.000	0.000
9	A	13	PRO	0	0.044	0.017	17.662	0.010	0.010	0.000	0.000	0.000	0.000
10	A	14	GLY	0	-0.044	-0.009	18.654	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.016	-0.001	20.052	0.006	0.006	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.853	-0.912	21.882	0.064	0.064	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.014	0.013	21.130	0.007	0.007	0.000	0.000	0.000	0.000
14	A	18	PRO	0	-0.013	0.003	17.055	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.788	0.846	19.222	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.038	0.017	18.619	0.003	0.003	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.032	-0.004	12.184	0.011	0.011	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.008	0.009	13.719	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.071	-0.056	9.722	0.073	0.073	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.010	0.015	8.912	-0.081	-0.081	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.841	-0.927	9.018	0.252	0.252	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.029	-0.001	8.300	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.712	-0.779	9.059	0.021	0.021	0.000	0.000	0.000	0.000
24	A	36	GLY	0	0.026	0.010	14.466	0.001	0.001	0.000	0.000	0.000	0.000
25	A	37	PHE	0	-0.036	-0.025	10.726	0.015	0.015	0.000	0.000	0.000	0.000
26	A	38	ASN	0	0.029	0.039	13.131	0.005	0.005	0.000	0.000	0.000	0.000
27	A	39	LEU	0	0.001	0.000	13.079	0.007	0.007	0.000	0.000	0.000	0.000
28	A	40	TYR	0	0.001	-0.017	13.700	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	41	VAL	0	0.039	0.005	15.408	0.014	0.014	0.000	0.000	0.000	0.000
30	A	42	THR	0	-0.038	-0.039	16.269	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	43	ASP	-1	-0.753	-0.873	18.473	0.147	0.147	0.000	0.000	0.000	0.000
32	A	44	ALA	0	-0.091	-0.045	18.747	0.000	0.000	0.000	0.000	0.000	0.000
33	A	45	ALA	0	-0.048	-0.011	20.075	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.838	-0.922	23.307	0.085	0.085	0.000	0.000	0.000	0.000
35	A	47	LEU	0	-0.037	-0.001	17.142	0.019	0.019	0.000	0.000	0.000	0.000
36	A	48	TRP	0	0.027	0.015	20.315	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	49	SER	0	0.022	-0.006	17.889	0.012	0.012	0.000	0.000	0.000	0.000
38	A	50	THR	0	0.021	0.010	17.868	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	51	CYS	0	-0.106	-0.040	19.807	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	52	PHE	0	0.023	0.000	17.116	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	53	THR	0	-0.016	-0.018	20.415	0.002	0.002	0.000	0.000	0.000	0.000
42	A	54	PRO	0	0.019	-0.017	20.311	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.813	-0.875	21.348	0.011	0.011	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.021	-0.029	23.511	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	57	LEU	0	0.007	0.014	16.291	0.001	0.001	0.000	0.000	0.000	0.000
46	A	58	ALA	0	0.017	0.008	20.694	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.013	-0.011	22.417	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	60	LEU	0	-0.031	-0.006	19.616	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.856	0.895	14.879	0.009	0.009	0.000	0.000	0.000	0.000
50	A	62	ALA	0	-0.006	0.007	21.424	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.904	0.958	24.917	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	64	PHE	0	-0.008	-0.011	21.891	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	GLY	0	-0.022	0.010	24.034	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	66	LEU	0	-0.089	-0.048	16.739	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	67	SER	0	-0.040	-0.025	20.953	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	68	ALA	0	-0.009	0.017	22.030	0.000	0.000	0.000	0.000	0.000	0.000
57	A	69	ALA	0	0.049	0.024	17.686	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.962	-0.968	14.855	0.000	0.000	0.000	0.000	0.000	0.000
59	A	71	ASP	-1	-0.830	-0.936	11.827	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	72	ILE	0	-0.030	-0.027	13.459	0.009	0.009	0.000	0.000	0.000	0.000
61	A	73	THR	0	-0.049	-0.067	6.760	0.000	0.000	0.000	0.000	0.000	0.000
62	A	74	PRO	0	-0.014	-0.007	9.648	0.031	0.031	0.000	0.000	0.000	0.000
63	A	75	ARG	1	0.990	0.997	10.565	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.029	0.016	9.880	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.880	0.932	3.185	-1.552	-0.521	0.056	-0.422	-0.666	0.001
66	A	78	ALA	0	0.021	0.021	8.978	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.023	0.007	11.573	-0.022	-0.022	0.000	0.000	0.000	0.000
68	A	80	CYS	0	-0.055	-0.024	9.413	0.024	0.024	0.000	0.000	0.000	0.000
69	A	81	GLU	-1	-0.954	-0.980	7.171	-0.400	-0.400	0.000	0.000	0.000	0.000
70	A	82	GLN	0	-0.062	-0.033	11.082	0.010	0.010	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.028	-0.008	13.909	0.034	0.034	0.000	0.000	0.000	0.000
72	A	84	ALA	0	-0.015	0.004	15.649	0.006	0.006	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.020	-0.022	14.434	0.004	0.004	0.000	0.000	0.000	0.000
74	A	86	ALA	0	-0.015	-0.002	17.727	0.002	0.002	0.000	0.000	0.000	0.000
75	A	87	LEU	0	0.016	0.001	19.858	0.004	0.004	0.000	0.000	0.000	0.000
76	A	88	THR	0	-0.054	-0.009	22.429	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	89	LEU	0	0.029	-0.003	24.340	0.004	0.004	0.000	0.000	0.000	0.000
78	A	90	GLN	0	-0.050	-0.041	26.743	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.858	-0.902	30.104	0.043	0.043	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.857	-0.943	28.705	0.072	0.072	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.820	0.903	26.581	-0.051	-0.051	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.040	0.030	23.415	0.002	0.002	0.000	0.000	0.000	0.000
83	A	95	SER	0	0.000	0.002	23.554	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	96	LEU	0	0.000	0.004	16.124	0.005	0.005	0.000	0.000	0.000	0.000
85	A	97	THR	0	-0.017	-0.019	20.737	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.024	-0.013	15.180	0.003	0.003	0.000	0.000	0.000	0.000
87	A	99	SER	0	0.015	0.000	18.457	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	100	GLY	0	0.051	0.019	18.003	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	101	GLY	0	-0.043	-0.012	19.063	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	102	PRO	0	0.010	-0.002	20.062	0.000	0.000	0.000	0.000	0.000	0.000
91	A	103	SER	0	-0.033	-0.019	22.695	0.001	0.001	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.003	0.011	21.977	0.001	0.001	0.000	0.000	0.000	0.000
93	A	105	LEU	0	-0.043	-0.011	17.840	0.000	0.000	0.000	0.000	0.000	0.000
94	A	106	ALA	0	0.008	0.014	21.149	0.004	0.004	0.000	0.000	0.000	0.000
95	A	107	PHE	0	-0.029	-0.020	17.522	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	108	ASP	-1	-0.890	-0.943	21.796	0.041	0.041	0.000	0.000	0.000	0.000
97	A	109	LEU	0	-0.044	-0.037	18.478	0.002	0.002	0.000	0.000	0.000	0.000
98	A	110	SER	0	-0.016	-0.021	22.960	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	111	LYS	1	0.814	0.930	23.579	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	112	VAL	0	-0.023	-0.012	20.800	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	113	PRO	0	0.024	0.014	24.229	0.003	0.003	0.000	0.000	0.000	0.000
102	A	114	GLY	0	0.071	0.030	25.328	0.007	0.007	0.000	0.000	0.000	0.000
103	A	115	PRO	0	-0.033	-0.033	25.285	0.010	0.010	0.000	0.000	0.000	0.000
104	A	116	GLU	-1	-0.879	-0.931	20.979	0.109	0.109	0.000	0.000	0.000	0.000
105	A	117	ALA	0	0.035	0.011	20.980	0.013	0.013	0.000	0.000	0.000	0.000
106	A	118	ALA	0	0.021	0.014	20.308	0.023	0.023	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.021	-0.022	19.917	0.022	0.022	0.000	0.000	0.000	0.000
108	A	120	ARG	1	0.877	0.935	15.268	-0.119	-0.119	0.000	0.000	0.000	0.000
109	A	121	LEU	0	0.053	0.033	15.787	0.057	0.057	0.000	0.000	0.000	0.000
110	A	122	ARG	1	0.942	0.982	17.077	-0.142	-0.142	0.000	0.000	0.000	0.000
111	A	123	ALA	0	-0.002	-0.014	13.966	0.031	0.031	0.000	0.000	0.000	0.000
112	A	124	LEU	0	0.012	0.024	11.387	0.115	0.115	0.000	0.000	0.000	0.000
113	A	125	THR	0	0.000	-0.008	12.600	0.113	0.113	0.000	0.000	0.000	0.000
114	A	126	LEU	0	-0.025	-0.019	14.123	0.040	0.040	0.000	0.000	0.000	0.000
115	A	127	GLY	0	-0.006	-0.005	10.553	0.024	0.024	0.000	0.000	0.000	0.000
116	A	128	LEU	0	0.002	-0.008	8.700	0.340	0.340	0.000	0.000	0.000	0.000
117	A	129	ALA	0	0.028	0.027	10.243	0.044	0.044	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.962	0.980	10.798	-0.541	-0.541	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.853	0.917	2.227	-10.719	-9.990	2.055	-1.112	-1.672	0.016
120	A	132	VAL	0	0.056	0.039	7.958	-0.139	-0.139	0.000	0.000	0.000	0.000
121	A	133	TRP	0	0.041	0.026	9.984	-0.126	-0.126	0.000	0.000	0.000	0.000
122	A	134	SER	0	-0.049	-0.029	8.179	-0.175	-0.175	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.029	-0.036	4.126	-0.311	-0.227	-0.001	-0.007	-0.076	0.000
124	A	136	GLU	-1	-0.887	-0.931	8.244	0.012	0.012	0.000	0.000	0.000	0.000
125	A	137	ARG	1	0.909	0.963	11.838	-0.153	-0.153	0.000	0.000	0.000	0.000
126	A	138	ARG	1	0.890	0.930	4.581	0.482	0.519	-0.001	-0.002	-0.034	0.000
127	A	139	LEU	0	-0.001	0.008	10.616	-0.050	-0.050	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.014	0.009	12.080	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	141	ALA	0	-0.078	-0.024	14.460	0.009	0.009	0.000	0.000	0.000	0.000
130	A	142	ALA	0	-0.012	0.004	13.721	-0.028	-0.028	0.000	0.000	0.000	0.000

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