FMO DATABASE

FMODB ID: 3QYML

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	OptAll
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	-1003973.260703
FMO2-HF: Nuclear repulsion	955070.397793
FMO2-HF: Total energy	-48902.86291
FMO2-MP2: Total energy	-49044.450361

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.
-13.418	-14.166	7.155	-2.759	-3.648	0.028

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 : 0.025 / q_NPA : 0.005

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	0.024	0.035	3.909	1.307	2.345	-0.007	-0.402	-0.628	0.001
4	A	8	LEU	0	0.021	-0.007	6.250	0.175	0.175	0.000	0.000	0.000	0.000
5	A	9	CYS	0	-0.014	0.006	8.994	-0.072	-0.072	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.022	0.005	11.785	0.049	0.049	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.006	0.019	14.787	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.037	0.007	18.522	0.013	0.013	0.000	0.000	0.000	0.000
9	A	13	PRO	0	0.022	0.023	17.406	0.012	0.012	0.000	0.000	0.000	0.000
10	A	14	GLY	0	-0.018	-0.015	18.360	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	15	PRO	0	-0.015	-0.014	19.790	0.009	0.009	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.832	-0.899	21.907	0.069	0.069	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.009	0.008	21.094	0.008	0.008	0.000	0.000	0.000	0.000
14	A	18	PRO	0	-0.010	0.004	16.846	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.787	0.856	19.208	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.025	0.018	18.733	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.037	-0.017	12.268	0.014	0.014	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.004	0.009	13.607	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.066	-0.066	9.610	0.079	0.079	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.019	0.008	9.024	-0.091	-0.091	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.816	-0.892	9.170	0.160	0.160	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.003	-0.022	8.573	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.707	-0.780	9.326	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	36	GLY	0	0.019	0.008	13.968	0.002	0.002	0.000	0.000	0.000	0.000
25	A	37	PHE	0	-0.023	-0.025	11.250	0.017	0.017	0.000	0.000	0.000	0.000
26	A	38	ASN	0	0.043	0.045	13.349	0.017	0.017	0.000	0.000	0.000	0.000
27	A	39	LEU	0	0.014	0.021	13.244	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	40	TYR	0	0.008	-0.008	13.734	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	41	VAL	0	0.021	-0.001	15.074	0.022	0.022	0.000	0.000	0.000	0.000
30	A	42	THR	0	-0.028	-0.037	16.195	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	43	ASP	-1	-0.746	-0.872	18.243	0.153	0.153	0.000	0.000	0.000	0.000
32	A	44	ALA	0	-0.082	-0.032	18.666	0.004	0.004	0.000	0.000	0.000	0.000
33	A	45	ALA	0	-0.052	-0.017	20.078	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.849	-0.920	23.224	0.077	0.077	0.000	0.000	0.000	0.000
35	A	47	LEU	0	-0.040	-0.010	17.067	0.022	0.022	0.000	0.000	0.000	0.000
36	A	48	TRP	0	0.018	0.016	20.129	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	49	SER	0	0.000	-0.021	17.803	0.010	0.010	0.000	0.000	0.000	0.000
38	A	50	THR	0	0.013	0.001	18.095	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	51	CYS	0	-0.108	-0.044	20.049	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	52	PHE	0	0.017	0.003	17.464	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	53	THR	0	0.006	0.008	20.564	0.001	0.001	0.000	0.000	0.000	0.000
42	A	54	PRO	0	0.010	-0.016	20.511	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.797	-0.868	21.542	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.001	-0.027	23.844	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	57	LEU	0	-0.001	0.007	16.700	0.000	0.000	0.000	0.000	0.000	0.000
46	A	58	ALA	0	0.010	0.006	21.069	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	59	ALA	0	-0.001	-0.005	22.835	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	60	LEU	0	-0.044	-0.011	19.879	0.000	0.000	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.827	0.888	15.154	0.051	0.051	0.000	0.000	0.000	0.000
50	A	62	ALA	0	-0.017	-0.002	21.630	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.904	0.952	25.296	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	64	PHE	0	-0.022	-0.006	22.042	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	GLY	0	-0.013	-0.001	23.619	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	66	LEU	0	-0.071	-0.033	17.113	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	67	SER	0	-0.044	-0.018	21.582	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	68	ALA	0	-0.019	0.005	22.219	0.001	0.001	0.000	0.000	0.000	0.000
57	A	69	ALA	0	-0.001	0.011	17.772	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.887	-0.950	15.414	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	71	ASP	-1	-0.862	-0.955	12.404	-0.071	-0.071	0.000	0.000	0.000	0.000
60	A	72	ILE	0	-0.013	-0.022	13.848	0.007	0.007	0.000	0.000	0.000	0.000
61	A	73	THR	0	-0.058	-0.065	7.230	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	74	PRO	0	-0.002	-0.002	10.064	0.003	0.003	0.000	0.000	0.000	0.000
63	A	75	ARG	1	0.969	0.988	11.209	0.014	0.014	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.029	0.005	9.939	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.833	0.910	3.257	0.193	0.706	0.008	-0.174	-0.347	0.000
66	A	78	ALA	0	0.043	0.027	9.304	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.019	0.023	11.983	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	80	CYS	0	-0.042	-0.025	9.701	0.029	0.029	0.000	0.000	0.000	0.000
69	A	81	GLU	-1	-0.894	-0.947	6.698	-0.576	-0.576	0.000	0.000	0.000	0.000
70	A	82	GLN	0	-0.081	-0.048	10.848	0.007	0.007	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.026	-0.013	13.722	0.041	0.041	0.000	0.000	0.000	0.000
72	A	84	ALA	0	-0.009	0.021	15.500	0.015	0.015	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.042	-0.039	14.445	0.000	0.000	0.000	0.000	0.000	0.000
74	A	86	ALA	0	-0.002	0.005	17.769	0.006	0.006	0.000	0.000	0.000	0.000
75	A	87	LEU	0	-0.003	-0.008	19.735	0.002	0.002	0.000	0.000	0.000	0.000
76	A	88	THR	0	-0.042	-0.010	22.244	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	89	LEU	0	0.014	-0.005	24.404	0.003	0.003	0.000	0.000	0.000	0.000
78	A	90	GLN	0	-0.051	-0.034	26.811	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.859	-0.915	30.353	0.037	0.037	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.833	-0.919	28.377	0.066	0.066	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.817	0.911	26.656	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.048	0.023	23.525	0.003	0.003	0.000	0.000	0.000	0.000
83	A	95	SER	0	-0.020	-0.009	23.551	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	96	LEU	0	0.003	0.008	16.093	0.005	0.005	0.000	0.000	0.000	0.000
85	A	97	THR	0	-0.006	-0.017	20.604	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.010	0.006	15.319	0.002	0.002	0.000	0.000	0.000	0.000
87	A	99	SER	0	0.011	-0.008	18.289	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	100	GLY	0	0.045	0.018	17.875	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	101	GLY	0	-0.023	-0.001	19.410	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	102	PRO	0	0.006	-0.006	20.160	0.003	0.003	0.000	0.000	0.000	0.000
91	A	103	SER	0	-0.025	-0.019	22.850	0.004	0.004	0.000	0.000	0.000	0.000
92	A	104	ALA	0	-0.007	0.005	21.739	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	105	LEU	0	-0.046	-0.014	17.968	0.000	0.000	0.000	0.000	0.000	0.000
94	A	106	ALA	0	0.011	0.013	20.768	0.004	0.004	0.000	0.000	0.000	0.000
95	A	107	PHE	0	-0.013	-0.016	17.775	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	108	ASP	-1	-0.887	-0.945	22.081	0.025	0.025	0.000	0.000	0.000	0.000
97	A	109	LEU	0	-0.041	-0.034	18.718	0.001	0.001	0.000	0.000	0.000	0.000
98	A	110	SER	0	0.011	-0.001	23.151	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	111	LYS	1	0.789	0.908	23.482	-0.067	-0.067	0.000	0.000	0.000	0.000
100	A	112	VAL	0	-0.012	-0.006	20.337	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	113	PRO	0	0.023	0.008	23.758	0.006	0.006	0.000	0.000	0.000	0.000
102	A	114	GLY	0	0.069	0.032	24.941	0.006	0.006	0.000	0.000	0.000	0.000
103	A	115	PRO	0	-0.028	-0.029	24.763	0.010	0.010	0.000	0.000	0.000	0.000
104	A	116	GLU	-1	-0.831	-0.898	20.550	0.088	0.088	0.000	0.000	0.000	0.000
105	A	117	ALA	0	0.015	0.004	20.523	0.013	0.013	0.000	0.000	0.000	0.000
106	A	118	ALA	0	0.033	0.018	19.943	0.024	0.024	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.031	-0.027	19.735	0.024	0.024	0.000	0.000	0.000	0.000
108	A	120	ARG	1	0.825	0.909	15.481	-0.084	-0.084	0.000	0.000	0.000	0.000
109	A	121	LEU	0	0.053	0.033	15.455	0.060	0.060	0.000	0.000	0.000	0.000
110	A	122	ARG	1	0.945	0.986	16.634	-0.140	-0.140	0.000	0.000	0.000	0.000
111	A	123	ALA	0	-0.002	-0.010	13.725	0.039	0.039	0.000	0.000	0.000	0.000
112	A	124	LEU	0	0.018	0.018	10.737	0.120	0.120	0.000	0.000	0.000	0.000
113	A	125	THR	0	-0.003	-0.010	11.938	0.150	0.150	0.000	0.000	0.000	0.000
114	A	126	LEU	0	-0.023	-0.016	13.606	0.054	0.054	0.000	0.000	0.000	0.000
115	A	127	GLY	0	-0.010	-0.006	9.823	0.040	0.040	0.000	0.000	0.000	0.000
116	A	128	LEU	0	-0.004	-0.007	8.378	0.429	0.429	0.000	0.000	0.000	0.000
117	A	129	ALA	0	0.038	0.026	9.661	0.092	0.092	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.952	0.974	10.166	-0.554	-0.554	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.830	0.895	1.917	-14.159	-16.576	7.155	-2.167	-2.571	0.027
120	A	132	VAL	0	0.053	0.034	7.287	-0.133	-0.133	0.000	0.000	0.000	0.000
121	A	133	TRP	0	0.053	0.031	9.407	-0.160	-0.160	0.000	0.000	0.000	0.000
122	A	134	SER	0	-0.037	-0.025	7.546	-0.134	-0.134	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.027	-0.003	3.899	-0.387	-0.269	-0.001	-0.016	-0.102	0.000
124	A	136	GLU	-1	-0.869	-0.935	7.881	0.066	0.066	0.000	0.000	0.000	0.000
125	A	137	ARG	1	0.911	0.956	11.607	-0.182	-0.182	0.000	0.000	0.000	0.000
126	A	138	ARG	1	0.850	0.910	4.959	-0.043	-0.043	0.000	0.000	0.000	0.000
127	A	139	LEU	0	0.014	0.014	10.721	-0.052	-0.052	0.000	0.000	0.000	0.000
128	A	140	ALA	0	-0.011	-0.010	12.198	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	141	ALA	0	-0.059	-0.020	14.356	0.013	0.013	0.000	0.000	0.000	0.000
130	A	142	ALA	0	-0.024	0.003	13.306	-0.017	-0.017	0.000	0.000	0.000	0.000

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