FMO DATABASE

FMODB ID: 39MVL

Calculation Name: 5TDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TDQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H3P7

Base Structure: X-ray

Registration Date: 2023-06-22

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	-1214239.149393
FMO2-HF: Nuclear repulsion	1161639.496424
FMO2-HF: Total energy	-52599.652969
FMO2-MP2: Total energy	-52755.952826

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:367:PRO)

Summations of interaction energy for fragment #1(A:367:PRO)

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.
-3.496	-1.132	-0.024	-0.915	-1.425	0.002

Interaction energy analysis for fragmet #1(A:367:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.023

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	369	ILE	0	0.042	0.019	3.823	-1.799	0.160	-0.026	-0.840	-1.094	0.002
4	A	370	ALA	0	-0.021	0.003	6.536	0.238	0.238	0.000	0.000	0.000	0.000
5	A	371	ALA	0	0.028	0.002	10.081	-0.059	-0.059	0.000	0.000	0.000	0.000
6	A	372	PRO	0	-0.003	0.009	12.832	0.023	0.023	0.000	0.000	0.000	0.000
7	A	373	SER	0	-0.041	-0.015	15.151	0.022	0.022	0.000	0.000	0.000	0.000
8	A	374	MET	0	0.001	-0.020	18.478	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	375	TRP	0	-0.064	-0.015	21.484	0.009	0.009	0.000	0.000	0.000	0.000
10	A	376	THR	0	0.021	0.014	25.322	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	377	ARG	1	0.839	0.897	28.480	0.051	0.051	0.000	0.000	0.000	0.000
12	A	378	PRO	0	0.118	0.051	31.539	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	379	GLN	0	-0.044	-0.011	34.108	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	380	ILE	0	0.047	0.013	33.765	0.000	0.000	0.000	0.000	0.000	0.000
15	A	381	LYS	1	0.929	0.954	35.379	0.031	0.031	0.000	0.000	0.000	0.000
16	A	382	ASP	-1	-0.831	-0.921	37.834	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	383	PHE	0	-0.068	-0.021	28.809	0.001	0.001	0.000	0.000	0.000	0.000
18	A	384	LYS	1	0.862	0.902	34.365	0.046	0.046	0.000	0.000	0.000	0.000
19	A	385	GLU	-1	-0.917	-0.941	35.693	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	386	LYS	1	0.863	0.920	36.095	0.033	0.033	0.000	0.000	0.000	0.000
21	A	387	ILE	0	-0.100	-0.028	30.665	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	388	GLN	0	-0.018	-0.024	34.493	0.000	0.000	0.000	0.000	0.000	0.000
23	A	389	GLN	0	-0.034	0.000	37.345	0.000	0.000	0.000	0.000	0.000	0.000
24	A	390	ASP	-1	-0.887	-0.956	37.347	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	391	ALA	0	-0.115	-0.042	34.429	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	392	ASP	-1	-0.837	-0.904	33.792	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	393	SER	0	-0.050	-0.037	29.220	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	394	VAL	0	-0.050	-0.030	30.212	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	395	ILE	0	-0.015	-0.001	26.971	0.000	0.000	0.000	0.000	0.000	0.000
30	A	396	THR	0	-0.008	-0.007	31.111	0.003	0.003	0.000	0.000	0.000	0.000
31	A	397	VAL	0	-0.008	-0.003	28.037	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	398	GLY	0	0.086	0.027	30.842	0.005	0.005	0.000	0.000	0.000	0.000
33	A	399	ARG	1	0.888	0.963	32.292	0.047	0.047	0.000	0.000	0.000	0.000
34	A	400	GLY	0	0.086	0.045	31.498	0.001	0.001	0.000	0.000	0.000	0.000
35	A	401	GLU	-1	-0.956	-0.960	28.759	-0.079	-0.079	0.000	0.000	0.000	0.000
36	A	402	VAL	0	0.012	-0.006	22.486	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	403	VAL	0	0.011	0.019	24.887	0.000	0.000	0.000	0.000	0.000	0.000
38	A	404	THR	0	-0.055	-0.042	18.956	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	405	VAL	0	0.021	0.017	21.266	0.005	0.005	0.000	0.000	0.000	0.000
40	A	406	ARG	1	0.840	0.927	16.867	0.164	0.164	0.000	0.000	0.000	0.000
41	A	407	VAL	0	-0.002	-0.015	17.642	0.019	0.019	0.000	0.000	0.000	0.000
42	A	408	PRO	0	0.025	0.013	16.182	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	409	THR	0	0.001	-0.005	12.065	0.004	0.004	0.000	0.000	0.000	0.000
44	A	410	HIS	0	-0.178	-0.055	15.473	0.012	0.012	0.000	0.000	0.000	0.000
45	A	411	GLU	-1	-0.862	-0.931	15.539	-0.094	-0.094	0.000	0.000	0.000	0.000
46	A	412	GLU	-1	-0.842	-0.921	16.740	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	413	GLY	0	-0.028	-0.017	18.618	0.009	0.009	0.000	0.000	0.000	0.000
48	A	414	SER	0	0.009	-0.001	15.071	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	415	TYR	0	-0.008	-0.019	14.391	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	416	LEU	0	-0.001	0.027	15.490	0.007	0.007	0.000	0.000	0.000	0.000
51	A	417	PHE	0	-0.011	-0.009	17.442	0.002	0.002	0.000	0.000	0.000	0.000
52	A	418	TRP	0	0.034	0.017	16.690	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	419	GLU	-1	-0.777	-0.830	22.322	-0.051	-0.051	0.000	0.000	0.000	0.000
54	A	420	PHE	0	-0.013	-0.024	23.252	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	421	ALA	0	0.026	0.014	27.238	0.003	0.003	0.000	0.000	0.000	0.000
56	A	422	THR	0	0.007	-0.027	29.749	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	423	ASP	-1	-0.751	-0.801	32.377	-0.043	-0.043	0.000	0.000	0.000	0.000
58	A	424	ASN	0	-0.054	-0.020	35.890	0.000	0.000	0.000	0.000	0.000	0.000
59	A	425	TYR	0	-0.030	-0.036	34.471	0.002	0.002	0.000	0.000	0.000	0.000
60	A	426	ASP	-1	-0.714	-0.802	30.154	-0.068	-0.068	0.000	0.000	0.000	0.000
61	A	427	ILE	0	-0.020	-0.027	26.602	0.001	0.001	0.000	0.000	0.000	0.000
62	A	428	GLY	0	0.002	0.010	24.707	0.000	0.000	0.000	0.000	0.000	0.000
63	A	429	PHE	0	0.010	0.001	19.875	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	430	GLY	0	0.051	0.020	18.263	0.001	0.001	0.000	0.000	0.000	0.000
65	A	431	VAL	0	-0.032	-0.007	13.882	0.010	0.010	0.000	0.000	0.000	0.000
66	A	432	TYR	0	0.033	0.020	11.765	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	433	PHE	0	-0.012	-0.015	7.824	0.046	0.046	0.000	0.000	0.000	0.000
68	A	434	GLU	-1	-0.852	-0.940	8.825	-0.324	-0.324	0.000	0.000	0.000	0.000
69	A	435	TRP	0	0.014	0.001	3.812	-0.251	0.128	0.003	-0.074	-0.308	0.000
70	A	436	THR	0	-0.039	-0.023	9.406	0.045	0.045	0.000	0.000	0.000	0.000
71	A	437	ASP	-1	-0.846	-0.908	13.056	-0.193	-0.193	0.000	0.000	0.000	0.000
72	A	438	SER	0	-0.072	-0.043	15.707	0.021	0.021	0.000	0.000	0.000	0.000
73	A	439	PRO	0	0.008	-0.002	18.026	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	440	ASN	0	-0.004	-0.017	20.562	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	441	THR	0	-0.026	-0.007	21.947	0.000	0.000	0.000	0.000	0.000	0.000
76	A	442	ALA	0	0.023	0.033	21.661	0.008	0.008	0.000	0.000	0.000	0.000
77	A	443	VAL	0	0.021	0.008	22.708	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	444	SER	0	-0.024	-0.011	23.027	0.004	0.004	0.000	0.000	0.000	0.000
79	A	445	VAL	0	0.021	0.018	24.675	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	476	LEU	0	-0.066	-0.049	8.825	0.002	0.002	0.000	0.000	0.000	0.000
81	A	477	ASP	-1	-0.855	-0.919	5.001	-1.441	-1.415	-0.001	-0.001	-0.023	0.000
82	A	478	GLU	-1	-0.931	-0.975	7.700	-0.175	-0.175	0.000	0.000	0.000	0.000
83	A	479	ILE	0	-0.061	-0.011	9.012	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	480	VAL	0	-0.047	-0.036	11.587	0.045	0.045	0.000	0.000	0.000	0.000
85	A	481	PRO	0	0.081	0.053	15.188	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	482	VAL	0	0.009	-0.013	16.728	0.020	0.020	0.000	0.000	0.000	0.000
87	A	483	TYR	0	-0.028	-0.010	19.280	0.006	0.006	0.000	0.000	0.000	0.000
88	A	484	ARG	1	0.856	0.926	22.902	0.067	0.067	0.000	0.000	0.000	0.000
89	A	485	ARG	1	0.846	0.927	20.118	0.122	0.122	0.000	0.000	0.000	0.000
90	A	486	ASP	-1	-0.794	-0.887	27.166	-0.055	-0.055	0.000	0.000	0.000	0.000
91	A	487	CYS	0	-0.070	-0.031	27.926	0.001	0.001	0.000	0.000	0.000	0.000
92	A	488	HIS	0	-0.022	0.006	30.020	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	489	GLU	-1	-0.956	-0.977	33.309	-0.039	-0.039	0.000	0.000	0.000	0.000
94	A	490	GLU	-1	-0.943	-0.974	31.467	-0.039	-0.039	0.000	0.000	0.000	0.000
95	A	491	VAL	0	-0.050	-0.025	28.762	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	492	TYR	0	0.024	0.007	24.843	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	493	ALA	0	-0.006	-0.012	24.400	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	494	GLY	0	0.010	-0.005	20.514	0.000	0.000	0.000	0.000	0.000	0.000
99	A	495	SER	0	-0.035	-0.012	18.621	0.001	0.001	0.000	0.000	0.000	0.000
100	A	496	HIS	0	0.067	0.087	9.783	0.036	0.036	0.000	0.000	0.000	0.000
101	A	497	GLN	0	0.006	0.023	11.569	0.019	0.019	0.000	0.000	0.000	0.000
102	A	498	TYR	0	0.050	0.005	11.022	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	499	PRO	0	-0.041	0.001	5.746	0.043	0.043	0.000	0.000	0.000	0.000
104	A	500	GLY	0	0.020	-0.007	6.236	0.028	0.028	0.000	0.000	0.000	0.000
105	A	501	ARG	1	0.891	0.948	8.018	0.150	0.150	0.000	0.000	0.000	0.000
106	A	502	GLY	0	0.000	-0.015	9.719	-0.060	-0.060	0.000	0.000	0.000	0.000
107	A	503	VAL	0	-0.005	0.018	12.051	0.049	0.049	0.000	0.000	0.000	0.000
108	A	504	TYR	0	-0.057	-0.085	11.948	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	505	LEU	0	-0.057	-0.029	13.799	0.038	0.038	0.000	0.000	0.000	0.000
110	A	506	LEU	0	0.015	0.015	15.957	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	507	LYS	1	0.915	0.955	17.397	0.192	0.192	0.000	0.000	0.000	0.000
112	A	508	PHE	0	0.028	0.017	20.328	0.004	0.004	0.000	0.000	0.000	0.000
113	A	509	ASP	-1	-0.831	-0.884	22.854	-0.113	-0.113	0.000	0.000	0.000	0.000
114	A	510	ASN	0	-0.024	-0.040	24.848	0.007	0.007	0.000	0.000	0.000	0.000
115	A	511	SER	0	-0.018	-0.042	25.922	0.008	0.008	0.000	0.000	0.000	0.000
116	A	512	TYR	0	-0.105	-0.055	27.878	0.004	0.004	0.000	0.000	0.000	0.000
117	A	513	SER	0	-0.094	-0.033	30.160	0.008	0.008	0.000	0.000	0.000	0.000
118	A	514	LEU	0	0.083	0.031	33.057	0.000	0.000	0.000	0.000	0.000	0.000
119	A	515	TRP	0	-0.031	-0.037	36.039	0.001	0.001	0.000	0.000	0.000	0.000
120	A	516	ARG	1	0.897	0.947	35.929	0.044	0.044	0.000	0.000	0.000	0.000
121	A	517	SER	0	0.036	0.027	34.317	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	518	LYS	1	0.798	0.891	31.048	0.069	0.069	0.000	0.000	0.000	0.000
123	A	519	SER	0	0.041	0.027	32.819	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	520	VAL	0	-0.006	-0.006	26.954	0.001	0.001	0.000	0.000	0.000	0.000
125	A	521	TYR	0	-0.057	-0.079	30.376	0.000	0.000	0.000	0.000	0.000	0.000
126	A	522	TYR	0	0.012	-0.009	23.975	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	523	ARG	1	0.960	0.987	26.159	0.059	0.059	0.000	0.000	0.000	0.000
128	A	524	VAL	0	-0.008	0.000	20.786	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	525	TYR	0	-0.103	-0.108	22.535	0.009	0.009	0.000	0.000	0.000	0.000
130	A	526	TYR	0	0.019	0.017	19.631	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:367:PRO)