FMO DATABASE

FMODB ID: VQKJ1

Calculation Name: 5D50-D-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5D50

Chain ID: D

ChEMBL ID:
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UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-636074.279425
FMO2-HF: Nuclear repulsion	596296.074185
FMO2-HF: Total energy	-39778.205239
FMO2-MP2: Total energy	-39893.301115

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(D:67:LEU)

Summations of interaction energy for fragment #1(D:67:LEU)

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.
-7.518	-3.744	1.984	-2.041	-3.717	-0.015

Interaction energy analysis for fragmet #1(D:67:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.076 / q_NPA : -0.054

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	D	69	VAL	0	0.026	0.000	3.826	-1.686	0.175	-0.021	-0.816	-1.024	-0.001
4	D	70	ASP	-1	-0.897	-0.949	4.477	-2.408	-2.302	-0.001	-0.010	-0.095	0.000
5	D	71	HIS	0	-0.080	-0.053	2.538	-2.190	-0.383	2.006	-1.215	-2.598	-0.014
6	D	72	GLU	-1	-0.888	-0.928	6.525	-0.529	-0.529	0.000	0.000	0.000	0.000
7	D	73	LEU	0	-0.061	-0.043	10.012	0.123	0.123	0.000	0.000	0.000	0.000
8	D	74	ASP	-1	-0.970	-0.973	7.837	-0.572	-0.572	0.000	0.000	0.000	0.000
9	D	75	ALA	0	-0.016	0.003	9.961	0.052	0.052	0.000	0.000	0.000	0.000
10	D	76	VAL	0	-0.078	-0.037	7.929	-0.123	-0.123	0.000	0.000	0.000	0.000
11	D	90	TRP	0	0.007	-0.015	22.846	0.009	0.009	0.000	0.000	0.000	0.000
12	D	91	THR	0	-0.027	-0.034	24.584	0.008	0.008	0.000	0.000	0.000	0.000
13	D	92	VAL	0	0.085	0.039	27.225	-0.009	-0.009	0.000	0.000	0.000	0.000
14	D	93	GLU	-1	-0.819	-0.900	29.463	-0.118	-0.118	0.000	0.000	0.000	0.000
15	D	94	LYS	1	0.891	0.949	23.707	0.154	0.154	0.000	0.000	0.000	0.000
16	D	95	GLN	0	0.012	0.029	23.818	-0.015	-0.015	0.000	0.000	0.000	0.000
17	D	96	ALA	0	0.024	0.021	26.211	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	97	ALA	0	-0.007	0.002	25.660	0.001	0.001	0.000	0.000	0.000	0.000
19	D	98	ALA	0	0.017	0.015	22.305	-0.004	-0.004	0.000	0.000	0.000	0.000
20	D	99	THR	0	0.013	-0.012	23.986	-0.011	-0.011	0.000	0.000	0.000	0.000
21	D	100	LEU	0	0.008	0.006	26.308	0.005	0.005	0.000	0.000	0.000	0.000
22	D	101	ASN	0	-0.067	-0.051	23.832	0.007	0.007	0.000	0.000	0.000	0.000
23	D	102	ALA	0	-0.025	0.002	23.334	-0.008	-0.008	0.000	0.000	0.000	0.000
24	D	103	TRP	0	-0.091	-0.041	24.616	0.006	0.006	0.000	0.000	0.000	0.000
25	D	104	MET	0	-0.008	0.005	25.548	0.016	0.016	0.000	0.000	0.000	0.000
26	D	120	ALA	0	-0.030	-0.005	41.919	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	121	GLY	0	0.077	0.009	39.328	-0.001	-0.001	0.000	0.000	0.000	0.000
28	D	122	ILE	0	-0.058	-0.015	40.272	0.003	0.003	0.000	0.000	0.000	0.000
29	D	123	GLY	0	0.072	0.028	41.335	0.004	0.004	0.000	0.000	0.000	0.000
30	D	124	PRO	0	0.037	0.016	38.659	-0.004	-0.004	0.000	0.000	0.000	0.000
31	D	125	ALA	0	0.026	0.008	37.268	-0.005	-0.005	0.000	0.000	0.000	0.000
32	D	126	THR	0	-0.005	-0.017	37.121	-0.002	-0.002	0.000	0.000	0.000	0.000
33	D	127	VAL	0	0.035	0.014	34.123	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	128	ASN	0	-0.033	-0.016	32.905	-0.010	-0.010	0.000	0.000	0.000	0.000
35	D	129	ARG	1	0.830	0.910	32.324	0.078	0.078	0.000	0.000	0.000	0.000
36	D	130	ILE	0	0.023	0.017	31.126	-0.004	-0.004	0.000	0.000	0.000	0.000
37	D	131	MET	0	0.003	0.011	27.871	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	132	LYS	1	0.875	0.929	26.499	0.092	0.092	0.000	0.000	0.000	0.000
39	D	133	ALA	0	0.049	0.025	27.737	0.003	0.003	0.000	0.000	0.000	0.000
40	D	134	GLU	-1	-0.882	-0.912	29.478	-0.086	-0.086	0.000	0.000	0.000	0.000
41	D	135	VAL	0	-0.042	-0.026	31.945	0.009	0.009	0.000	0.000	0.000	0.000
42	D	136	SER	0	0.006	-0.009	33.516	-0.006	-0.006	0.000	0.000	0.000	0.000
43	D	137	THR	0	-0.009	0.012	35.268	0.004	0.004	0.000	0.000	0.000	0.000
44	D	138	THR	0	0.030	0.001	37.241	-0.002	-0.002	0.000	0.000	0.000	0.000
45	D	139	ILE	0	0.094	0.032	38.485	-0.002	-0.002	0.000	0.000	0.000	0.000
46	D	140	GLY	0	-0.002	0.005	40.159	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	141	VAL	0	-0.017	-0.019	39.122	0.001	0.001	0.000	0.000	0.000	0.000
48	D	142	LEU	0	-0.017	-0.004	33.930	-0.001	-0.001	0.000	0.000	0.000	0.000
49	D	143	SER	0	-0.009	-0.005	37.421	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	144	SER	0	-0.018	-0.017	39.632	-0.003	-0.003	0.000	0.000	0.000	0.000
51	D	145	LEU	0	0.002	0.007	34.663	0.001	0.001	0.000	0.000	0.000	0.000
52	D	146	ALA	0	0.029	0.022	35.462	-0.003	-0.003	0.000	0.000	0.000	0.000
53	D	147	ARG	1	0.867	0.905	36.383	0.083	0.083	0.000	0.000	0.000	0.000
54	D	148	ALA	0	-0.035	0.005	36.897	0.001	0.001	0.000	0.000	0.000	0.000
55	D	149	PHE	0	-0.003	0.002	31.993	0.001	0.001	0.000	0.000	0.000	0.000
56	D	150	GLY	0	-0.045	-0.017	35.200	-0.003	-0.003	0.000	0.000	0.000	0.000
57	D	151	HIS	1	0.767	0.871	30.844	0.144	0.144	0.000	0.000	0.000	0.000
58	D	152	GLU	-1	-0.811	-0.907	35.416	-0.086	-0.086	0.000	0.000	0.000	0.000
59	D	153	ALA	0	-0.021	-0.021	35.061	-0.005	-0.005	0.000	0.000	0.000	0.000
60	D	154	TYR	0	-0.028	-0.045	33.175	0.000	0.000	0.000	0.000	0.000	0.000
61	D	155	GLU	-1	-0.721	-0.837	31.238	-0.144	-0.144	0.000	0.000	0.000	0.000
62	D	156	MET	0	0.008	0.013	29.769	-0.008	-0.008	0.000	0.000	0.000	0.000
63	D	157	ILE	0	-0.052	-0.029	29.214	-0.006	-0.006	0.000	0.000	0.000	0.000
64	D	158	ILE	0	-0.016	0.009	28.087	0.003	0.003	0.000	0.000	0.000	0.000
65	D	159	PRO	0	-0.034	-0.013	26.054	-0.009	-0.009	0.000	0.000	0.000	0.000
66	D	160	VAL	0	0.038	0.020	21.451	0.003	0.003	0.000	0.000	0.000	0.000
67	D	161	GLY	0	0.004	0.005	21.610	-0.017	-0.017	0.000	0.000	0.000	0.000
68	D	162	ALA	0	0.023	-0.014	20.886	0.001	0.001	0.000	0.000	0.000	0.000
69	D	163	PRO	0	-0.023	-0.009	22.055	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	164	GLY	0	-0.002	-0.001	25.674	0.003	0.003	0.000	0.000	0.000	0.000
71	D	165	ILE	0	0.002	0.012	18.694	0.003	0.003	0.000	0.000	0.000	0.000
72	D	166	ILE	0	-0.019	-0.007	22.493	-0.016	-0.016	0.000	0.000	0.000	0.000
73	D	167	ASP	-1	-0.936	-0.955	21.068	-0.273	-0.273	0.000	0.000	0.000	0.000
74	D	168	TYR	0	-0.023	-0.024	23.844	-0.002	-0.002	0.000	0.000	0.000	0.000
75	D	169	ASP	-1	-0.753	-0.887	26.499	-0.149	-0.149	0.000	0.000	0.000	0.000
76	D	170	HIS	0	0.053	0.025	29.075	0.017	0.017	0.000	0.000	0.000	0.000
77	D	171	ARG	1	0.880	0.955	31.569	0.143	0.143	0.000	0.000	0.000	0.000
78	D	172	MET	0	-0.066	-0.033	28.795	0.006	0.006	0.000	0.000	0.000	0.000
79	D	173	TYR	0	0.056	0.023	32.339	0.008	0.008	0.000	0.000	0.000	0.000
80	D	174	ALA	0	0.000	-0.010	34.208	0.007	0.007	0.000	0.000	0.000	0.000
81	D	175	ALA	0	-0.002	0.004	37.137	0.006	0.006	0.000	0.000	0.000	0.000
82	D	176	LEU	0	-0.032	0.007	33.759	0.004	0.004	0.000	0.000	0.000	0.000
83	D	177	PRO	0	0.061	0.034	38.257	0.003	0.003	0.000	0.000	0.000	0.000
84	D	178	GLN	0	-0.009	-0.014	39.913	-0.005	-0.005	0.000	0.000	0.000	0.000
85	D	179	GLU	-1	-0.843	-0.940	40.471	-0.084	-0.084	0.000	0.000	0.000	0.000
86	D	180	GLU	-1	-0.828	-0.905	36.883	-0.104	-0.104	0.000	0.000	0.000	0.000
87	D	181	LYS	1	0.815	0.912	36.053	0.094	0.094	0.000	0.000	0.000	0.000
88	D	182	ASN	0	-0.042	-0.022	36.059	-0.003	-0.003	0.000	0.000	0.000	0.000
89	D	183	LYS	1	0.847	0.915	34.924	0.099	0.099	0.000	0.000	0.000	0.000
90	D	184	ILE	0	0.011	0.015	30.515	-0.005	-0.005	0.000	0.000	0.000	0.000
91	D	185	THR	0	0.008	-0.004	31.962	-0.004	-0.004	0.000	0.000	0.000	0.000
92	D	186	SER	0	-0.003	0.005	34.108	0.002	0.002	0.000	0.000	0.000	0.000
93	D	187	PHE	0	-0.012	-0.002	26.390	0.001	0.001	0.000	0.000	0.000	0.000
94	D	188	ILE	0	0.009	0.005	28.318	-0.004	-0.004	0.000	0.000	0.000	0.000
95	D	189	ASN	0	0.000	-0.016	29.933	-0.007	-0.007	0.000	0.000	0.000	0.000
96	D	190	PHE	0	-0.013	0.011	30.187	0.004	0.004	0.000	0.000	0.000	0.000
97	D	191	VAL	0	0.003	-0.005	25.306	0.000	0.000	0.000	0.000	0.000	0.000
98	D	192	PHE	0	-0.049	-0.029	27.319	-0.005	-0.005	0.000	0.000	0.000	0.000
99	D	193	GLU	-1	-0.816	-0.902	29.473	-0.105	-0.105	0.000	0.000	0.000	0.000
100	D	194	GLN	0	-0.068	-0.012	28.091	0.011	0.011	0.000	0.000	0.000	0.000
101	D	195	ASN	0	-0.094	-0.020	25.139	-0.011	-0.011	0.000	0.000	0.000	0.000
102	D	196	LYS	1	0.868	0.911	28.153	0.132	0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:67:LEU)