FMO DATABASE

FMODB ID: ZVNKN

Calculation Name: 5D50-L-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: L

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-660248.681279
FMO2-HF: Nuclear repulsion	619525.141091
FMO2-HF: Total energy	-40723.540188
FMO2-MP2: Total energy	-40841.500316

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(L:67:LEU)

Summations of interaction energy for fragment #1(L: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.
1.54	3.66	-0.024	-1.025	-1.07	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.062

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	L	69	VAL	0	-0.026	-0.011	3.859	-0.730	1.295	-0.023	-1.020	-0.981	-0.002
4	L	70	ASP	-1	-0.908	-0.951	5.201	2.011	2.106	-0.001	-0.005	-0.089	0.000
5	L	71	HIS	0	-0.034	-0.041	7.423	-0.185	-0.185	0.000	0.000	0.000	0.000
6	L	72	GLU	-1	-1.013	-1.014	9.581	0.066	0.066	0.000	0.000	0.000	0.000
7	L	73	LEU	0	0.009	0.022	11.041	-0.071	-0.071	0.000	0.000	0.000	0.000
8	L	74	ASP	-1	-0.879	-0.932	14.602	0.378	0.378	0.000	0.000	0.000	0.000
9	L	75	ALA	0	-0.064	-0.032	14.196	-0.019	-0.019	0.000	0.000	0.000	0.000
10	L	76	VAL	0	-0.072	-0.026	15.091	-0.049	-0.049	0.000	0.000	0.000	0.000
11	L	90	TRP	0	-0.056	-0.054	17.883	0.005	0.005	0.000	0.000	0.000	0.000
12	L	91	THR	0	-0.005	-0.002	19.849	0.001	0.001	0.000	0.000	0.000	0.000
13	L	92	VAL	0	0.070	0.028	21.727	-0.005	-0.005	0.000	0.000	0.000	0.000
14	L	93	GLU	-1	-0.797	-0.850	23.800	-0.010	-0.010	0.000	0.000	0.000	0.000
15	L	94	LYS	1	0.991	0.984	14.935	-0.023	-0.023	0.000	0.000	0.000	0.000
16	L	95	GLN	0	0.003	0.032	17.170	0.004	0.004	0.000	0.000	0.000	0.000
17	L	96	ALA	0	0.038	0.019	19.804	-0.012	-0.012	0.000	0.000	0.000	0.000
18	L	97	ALA	0	-0.028	-0.012	20.537	-0.011	-0.011	0.000	0.000	0.000	0.000
19	L	98	ALA	0	-0.053	-0.026	15.597	-0.011	-0.011	0.000	0.000	0.000	0.000
20	L	99	THR	0	0.030	0.000	16.747	-0.024	-0.024	0.000	0.000	0.000	0.000
21	L	100	LEU	0	-0.012	0.003	18.633	-0.012	-0.012	0.000	0.000	0.000	0.000
22	L	101	ASN	0	-0.007	0.002	14.186	-0.009	-0.009	0.000	0.000	0.000	0.000
23	L	102	ALA	0	0.049	0.040	15.289	-0.016	-0.016	0.000	0.000	0.000	0.000
24	L	103	TRP	0	0.006	-0.018	16.514	-0.017	-0.017	0.000	0.000	0.000	0.000
25	L	104	MET	0	-0.048	-0.033	16.288	-0.004	-0.004	0.000	0.000	0.000	0.000
26	L	105	ARG	1	0.925	0.985	19.994	0.109	0.109	0.000	0.000	0.000	0.000
27	L	106	LYS	1	0.934	0.979	17.755	0.223	0.223	0.000	0.000	0.000	0.000
28	L	120	ALA	0	-0.025	-0.029	29.090	-0.002	-0.002	0.000	0.000	0.000	0.000
29	L	121	GLY	0	0.032	0.019	29.974	-0.001	-0.001	0.000	0.000	0.000	0.000
30	L	122	ILE	0	0.005	-0.003	31.897	0.001	0.001	0.000	0.000	0.000	0.000
31	L	123	GLY	0	-0.002	0.014	33.937	0.003	0.003	0.000	0.000	0.000	0.000
32	L	124	PRO	0	0.009	-0.013	33.701	-0.002	-0.002	0.000	0.000	0.000	0.000
33	L	125	ALA	0	0.057	0.041	31.718	-0.002	-0.002	0.000	0.000	0.000	0.000
34	L	126	THR	0	-0.011	-0.027	29.176	-0.004	-0.004	0.000	0.000	0.000	0.000
35	L	127	VAL	0	0.045	0.018	29.020	0.001	0.001	0.000	0.000	0.000	0.000
36	L	128	ASN	0	0.041	0.013	26.016	0.006	0.006	0.000	0.000	0.000	0.000
37	L	129	ARG	1	0.959	0.990	23.051	0.054	0.054	0.000	0.000	0.000	0.000
38	L	130	ILE	0	0.010	-0.004	23.902	0.002	0.002	0.000	0.000	0.000	0.000
39	L	131	MET	0	-0.015	0.000	24.881	0.004	0.004	0.000	0.000	0.000	0.000
40	L	132	LYS	1	0.856	0.941	20.267	0.019	0.019	0.000	0.000	0.000	0.000
41	L	133	ALA	0	-0.094	-0.051	20.715	0.005	0.005	0.000	0.000	0.000	0.000
42	L	134	GLU	-1	-0.828	-0.923	22.888	-0.012	-0.012	0.000	0.000	0.000	0.000
43	L	135	VAL	0	-0.059	-0.014	26.468	0.001	0.001	0.000	0.000	0.000	0.000
44	L	136	SER	0	-0.024	-0.053	27.755	0.001	0.001	0.000	0.000	0.000	0.000
45	L	137	THR	0	0.015	0.003	27.822	0.001	0.001	0.000	0.000	0.000	0.000
46	L	138	THR	0	0.041	0.028	30.432	0.001	0.001	0.000	0.000	0.000	0.000
47	L	139	ILE	0	0.098	0.025	31.172	-0.003	-0.003	0.000	0.000	0.000	0.000
48	L	140	GLY	0	0.016	0.018	32.478	-0.003	-0.003	0.000	0.000	0.000	0.000
49	L	141	VAL	0	0.017	0.014	30.625	-0.003	-0.003	0.000	0.000	0.000	0.000
50	L	142	LEU	0	0.049	0.015	26.502	-0.004	-0.004	0.000	0.000	0.000	0.000
51	L	143	SER	0	0.001	-0.001	29.550	-0.006	-0.006	0.000	0.000	0.000	0.000
52	L	144	SER	0	-0.027	-0.020	31.881	-0.003	-0.003	0.000	0.000	0.000	0.000
53	L	145	LEU	0	-0.066	-0.032	26.292	-0.003	-0.003	0.000	0.000	0.000	0.000
54	L	146	ALA	0	0.015	0.009	27.835	-0.007	-0.007	0.000	0.000	0.000	0.000
55	L	147	ARG	1	0.856	0.911	28.831	0.037	0.037	0.000	0.000	0.000	0.000
56	L	148	ALA	0	-0.026	-0.001	31.536	-0.002	-0.002	0.000	0.000	0.000	0.000
57	L	149	PHE	0	-0.085	-0.038	26.756	-0.003	-0.003	0.000	0.000	0.000	0.000
58	L	150	GLY	0	0.002	0.013	27.403	-0.007	-0.007	0.000	0.000	0.000	0.000
59	L	151	HIS	1	0.803	0.895	23.809	0.092	0.092	0.000	0.000	0.000	0.000
60	L	152	GLU	-1	-0.811	-0.900	28.166	-0.040	-0.040	0.000	0.000	0.000	0.000
61	L	153	ALA	0	0.009	-0.015	27.717	-0.003	-0.003	0.000	0.000	0.000	0.000
62	L	154	TYR	0	-0.024	-0.027	27.439	0.000	0.000	0.000	0.000	0.000	0.000
63	L	155	GLU	-1	-0.803	-0.906	24.420	-0.071	-0.071	0.000	0.000	0.000	0.000
64	L	156	MET	0	-0.078	-0.024	23.007	-0.003	-0.003	0.000	0.000	0.000	0.000
65	L	157	ILE	0	-0.010	-0.013	22.204	0.000	0.000	0.000	0.000	0.000	0.000
66	L	158	ILE	0	0.023	0.025	21.348	0.009	0.009	0.000	0.000	0.000	0.000
67	L	159	PRO	0	-0.017	-0.004	19.452	-0.007	-0.007	0.000	0.000	0.000	0.000
68	L	160	VAL	0	0.002	-0.009	15.367	0.009	0.009	0.000	0.000	0.000	0.000
69	L	161	GLY	0	-0.012	-0.002	14.219	-0.002	-0.002	0.000	0.000	0.000	0.000
70	L	162	ALA	0	-0.034	-0.012	14.908	0.017	0.017	0.000	0.000	0.000	0.000
71	L	163	PRO	0	0.030	0.002	17.036	-0.010	-0.010	0.000	0.000	0.000	0.000
72	L	164	GLY	0	-0.009	-0.002	18.106	-0.008	-0.008	0.000	0.000	0.000	0.000
73	L	165	ILE	0	-0.056	-0.013	19.792	-0.003	-0.003	0.000	0.000	0.000	0.000
74	L	166	ILE	0	0.025	0.016	19.061	-0.004	-0.004	0.000	0.000	0.000	0.000
75	L	167	ASP	-1	-0.917	-0.956	15.516	-0.145	-0.145	0.000	0.000	0.000	0.000
76	L	168	TYR	0	-0.028	-0.021	18.429	-0.010	-0.010	0.000	0.000	0.000	0.000
77	L	169	ASP	-1	-0.825	-0.930	20.897	-0.099	-0.099	0.000	0.000	0.000	0.000
78	L	170	HIS	0	0.083	0.036	22.992	0.008	0.008	0.000	0.000	0.000	0.000
79	L	171	ARG	1	0.968	0.997	25.843	0.104	0.104	0.000	0.000	0.000	0.000
80	L	172	MET	0	-0.073	-0.045	24.790	0.001	0.001	0.000	0.000	0.000	0.000
81	L	173	TYR	0	0.049	0.025	26.894	0.005	0.005	0.000	0.000	0.000	0.000
82	L	174	ALA	0	-0.014	-0.014	28.685	0.005	0.005	0.000	0.000	0.000	0.000
83	L	175	ALA	0	-0.057	-0.023	30.957	0.003	0.003	0.000	0.000	0.000	0.000
84	L	176	LEU	0	-0.022	0.009	28.439	0.002	0.002	0.000	0.000	0.000	0.000
85	L	177	PRO	0	0.068	0.040	32.499	0.005	0.005	0.000	0.000	0.000	0.000
86	L	178	GLN	0	-0.002	-0.021	34.615	-0.003	-0.003	0.000	0.000	0.000	0.000
87	L	179	GLU	-1	-0.906	-0.954	35.758	-0.041	-0.041	0.000	0.000	0.000	0.000
88	L	180	GLU	-1	-0.846	-0.934	31.518	-0.054	-0.054	0.000	0.000	0.000	0.000
89	L	181	LYS	1	0.856	0.943	30.976	0.042	0.042	0.000	0.000	0.000	0.000
90	L	182	ASN	0	0.005	-0.006	31.387	0.001	0.001	0.000	0.000	0.000	0.000
91	L	183	LYS	1	0.872	0.942	31.036	0.050	0.050	0.000	0.000	0.000	0.000
92	L	184	ILE	0	0.024	0.018	26.201	0.001	0.001	0.000	0.000	0.000	0.000
93	L	185	THR	0	0.005	-0.003	28.080	0.003	0.003	0.000	0.000	0.000	0.000
94	L	186	SER	0	-0.041	-0.012	30.015	0.005	0.005	0.000	0.000	0.000	0.000
95	L	187	PHE	0	0.014	0.002	23.560	0.004	0.004	0.000	0.000	0.000	0.000
96	L	188	ILE	0	0.006	0.006	25.001	0.003	0.003	0.000	0.000	0.000	0.000
97	L	189	ASN	0	0.000	-0.010	27.016	0.005	0.005	0.000	0.000	0.000	0.000
98	L	190	PHE	0	-0.015	0.006	28.228	0.005	0.005	0.000	0.000	0.000	0.000
99	L	191	VAL	0	0.057	0.027	23.022	0.006	0.006	0.000	0.000	0.000	0.000
100	L	192	PHE	0	-0.020	0.000	24.317	0.007	0.007	0.000	0.000	0.000	0.000
101	L	193	GLU	-1	-0.914	-0.958	27.594	0.019	0.019	0.000	0.000	0.000	0.000
102	L	194	GLN	0	-0.087	-0.037	26.597	0.003	0.003	0.000	0.000	0.000	0.000
103	L	195	ASN	0	-0.110	-0.064	23.570	0.014	0.014	0.000	0.000	0.000	0.000
104	L	196	LYS	1	0.933	0.982	26.746	-0.043	-0.043	0.000	0.000	0.000	0.000

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