FMO DATABASE

FMODB ID: R8Y68

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

Total energy (hartree)

FMO2-HF: Electronic energy	-660748.272612
FMO2-HF: Nuclear repulsion	620024.345682
FMO2-HF: Total energy	-40723.926931
FMO2-MP2: Total energy	-40841.913623

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.
-4.23	-1.997	-0.024	-1.094	-1.117	-0.001

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 : -0.013 / 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

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	-0.034	-0.020	3.859	-0.123	1.976	-0.023	-1.067	-1.010	-0.001
4	L	70	ASP	-1	-0.909	-0.940	4.276	-3.771	-3.637	-0.001	-0.027	-0.107	0.000
5	L	71	HIS	0	-0.037	-0.048	6.442	0.132	0.132	0.000	0.000	0.000	0.000
6	L	72	GLU	-1	-0.982	-1.004	8.595	-0.382	-0.382	0.000	0.000	0.000	0.000
7	L	73	LEU	0	-0.015	0.017	10.322	0.108	0.108	0.000	0.000	0.000	0.000
8	L	74	ASP	-1	-0.850	-0.891	13.753	-0.007	-0.007	0.000	0.000	0.000	0.000
9	L	75	ALA	0	-0.053	-0.021	13.801	0.048	0.048	0.000	0.000	0.000	0.000
10	L	76	VAL	0	-0.112	-0.081	14.645	0.043	0.043	0.000	0.000	0.000	0.000
11	L	90	TRP	0	-0.022	-0.015	17.768	0.015	0.015	0.000	0.000	0.000	0.000
12	L	91	THR	0	-0.047	-0.056	19.843	-0.014	-0.014	0.000	0.000	0.000	0.000
13	L	92	VAL	0	0.051	0.023	21.882	0.002	0.002	0.000	0.000	0.000	0.000
14	L	93	GLU	-1	-0.781	-0.848	24.060	0.121	0.121	0.000	0.000	0.000	0.000
15	L	94	LYS	1	0.985	0.979	15.436	-0.316	-0.316	0.000	0.000	0.000	0.000
16	L	95	GLN	0	0.022	0.037	17.600	0.028	0.028	0.000	0.000	0.000	0.000
17	L	96	ALA	0	0.034	0.015	20.093	-0.018	-0.018	0.000	0.000	0.000	0.000
18	L	97	ALA	0	-0.030	-0.013	20.810	-0.017	-0.017	0.000	0.000	0.000	0.000
19	L	98	ALA	0	-0.051	-0.027	15.984	-0.006	-0.006	0.000	0.000	0.000	0.000
20	L	99	THR	0	0.016	-0.004	16.967	-0.016	-0.016	0.000	0.000	0.000	0.000
21	L	100	LEU	0	-0.016	0.000	18.889	-0.026	-0.026	0.000	0.000	0.000	0.000
22	L	101	ASN	0	-0.015	-0.001	14.567	-0.028	-0.028	0.000	0.000	0.000	0.000
23	L	102	ALA	0	0.065	0.048	15.475	-0.029	-0.029	0.000	0.000	0.000	0.000
24	L	103	TRP	0	0.026	-0.007	16.746	-0.037	-0.037	0.000	0.000	0.000	0.000
25	L	104	MET	0	-0.057	-0.034	16.678	-0.021	-0.021	0.000	0.000	0.000	0.000
26	L	105	ARG	1	0.927	0.977	20.313	0.065	0.065	0.000	0.000	0.000	0.000
27	L	106	LYS	1	0.914	0.971	17.805	0.163	0.163	0.000	0.000	0.000	0.000
28	L	120	ALA	0	-0.030	-0.028	29.146	0.000	0.000	0.000	0.000	0.000	0.000
29	L	121	GLY	0	0.042	0.021	30.192	-0.006	-0.006	0.000	0.000	0.000	0.000
30	L	122	ILE	0	0.003	-0.007	32.092	0.001	0.001	0.000	0.000	0.000	0.000
31	L	123	GLY	0	0.002	0.020	34.077	0.002	0.002	0.000	0.000	0.000	0.000
32	L	124	PRO	0	0.017	-0.006	33.873	-0.003	-0.003	0.000	0.000	0.000	0.000
33	L	125	ALA	0	0.057	0.037	31.860	0.000	0.000	0.000	0.000	0.000	0.000
34	L	126	THR	0	0.015	-0.016	29.451	0.000	0.000	0.000	0.000	0.000	0.000
35	L	127	VAL	0	0.042	0.016	29.172	0.008	0.008	0.000	0.000	0.000	0.000
36	L	128	ASN	0	-0.001	-0.007	26.163	0.010	0.010	0.000	0.000	0.000	0.000
37	L	129	ARG	1	0.954	0.991	23.463	-0.069	-0.069	0.000	0.000	0.000	0.000
38	L	130	ILE	0	0.010	-0.004	24.151	0.014	0.014	0.000	0.000	0.000	0.000
39	L	131	MET	0	-0.009	0.002	25.237	0.007	0.007	0.000	0.000	0.000	0.000
40	L	132	LYS	1	0.771	0.876	20.699	-0.151	-0.151	0.000	0.000	0.000	0.000
41	L	133	ALA	0	-0.083	-0.050	21.062	0.023	0.023	0.000	0.000	0.000	0.000
42	L	134	GLU	-1	-0.754	-0.859	23.269	0.145	0.145	0.000	0.000	0.000	0.000
43	L	135	VAL	0	-0.056	-0.014	26.821	-0.006	-0.006	0.000	0.000	0.000	0.000
44	L	136	SER	0	-0.008	-0.023	27.938	-0.007	-0.007	0.000	0.000	0.000	0.000
45	L	137	THR	0	0.013	-0.001	28.239	-0.004	-0.004	0.000	0.000	0.000	0.000
46	L	138	THR	0	0.038	0.027	30.719	0.000	0.000	0.000	0.000	0.000	0.000
47	L	139	ILE	0	0.107	0.031	31.430	-0.002	-0.002	0.000	0.000	0.000	0.000
48	L	140	GLY	0	0.023	0.024	32.851	-0.006	-0.006	0.000	0.000	0.000	0.000
49	L	141	VAL	0	0.005	0.003	30.928	-0.006	-0.006	0.000	0.000	0.000	0.000
50	L	142	LEU	0	0.050	0.015	27.048	-0.005	-0.005	0.000	0.000	0.000	0.000
51	L	143	SER	0	0.028	0.009	29.816	-0.007	-0.007	0.000	0.000	0.000	0.000
52	L	144	SER	0	-0.067	-0.028	32.093	-0.008	-0.008	0.000	0.000	0.000	0.000
53	L	145	LEU	0	-0.061	-0.032	26.569	-0.006	-0.006	0.000	0.000	0.000	0.000
54	L	146	ALA	0	0.020	0.014	28.004	-0.005	-0.005	0.000	0.000	0.000	0.000
55	L	147	ARG	1	0.801	0.857	28.995	-0.003	-0.003	0.000	0.000	0.000	0.000
56	L	148	ALA	0	-0.027	-0.003	31.754	-0.006	-0.006	0.000	0.000	0.000	0.000
57	L	149	PHE	0	-0.082	-0.039	26.770	-0.006	-0.006	0.000	0.000	0.000	0.000
58	L	150	GLY	0	0.005	0.016	27.685	-0.008	-0.008	0.000	0.000	0.000	0.000
59	L	151	HIS	1	0.800	0.882	24.149	0.047	0.047	0.000	0.000	0.000	0.000
60	L	152	GLU	-1	-0.790	-0.874	28.383	-0.003	-0.003	0.000	0.000	0.000	0.000
61	L	153	ALA	0	0.002	-0.011	28.032	0.003	0.003	0.000	0.000	0.000	0.000
62	L	154	TYR	0	-0.009	-0.020	27.766	0.007	0.007	0.000	0.000	0.000	0.000
63	L	155	GLU	-1	-0.751	-0.862	24.684	-0.028	-0.028	0.000	0.000	0.000	0.000
64	L	156	MET	0	-0.075	-0.022	23.369	0.002	0.002	0.000	0.000	0.000	0.000
65	L	157	ILE	0	-0.011	-0.011	22.627	0.012	0.012	0.000	0.000	0.000	0.000
66	L	158	ILE	0	0.022	0.022	21.980	0.013	0.013	0.000	0.000	0.000	0.000
67	L	159	PRO	0	-0.015	-0.003	19.709	0.003	0.003	0.000	0.000	0.000	0.000
68	L	160	VAL	0	-0.003	-0.009	16.176	0.009	0.009	0.000	0.000	0.000	0.000
69	L	161	GLY	0	-0.008	0.001	14.514	-0.008	-0.008	0.000	0.000	0.000	0.000
70	L	162	ALA	0	-0.032	-0.010	15.125	0.027	0.027	0.000	0.000	0.000	0.000
71	L	163	PRO	0	0.037	0.006	17.010	-0.022	-0.022	0.000	0.000	0.000	0.000
72	L	164	GLY	0	-0.013	-0.003	18.241	-0.025	-0.025	0.000	0.000	0.000	0.000
73	L	165	ILE	0	-0.063	-0.019	20.123	-0.013	-0.013	0.000	0.000	0.000	0.000
74	L	166	ILE	0	0.021	0.014	19.416	0.000	0.000	0.000	0.000	0.000	0.000
75	L	167	ASP	-1	-0.905	-0.949	15.774	-0.063	-0.063	0.000	0.000	0.000	0.000
76	L	168	TYR	0	-0.039	-0.032	18.850	-0.033	-0.033	0.000	0.000	0.000	0.000
77	L	169	ASP	-1	-0.791	-0.896	21.176	-0.069	-0.069	0.000	0.000	0.000	0.000
78	L	170	HIS	0	0.097	0.037	23.219	-0.004	-0.004	0.000	0.000	0.000	0.000
79	L	171	ARG	1	0.888	0.952	25.565	0.096	0.096	0.000	0.000	0.000	0.000
80	L	172	MET	0	-0.046	-0.035	25.252	-0.003	-0.003	0.000	0.000	0.000	0.000
81	L	173	TYR	0	0.060	0.037	27.141	0.000	0.000	0.000	0.000	0.000	0.000
82	L	174	ALA	0	0.004	-0.004	28.929	0.002	0.002	0.000	0.000	0.000	0.000
83	L	175	ALA	0	-0.042	-0.020	31.225	0.003	0.003	0.000	0.000	0.000	0.000
84	L	176	LEU	0	-0.029	0.005	28.775	-0.001	-0.001	0.000	0.000	0.000	0.000
85	L	177	PRO	0	0.064	0.047	32.803	0.008	0.008	0.000	0.000	0.000	0.000
86	L	178	GLN	0	0.003	-0.012	35.005	-0.002	-0.002	0.000	0.000	0.000	0.000
87	L	179	GLU	-1	-0.912	-0.961	36.112	-0.074	-0.074	0.000	0.000	0.000	0.000
88	L	180	GLU	-1	-0.803	-0.895	31.867	-0.105	-0.105	0.000	0.000	0.000	0.000
89	L	181	LYS	1	0.807	0.898	31.325	0.051	0.051	0.000	0.000	0.000	0.000
90	L	182	ASN	0	0.012	0.006	31.703	0.003	0.003	0.000	0.000	0.000	0.000
91	L	183	LYS	1	0.834	0.912	31.437	0.101	0.101	0.000	0.000	0.000	0.000
92	L	184	ILE	0	0.010	0.012	26.253	-0.003	-0.003	0.000	0.000	0.000	0.000
93	L	185	THR	0	0.000	-0.014	28.360	0.001	0.001	0.000	0.000	0.000	0.000
94	L	186	SER	0	-0.038	-0.010	30.243	0.004	0.004	0.000	0.000	0.000	0.000
95	L	187	PHE	0	0.020	0.005	23.712	0.003	0.003	0.000	0.000	0.000	0.000
96	L	188	ILE	0	0.000	0.001	25.053	-0.002	-0.002	0.000	0.000	0.000	0.000
97	L	189	ASN	0	-0.002	-0.011	27.222	0.006	0.006	0.000	0.000	0.000	0.000
98	L	190	PHE	0	-0.016	0.008	28.322	0.006	0.006	0.000	0.000	0.000	0.000
99	L	191	VAL	0	0.056	0.026	23.153	0.002	0.002	0.000	0.000	0.000	0.000
100	L	192	PHE	0	-0.011	-0.006	24.456	0.006	0.006	0.000	0.000	0.000	0.000
101	L	193	GLU	-1	-0.912	-0.954	27.668	-0.016	-0.016	0.000	0.000	0.000	0.000
102	L	194	GLN	0	-0.076	-0.033	26.871	-0.003	-0.003	0.000	0.000	0.000	0.000
103	L	195	ASN	0	-0.092	-0.041	23.633	0.003	0.003	0.000	0.000	0.000	0.000
104	L	196	LYS	1	0.900	0.961	26.752	0.019	0.019	0.000	0.000	0.000	0.000

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