FMO DATABASE

FMODB ID: QVNZY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-663997.248314
FMO2-HF: Nuclear repulsion	623272.999342
FMO2-HF: Total energy	-40724.248972
FMO2-MP2: Total energy	-40842.213149

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.
-4.047	-0.832	-0.018	-1.654	-1.541	0

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 : -0.019

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].
3	L	69	VAL	0	-0.053	-0.034	3.110	-0.119	2.883	-0.017	-1.587	-1.397
4	L	70	ASP	-1	-0.928	-0.946	4.027	-3.622	-3.409	-0.001	-0.067	-0.144
5	L	71	HIS	0	-0.031	-0.034	6.321	0.096	0.096	0.000	0.000	0.000
6	L	72	GLU	-1	-0.955	-0.982	8.818	-0.344	-0.344	0.000	0.000	0.000
7	L	73	LEU	0	-0.028	0.005	10.505	0.124	0.124	0.000	0.000	0.000
8	L	74	ASP	-1	-0.845	-0.905	13.703	0.005	0.005	0.000	0.000	0.000
9	L	75	ALA	0	-0.061	-0.022	13.636	0.045	0.045	0.000	0.000	0.000
10	L	76	VAL	0	-0.116	-0.078	14.553	0.049	0.049	0.000	0.000	0.000
11	L	90	TRP	0	-0.009	-0.010	18.125	0.015	0.015	0.000	0.000	0.000
12	L	91	THR	0	-0.050	-0.056	20.051	-0.017	-0.017	0.000	0.000	0.000
13	L	92	VAL	0	0.045	0.025	22.332	0.005	0.005	0.000	0.000	0.000
14	L	93	GLU	-1	-0.770	-0.850	24.082	0.141	0.141	0.000	0.000	0.000
15	L	94	LYS	1	0.964	0.974	16.083	-0.344	-0.344	0.000	0.000	0.000
16	L	95	GLN	0	0.022	0.039	17.817	0.036	0.036	0.000	0.000	0.000
17	L	96	ALA	0	0.053	0.036	20.334	-0.016	-0.016	0.000	0.000	0.000
18	L	97	ALA	0	-0.038	-0.013	20.595	-0.016	-0.016	0.000	0.000	0.000
19	L	98	ALA	0	-0.026	-0.016	15.962	-0.010	-0.010	0.000	0.000	0.000
20	L	99	THR	0	0.001	-0.011	17.266	-0.020	-0.020	0.000	0.000	0.000
21	L	100	LEU	0	-0.006	-0.005	19.329	-0.027	-0.027	0.000	0.000	0.000
22	L	101	ASN	0	-0.039	-0.021	14.798	-0.029	-0.029	0.000	0.000	0.000
23	L	102	ALA	0	0.044	0.027	15.806	-0.030	-0.030	0.000	0.000	0.000
24	L	103	TRP	0	0.035	0.006	17.063	-0.040	-0.040	0.000	0.000	0.000
25	L	104	MET	0	-0.008	0.017	16.792	-0.032	-0.032	0.000	0.000	0.000
26	L	105	ARG	1	0.919	0.963	20.596	0.045	0.045	0.000	0.000	0.000
27	L	106	LYS	1	0.846	0.923	17.847	0.130	0.130	0.000	0.000	0.000
28	L	120	ALA	0	-0.024	-0.025	29.357	0.000	0.000	0.000	0.000	0.000
29	L	121	GLY	0	0.067	0.037	30.404	-0.006	-0.006	0.000	0.000	0.000
30	L	122	ILE	0	-0.007	-0.002	32.236	0.000	0.000	0.000	0.000	0.000
31	L	123	GLY	0	0.016	0.003	34.651	0.003	0.003	0.000	0.000	0.000
32	L	124	PRO	0	-0.007	-0.010	33.909	-0.003	-0.003	0.000	0.000	0.000
33	L	125	ALA	0	0.052	0.035	31.425	0.003	0.003	0.000	0.000	0.000
34	L	126	THR	0	0.021	-0.006	29.611	0.002	0.002	0.000	0.000	0.000
35	L	127	VAL	0	0.043	0.026	28.808	0.008	0.008	0.000	0.000	0.000
36	L	128	ASN	0	0.017	0.000	26.080	0.011	0.011	0.000	0.000	0.000
37	L	129	ARG	1	0.942	0.978	23.780	-0.075	-0.075	0.000	0.000	0.000
38	L	130	ILE	0	-0.020	-0.022	24.425	0.014	0.014	0.000	0.000	0.000
39	L	131	MET	0	-0.016	-0.011	25.286	0.007	0.007	0.000	0.000	0.000
40	L	132	LYS	1	0.778	0.877	20.680	-0.162	-0.162	0.000	0.000	0.000
41	L	133	ALA	0	-0.043	-0.027	20.995	0.027	0.027	0.000	0.000	0.000
42	L	134	GLU	-1	-0.756	-0.858	23.311	0.159	0.159	0.000	0.000	0.000
43	L	135	VAL	0	-0.056	-0.018	26.968	-0.007	-0.007	0.000	0.000	0.000
44	L	136	SER	0	-0.009	-0.020	28.505	-0.011	-0.011	0.000	0.000	0.000
45	L	137	THR	0	0.019	0.006	28.578	-0.005	-0.005	0.000	0.000	0.000
46	L	138	THR	0	0.034	0.019	31.053	0.000	0.000	0.000	0.000	0.000
47	L	139	ILE	0	0.089	0.026	31.453	-0.002	-0.002	0.000	0.000	0.000
48	L	140	GLY	0	0.025	0.028	32.932	-0.006	-0.006	0.000	0.000	0.000
49	L	141	VAL	0	0.000	0.010	31.141	-0.006	-0.006	0.000	0.000	0.000
50	L	142	LEU	0	0.031	0.009	27.283	-0.005	-0.005	0.000	0.000	0.000
51	L	143	SER	0	-0.003	-0.002	30.005	-0.007	-0.007	0.000	0.000	0.000
52	L	144	SER	0	-0.027	-0.029	32.469	-0.008	-0.008	0.000	0.000	0.000
53	L	145	LEU	0	-0.054	-0.029	26.789	-0.006	-0.006	0.000	0.000	0.000
54	L	146	ALA	0	0.044	0.018	28.082	-0.006	-0.006	0.000	0.000	0.000
55	L	147	ARG	1	0.822	0.893	29.054	-0.017	-0.017	0.000	0.000	0.000
56	L	148	ALA	0	-0.029	-0.011	31.743	-0.007	-0.007	0.000	0.000	0.000
57	L	149	PHE	0	-0.075	-0.034	26.665	-0.007	-0.007	0.000	0.000	0.000
58	L	150	GLY	0	0.006	0.015	27.939	-0.007	-0.007	0.000	0.000	0.000
59	L	151	HIS	1	0.773	0.867	24.587	0.027	0.027	0.000	0.000	0.000
60	L	152	GLU	-1	-0.764	-0.869	28.480	0.013	0.013	0.000	0.000	0.000
61	L	153	ALA	0	-0.028	-0.024	28.161	0.005	0.005	0.000	0.000	0.000
62	L	154	TYR	0	-0.016	-0.023	27.474	0.008	0.008	0.000	0.000	0.000
63	L	155	GLU	-1	-0.745	-0.858	24.566	-0.005	-0.005	0.000	0.000	0.000
64	L	156	MET	0	-0.070	-0.020	23.265	0.004	0.004	0.000	0.000	0.000
65	L	157	ILE	0	-0.015	-0.013	22.829	0.015	0.015	0.000	0.000	0.000
66	L	158	ILE	0	0.042	0.033	21.933	0.011	0.011	0.000	0.000	0.000
67	L	159	PRO	0	-0.003	0.004	20.303	0.007	0.007	0.000	0.000	0.000
68	L	160	VAL	0	0.000	-0.016	16.254	0.014	0.014	0.000	0.000	0.000
69	L	161	GLY	0	0.005	0.014	14.916	-0.007	-0.007	0.000	0.000	0.000
70	L	162	ALA	0	-0.027	-0.009	15.621	0.038	0.038	0.000	0.000	0.000
71	L	163	PRO	0	0.024	-0.011	16.752	-0.028	-0.028	0.000	0.000	0.000
72	L	164	GLY	0	-0.010	0.012	18.521	-0.023	-0.023	0.000	0.000	0.000
73	L	165	ILE	0	-0.077	-0.034	19.994	-0.017	-0.017	0.000	0.000	0.000
74	L	166	ILE	0	0.019	0.018	19.382	0.002	0.002	0.000	0.000	0.000
75	L	167	ASP	-1	-0.905	-0.957	16.154	-0.015	-0.015	0.000	0.000	0.000
76	L	168	TYR	0	-0.028	-0.019	18.971	-0.031	-0.031	0.000	0.000	0.000
77	L	169	ASP	-1	-0.785	-0.886	21.318	-0.045	-0.045	0.000	0.000	0.000
78	L	170	HIS	0	0.099	0.043	23.592	-0.007	-0.007	0.000	0.000	0.000
79	L	171	ARG	1	0.878	0.936	25.990	0.070	0.070	0.000	0.000	0.000
80	L	172	MET	0	-0.041	-0.025	25.510	-0.005	-0.005	0.000	0.000	0.000
81	L	173	TYR	0	0.048	0.029	27.179	0.000	0.000	0.000	0.000	0.000
82	L	174	ALA	0	-0.011	-0.004	28.969	0.002	0.002	0.000	0.000	0.000
83	L	175	ALA	0	-0.019	-0.014	31.507	0.001	0.001	0.000	0.000	0.000
84	L	176	LEU	0	-0.020	0.015	28.676	-0.003	-0.003	0.000	0.000	0.000
85	L	177	PRO	0	0.064	0.035	32.851	0.008	0.008	0.000	0.000	0.000
86	L	178	GLN	0	0.019	-0.004	34.949	-0.001	-0.001	0.000	0.000	0.000
87	L	179	GLU	-1	-0.864	-0.923	36.182	-0.068	-0.068	0.000	0.000	0.000
88	L	180	GLU	-1	-0.802	-0.892	31.666	-0.093	-0.093	0.000	0.000	0.000
89	L	181	LYS	1	0.784	0.886	31.487	0.041	0.041	0.000	0.000	0.000
90	L	182	ASN	0	0.000	0.016	32.087	0.005	0.005	0.000	0.000	0.000
91	L	183	LYS	1	0.781	0.869	32.053	0.085	0.085	0.000	0.000	0.000
92	L	184	ILE	0	0.016	0.007	26.759	-0.003	-0.003	0.000	0.000	0.000
93	L	185	THR	0	-0.008	-0.028	28.839	0.002	0.002	0.000	0.000	0.000
94	L	186	SER	0	-0.038	-0.014	30.746	0.006	0.006	0.000	0.000	0.000
95	L	187	PHE	0	0.021	0.012	23.868	0.003	0.003	0.000	0.000	0.000
96	L	188	ILE	0	0.010	0.006	25.318	0.000	0.000	0.000	0.000	0.000
97	L	189	ASN	0	0.017	0.003	27.417	0.008	0.008	0.000	0.000	0.000
98	L	190	PHE	0	-0.021	0.001	28.467	0.005	0.005	0.000	0.000	0.000
99	L	191	VAL	0	0.035	0.014	23.342	0.001	0.001	0.000	0.000	0.000
100	L	192	PHE	0	-0.017	-0.010	24.728	0.007	0.007	0.000	0.000	0.000
101	L	193	GLU	-1	-0.920	-0.958	27.880	-0.005	-0.005	0.000	0.000	0.000
102	L	194	GLN	0	-0.075	-0.037	26.792	0.000	0.000	0.000	0.000	0.000
103	L	195	ASN	0	-0.070	-0.028	23.652	0.005	0.005	0.000	0.000	0.000
104	L	196	LYS	1	0.885	0.951	26.767	0.010	0.010	0.000	0.000	0.000

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