FMO DATABASE

FMODB ID: ZY4GN

Calculation Name: 3UAF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UAF

Chain ID: A

ChEMBL ID:

UniProt ID: G5ED35

Base Structure: X-ray

Registration Date: 2023-06-20

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-914409.312007
FMO2-HF: Nuclear repulsion	867923.15437
FMO2-HF: Total energy	-46486.157637
FMO2-MP2: Total energy	-46619.305338

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:21:LYS)

Summations of interaction energy for fragment #1(A:21:LYS)

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.
-115.573	-112.447	-0.023	-1.423	-1.679	0.005

Interaction energy analysis for fragmet #1(A:21:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.015 / q_NPA : 1.009

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	A	23	SER	0	-0.026	0.005	3.689	-4.386	-1.727	-0.026	-1.227	-1.405	0.005
4	A	24	CYS	0	-0.077	-0.034	5.116	2.042	2.085	-0.002	-0.001	-0.040	0.000
5	A	25	LEU	0	0.057	0.025	8.855	-0.887	-0.887	0.000	0.000	0.000	0.000
6	A	26	MET	0	-0.006	0.002	11.717	1.283	1.283	0.000	0.000	0.000	0.000
7	A	27	ALA	0	0.055	0.044	15.334	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	28	THR	0	-0.055	-0.040	18.055	0.829	0.829	0.000	0.000	0.000	0.000
9	A	29	GLY	0	0.062	0.022	21.623	-0.224	-0.224	0.000	0.000	0.000	0.000
10	A	30	VAL	0	-0.061	-0.029	24.922	0.235	0.235	0.000	0.000	0.000	0.000
11	A	31	LEU	0	0.033	0.035	27.136	0.070	0.070	0.000	0.000	0.000	0.000
12	A	32	LYS	1	0.882	0.934	30.107	9.975	9.975	0.000	0.000	0.000	0.000
13	A	33	CYS	0	0.000	0.034	33.386	0.185	0.185	0.000	0.000	0.000	0.000
14	A	34	PRO	0	-0.033	-0.026	35.906	0.190	0.190	0.000	0.000	0.000	0.000
15	A	35	THR	0	-0.007	-0.018	39.068	0.165	0.165	0.000	0.000	0.000	0.000
16	A	36	ASP	-1	-0.829	-0.929	39.554	-7.640	-7.640	0.000	0.000	0.000	0.000
17	A	37	PRO	0	-0.012	0.001	38.431	-0.215	-0.215	0.000	0.000	0.000	0.000
18	A	38	GLU	-1	-0.804	-0.885	38.039	-8.021	-8.021	0.000	0.000	0.000	0.000
19	A	39	ALA	0	-0.012	-0.002	36.282	-0.190	-0.190	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.038	-0.007	33.124	-0.307	-0.307	0.000	0.000	0.000	0.000
21	A	41	LYS	1	0.736	0.860	32.489	7.770	7.770	0.000	0.000	0.000	0.000
22	A	42	LYS	1	0.888	0.952	31.741	8.764	8.764	0.000	0.000	0.000	0.000
23	A	43	VAL	0	0.038	0.024	28.809	0.109	0.109	0.000	0.000	0.000	0.000
24	A	44	HIS	0	-0.062	-0.023	24.292	0.086	0.086	0.000	0.000	0.000	0.000
25	A	45	ILE	0	-0.012	-0.021	22.044	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	46	ASP	-1	-0.688	-0.799	20.639	-13.609	-13.609	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.046	-0.027	14.015	0.045	0.045	0.000	0.000	0.000	0.000
28	A	48	TRP	0	0.000	-0.010	16.062	-0.346	-0.346	0.000	0.000	0.000	0.000
29	A	49	ASP	-1	-0.703	-0.842	10.547	-28.256	-28.256	0.000	0.000	0.000	0.000
30	A	50	ALA	0	0.032	0.009	13.857	0.563	0.563	0.000	0.000	0.000	0.000
31	A	51	ALA	0	-0.042	-0.018	11.143	0.685	0.685	0.000	0.000	0.000	0.000
32	A	52	ALA	0	0.011	0.009	11.855	0.440	0.440	0.000	0.000	0.000	0.000
33	A	53	ALA	0	0.034	0.018	13.014	0.975	0.975	0.000	0.000	0.000	0.000
34	A	54	ALA	0	-0.058	-0.017	15.251	0.811	0.811	0.000	0.000	0.000	0.000
35	A	55	ALA	0	-0.080	-0.032	12.737	0.497	0.497	0.000	0.000	0.000	0.000
36	A	56	GLU	-1	-0.970	-0.981	14.680	-14.067	-14.067	0.000	0.000	0.000	0.000
37	A	57	SER	0	-0.105	-0.052	12.831	0.061	0.061	0.000	0.000	0.000	0.000
38	A	58	ASP	-1	-0.924	-0.974	14.613	-15.960	-15.960	0.000	0.000	0.000	0.000
39	A	59	ASP	-1	-0.876	-0.937	13.985	-17.619	-17.619	0.000	0.000	0.000	0.000
40	A	60	LEU	0	-0.036	-0.010	15.697	-0.382	-0.382	0.000	0.000	0.000	0.000
41	A	61	MET	0	-0.064	-0.011	10.380	-0.465	-0.465	0.000	0.000	0.000	0.000
42	A	62	GLY	0	-0.001	-0.013	14.378	-0.037	-0.037	0.000	0.000	0.000	0.000
43	A	63	ARG	1	0.807	0.866	17.214	13.278	13.278	0.000	0.000	0.000	0.000
44	A	64	THR	0	-0.064	-0.028	21.004	0.325	0.325	0.000	0.000	0.000	0.000
45	A	65	TRP	0	0.006	-0.002	23.594	0.306	0.306	0.000	0.000	0.000	0.000
46	A	66	SER	0	-0.047	-0.014	27.215	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	67	ASP	-1	-0.784	-0.914	28.819	-9.580	-9.580	0.000	0.000	0.000	0.000
48	A	68	ARG	1	0.925	0.957	31.432	8.918	8.918	0.000	0.000	0.000	0.000
49	A	69	ASN	0	-0.098	-0.062	33.058	0.491	0.491	0.000	0.000	0.000	0.000
50	A	70	GLY	0	0.063	0.043	31.639	0.014	0.014	0.000	0.000	0.000	0.000
51	A	71	ASN	0	-0.071	-0.026	28.178	-0.403	-0.403	0.000	0.000	0.000	0.000
52	A	72	PHE	0	0.045	0.025	21.953	0.180	0.180	0.000	0.000	0.000	0.000
53	A	73	GLN	0	-0.013	-0.022	21.076	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	74	VAL	0	0.012	0.020	17.883	0.416	0.416	0.000	0.000	0.000	0.000
55	A	75	THR	0	-0.007	-0.021	13.924	-0.390	-0.390	0.000	0.000	0.000	0.000
56	A	76	GLY	0	0.067	0.042	13.313	1.015	1.015	0.000	0.000	0.000	0.000
57	A	78	ALA	0	0.103	0.061	7.655	2.092	2.092	0.000	0.000	0.000	0.000
58	A	79	SER	0	-0.044	-0.055	3.330	-4.654	-4.230	0.005	-0.195	-0.234	0.000
59	A	80	ASH	0	-0.034	-0.033	5.773	4.104	4.104	0.000	0.000	0.000	0.000
60	A	81	PHE	0	-0.010	-0.007	5.501	-4.520	-4.520	0.000	0.000	0.000	0.000
61	A	82	GLY	0	0.030	0.023	7.633	1.978	1.978	0.000	0.000	0.000	0.000
62	A	83	PRO	0	-0.026	-0.033	10.215	-2.160	-2.160	0.000	0.000	0.000	0.000
63	A	84	ILE	0	0.030	0.020	11.373	-1.373	-1.373	0.000	0.000	0.000	0.000
64	A	85	ASN	0	-0.034	-0.019	6.143	-3.647	-3.647	0.000	0.000	0.000	0.000
65	A	86	THR	0	-0.053	-0.027	6.084	-8.018	-8.018	0.000	0.000	0.000	0.000
66	A	87	PRO	0	-0.037	-0.018	5.935	3.389	3.389	0.000	0.000	0.000	0.000
67	A	88	ASP	-1	-0.857	-0.940	8.838	-22.894	-22.894	0.000	0.000	0.000	0.000
68	A	89	PRO	0	-0.041	-0.006	10.950	1.546	1.546	0.000	0.000	0.000	0.000
69	A	90	TYR	0	0.039	0.021	13.793	1.306	1.306	0.000	0.000	0.000	0.000
70	A	91	LEU	0	-0.083	-0.045	17.577	-0.066	-0.066	0.000	0.000	0.000	0.000
71	A	92	TYR	0	0.002	0.017	20.354	0.635	0.635	0.000	0.000	0.000	0.000
72	A	93	ILE	0	0.008	-0.006	23.293	0.109	0.109	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.012	0.010	26.397	0.108	0.108	0.000	0.000	0.000	0.000
74	A	95	HIS	0	-0.015	-0.014	29.402	0.190	0.190	0.000	0.000	0.000	0.000
75	A	96	ASN	0	0.009	-0.006	32.450	0.105	0.105	0.000	0.000	0.000	0.000
76	A	98	PRO	0	0.036	0.021	36.476	-0.137	-0.137	0.000	0.000	0.000	0.000
77	A	99	HIS	0	-0.062	-0.026	35.631	0.226	0.226	0.000	0.000	0.000	0.000
78	A	100	ARG	1	0.864	0.920	36.541	8.822	8.822	0.000	0.000	0.000	0.000
79	A	101	ASP	-1	-0.939	-0.961	40.456	-7.697	-7.697	0.000	0.000	0.000	0.000
80	A	102	SER	0	-0.020	-0.025	39.580	0.152	0.152	0.000	0.000	0.000	0.000
81	A	103	ASN	0	-0.065	-0.035	41.164	0.070	0.070	0.000	0.000	0.000	0.000
82	A	104	ALA	0	0.002	0.015	37.124	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	105	THR	0	0.034	0.015	35.757	0.060	0.060	0.000	0.000	0.000	0.000
84	A	106	ASN	0	-0.018	0.001	32.672	0.002	0.002	0.000	0.000	0.000	0.000
85	A	107	PRO	0	0.016	0.002	28.478	-0.086	-0.086	0.000	0.000	0.000	0.000
86	A	108	ILE	0	-0.025	0.003	26.331	0.024	0.024	0.000	0.000	0.000	0.000
87	A	109	GLN	0	0.064	0.030	22.373	-0.631	-0.631	0.000	0.000	0.000	0.000
88	A	110	ILE	0	-0.086	-0.051	20.780	0.336	0.336	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.867	-0.931	17.957	-17.674	-17.674	0.000	0.000	0.000	0.000
90	A	112	VAL	0	-0.087	-0.033	14.885	0.353	0.353	0.000	0.000	0.000	0.000
91	A	113	ILE	0	0.045	0.021	14.715	-1.039	-1.039	0.000	0.000	0.000	0.000
92	A	114	PRO	0	0.067	0.024	10.095	-0.437	-0.437	0.000	0.000	0.000	0.000
93	A	115	LEU	0	-0.062	-0.025	9.731	-2.485	-2.485	0.000	0.000	0.000	0.000
94	A	116	PHE	0	0.014	-0.002	7.026	0.187	0.187	0.000	0.000	0.000	0.000
95	A	117	LEU	0	-0.004	0.001	9.125	0.985	0.985	0.000	0.000	0.000	0.000
96	A	118	PRO	0	-0.050	-0.045	8.611	-3.203	-3.203	0.000	0.000	0.000	0.000
97	A	119	SER	0	-0.048	-0.007	10.980	2.608	2.608	0.000	0.000	0.000	0.000
98	A	120	ILE	0	-0.032	-0.017	13.057	-0.445	-0.445	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.036	0.022	14.648	0.694	0.694	0.000	0.000	0.000	0.000
100	A	122	ARG	1	0.881	0.935	17.327	15.060	15.060	0.000	0.000	0.000	0.000
101	A	123	LEU	0	0.048	0.019	19.869	0.187	0.187	0.000	0.000	0.000	0.000
102	A	124	GLY	0	-0.013	0.008	22.850	0.443	0.443	0.000	0.000	0.000	0.000
103	A	125	ASN	0	-0.045	-0.040	26.334	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	126	VAL	0	0.035	0.016	25.035	-0.079	-0.079	0.000	0.000	0.000	0.000
105	A	127	TYR	0	-0.046	-0.034	28.314	0.229	0.229	0.000	0.000	0.000	0.000
106	A	128	LEU	0	0.028	0.012	29.089	-0.209	-0.209	0.000	0.000	0.000	0.000
107	A	129	ASP	-1	-0.724	-0.850	32.298	-8.820	-8.820	0.000	0.000	0.000	0.000
108	A	130	ARG	1	0.755	0.847	32.638	9.373	9.373	0.000	0.000	0.000	0.000
109	A	131	TYR	0	0.048	0.016	31.184	-0.233	-0.233	0.000	0.000	0.000	0.000
110	A	132	LEU	0	0.014	0.015	25.940	0.180	0.180	0.000	0.000	0.000	0.000
111	A	133	GLU	-1	-0.879	-0.960	30.026	-10.313	-10.313	0.000	0.000	0.000	0.000
112	A	134	ASP	-1	-0.810	-0.883	32.524	-8.830	-8.830	0.000	0.000	0.000	0.000
113	A	135	TYR	0	-0.051	-0.025	32.298	0.317	0.317	0.000	0.000	0.000	0.000
114	A	136	HIS	0	0.004	-0.002	27.209	0.420	0.420	0.000	0.000	0.000	0.000
115	A	137	HIS	0	-0.066	-0.013	32.816	0.400	0.400	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:LYS)