FMO DATABASE

FMODB ID: 661RZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-914019.575691
FMO2-HF: Nuclear repulsion	867533.942925
FMO2-HF: Total energy	-46485.632766
FMO2-MP2: Total energy	-46618.794074

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.
-113.092	-111.021	-0.024	-0.764	-1.28	0

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 : 0.962 / q_NPA : 0.961

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	A	23	SER	0	-0.009	0.008	3.780	-4.873	-3.040	-0.022	-0.692	-1.118
4	A	24	CYS	0	-0.072	-0.022	5.085	2.277	2.327	-0.002	-0.001	-0.046
5	A	25	LEU	0	0.065	0.013	8.809	-1.090	-1.090	0.000	0.000	0.000
6	A	26	MET	0	-0.006	-0.001	11.710	1.319	1.319	0.000	0.000	0.000
7	A	27	ALA	0	0.049	0.041	15.281	-0.148	-0.148	0.000	0.000	0.000
8	A	28	THR	0	-0.060	-0.041	18.073	0.822	0.822	0.000	0.000	0.000
9	A	29	GLY	0	0.061	0.017	21.602	-0.234	-0.234	0.000	0.000	0.000
10	A	30	VAL	0	-0.056	-0.016	24.934	0.211	0.211	0.000	0.000	0.000
11	A	31	LEU	0	0.029	0.024	27.434	0.070	0.070	0.000	0.000	0.000
12	A	32	LYS	1	0.905	0.943	30.194	9.744	9.744	0.000	0.000	0.000
13	A	33	CYS	0	-0.021	0.022	33.487	0.174	0.174	0.000	0.000	0.000
14	A	34	PRO	0	-0.044	-0.031	36.013	0.189	0.189	0.000	0.000	0.000
15	A	35	THR	0	-0.005	-0.027	39.230	0.163	0.163	0.000	0.000	0.000
16	A	36	ASP	-1	-0.834	-0.928	39.710	-7.547	-7.547	0.000	0.000	0.000
17	A	37	PRO	0	-0.011	-0.003	38.536	-0.213	-0.213	0.000	0.000	0.000
18	A	38	GLU	-1	-0.825	-0.905	38.124	-7.922	-7.922	0.000	0.000	0.000
19	A	39	ALA	0	-0.023	-0.009	36.350	-0.185	-0.185	0.000	0.000	0.000
20	A	40	VAL	0	-0.031	-0.006	33.188	-0.300	-0.300	0.000	0.000	0.000
21	A	41	LYS	1	0.771	0.895	32.534	7.701	7.701	0.000	0.000	0.000
22	A	42	LYS	1	0.890	0.954	31.806	8.757	8.757	0.000	0.000	0.000
23	A	43	VAL	0	0.030	0.021	28.712	0.108	0.108	0.000	0.000	0.000
24	A	44	HIS	0	-0.047	-0.023	24.501	0.081	0.081	0.000	0.000	0.000
25	A	45	ILE	0	-0.024	-0.022	22.019	-0.004	-0.004	0.000	0.000	0.000
26	A	46	ASP	-1	-0.693	-0.826	20.644	-13.316	-13.316	0.000	0.000	0.000
27	A	47	LEU	0	-0.056	-0.032	14.074	0.032	0.032	0.000	0.000	0.000
28	A	48	TRP	0	0.007	0.001	16.172	-0.335	-0.335	0.000	0.000	0.000
29	A	49	ASP	-1	-0.701	-0.835	10.791	-27.156	-27.156	0.000	0.000	0.000
30	A	50	ALA	0	0.038	0.008	14.015	0.579	0.579	0.000	0.000	0.000
31	A	51	ALA	0	-0.039	-0.019	11.262	0.659	0.659	0.000	0.000	0.000
32	A	52	ALA	0	0.008	0.008	11.698	0.423	0.423	0.000	0.000	0.000
33	A	53	ALA	0	0.023	0.011	12.843	0.969	0.969	0.000	0.000	0.000
34	A	54	ALA	0	-0.055	-0.017	15.169	0.781	0.781	0.000	0.000	0.000
35	A	55	ALA	0	-0.069	-0.024	12.650	0.427	0.427	0.000	0.000	0.000
36	A	56	GLU	-1	-0.966	-0.982	14.571	-13.994	-13.994	0.000	0.000	0.000
37	A	57	SER	0	-0.110	-0.055	12.643	0.049	0.049	0.000	0.000	0.000
38	A	58	ASP	-1	-0.927	-0.973	14.320	-15.626	-15.626	0.000	0.000	0.000
39	A	59	ASP	-1	-0.878	-0.936	13.709	-17.119	-17.119	0.000	0.000	0.000
40	A	60	LEU	0	-0.024	-0.008	15.445	-0.399	-0.399	0.000	0.000	0.000
41	A	61	MET	0	-0.072	-0.012	10.467	-0.466	-0.466	0.000	0.000	0.000
42	A	62	GLY	0	-0.009	-0.018	14.455	-0.042	-0.042	0.000	0.000	0.000
43	A	63	ARG	1	0.831	0.905	17.253	12.919	12.919	0.000	0.000	0.000
44	A	64	THR	0	-0.061	-0.027	21.044	0.301	0.301	0.000	0.000	0.000
45	A	65	TRP	0	-0.001	0.000	23.608	0.300	0.300	0.000	0.000	0.000
46	A	66	SER	0	-0.058	-0.024	27.232	-0.033	-0.033	0.000	0.000	0.000
47	A	67	ASP	-1	-0.791	-0.908	28.821	-9.746	-9.746	0.000	0.000	0.000
48	A	68	ARG	1	0.915	0.936	31.412	8.866	8.866	0.000	0.000	0.000
49	A	69	ASN	0	-0.064	-0.046	33.239	0.471	0.471	0.000	0.000	0.000
50	A	70	GLY	0	0.057	0.045	31.682	0.018	0.018	0.000	0.000	0.000
51	A	71	ASN	0	-0.071	-0.023	28.056	-0.424	-0.424	0.000	0.000	0.000
52	A	72	PHE	0	0.039	0.020	21.835	0.182	0.182	0.000	0.000	0.000
53	A	73	GLN	0	-0.014	-0.017	20.840	-0.002	-0.002	0.000	0.000	0.000
54	A	74	VAL	0	0.011	0.015	17.763	0.408	0.408	0.000	0.000	0.000
55	A	75	THR	0	-0.009	-0.018	13.787	-0.646	-0.646	0.000	0.000	0.000
56	A	76	GLY	0	0.056	0.031	13.318	1.052	1.052	0.000	0.000	0.000
57	A	78	ALA	0	0.102	0.054	7.705	2.137	2.137	0.000	0.000	0.000
58	A	79	SER	0	-0.041	-0.044	3.940	-7.219	-7.031	0.000	-0.071	-0.116
59	A	80	ASH	0	-0.034	-0.032	5.545	4.080	4.080	0.000	0.000	0.000
60	A	81	PHE	0	-0.022	-0.015	5.490	-4.612	-4.612	0.000	0.000	0.000
61	A	82	GLY	0	0.016	0.013	7.648	1.941	1.941	0.000	0.000	0.000
62	A	83	PRO	0	-0.041	-0.037	10.269	-1.877	-1.877	0.000	0.000	0.000
63	A	84	ILE	0	0.036	0.024	11.670	-1.238	-1.238	0.000	0.000	0.000
64	A	85	ASN	0	0.008	0.002	6.075	-0.210	-0.210	0.000	0.000	0.000
65	A	86	THR	0	-0.071	-0.038	6.196	-7.512	-7.512	0.000	0.000	0.000
66	A	87	PRO	0	-0.040	-0.023	6.299	3.089	3.089	0.000	0.000	0.000
67	A	88	ASP	-1	-0.887	-0.951	9.210	-22.229	-22.229	0.000	0.000	0.000
68	A	89	PRO	0	-0.051	-0.006	11.335	1.372	1.372	0.000	0.000	0.000
69	A	90	TYR	0	0.082	0.042	14.119	1.151	1.151	0.000	0.000	0.000
70	A	91	LEU	0	-0.082	-0.047	17.891	-0.071	-0.071	0.000	0.000	0.000
71	A	92	TYR	0	0.007	0.019	20.605	0.649	0.649	0.000	0.000	0.000
72	A	93	ILE	0	0.014	-0.004	23.398	0.112	0.112	0.000	0.000	0.000
73	A	94	GLN	0	0.014	0.007	26.496	0.021	0.021	0.000	0.000	0.000
74	A	95	HIS	0	-0.016	-0.010	29.495	0.205	0.205	0.000	0.000	0.000
75	A	96	ASN	0	0.007	-0.008	32.528	0.139	0.139	0.000	0.000	0.000
76	A	98	PRO	0	0.029	0.026	36.715	-0.121	-0.121	0.000	0.000	0.000
77	A	99	HIS	0	-0.076	-0.046	35.875	0.205	0.205	0.000	0.000	0.000
78	A	100	ARG	1	0.923	0.954	37.519	8.611	8.611	0.000	0.000	0.000
79	A	101	ASP	-1	-0.937	-0.959	40.727	-7.562	-7.562	0.000	0.000	0.000
80	A	102	SER	0	-0.019	-0.019	39.821	0.155	0.155	0.000	0.000	0.000
81	A	103	ASN	0	-0.028	-0.019	41.464	0.021	0.021	0.000	0.000	0.000
82	A	104	ALA	0	-0.019	0.001	37.382	-0.025	-0.025	0.000	0.000	0.000
83	A	105	THR	0	0.035	0.019	36.045	0.055	0.055	0.000	0.000	0.000
84	A	106	ASN	0	-0.030	-0.004	33.074	-0.048	-0.048	0.000	0.000	0.000
85	A	107	PRO	0	0.012	0.000	28.621	-0.105	-0.105	0.000	0.000	0.000
86	A	108	ILE	0	-0.014	0.009	26.386	0.030	0.030	0.000	0.000	0.000
87	A	109	GLN	0	0.054	0.019	22.755	-0.659	-0.659	0.000	0.000	0.000
88	A	110	ILE	0	-0.083	-0.046	20.882	0.328	0.328	0.000	0.000	0.000
89	A	111	ASP	-1	-0.850	-0.929	18.241	-17.392	-17.392	0.000	0.000	0.000
90	A	112	VAL	0	-0.098	-0.033	14.548	0.308	0.308	0.000	0.000	0.000
91	A	113	ILE	0	0.032	0.012	14.485	-1.005	-1.005	0.000	0.000	0.000
92	A	114	PRO	0	0.062	0.023	10.575	-0.394	-0.394	0.000	0.000	0.000
93	A	115	LEU	0	-0.053	-0.019	10.025	-2.533	-2.533	0.000	0.000	0.000
94	A	116	PHE	0	-0.001	-0.014	6.552	0.304	0.304	0.000	0.000	0.000
95	A	117	LEU	0	-0.008	0.003	9.062	0.793	0.793	0.000	0.000	0.000
96	A	118	PRO	0	-0.048	-0.042	8.447	-3.400	-3.400	0.000	0.000	0.000
97	A	119	SER	0	-0.066	-0.002	11.287	2.933	2.933	0.000	0.000	0.000
98	A	120	ILE	0	-0.004	-0.008	12.892	-0.429	-0.429	0.000	0.000	0.000
99	A	121	VAL	0	0.033	0.020	14.698	0.671	0.671	0.000	0.000	0.000
100	A	122	ARG	1	0.892	0.942	17.307	15.022	15.022	0.000	0.000	0.000
101	A	123	LEU	0	0.047	0.019	20.056	0.175	0.175	0.000	0.000	0.000
102	A	124	GLY	0	-0.017	0.008	22.899	0.433	0.433	0.000	0.000	0.000
103	A	125	ASN	0	-0.042	-0.038	26.347	-0.108	-0.108	0.000	0.000	0.000
104	A	126	VAL	0	0.038	0.018	25.277	-0.074	-0.074	0.000	0.000	0.000
105	A	127	TYR	0	-0.058	-0.041	28.437	0.254	0.254	0.000	0.000	0.000
106	A	128	LEU	0	0.028	0.009	29.263	-0.197	-0.197	0.000	0.000	0.000
107	A	129	ASP	-1	-0.723	-0.860	32.500	-8.722	-8.722	0.000	0.000	0.000
108	A	130	ARG	1	0.772	0.863	32.940	9.317	9.317	0.000	0.000	0.000
109	A	131	TYR	0	0.035	0.005	31.471	-0.200	-0.200	0.000	0.000	0.000
110	A	132	LEU	0	0.010	0.010	26.246	0.160	0.160	0.000	0.000	0.000
111	A	133	GLU	-1	-0.881	-0.965	30.340	-10.158	-10.158	0.000	0.000	0.000
112	A	134	ASP	-1	-0.836	-0.878	32.880	-8.779	-8.779	0.000	0.000	0.000
113	A	135	TYR	0	-0.083	-0.041	32.907	0.312	0.312	0.000	0.000	0.000
114	A	136	HIS	0	-0.015	-0.015	27.539	0.364	0.364	0.000	0.000	0.000
115	A	137	HIS	0	-0.022	0.017	32.955	0.208	0.208	0.000	0.000	0.000

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