FMO DATABASE

FMODB ID: R57K8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-913750.662159
FMO2-HF: Nuclear repulsion	867264.277881
FMO2-HF: Total energy	-46486.384278
FMO2-MP2: Total energy	-46619.544852

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.
-124.779	-120.924	0.155	-1.882	-2.128	-0.001

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 : 1.016 / q_NPA : 1.008

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

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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	-0.075	-0.029	3.147	-8.885	-5.796	0.151	-1.518	-1.722	-0.001
4	A	24	CYS	0	-0.086	-0.044	5.030	2.168	2.210	-0.002	-0.002	-0.038	0.000
5	A	25	LEU	0	0.054	0.033	8.835	-1.276	-1.276	0.000	0.000	0.000	0.000
6	A	26	MET	0	-0.015	-0.003	11.446	1.248	1.248	0.000	0.000	0.000	0.000
7	A	27	ALA	0	0.039	0.029	15.134	-0.207	-0.207	0.000	0.000	0.000	0.000
8	A	28	THR	0	-0.056	-0.036	17.879	0.900	0.900	0.000	0.000	0.000	0.000
9	A	29	GLY	0	0.047	0.016	21.473	-0.193	-0.193	0.000	0.000	0.000	0.000
10	A	30	VAL	0	-0.043	-0.026	24.921	0.239	0.239	0.000	0.000	0.000	0.000
11	A	31	LEU	0	0.034	0.036	27.023	0.100	0.100	0.000	0.000	0.000	0.000
12	A	32	LYS	1	0.831	0.905	30.025	10.116	10.116	0.000	0.000	0.000	0.000
13	A	33	CYS	0	0.007	0.037	33.290	0.218	0.218	0.000	0.000	0.000	0.000
14	A	34	PRO	0	-0.041	-0.028	36.118	0.188	0.188	0.000	0.000	0.000	0.000
15	A	35	THR	0	-0.008	-0.017	39.016	0.175	0.175	0.000	0.000	0.000	0.000
16	A	36	ASP	-1	-0.807	-0.920	39.354	-7.780	-7.780	0.000	0.000	0.000	0.000
17	A	37	PRO	0	-0.016	-0.016	38.403	-0.241	-0.241	0.000	0.000	0.000	0.000
18	A	38	GLU	-1	-0.816	-0.894	38.130	-8.091	-8.091	0.000	0.000	0.000	0.000
19	A	39	ALA	0	0.002	0.015	36.288	-0.225	-0.225	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.021	0.002	33.037	-0.311	-0.311	0.000	0.000	0.000	0.000
21	A	41	LYS	1	0.726	0.873	32.227	7.851	7.851	0.000	0.000	0.000	0.000
22	A	42	LYS	1	0.896	0.945	31.679	8.855	8.855	0.000	0.000	0.000	0.000
23	A	43	VAL	0	0.021	0.018	28.404	0.077	0.077	0.000	0.000	0.000	0.000
24	A	44	HIS	0	-0.062	-0.028	24.027	0.154	0.154	0.000	0.000	0.000	0.000
25	A	45	ILE	0	-0.008	-0.016	21.862	0.022	0.022	0.000	0.000	0.000	0.000
26	A	46	ASP	-1	-0.688	-0.799	20.320	-13.776	-13.776	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.044	-0.022	13.648	0.018	0.018	0.000	0.000	0.000	0.000
28	A	48	TRP	0	-0.041	-0.030	15.812	-0.215	-0.215	0.000	0.000	0.000	0.000
29	A	49	ASP	-1	-0.705	-0.855	10.637	-29.125	-29.125	0.000	0.000	0.000	0.000
30	A	50	ALA	0	0.039	0.021	13.870	0.616	0.616	0.000	0.000	0.000	0.000
31	A	51	ALA	0	-0.049	-0.019	10.860	0.688	0.688	0.000	0.000	0.000	0.000
32	A	52	ALA	0	0.013	0.010	11.774	0.596	0.596	0.000	0.000	0.000	0.000
33	A	53	ALA	0	0.024	0.015	12.925	1.083	1.083	0.000	0.000	0.000	0.000
34	A	54	ALA	0	-0.068	-0.029	15.085	0.941	0.941	0.000	0.000	0.000	0.000
35	A	55	ALA	0	-0.066	-0.030	12.519	0.122	0.122	0.000	0.000	0.000	0.000
36	A	56	GLU	-1	-0.972	-0.974	14.454	-14.507	-14.507	0.000	0.000	0.000	0.000
37	A	57	SER	0	-0.089	-0.049	13.004	0.233	0.233	0.000	0.000	0.000	0.000
38	A	58	ASP	-1	-0.940	-0.977	14.880	-16.362	-16.362	0.000	0.000	0.000	0.000
39	A	59	ASP	-1	-0.847	-0.925	13.875	-18.342	-18.342	0.000	0.000	0.000	0.000
40	A	60	LEU	0	-0.026	-0.007	15.224	-0.573	-0.573	0.000	0.000	0.000	0.000
41	A	61	MET	0	-0.069	-0.018	10.011	-0.314	-0.314	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.006	-0.003	13.984	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	63	ARG	1	0.808	0.868	17.042	13.583	13.583	0.000	0.000	0.000	0.000
44	A	64	THR	0	-0.071	-0.045	20.870	0.303	0.303	0.000	0.000	0.000	0.000
45	A	65	TRP	0	0.012	0.000	23.543	0.320	0.320	0.000	0.000	0.000	0.000
46	A	66	SER	0	-0.061	-0.024	27.256	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	67	ASP	-1	-0.714	-0.865	29.101	-9.341	-9.341	0.000	0.000	0.000	0.000
48	A	68	ARG	1	0.876	0.933	31.456	9.058	9.058	0.000	0.000	0.000	0.000
49	A	69	ASN	0	-0.080	-0.057	33.348	0.484	0.484	0.000	0.000	0.000	0.000
50	A	70	GLY	0	0.045	0.024	31.663	0.026	0.026	0.000	0.000	0.000	0.000
51	A	71	ASN	0	-0.097	-0.043	28.320	-0.463	-0.463	0.000	0.000	0.000	0.000
52	A	72	PHE	0	0.049	0.022	21.806	0.200	0.200	0.000	0.000	0.000	0.000
53	A	73	GLN	0	0.000	-0.012	21.013	-0.278	-0.278	0.000	0.000	0.000	0.000
54	A	74	VAL	0	0.026	0.033	17.568	0.496	0.496	0.000	0.000	0.000	0.000
55	A	75	THR	0	-0.006	-0.016	14.118	-0.355	-0.355	0.000	0.000	0.000	0.000
56	A	76	GLY	0	0.061	0.033	13.445	1.128	1.128	0.000	0.000	0.000	0.000
57	A	78	ALA	0	0.111	0.064	7.722	2.210	2.210	0.000	0.000	0.000	0.000
58	A	79	SER	0	-0.048	-0.063	3.219	-4.426	-3.702	0.006	-0.362	-0.368	0.000
59	A	80	ASH	0	-0.021	-0.014	5.389	4.866	4.866	0.000	0.000	0.000	0.000
60	A	81	PHE	0	-0.007	-0.005	5.566	-4.617	-4.617	0.000	0.000	0.000	0.000
61	A	82	GLY	0	0.025	0.018	7.713	1.829	1.829	0.000	0.000	0.000	0.000
62	A	83	PRO	0	-0.015	-0.030	10.010	-2.408	-2.408	0.000	0.000	0.000	0.000
63	A	84	ILE	0	0.022	0.024	10.643	-1.204	-1.204	0.000	0.000	0.000	0.000
64	A	85	ASN	0	-0.039	-0.025	5.781	-4.895	-4.895	0.000	0.000	0.000	0.000
65	A	86	THR	0	-0.052	-0.023	5.366	-10.491	-10.491	0.000	0.000	0.000	0.000
66	A	87	PRO	0	-0.020	-0.015	5.755	3.713	3.713	0.000	0.000	0.000	0.000
67	A	88	ASP	-1	-0.847	-0.912	8.683	-23.943	-23.943	0.000	0.000	0.000	0.000
68	A	89	PRO	0	-0.041	-0.015	10.684	1.600	1.600	0.000	0.000	0.000	0.000
69	A	90	TYR	0	-0.002	-0.017	13.403	1.410	1.410	0.000	0.000	0.000	0.000
70	A	91	LEU	0	-0.075	-0.042	17.180	-0.133	-0.133	0.000	0.000	0.000	0.000
71	A	92	TYR	0	-0.011	0.005	19.950	0.645	0.645	0.000	0.000	0.000	0.000
72	A	93	ILE	0	-0.003	-0.009	22.805	0.048	0.048	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.032	0.022	26.030	0.121	0.121	0.000	0.000	0.000	0.000
74	A	95	HIS	0	-0.009	-0.012	29.279	0.212	0.212	0.000	0.000	0.000	0.000
75	A	96	ASN	0	0.019	0.001	32.111	0.077	0.077	0.000	0.000	0.000	0.000
76	A	98	PRO	0	0.039	0.019	36.361	-0.110	-0.110	0.000	0.000	0.000	0.000
77	A	99	HIS	0	-0.028	0.004	35.499	0.212	0.212	0.000	0.000	0.000	0.000
78	A	100	ARG	1	0.822	0.885	36.377	8.944	8.944	0.000	0.000	0.000	0.000
79	A	101	ASP	-1	-0.890	-0.929	39.879	-7.879	-7.879	0.000	0.000	0.000	0.000
80	A	102	SER	0	-0.042	-0.042	39.476	0.139	0.139	0.000	0.000	0.000	0.000
81	A	103	ASN	0	-0.085	-0.047	41.250	0.085	0.085	0.000	0.000	0.000	0.000
82	A	104	ALA	0	0.013	0.026	37.327	0.003	0.003	0.000	0.000	0.000	0.000
83	A	105	THR	0	0.017	0.000	35.701	0.039	0.039	0.000	0.000	0.000	0.000
84	A	106	ASN	0	0.002	0.008	32.287	0.017	0.017	0.000	0.000	0.000	0.000
85	A	107	PRO	0	0.015	0.001	28.584	-0.108	-0.108	0.000	0.000	0.000	0.000
86	A	108	ILE	0	-0.036	-0.001	25.956	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	109	GLN	0	0.058	0.023	21.855	-0.640	-0.640	0.000	0.000	0.000	0.000
88	A	110	ILE	0	-0.080	-0.038	20.608	0.341	0.341	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.855	-0.930	17.916	-18.137	-18.137	0.000	0.000	0.000	0.000
90	A	112	VAL	0	-0.079	-0.031	14.372	0.568	0.568	0.000	0.000	0.000	0.000
91	A	113	ILE	0	0.057	0.024	14.333	-1.266	-1.266	0.000	0.000	0.000	0.000
92	A	114	PRO	0	0.065	0.024	9.233	-0.362	-0.362	0.000	0.000	0.000	0.000
93	A	115	LEU	0	-0.076	-0.030	9.264	-2.583	-2.583	0.000	0.000	0.000	0.000
94	A	116	PHE	0	0.021	-0.004	6.732	0.259	0.259	0.000	0.000	0.000	0.000
95	A	117	LEU	0	-0.024	0.002	8.924	1.563	1.563	0.000	0.000	0.000	0.000
96	A	118	PRO	0	-0.048	-0.033	8.721	-3.074	-3.074	0.000	0.000	0.000	0.000
97	A	119	SER	0	-0.039	-0.015	11.101	2.566	2.566	0.000	0.000	0.000	0.000
98	A	120	ILE	0	-0.025	-0.023	13.373	-0.273	-0.273	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.039	0.033	14.676	0.914	0.914	0.000	0.000	0.000	0.000
100	A	122	ARG	1	0.885	0.929	17.323	15.316	15.316	0.000	0.000	0.000	0.000
101	A	123	LEU	0	0.058	0.029	19.946	0.302	0.302	0.000	0.000	0.000	0.000
102	A	124	GLY	0	-0.008	0.012	22.971	0.478	0.478	0.000	0.000	0.000	0.000
103	A	125	ASN	0	-0.026	-0.028	26.433	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	126	VAL	0	0.029	0.023	24.842	0.020	0.020	0.000	0.000	0.000	0.000
105	A	127	TYR	0	-0.041	-0.037	28.109	0.242	0.242	0.000	0.000	0.000	0.000
106	A	128	LEU	0	0.019	0.013	29.100	-0.280	-0.280	0.000	0.000	0.000	0.000
107	A	129	ASP	-1	-0.779	-0.883	32.258	-8.949	-8.949	0.000	0.000	0.000	0.000
108	A	130	ARG	1	0.803	0.884	32.531	9.487	9.487	0.000	0.000	0.000	0.000
109	A	131	TYR	0	0.045	0.016	31.073	-0.225	-0.225	0.000	0.000	0.000	0.000
110	A	132	LEU	0	0.000	0.012	26.019	0.130	0.130	0.000	0.000	0.000	0.000
111	A	133	GLU	-1	-0.863	-0.955	30.094	-10.452	-10.452	0.000	0.000	0.000	0.000
112	A	134	ASP	-1	-0.800	-0.878	32.548	-8.987	-8.987	0.000	0.000	0.000	0.000
113	A	135	TYR	0	-0.067	-0.021	31.694	0.352	0.352	0.000	0.000	0.000	0.000
114	A	136	HIS	0	0.011	-0.008	26.769	0.413	0.413	0.000	0.000	0.000	0.000
115	A	137	HIS	0	-0.073	-0.015	32.387	0.437	0.437	0.000	0.000	0.000	0.000

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