FMO DATABASE

FMODB ID: 3JK6L

Calculation Name: 1TWU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TWU

Chain ID: A

ChEMBL ID:

UniProt ID: P37479

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:

Apendix: None

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1178141.216056
FMO2-HF: Nuclear repulsion	1124221.654697
FMO2-HF: Total energy	-53919.561359
FMO2-MP2: Total energy	-54077.459342

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:3:LYS)

Summations of interaction energy for fragment #1(A:3: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.
-161.817	-148.24	11.371	-9.446	-15.5	-0.101

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.965

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	5	PHE	0	0.002	0.005	2.738	1.720	3.941	0.150	-0.789	-1.581	0.002
4	A	6	SER	0	-0.011	-0.021	5.832	1.125	1.125	0.000	0.000	0.000	0.000
5	A	7	SER	0	0.000	0.002	9.475	1.179	1.179	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.013	0.009	6.394	1.518	1.518	0.000	0.000	0.000	0.000
7	A	9	GLN	0	0.020	0.016	2.718	2.989	3.645	0.244	-0.209	-0.691	0.001
8	A	10	ALA	0	0.013	0.012	2.850	2.665	3.493	0.096	-0.202	-0.722	-0.001
9	A	11	ALA	0	0.008	-0.004	2.244	-17.437	-15.832	3.432	-2.213	-2.823	-0.031
10	A	12	GLN	0	-0.010	-0.016	2.263	-12.421	-11.920	4.603	-1.928	-3.177	-0.025
11	A	13	ILE	0	-0.058	-0.023	2.935	3.317	4.007	0.044	-0.046	-0.688	-0.001
12	A	14	ARG	1	0.868	0.923	4.828	26.056	26.103	-0.001	-0.001	-0.044	0.000
13	A	15	ILE	0	-0.024	0.010	8.321	1.154	1.154	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.011	-0.006	11.229	0.392	0.392	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.914	0.966	14.336	17.033	17.033	0.000	0.000	0.000	0.000
16	A	18	PRO	0	0.002	0.018	17.778	-0.117	-0.117	0.000	0.000	0.000	0.000
17	A	19	THR	0	0.022	-0.024	21.253	0.246	0.246	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.028	0.011	23.856	0.110	0.110	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.095	-0.064	26.126	0.762	0.762	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.050	0.007	20.922	-0.369	-0.369	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.894	-0.945	24.022	-11.787	-11.787	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.930	-0.964	26.184	-10.938	-10.938	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.070	-0.027	20.382	-0.348	-0.348	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.013	-0.011	21.594	-0.689	-0.689	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.921	0.974	22.668	10.480	10.480	0.000	0.000	0.000	0.000
26	A	28	PHE	0	0.019	0.006	20.277	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	29	TYR	0	-0.058	-0.052	17.366	-0.695	-0.695	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.836	-0.907	19.432	-15.555	-15.555	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.964	-0.978	20.973	-11.460	-11.460	0.000	0.000	0.000	0.000
30	A	32	GLY	0	-0.015	-0.032	23.625	0.341	0.341	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.083	-0.049	17.585	0.031	0.031	0.000	0.000	0.000	0.000
32	A	34	CYS	0	-0.089	-0.022	19.783	0.057	0.057	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.017	0.006	14.279	-0.865	-0.865	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.959	0.973	13.224	21.051	21.051	0.000	0.000	0.000	0.000
35	A	37	ARG	1	0.909	0.940	14.707	13.193	13.193	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.153	-0.085	9.886	0.204	0.204	0.000	0.000	0.000	0.000
37	A	39	GLY	0	-0.002	-0.001	13.720	-0.754	-0.754	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.871	-0.940	15.687	-14.256	-14.256	0.000	0.000	0.000	0.000
39	A	41	PHE	0	-0.081	-0.025	17.785	-0.060	-0.060	0.000	0.000	0.000	0.000
40	A	42	SER	0	0.024	0.020	21.294	0.285	0.285	0.000	0.000	0.000	0.000
41	A	43	GLN	0	-0.004	-0.011	24.992	0.385	0.385	0.000	0.000	0.000	0.000
42	A	44	HIS	0	-0.013	0.003	21.176	0.438	0.438	0.000	0.000	0.000	0.000
43	A	45	ASN	0	-0.069	-0.050	23.132	0.122	0.122	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.060	0.030	26.383	0.018	0.018	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.035	-0.011	22.633	0.103	0.103	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.801	-0.879	23.559	-12.165	-12.165	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.023	-0.020	19.566	-0.197	-0.197	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.015	0.008	17.962	0.113	0.113	0.000	0.000	0.000	0.000
49	A	51	MET	0	-0.044	-0.024	12.706	-0.560	-0.560	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.015	0.003	13.525	0.461	0.461	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.005	-0.012	10.487	-2.096	-2.096	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.028	0.015	8.849	2.278	2.278	0.000	0.000	0.000	0.000
53	A	55	PRO	0	-0.006	-0.021	8.781	-2.828	-2.828	0.000	0.000	0.000	0.000
54	A	56	HIS	0	0.021	-0.005	7.122	2.449	2.449	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.087	0.027	6.825	0.008	0.008	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.943	-0.958	2.254	-71.273	-68.769	1.548	-1.709	-2.342	-0.016
57	A	59	TYR	0	-0.002	-0.021	2.535	-30.159	-25.669	1.256	-2.348	-3.399	-0.030
58	A	60	HIS	0	-0.023	0.013	5.242	7.465	7.500	-0.001	-0.001	-0.033	0.000
59	A	61	LEU	0	0.013	0.010	8.721	-0.700	-0.700	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.831	-0.937	11.924	-20.561	-20.561	0.000	0.000	0.000	0.000
61	A	63	PHE	0	0.003	0.009	14.339	0.156	0.156	0.000	0.000	0.000	0.000
62	A	64	THR	0	0.013	0.002	17.995	0.423	0.423	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.097	0.051	20.540	-0.149	-0.149	0.000	0.000	0.000	0.000
64	A	66	TYR	0	-0.043	-0.032	24.338	0.085	0.085	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.911	-0.960	26.723	-9.924	-9.924	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.042	-0.011	29.898	0.369	0.369	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.051	-0.016	31.076	0.138	0.138	0.000	0.000	0.000	0.000
68	A	70	SER	0	-0.022	-0.016	25.055	-0.246	-0.246	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.005	-0.001	27.030	0.302	0.302	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.019	0.021	23.804	-0.428	-0.428	0.000	0.000	0.000	0.000
71	A	73	PRO	0	-0.092	-0.052	20.564	0.332	0.332	0.000	0.000	0.000	0.000
72	A	74	VAL	0	0.010	0.009	23.853	0.236	0.236	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.007	0.005	25.074	-0.340	-0.340	0.000	0.000	0.000	0.000
74	A	76	HIS	0	0.012	0.010	24.198	0.248	0.248	0.000	0.000	0.000	0.000
75	A	77	PRO	0	-0.012	0.002	24.663	-0.517	-0.517	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.841	-0.936	24.328	-11.958	-11.958	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.110	-0.050	20.105	-0.851	-0.851	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.026	-0.029	19.389	0.196	0.196	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.008	0.023	13.291	-1.235	-1.235	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.030	-0.022	15.928	0.800	0.800	0.000	0.000	0.000	0.000
81	A	83	PHE	0	-0.002	0.006	13.668	-1.706	-1.706	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.023	-0.023	15.092	0.968	0.968	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.003	-0.001	17.131	-0.718	-0.718	0.000	0.000	0.000	0.000
84	A	86	PRO	0	-0.028	-0.017	18.676	0.803	0.803	0.000	0.000	0.000	0.000
85	A	87	ASN	0	0.022	0.019	21.632	1.105	1.105	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.076	0.012	23.836	-0.089	-0.089	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.002	0.010	26.463	0.218	0.218	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.921	-0.961	21.394	-14.400	-14.400	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.029	0.003	23.054	-0.073	-0.073	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.015	-0.002	24.305	0.071	0.071	0.000	0.000	0.000	0.000
91	A	93	ALA	0	-0.014	-0.005	26.187	0.237	0.237	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.008	0.005	21.585	0.195	0.195	0.000	0.000	0.000	0.000
93	A	95	THR	0	0.002	-0.012	24.693	0.304	0.304	0.000	0.000	0.000	0.000
94	A	96	SER	0	0.011	0.007	26.427	0.405	0.405	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.877	0.952	24.648	12.979	12.979	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.014	0.007	22.924	0.212	0.212	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.896	0.949	27.470	10.188	10.188	0.000	0.000	0.000	0.000
98	A	100	HIS	0	-0.082	-0.033	30.712	0.293	0.293	0.000	0.000	0.000	0.000
99	A	101	MET	0	-0.066	-0.009	26.661	0.131	0.131	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.020	0.008	31.023	0.079	0.079	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.001	0.009	27.050	0.045	0.045	0.000	0.000	0.000	0.000
102	A	104	GLN	0	0.037	0.009	29.477	0.259	0.259	0.000	0.000	0.000	0.000
103	A	105	GLU	-1	-0.863	-0.935	28.755	-10.783	-10.783	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.054	-0.033	27.815	0.338	0.338	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.896	-0.956	29.595	-9.867	-9.867	0.000	0.000	0.000	0.000
106	A	108	SER	0	-0.080	-0.038	27.069	-0.157	-0.157	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.870	-0.936	27.740	-9.946	-9.946	0.000	0.000	0.000	0.000
108	A	110	ASN	0	-0.021	-0.015	26.453	0.561	0.561	0.000	0.000	0.000	0.000
109	A	111	PRO	0	0.048	0.013	28.472	-0.216	-0.216	0.000	0.000	0.000	0.000
110	A	112	TYR	0	-0.035	-0.013	22.278	0.136	0.136	0.000	0.000	0.000	0.000
111	A	113	TRP	0	-0.007	-0.033	19.518	-0.231	-0.231	0.000	0.000	0.000	0.000
112	A	114	SER	0	0.051	0.040	25.930	-0.060	-0.060	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.039	-0.015	28.683	0.500	0.500	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.031	-0.019	27.460	-0.309	-0.309	0.000	0.000	0.000	0.000
115	A	117	GLY	0	-0.005	-0.022	25.077	-0.595	-0.595	0.000	0.000	0.000	0.000
116	A	118	VAL	0	0.015	0.027	24.822	0.408	0.408	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.006	-0.004	24.160	-0.834	-0.834	0.000	0.000	0.000	0.000
118	A	120	ILE	0	-0.022	-0.005	24.242	0.590	0.590	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.900	-0.952	23.941	-11.707	-11.707	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.814	-0.883	21.178	-14.190	-14.190	0.000	0.000	0.000	0.000
121	A	123	PRO	0	0.006	-0.020	23.360	0.378	0.378	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.832	-0.890	23.524	-12.220	-12.220	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.010	0.009	25.382	0.056	0.056	0.000	0.000	0.000	0.000
124	A	126	TRP	0	-0.099	-0.046	14.476	-0.556	-0.556	0.000	0.000	0.000	0.000
125	A	127	ARG	1	0.908	0.964	22.032	11.832	11.832	0.000	0.000	0.000	0.000
126	A	128	ILE	0	0.020	0.007	18.555	-0.917	-0.917	0.000	0.000	0.000	0.000
127	A	129	VAL	0	-0.002	-0.002	19.837	0.733	0.733	0.000	0.000	0.000	0.000
128	A	130	PHE	0	0.020	0.017	19.566	-1.073	-1.073	0.000	0.000	0.000	0.000
129	A	131	MET	0	-0.016	0.013	20.276	0.785	0.785	0.000	0.000	0.000	0.000
130	A	132	ASN	0	0.033	0.019	20.997	-1.028	-1.028	0.000	0.000	0.000	0.000
131	A	133	SER	0	-0.025	-0.027	20.855	0.192	0.192	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.966	0.963	17.338	13.684	13.684	0.000	0.000	0.000	0.000
133	A	135	GLY	0	0.030	0.042	16.070	-1.082	-1.082	0.000	0.000	0.000	0.000
134	A	136	ILE	0	-0.010	-0.004	13.902	1.075	1.075	0.000	0.000	0.000	0.000
135	A	137	SER	0	-0.013	-0.018	14.788	-0.944	-0.944	0.000	0.000	0.000	0.000
136	A	138	GLY	0	0.036	0.026	13.415	-0.866	-0.866	0.000	0.000	0.000	0.000
137	A	139	LYS	1	0.937	0.973	14.467	13.920	13.920	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)