FMO DATABASE

FMODB ID: JQ239

Calculation Name: 5LP5-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LP5

Chain ID: F

ChEMBL ID:

UniProt ID: O26085

Base Structure: X-ray

Registration Date: 2023-09-21

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1442420.39748
FMO2-HF: Nuclear repulsion	1383095.535764
FMO2-HF: Total energy	-59324.861716
FMO2-MP2: Total energy	-59499.094262

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(F:92:LYS)

Summations of interaction energy for fragment #1(F:92: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.
-41.831	-38.147	-0.036	-1.798	-1.848	0.002

Interaction energy analysis for fragmet #1(F:92:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 0.978

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	F	94	THR	0	0.005	0.019	3.791	-6.446	-3.216	-0.036	-1.747	-1.447	0.002
4	F	95	TYR	0	0.025	0.021	6.165	2.734	2.734	0.000	0.000	0.000	0.000
5	F	96	THR	0	0.007	0.003	9.867	-0.689	-0.689	0.000	0.000	0.000	0.000
6	F	97	PRO	0	-0.020	0.007	12.377	0.768	0.768	0.000	0.000	0.000	0.000
7	F	98	THR	0	-0.006	-0.016	16.051	0.321	0.321	0.000	0.000	0.000	0.000
8	F	99	PHE	0	-0.030	-0.009	18.863	0.273	0.273	0.000	0.000	0.000	0.000
9	F	100	MET	0	0.030	0.039	22.288	0.195	0.195	0.000	0.000	0.000	0.000
10	F	101	THR	0	-0.048	-0.024	24.839	0.340	0.340	0.000	0.000	0.000	0.000
11	F	102	SER	0	-0.014	-0.011	27.695	0.448	0.448	0.000	0.000	0.000	0.000
12	F	103	PHE	0	0.038	0.014	28.606	-0.357	-0.357	0.000	0.000	0.000	0.000
13	F	104	ILE	0	-0.062	-0.014	26.383	0.195	0.195	0.000	0.000	0.000	0.000
14	F	105	SER	0	-0.009	-0.005	30.764	0.308	0.308	0.000	0.000	0.000	0.000
15	F	106	LEU	0	-0.005	-0.009	33.504	-0.018	-0.018	0.000	0.000	0.000	0.000
16	F	107	GLU	-1	-0.962	-0.978	36.088	-7.576	-7.576	0.000	0.000	0.000	0.000
17	F	108	ASP	-1	-0.935	-0.971	32.228	-9.179	-9.179	0.000	0.000	0.000	0.000
18	F	109	THR	0	-0.049	-0.057	31.464	0.009	0.009	0.000	0.000	0.000	0.000
19	F	110	HIS	0	0.027	0.003	28.647	-0.543	-0.543	0.000	0.000	0.000	0.000
20	F	111	SER	0	0.012	0.000	26.719	-0.545	-0.545	0.000	0.000	0.000	0.000
21	F	112	VAL	0	0.000	-0.007	23.917	0.362	0.362	0.000	0.000	0.000	0.000
22	F	113	SER	0	0.020	0.013	24.842	-0.340	-0.340	0.000	0.000	0.000	0.000
23	F	114	LEU	0	-0.012	-0.008	19.104	0.140	0.140	0.000	0.000	0.000	0.000
24	F	115	ASN	0	-0.020	-0.005	21.327	0.575	0.575	0.000	0.000	0.000	0.000
25	F	116	PRO	0	0.021	0.006	20.000	-0.685	-0.685	0.000	0.000	0.000	0.000
26	F	117	ILE	0	0.012	0.009	13.772	-0.112	-0.112	0.000	0.000	0.000	0.000
27	F	118	VAL	0	-0.049	-0.028	15.479	0.177	0.177	0.000	0.000	0.000	0.000
28	F	119	ASN	0	-0.038	-0.035	13.784	-1.623	-1.623	0.000	0.000	0.000	0.000
29	F	120	LEU	0	0.044	0.055	12.240	-1.254	-1.254	0.000	0.000	0.000	0.000
30	F	121	GLU	-1	-0.935	-0.982	11.298	-21.270	-21.270	0.000	0.000	0.000	0.000
31	F	122	GLU	-1	-0.943	-0.975	15.143	-12.809	-12.809	0.000	0.000	0.000	0.000
32	F	123	ASN	0	-0.055	-0.047	18.105	-0.172	-0.172	0.000	0.000	0.000	0.000
33	F	124	LYS	1	0.872	0.960	8.600	26.251	26.251	0.000	0.000	0.000	0.000
34	F	125	ILE	0	-0.012	-0.010	14.949	0.379	0.379	0.000	0.000	0.000	0.000
35	F	126	TYR	0	0.032	0.024	10.444	-0.648	-0.648	0.000	0.000	0.000	0.000
36	F	127	GLY	0	0.058	0.030	12.734	1.410	1.410	0.000	0.000	0.000	0.000
37	F	128	LEU	0	-0.055	-0.025	14.177	-0.620	-0.620	0.000	0.000	0.000	0.000
38	F	129	VAL	0	0.057	0.023	13.663	0.514	0.514	0.000	0.000	0.000	0.000
39	F	130	SER	0	0.002	-0.011	16.796	0.158	0.158	0.000	0.000	0.000	0.000
40	F	131	HIS	0	-0.043	-0.012	19.050	-0.662	-0.662	0.000	0.000	0.000	0.000
41	F	132	ASN	0	-0.028	-0.026	16.140	-0.493	-0.493	0.000	0.000	0.000	0.000
42	F	133	GLN	0	0.020	0.024	18.056	0.399	0.399	0.000	0.000	0.000	0.000
43	F	134	ALA	0	0.056	0.034	16.763	-0.436	-0.436	0.000	0.000	0.000	0.000
44	F	135	ILE	0	-0.045	-0.028	18.297	0.779	0.779	0.000	0.000	0.000	0.000
45	F	136	GLY	0	0.037	0.012	19.204	0.801	0.801	0.000	0.000	0.000	0.000
46	F	137	ILE	0	0.003	0.015	17.099	-0.907	-0.907	0.000	0.000	0.000	0.000
47	F	138	ALA	0	-0.023	-0.018	16.691	0.769	0.769	0.000	0.000	0.000	0.000
48	F	139	VAL	0	0.000	0.013	17.048	-0.715	-0.715	0.000	0.000	0.000	0.000
49	F	140	LEU	0	0.014	0.019	18.035	0.589	0.589	0.000	0.000	0.000	0.000
50	F	141	GLU	-1	-0.818	-0.924	19.630	-12.024	-12.024	0.000	0.000	0.000	0.000
51	F	142	LYS	1	0.927	0.965	23.062	10.696	10.696	0.000	0.000	0.000	0.000
52	F	143	GLY	0	0.010	0.004	23.056	0.351	0.351	0.000	0.000	0.000	0.000
53	F	144	ARG	1	0.913	0.962	23.856	10.409	10.409	0.000	0.000	0.000	0.000
54	F	145	LEU	0	0.014	0.017	17.293	-0.226	-0.226	0.000	0.000	0.000	0.000
55	F	146	ASN	0	0.015	0.008	21.198	0.416	0.416	0.000	0.000	0.000	0.000
56	F	147	GLY	0	0.036	0.012	21.108	-0.621	-0.621	0.000	0.000	0.000	0.000
57	F	148	PHE	0	-0.043	-0.029	21.754	0.764	0.764	0.000	0.000	0.000	0.000
58	F	149	LEU	0	-0.004	-0.012	22.343	-0.489	-0.489	0.000	0.000	0.000	0.000
59	F	150	ASN	0	0.065	-0.003	22.054	-0.037	-0.037	0.000	0.000	0.000	0.000
60	F	151	ALA	0	-0.003	0.012	24.258	0.081	0.081	0.000	0.000	0.000	0.000
61	F	152	HIS	0	-0.006	0.012	25.692	0.192	0.192	0.000	0.000	0.000	0.000
62	F	153	LYS	1	0.986	0.987	26.327	9.035	9.035	0.000	0.000	0.000	0.000
63	F	154	ARG	1	0.821	0.902	22.860	11.800	11.800	0.000	0.000	0.000	0.000
64	F	155	CYS	0	-0.075	0.005	21.747	-0.726	-0.726	0.000	0.000	0.000	0.000
65	F	156	ALA	0	0.044	0.029	20.559	0.375	0.375	0.000	0.000	0.000	0.000
66	F	157	TYR	0	-0.033	-0.036	15.763	-0.725	-0.725	0.000	0.000	0.000	0.000
67	F	158	SER	0	-0.017	0.016	14.557	0.588	0.588	0.000	0.000	0.000	0.000
68	F	159	VAL	0	-0.011	-0.005	15.378	-0.862	-0.862	0.000	0.000	0.000	0.000
69	F	160	MET	0	-0.054	-0.016	14.138	0.130	0.130	0.000	0.000	0.000	0.000
70	F	161	ILE	0	0.008	-0.001	18.472	-0.042	-0.042	0.000	0.000	0.000	0.000
71	F	162	GLY	0	0.046	0.026	21.783	0.129	0.129	0.000	0.000	0.000	0.000
72	F	163	GLN	0	-0.019	-0.019	21.012	-0.669	-0.669	0.000	0.000	0.000	0.000
73	F	164	ASN	0	-0.016	-0.011	20.949	-0.592	-0.592	0.000	0.000	0.000	0.000
74	F	165	GLN	0	-0.059	-0.027	14.837	-0.292	-0.292	0.000	0.000	0.000	0.000
75	F	166	VAL	0	0.037	0.024	19.288	-0.213	-0.213	0.000	0.000	0.000	0.000
76	F	167	LEU	0	-0.008	-0.003	16.203	-0.242	-0.242	0.000	0.000	0.000	0.000
77	F	168	GLY	0	0.045	0.026	19.826	0.624	0.624	0.000	0.000	0.000	0.000
78	F	169	PHE	0	-0.067	-0.040	17.669	-0.822	-0.822	0.000	0.000	0.000	0.000
79	F	170	ILE	0	-0.024	-0.003	20.294	0.521	0.521	0.000	0.000	0.000	0.000
80	F	171	GLY	0	0.042	0.012	22.252	-0.129	-0.129	0.000	0.000	0.000	0.000
81	F	172	THR	0	-0.049	-0.024	25.517	0.111	0.111	0.000	0.000	0.000	0.000
82	F	173	ASN	0	0.077	0.037	29.039	0.089	0.089	0.000	0.000	0.000	0.000
83	F	174	PHE	0	0.009	-0.019	32.575	0.020	0.020	0.000	0.000	0.000	0.000
84	F	175	LYS	1	0.882	0.963	35.486	8.014	8.014	0.000	0.000	0.000	0.000
85	F	176	GLN	0	-0.042	-0.012	32.680	0.073	0.073	0.000	0.000	0.000	0.000
86	F	177	GLU	-1	-0.853	-0.924	31.840	-8.447	-8.447	0.000	0.000	0.000	0.000
87	F	178	LEU	0	-0.032	-0.020	23.800	-0.105	-0.105	0.000	0.000	0.000	0.000
88	F	179	VAL	0	-0.015	-0.010	26.992	0.123	0.123	0.000	0.000	0.000	0.000
89	F	180	VAL	0	-0.032	-0.007	22.827	-0.437	-0.437	0.000	0.000	0.000	0.000
90	F	181	ASP	-1	-0.802	-0.900	24.633	-9.406	-9.406	0.000	0.000	0.000	0.000
91	F	182	PHE	0	-0.059	-0.060	24.033	-0.461	-0.461	0.000	0.000	0.000	0.000
92	F	183	ILE	0	0.002	0.020	24.706	-0.268	-0.268	0.000	0.000	0.000	0.000
93	F	184	VAL	0	0.011	-0.003	25.628	0.377	0.377	0.000	0.000	0.000	0.000
94	F	185	PRO	0	0.083	0.026	27.984	-0.059	-0.059	0.000	0.000	0.000	0.000
95	F	186	SER	0	-0.067	-0.039	30.422	0.066	0.066	0.000	0.000	0.000	0.000
96	F	187	ALA	0	-0.012	0.008	26.800	0.009	0.009	0.000	0.000	0.000	0.000
97	F	188	GLU	-1	-0.951	-0.972	28.337	-8.709	-8.709	0.000	0.000	0.000	0.000
98	F	189	ILE	0	-0.040	-0.020	25.775	-0.312	-0.312	0.000	0.000	0.000	0.000
99	F	190	ASN	0	-0.007	-0.022	28.443	0.607	0.607	0.000	0.000	0.000	0.000
100	F	191	ILE	0	-0.027	-0.019	29.343	-0.250	-0.250	0.000	0.000	0.000	0.000
101	F	192	GLY	0	-0.045	-0.023	29.699	0.127	0.127	0.000	0.000	0.000	0.000
102	F	193	ASP	-1	-0.859	-0.905	25.194	-10.611	-10.611	0.000	0.000	0.000	0.000
103	F	194	GLN	0	0.024	-0.004	21.634	0.231	0.231	0.000	0.000	0.000	0.000
104	F	195	VAL	0	0.008	0.008	20.403	-0.101	-0.101	0.000	0.000	0.000	0.000
105	F	196	LEU	0	-0.015	-0.006	15.996	-0.176	-0.176	0.000	0.000	0.000	0.000
106	F	197	THR	0	0.013	-0.008	12.122	0.491	0.491	0.000	0.000	0.000	0.000
107	F	198	SER	0	0.028	-0.019	13.571	-0.951	-0.951	0.000	0.000	0.000	0.000
108	F	199	GLY	0	-0.027	-0.011	9.492	-0.571	-0.571	0.000	0.000	0.000	0.000
109	F	200	LEU	0	-0.044	-0.029	8.609	-1.546	-1.546	0.000	0.000	0.000	0.000
110	F	201	ASP	-1	-0.774	-0.904	10.905	-18.747	-18.747	0.000	0.000	0.000	0.000
111	F	202	GLY	0	-0.025	-0.001	8.444	0.228	0.228	0.000	0.000	0.000	0.000
112	F	203	ILE	0	-0.059	0.001	9.510	-0.333	-0.333	0.000	0.000	0.000	0.000
113	F	204	PHE	0	-0.012	-0.009	10.410	-0.783	-0.783	0.000	0.000	0.000	0.000
114	F	205	GLY	0	0.036	0.013	7.428	-1.191	-1.191	0.000	0.000	0.000	0.000
115	F	206	ALA	0	0.002	0.002	8.128	1.927	1.927	0.000	0.000	0.000	0.000
116	F	207	GLY	0	-0.011	-0.007	10.445	-0.810	-0.810	0.000	0.000	0.000	0.000
117	F	208	VAL	0	-0.009	0.006	12.163	0.556	0.556	0.000	0.000	0.000	0.000
118	F	209	PHE	0	0.000	0.003	14.775	0.399	0.399	0.000	0.000	0.000	0.000
119	F	210	VAL	0	-0.001	-0.004	18.019	-0.187	-0.187	0.000	0.000	0.000	0.000
120	F	211	GLY	0	0.030	-0.004	20.457	0.397	0.397	0.000	0.000	0.000	0.000
121	F	212	GLU	-1	-0.938	-0.949	23.605	-10.518	-10.518	0.000	0.000	0.000	0.000
122	F	213	VAL	0	0.022	0.017	26.151	0.232	0.232	0.000	0.000	0.000	0.000
123	F	214	SER	0	-0.055	-0.039	28.276	0.249	0.249	0.000	0.000	0.000	0.000
124	F	215	SER	0	0.004	0.000	31.671	0.327	0.327	0.000	0.000	0.000	0.000
125	F	216	ILE	0	0.033	-0.002	30.639	-0.290	-0.290	0.000	0.000	0.000	0.000
126	F	217	GLU	-1	-0.966	-0.959	32.754	-8.011	-8.011	0.000	0.000	0.000	0.000
127	F	218	ASP	-1	-0.909	-0.970	33.268	-8.277	-8.277	0.000	0.000	0.000	0.000
128	F	219	HIS	0	-0.027	-0.012	33.121	0.331	0.331	0.000	0.000	0.000	0.000
129	F	220	TYR	0	-0.025	0.003	35.926	0.097	0.097	0.000	0.000	0.000	0.000
130	F	221	THR	0	-0.051	-0.043	34.101	-0.126	-0.126	0.000	0.000	0.000	0.000
131	F	222	TYR	0	-0.024	-0.011	29.495	-0.167	-0.167	0.000	0.000	0.000	0.000
132	F	223	LYS	1	0.909	0.981	29.149	9.190	9.190	0.000	0.000	0.000	0.000
133	F	224	SER	0	0.002	-0.002	28.651	-0.231	-0.231	0.000	0.000	0.000	0.000
134	F	225	ALA	0	-0.009	-0.010	26.804	0.229	0.229	0.000	0.000	0.000	0.000
135	F	226	VAL	0	0.022	0.035	27.924	-0.324	-0.324	0.000	0.000	0.000	0.000
136	F	227	LEU	0	0.002	0.004	23.863	-0.016	-0.016	0.000	0.000	0.000	0.000
137	F	228	LYS	1	0.896	0.948	28.169	9.674	9.674	0.000	0.000	0.000	0.000
138	F	229	ASN	0	-0.048	-0.042	27.329	-0.180	-0.180	0.000	0.000	0.000	0.000
139	F	230	ALA	0	0.102	0.070	24.633	-0.346	-0.346	0.000	0.000	0.000	0.000
140	F	231	PHE	0	-0.059	-0.029	23.685	0.355	0.355	0.000	0.000	0.000	0.000
141	F	232	LEU	0	0.051	0.033	25.588	-0.022	-0.022	0.000	0.000	0.000	0.000
142	F	233	SER	0	-0.003	-0.014	26.481	-0.112	-0.112	0.000	0.000	0.000	0.000
143	F	234	GLY	0	0.033	0.056	28.586	0.269	0.269	0.000	0.000	0.000	0.000
144	F	235	ALA	0	0.045	0.010	30.904	-0.136	-0.136	0.000	0.000	0.000	0.000
145	F	236	LYS	1	0.898	0.962	29.009	10.056	10.056	0.000	0.000	0.000	0.000
146	F	237	LEU	0	0.048	0.028	28.183	-0.254	-0.254	0.000	0.000	0.000	0.000
147	F	238	LEU	0	-0.058	-0.044	23.846	0.087	0.087	0.000	0.000	0.000	0.000
148	F	239	ARG	1	0.937	0.953	24.676	10.357	10.357	0.000	0.000	0.000	0.000
149	F	240	HIS	0	0.011	0.000	21.200	-0.518	-0.518	0.000	0.000	0.000	0.000
150	F	241	VAL	0	0.025	0.034	18.077	-0.120	-0.120	0.000	0.000	0.000	0.000
151	F	242	PHE	0	-0.001	-0.009	13.657	-0.238	-0.238	0.000	0.000	0.000	0.000
152	F	243	LEU	0	-0.009	-0.014	12.480	0.394	0.394	0.000	0.000	0.000	0.000
153	F	244	SER	0	-0.047	-0.033	9.996	-2.085	-2.085	0.000	0.000	0.000	0.000
154	F	245	ASP	-1	-0.842	-0.939	7.494	-28.063	-28.063	0.000	0.000	0.000	0.000
155	F	246	VAL	0	0.038	0.033	4.678	-5.412	-5.323	-0.001	-0.017	-0.070	0.000
156	F	247	LYS	1	0.976	0.989	3.888	34.189	34.554	0.001	-0.034	-0.331	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:92:LYS)