FMO DATABASE

FMODB ID: ZV9JN

Calculation Name: 5T8L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T8L

Chain ID: A

ChEMBL ID:

UniProt ID: P39929

Base Structure: X-ray

Registration Date: 2023-09-23

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-784475.207421
FMO2-HF: Nuclear repulsion	733478.026569
FMO2-HF: Total energy	-50997.180852
FMO2-MP2: Total energy	-51142.307885

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:18:SER)

Summations of interaction energy for fragment #1(A:18:SER)

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.
-16.455	-13.224	9.885	-5.481	-7.635	0.044

Interaction energy analysis for fragmet #1(A:18:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.008

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

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	20	THR	0	0.065	0.035	2.022	-4.432	-4.304	5.666	-2.499	-3.295	0.018
4	A	21	LYS	1	0.907	0.963	2.249	-8.759	-6.192	4.205	-2.785	-3.987	0.025
5	A	22	ALA	0	0.034	0.011	3.865	-1.818	-1.282	0.014	-0.197	-0.353	0.001
6	A	23	ILE	0	0.053	0.033	5.755	0.108	0.108	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.008	-0.001	6.548	-0.374	-0.374	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.980	0.990	6.778	-0.594	-0.594	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.020	0.028	9.750	-0.141	-0.141	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.988	1.006	11.432	-0.963	-0.963	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.938	-0.965	11.980	0.688	0.688	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.076	-0.049	12.637	-0.147	-0.147	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.040	0.017	15.520	-0.041	-0.041	0.000	0.000	0.000	0.000
14	A	31	ASN	0	-0.031	-0.020	17.352	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.015	-0.012	18.645	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.018	-0.022	18.651	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	34	SER	0	0.073	0.043	21.666	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.961	0.979	22.017	-0.258	-0.258	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.934	0.970	21.995	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	37	GLN	0	-0.027	-0.020	25.913	0.004	0.004	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.016	-0.006	27.780	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	39	HIS	0	-0.010	-0.003	29.310	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.005	-0.017	28.543	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.955	0.970	29.261	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.009	0.019	33.968	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.028	-0.022	33.825	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	44	ILE	0	0.001	0.009	34.272	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.011	0.009	38.002	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	46	ASN	0	-0.016	-0.017	38.868	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.009	-0.007	40.180	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.888	-0.937	42.407	0.020	0.020	0.000	0.000	0.000	0.000
32	A	49	ASN	0	-0.007	-0.021	44.207	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.914	-0.961	44.622	0.023	0.023	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.020	0.000	46.733	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.962	0.971	48.423	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.050	0.032	49.312	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	54	PHE	0	0.006	-0.007	48.209	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.025	-0.007	52.633	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.043	-0.007	54.852	0.000	0.000	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.929	0.968	54.486	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	58	GLY	0	0.024	0.014	57.857	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	59	ASN	0	-0.017	-0.005	54.738	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.022	0.990	54.252	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	61	VAL	0	0.011	0.005	52.649	0.000	0.000	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.014	0.005	49.160	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.043	0.033	49.220	0.001	0.001	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.953	0.981	48.448	0.004	0.004	0.000	0.000	0.000	0.000
48	A	65	ASN	0	-0.021	-0.024	47.024	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.036	0.027	44.810	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.038	0.015	43.547	0.001	0.001	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.942	0.977	42.332	0.011	0.011	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.959	0.980	38.773	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.943	0.972	38.957	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.961	0.993	38.250	0.010	0.010	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.022	-0.012	35.538	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	73	ILE	0	-0.027	-0.011	33.861	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.903	-0.948	33.176	0.019	0.019	0.000	0.000	0.000	0.000
58	A	75	GLN	0	-0.028	-0.020	32.971	0.000	0.000	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.029	-0.012	28.378	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.003	-0.007	28.655	0.001	0.001	0.000	0.000	0.000	0.000
61	A	78	SER	0	0.015	0.021	28.349	0.000	0.000	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.963	0.974	26.434	0.046	0.046	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.045	-0.017	23.876	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.774	-0.890	23.306	0.049	0.049	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.068	0.045	23.662	0.000	0.000	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.066	-0.039	18.925	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.028	-0.025	19.090	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.900	-0.939	19.153	0.011	0.011	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.019	-0.005	18.238	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.082	-0.046	14.808	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.901	-0.953	14.969	0.194	0.194	0.000	0.000	0.000	0.000
72	A	89	GLN	0	-0.001	0.004	16.787	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.017	-0.008	11.451	-0.088	-0.088	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.013	-0.012	11.249	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.081	0.045	12.867	0.015	0.015	0.000	0.000	0.000	0.000
76	A	93	SER	0	-0.009	0.009	13.919	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.060	-0.026	7.847	-0.102	-0.102	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.951	-0.984	10.411	0.562	0.562	0.000	0.000	0.000	0.000
79	A	96	SER	0	0.004	-0.016	11.893	0.024	0.024	0.000	0.000	0.000	0.000
80	A	97	ALA	0	-0.014	0.000	11.126	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.021	-0.024	6.321	-0.271	-0.271	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.029	0.031	10.329	0.023	0.023	0.000	0.000	0.000	0.000
83	A	100	ASN	0	0.002	-0.003	13.765	0.023	0.023	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.027	-0.022	8.911	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.953	-0.977	12.630	0.315	0.315	0.000	0.000	0.000	0.000
86	A	103	THR	0	0.010	0.007	13.704	0.005	0.005	0.000	0.000	0.000	0.000
87	A	104	MET	0	-0.009	-0.001	15.419	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.960	0.971	11.912	0.048	0.048	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.035	0.038	16.020	0.009	0.009	0.000	0.000	0.000	0.000
90	A	107	MET	0	-0.012	-0.009	18.733	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	108	GLN	0	-0.028	-0.012	17.530	0.000	0.000	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-1.010	-1.008	19.294	0.061	0.061	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.039	0.020	21.143	0.007	0.007	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.017	-0.001	23.805	0.002	0.002	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.910	0.948	19.837	0.043	0.043	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.009	0.011	25.494	0.002	0.002	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.027	-0.001	27.327	0.005	0.005	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.970	0.998	28.760	0.060	0.060	0.000	0.000	0.000	0.000
99	A	116	THR	0	-0.048	-0.024	28.834	0.000	0.000	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.030	-0.019	31.152	0.002	0.002	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.018	0.003	33.389	0.002	0.002	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.012	-0.009	34.729	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	120	GLY	0	-0.036	-0.003	36.572	0.000	0.000	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.021	-0.016	37.370	0.004	0.004	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.943	-0.963	39.166	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.086	-0.051	41.619	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.927	-0.956	45.341	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.934	0.954	43.969	0.026	0.026	0.000	0.000	0.000	0.000
109	A	126	VAL	0	0.042	0.025	43.736	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.953	-0.981	39.735	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.859	-0.945	42.604	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.007	0.011	44.758	0.000	0.000	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.104	-0.056	42.707	0.001	0.001	0.000	0.000	0.000	0.000
114	A	131	ASP	-1	-0.850	-0.924	41.650	-0.040	-0.040	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.886	-0.940	44.758	-0.027	-0.027	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.058	-0.034	48.487	0.000	0.000	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.801	0.901	42.056	0.034	0.034	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.886	-0.938	46.285	-0.043	-0.043	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.103	-0.053	48.259	0.002	0.002	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.095	-0.045	48.809	0.001	0.001	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.886	-0.939	44.767	-0.041	-0.041	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.023	0.005	49.354	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.066	-0.044	52.127	0.002	0.002	0.000	0.000	0.000	0.000
124	A	141	ASP	-1	-0.994	-0.985	48.040	-0.037	-0.037	0.000	0.000	0.000	0.000
125	A	142	GLU	-1	-1.050	-1.023	48.071	-0.041	-0.041	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:18:SER)