FMO DATABASE

FMODB ID: 3Q5VL

Calculation Name: 5CLV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CLV

Chain ID: A

ChEMBL ID:

UniProt ID: P03052

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	OptHSide
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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-589545.363109
FMO2-HF: Nuclear repulsion	553530.399014
FMO2-HF: Total energy	-36014.964094
FMO2-MP2: Total energy	-36123.161803

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:2:LYS)

Summations of interaction energy for fragment #1(A:2: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.
10.292	12.037	-0.004	-0.749	-0.993	0.001

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.964 / q_NPA : 0.967

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	4	ARG	1	0.878	0.926	3.581	32.999	34.744	-0.004	-0.749	-0.993	0.001
4	A	5	LEU	0	-0.015	-0.001	5.897	-0.301	-0.301	0.000	0.000	0.000	0.000
5	A	6	THR	0	0.012	-0.017	9.663	1.359	1.359	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.733	-0.873	12.388	-15.735	-15.735	0.000	0.000	0.000	0.000
7	A	8	SER	0	0.004	-0.008	15.005	0.801	0.801	0.000	0.000	0.000	0.000
8	A	9	GLN	0	0.053	0.054	11.311	-0.374	-0.374	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.004	0.003	11.818	0.226	0.226	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.014	-0.019	14.422	0.646	0.646	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.855	-0.922	17.322	-16.230	-16.230	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.013	0.002	15.104	0.636	0.636	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.035	-0.020	16.086	0.481	0.481	0.000	0.000	0.000	0.000
14	A	15	GLN	0	-0.004	0.007	18.685	0.449	0.449	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.002	-0.005	22.078	0.041	0.041	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.059	-0.015	17.769	0.161	0.161	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.900	-0.951	22.083	-10.399	-10.399	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.068	-0.039	18.371	-0.329	-0.329	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.040	0.030	21.616	0.226	0.226	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.079	0.020	20.322	-0.325	-0.325	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.039	0.014	18.320	-0.500	-0.500	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.013	-0.009	15.766	-0.374	-0.374	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.038	0.026	15.039	-0.975	-0.975	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.929	-0.962	14.996	-13.906	-13.906	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.016	-0.016	12.079	-0.780	-0.780	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.006	-0.001	10.463	-1.146	-1.146	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.876	0.954	10.120	13.974	13.974	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.013	0.000	11.008	-0.844	-0.844	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.051	-0.018	5.894	-1.024	-1.024	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.039	-0.031	5.914	-3.009	-3.009	0.000	0.000	0.000	0.000
31	A	32	VAL	0	0.020	0.040	7.321	-2.175	-2.175	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.829	-0.895	9.681	-18.657	-18.657	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.082	-0.033	5.741	-0.197	-0.197	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.848	0.918	6.381	16.216	16.216	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.031	-0.001	6.665	-0.871	-0.871	0.000	0.000	0.000	0.000
36	A	37	GLN	0	0.072	0.027	7.207	2.034	2.034	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.009	0.001	9.413	1.148	1.148	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.061	0.042	11.580	0.692	0.692	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.040	0.047	11.176	0.737	0.737	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.033	-0.009	13.923	0.626	0.626	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.044	-0.045	15.766	0.706	0.706	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.052	-0.050	16.497	0.533	0.533	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.010	0.000	16.792	0.445	0.445	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.012	0.028	19.904	0.381	0.381	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.030	0.003	17.374	0.191	0.191	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.027	-0.006	18.064	-0.578	-0.578	0.000	0.000	0.000	0.000
47	A	48	ARG	1	1.000	0.969	13.719	14.819	14.819	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.002	0.010	13.969	-0.751	-0.751	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.033	0.023	15.466	-0.455	-0.455	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.057	0.023	11.263	-0.290	-0.290	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.004	0.006	10.881	-0.891	-0.891	0.000	0.000	0.000	0.000
52	A	53	GLN	0	0.024	0.006	11.930	-0.326	-0.326	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.034	-0.013	13.994	0.070	0.070	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.027	0.002	7.550	-0.134	-0.134	0.000	0.000	0.000	0.000
55	A	56	HIS	0	-0.026	-0.008	11.025	-1.601	-1.601	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.924	0.964	12.192	13.777	13.777	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.049	0.031	12.532	0.157	0.157	0.000	0.000	0.000	0.000
58	A	59	TRP	0	-0.038	-0.039	7.110	-1.763	-1.763	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.003	-0.015	11.692	-0.354	-0.354	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.049	0.024	14.178	0.388	0.388	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.037	-0.030	11.236	0.232	0.232	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.868	-0.916	10.457	-25.903	-25.903	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.938	-0.942	14.497	-15.129	-15.129	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.756	0.900	17.508	15.235	15.235	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.010	0.005	13.159	-0.315	-0.315	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.038	-0.008	16.647	-0.574	-0.574	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.029	-0.018	19.381	0.326	0.326	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.879	-0.946	22.218	-11.761	-11.761	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.024	-0.008	24.967	0.309	0.309	0.000	0.000	0.000	0.000
70	A	71	TYR	0	-0.090	-0.041	23.650	0.393	0.393	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.039	0.009	23.372	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.836	0.908	16.177	17.264	17.264	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.001	-0.002	22.315	0.300	0.300	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.038	-0.026	22.543	-0.157	-0.157	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.031	0.013	25.041	0.292	0.292	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.013	0.008	28.262	-0.166	-0.166	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.003	-0.008	30.358	0.287	0.287	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.032	0.007	33.176	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.888	-0.942	34.603	-8.593	-8.593	0.000	0.000	0.000	0.000
80	A	81	HIS	0	0.053	0.025	34.937	-0.254	-0.254	0.000	0.000	0.000	0.000
81	A	82	GLN	0	0.038	-0.002	34.561	-0.212	-0.212	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.014	0.014	30.891	-0.282	-0.282	0.000	0.000	0.000	0.000
83	A	84	TYR	0	-0.028	-0.007	30.714	-0.365	-0.365	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.002	0.002	32.045	-0.198	-0.198	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.018	0.010	27.454	-0.172	-0.172	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.911	0.945	26.760	10.597	10.597	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.886	0.941	27.817	9.093	9.093	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.007	-0.010	29.452	-0.162	-0.162	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.794	-0.874	21.719	-14.588	-14.588	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.030	0.019	24.917	-0.404	-0.404	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.858	-0.921	26.674	-10.072	-10.072	0.000	0.000	0.000	0.000
92	A	93	ALA	0	-0.014	0.000	25.316	0.053	0.053	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.803	0.888	19.164	15.061	15.061	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.839	0.919	23.998	10.471	10.471	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.949	0.992	23.977	10.161	10.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)