FMO DATABASE

FMODB ID: K3643

Calculation Name: 5DTC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12024

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-617618.344637
FMO2-HF: Nuclear repulsion	583131.195163
FMO2-HF: Total energy	-34487.149474
FMO2-MP2: Total energy	-34589.866542

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:5:LYS)

Summations of interaction energy for fragment #1(A:5: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.
-101.251	-99.012	16.557	-10.177	-8.617	-0.11

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.929 / q_NPA : 0.931

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	7	GLN	0	-0.016	-0.011	2.949	4.479	6.528	0.014	-0.891	-1.172	0.002
4	A	8	VAL	0	0.019	0.021	3.832	-7.500	-7.124	0.005	-0.149	-0.231	-0.001
5	A	9	LYS	1	0.913	0.973	6.540	26.150	26.150	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.010	-0.003	9.812	-0.313	-0.313	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.938	0.966	13.050	15.851	15.851	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.004	-0.003	16.738	-0.328	-0.328	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.023	0.021	19.726	0.487	0.487	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.035	-0.011	23.072	0.048	0.048	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.934	0.970	26.071	10.434	10.434	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.770	-0.841	29.135	-9.096	-9.096	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.922	0.948	31.130	8.019	8.019	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.892	-0.935	33.273	-8.407	-8.407	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.890	-0.945	32.358	-8.664	-8.664	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.012	-0.007	31.914	-0.211	-0.211	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.038	-0.017	28.984	-0.216	-0.216	0.000	0.000	0.000	0.000
18	A	22	HIS	0	-0.043	-0.006	27.652	-0.536	-0.536	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.008	0.008	22.095	0.085	0.085	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.018	-0.020	23.149	0.028	0.028	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.918	-0.965	21.987	-13.786	-13.786	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.025	-0.003	18.204	-0.578	-0.578	0.000	0.000	0.000	0.000
23	A	27	PRO	0	-0.043	-0.016	14.439	-0.405	-0.405	0.000	0.000	0.000	0.000
24	A	28	MET	0	-0.003	0.002	13.618	0.709	0.709	0.000	0.000	0.000	0.000
25	A	29	TYR	0	0.000	-0.015	7.049	-0.881	-0.881	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.050	0.031	8.974	1.699	1.699	0.000	0.000	0.000	0.000
27	A	31	PRO	0	0.036	0.011	7.794	-2.672	-2.672	0.000	0.000	0.000	0.000
28	A	32	ILE	0	0.025	0.016	4.411	1.790	1.953	-0.001	-0.019	-0.142	0.000
29	A	33	SER	0	-0.014	-0.007	7.926	1.035	1.035	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.015	0.004	10.915	1.635	1.635	0.000	0.000	0.000	0.000
31	A	35	LYS	1	0.980	0.976	13.412	15.925	15.925	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.875	0.925	16.523	11.786	11.786	0.000	0.000	0.000	0.000
33	A	37	TYR	0	0.031	0.012	19.735	0.195	0.195	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.087	0.058	17.588	0.269	0.269	0.000	0.000	0.000	0.000
35	A	39	LEU	0	-0.025	-0.012	14.335	-0.116	-0.116	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.035	0.014	18.237	0.399	0.399	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.942	-0.961	20.257	-12.270	-12.270	0.000	0.000	0.000	0.000
38	A	42	ILE	0	-0.009	-0.007	15.275	0.180	0.180	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.011	0.005	19.614	0.211	0.211	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.026	-0.025	22.224	0.733	0.733	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.014	0.004	21.340	0.451	0.451	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.060	-0.042	19.059	0.176	0.176	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.037	-0.001	23.312	0.170	0.170	0.000	0.000	0.000	0.000
44	A	48	GLY	0	-0.026	0.005	26.381	0.351	0.351	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.059	-0.048	27.960	0.328	0.328	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.854	-0.902	29.883	-7.974	-7.974	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.832	0.890	32.209	8.059	8.059	0.000	0.000	0.000	0.000
48	A	52	PRO	0	-0.019	-0.001	27.829	-0.097	-0.097	0.000	0.000	0.000	0.000
49	A	53	VAL	0	0.043	0.023	28.563	0.208	0.208	0.000	0.000	0.000	0.000
50	A	54	PRO	0	-0.033	0.001	27.234	-0.417	-0.417	0.000	0.000	0.000	0.000
51	A	55	PHE	0	0.048	0.005	23.918	0.181	0.181	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.834	-0.905	23.584	-11.770	-11.770	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.017	0.003	19.175	-0.090	-0.090	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.046	-0.017	20.476	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	59	ILE	0	0.004	0.004	14.334	-0.480	-0.480	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.844	-0.910	18.462	-15.292	-15.292	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.033	0.031	20.926	0.353	0.353	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.895	-0.929	19.686	-15.079	-15.079	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.008	-0.005	20.394	-0.498	-0.498	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.003	-0.007	14.882	-0.259	-0.259	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.912	0.946	19.014	12.185	12.185	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.061	-0.053	15.859	0.521	0.521	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.076	-0.052	12.456	-0.204	-0.204	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.040	0.019	10.148	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	69	HIS	0	0.055	0.028	7.598	-3.149	-3.149	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.789	-0.849	9.407	-20.199	-20.199	0.000	0.000	0.000	0.000
67	A	71	TYR	0	-0.019	-0.017	12.679	-0.072	-0.072	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.012	-0.013	6.655	0.272	0.272	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.008	-0.013	9.805	-0.811	-0.811	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.892	0.947	10.992	16.767	16.767	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.809	0.890	13.056	18.281	18.281	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.001	0.017	10.787	0.380	0.380	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.045	-0.015	9.182	-1.207	-1.207	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.005	-0.029	3.768	2.762	2.950	0.001	-0.035	-0.154	0.000
75	A	79	SER	0	-0.015	-0.034	2.395	-2.125	-0.889	2.352	-1.768	-1.820	-0.015
76	A	80	GLU	-1	-0.834	-0.886	1.720	-124.419	-126.192	14.186	-7.315	-5.098	-0.096
77	A	81	ALA	0	-0.019	0.009	6.047	5.348	5.348	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.027	-0.035	8.802	0.195	0.195	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.030	-0.006	10.352	1.321	1.321	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.009	-0.015	13.284	0.608	0.608	0.000	0.000	0.000	0.000
81	A	85	VAL	0	-0.019	-0.015	15.113	0.252	0.252	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.850	-0.918	17.956	-11.472	-11.472	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.051	-0.058	21.137	-0.504	-0.504	0.000	0.000	0.000	0.000
84	A	88	THR	0	0.003	0.014	23.353	0.482	0.482	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.851	0.892	26.477	8.768	8.768	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.040	-0.022	27.587	-0.063	-0.063	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.057	-0.025	27.551	0.480	0.480	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)