FMO DATABASE

FMODB ID: 76J1K

Calculation Name: 4ID3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ID3

Chain ID: A

ChEMBL ID:

UniProt ID: P12689

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-641308.027502
FMO2-HF: Nuclear repulsion	606598.937047
FMO2-HF: Total energy	-34709.090454
FMO2-MP2: Total energy	-34812.30784

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:164:LYS)

Summations of interaction energy for fragment #1(A:164: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.
112.53	113.428	11.843	-4.214	-8.526	-0.032

Interaction energy analysis for fragmet #1(A:164:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.953 / q_NPA : 0.966

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	166	PHE	0	-0.005	0.008	3.333	1.822	4.054	-0.006	-1.017	-1.208	0.001
4	A	167	LYS	1	0.972	0.991	2.763	34.832	35.784	0.142	-0.242	-0.852	0.000
5	A	168	ASN	0	-0.044	-0.034	4.342	3.820	3.954	0.000	-0.026	-0.108	0.000
6	A	169	CYS	0	-0.021	0.017	7.422	4.179	4.179	0.000	0.000	0.000	0.000
7	A	170	VAL	0	-0.021	-0.024	9.028	-2.550	-2.550	0.000	0.000	0.000	0.000
8	A	171	ILE	0	0.035	0.019	9.948	2.084	2.084	0.000	0.000	0.000	0.000
9	A	172	TYR	0	0.006	0.011	13.673	-0.178	-0.178	0.000	0.000	0.000	0.000
10	A	173	ILE	0	-0.004	0.002	14.728	0.408	0.408	0.000	0.000	0.000	0.000
11	A	174	ASN	0	0.024	0.004	18.370	0.539	0.539	0.000	0.000	0.000	0.000
12	A	175	GLY	0	-0.002	0.000	22.052	0.178	0.178	0.000	0.000	0.000	0.000
13	A	176	TYR	0	0.021	0.006	22.846	-0.507	-0.507	0.000	0.000	0.000	0.000
14	A	177	THR	0	-0.029	-0.029	19.295	0.059	0.059	0.000	0.000	0.000	0.000
15	A	178	LYS	1	0.920	0.984	21.156	11.692	11.692	0.000	0.000	0.000	0.000
16	A	179	PRO	0	0.117	0.052	16.272	0.118	0.118	0.000	0.000	0.000	0.000
17	A	180	GLY	0	0.070	0.047	18.858	0.031	0.031	0.000	0.000	0.000	0.000
18	A	181	ARG	1	0.916	0.937	17.498	14.605	14.605	0.000	0.000	0.000	0.000
19	A	182	LEU	0	0.022	0.013	15.443	-1.043	-1.043	0.000	0.000	0.000	0.000
20	A	183	GLN	0	0.119	0.058	14.864	-0.553	-0.553	0.000	0.000	0.000	0.000
21	A	184	LEU	0	0.015	0.001	13.012	-1.534	-1.534	0.000	0.000	0.000	0.000
22	A	185	HIS	1	0.873	0.931	11.401	18.997	18.997	0.000	0.000	0.000	0.000
23	A	186	GLU	-1	-0.882	-0.927	10.283	-24.379	-24.379	0.000	0.000	0.000	0.000
24	A	187	MET	0	-0.019	0.000	8.908	-2.875	-2.875	0.000	0.000	0.000	0.000
25	A	188	ILE	0	-0.009	-0.002	6.963	-2.811	-2.811	0.000	0.000	0.000	0.000
26	A	189	VAL	0	-0.031	-0.019	5.923	-5.119	-5.119	0.000	0.000	0.000	0.000
27	A	190	LEU	0	0.005	0.008	4.314	-12.733	-12.577	-0.001	-0.024	-0.130	0.000
28	A	191	HIS	0	-0.019	0.000	2.771	-7.734	-6.483	0.298	-0.329	-1.220	-0.001
29	A	192	GLY	0	-0.078	-0.055	2.261	-5.846	-7.216	11.285	-5.703	-4.213	-0.027
30	A	193	GLY	0	0.037	0.037	2.900	5.928	3.471	0.125	3.127	-0.795	-0.005
31	A	194	LYS	1	0.926	0.955	6.091	35.661	35.661	0.000	0.000	0.000	0.000
32	A	195	PHE	0	0.011	-0.002	8.728	1.713	1.713	0.000	0.000	0.000	0.000
33	A	196	LEU	0	-0.005	0.007	12.213	0.040	0.040	0.000	0.000	0.000	0.000
34	A	197	HIS	0	-0.001	-0.014	15.557	0.676	0.676	0.000	0.000	0.000	0.000
35	A	198	TYR	0	0.022	0.007	18.430	0.698	0.698	0.000	0.000	0.000	0.000
36	A	199	LEU	0	-0.014	-0.002	19.719	-0.764	-0.764	0.000	0.000	0.000	0.000
37	A	200	SER	0	0.024	0.023	19.161	0.609	0.609	0.000	0.000	0.000	0.000
38	A	201	SER	0	0.047	0.009	20.753	0.548	0.548	0.000	0.000	0.000	0.000
39	A	202	LYS	1	0.968	0.980	20.037	12.022	12.022	0.000	0.000	0.000	0.000
40	A	203	LYS	1	0.946	0.991	19.322	13.890	13.890	0.000	0.000	0.000	0.000
41	A	204	THR	0	-0.035	-0.018	15.883	-0.630	-0.630	0.000	0.000	0.000	0.000
42	A	205	VAL	0	-0.011	0.000	14.970	-1.233	-1.233	0.000	0.000	0.000	0.000
43	A	206	THR	0	-0.007	-0.021	12.299	0.060	0.060	0.000	0.000	0.000	0.000
44	A	207	HIS	0	-0.010	0.022	12.335	0.396	0.396	0.000	0.000	0.000	0.000
45	A	208	ILE	0	0.006	0.014	15.814	-0.602	-0.602	0.000	0.000	0.000	0.000
46	A	209	VAL	0	-0.017	0.007	14.534	0.111	0.111	0.000	0.000	0.000	0.000
47	A	210	ALA	0	0.000	-0.011	17.798	0.311	0.311	0.000	0.000	0.000	0.000
48	A	211	SER	0	0.037	0.008	21.220	-0.178	-0.178	0.000	0.000	0.000	0.000
49	A	212	ASN	0	0.003	-0.007	23.307	0.100	0.100	0.000	0.000	0.000	0.000
50	A	213	LEU	0	-0.008	-0.005	24.446	-0.208	-0.208	0.000	0.000	0.000	0.000
51	A	214	PRO	0	0.057	0.041	28.034	0.316	0.316	0.000	0.000	0.000	0.000
52	A	215	LEU	0	0.105	0.039	30.907	-0.281	-0.281	0.000	0.000	0.000	0.000
53	A	216	LYS	1	1.012	1.002	31.994	9.364	9.364	0.000	0.000	0.000	0.000
54	A	217	LYS	1	0.825	0.895	27.065	11.096	11.096	0.000	0.000	0.000	0.000
55	A	218	ARG	1	0.934	0.976	27.934	9.489	9.489	0.000	0.000	0.000	0.000
56	A	219	ILE	0	0.003	0.008	29.297	-0.116	-0.116	0.000	0.000	0.000	0.000
57	A	220	GLU	-1	-0.859	-0.912	27.425	-11.330	-11.330	0.000	0.000	0.000	0.000
58	A	221	PHE	0	-0.039	-0.036	24.099	-0.390	-0.390	0.000	0.000	0.000	0.000
59	A	222	ALA	0	0.062	0.036	25.102	-0.347	-0.347	0.000	0.000	0.000	0.000
60	A	223	ASN	0	-0.052	-0.039	25.178	-0.289	-0.289	0.000	0.000	0.000	0.000
61	A	224	TYR	0	0.042	0.030	20.200	-0.598	-0.598	0.000	0.000	0.000	0.000
62	A	225	LYS	1	0.906	0.968	16.629	16.418	16.418	0.000	0.000	0.000	0.000
63	A	226	VAL	0	0.003	-0.002	18.834	-0.645	-0.645	0.000	0.000	0.000	0.000
64	A	227	VAL	0	0.006	0.010	15.273	0.454	0.454	0.000	0.000	0.000	0.000
65	A	228	SER	0	0.077	0.027	18.668	-0.309	-0.309	0.000	0.000	0.000	0.000
66	A	229	PRO	0	-0.030	-0.050	16.198	-0.760	-0.760	0.000	0.000	0.000	0.000
67	A	230	ASP	-1	-0.849	-0.915	15.164	-14.952	-14.952	0.000	0.000	0.000	0.000
68	A	231	TRP	0	-0.025	0.001	11.123	-0.998	-0.998	0.000	0.000	0.000	0.000
69	A	232	ILE	0	-0.038	-0.021	9.855	-1.018	-1.018	0.000	0.000	0.000	0.000
70	A	233	VAL	0	0.000	-0.019	10.676	-1.182	-1.182	0.000	0.000	0.000	0.000
71	A	234	ASP	-1	-0.761	-0.847	12.649	-15.757	-15.757	0.000	0.000	0.000	0.000
72	A	235	SER	0	-0.032	-0.024	8.992	-0.169	-0.169	0.000	0.000	0.000	0.000
73	A	236	VAL	0	-0.046	-0.032	7.282	-0.914	-0.914	0.000	0.000	0.000	0.000
74	A	237	LYS	1	0.880	0.946	9.093	16.455	16.455	0.000	0.000	0.000	0.000
75	A	238	GLU	-1	-0.904	-0.950	11.548	-15.815	-15.815	0.000	0.000	0.000	0.000
76	A	239	ALA	0	-0.037	0.002	7.062	-0.213	-0.213	0.000	0.000	0.000	0.000
77	A	240	ARG	1	0.920	0.942	7.091	17.314	17.314	0.000	0.000	0.000	0.000
78	A	241	LEU	0	-0.055	-0.018	7.772	0.499	0.499	0.000	0.000	0.000	0.000
79	A	242	LEU	0	0.046	0.033	9.212	1.062	1.062	0.000	0.000	0.000	0.000
80	A	243	PRO	0	0.021	0.007	12.894	-0.628	-0.628	0.000	0.000	0.000	0.000
81	A	244	TRP	0	0.046	0.012	14.795	0.598	0.598	0.000	0.000	0.000	0.000
82	A	245	GLN	0	0.010	-0.011	16.147	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	246	ASN	0	0.024	0.015	18.250	0.850	0.850	0.000	0.000	0.000	0.000
84	A	247	TYR	0	-0.034	-0.061	16.037	0.064	0.064	0.000	0.000	0.000	0.000
85	A	248	SER	0	-0.043	-0.017	19.366	-0.205	-0.205	0.000	0.000	0.000	0.000
86	A	249	LEU	0	0.005	0.007	21.302	0.436	0.436	0.000	0.000	0.000	0.000
87	A	250	THR	0	-0.057	-0.017	24.054	0.395	0.395	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:164:LYS)