FMO DATABASE

FMODB ID: YZ5Q2

Calculation Name: 2BH8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BH8

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9X9

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	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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-424443.642203
FMO2-HF: Nuclear repulsion	393300.482064
FMO2-HF: Total energy	-31143.160139
FMO2-MP2: Total energy	-31235.249253

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:LYS)

Summations of interaction energy for fragment #1(A:18: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.
-160.179	-156.189	29.195	-17.339	-15.845	-0.17

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.863

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	20	THR	0	-0.023	-0.011	3.366	-6.034	-3.507	-0.003	-1.130	-1.393	0.000
4	A	21	GLY	0	0.059	0.024	5.434	5.077	5.077	0.000	0.000	0.000	0.000
5	A	22	ILE	0	-0.043	-0.005	9.050	-0.730	-0.730	0.000	0.000	0.000	0.000
6	A	23	VAL	0	-0.008	0.000	12.192	0.771	0.771	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.819	0.894	14.390	19.124	19.124	0.000	0.000	0.000	0.000
8	A	25	TRP	0	0.045	0.009	17.447	1.012	1.012	0.000	0.000	0.000	0.000
9	A	26	PHE	0	0.011	-0.007	12.718	-1.062	-1.062	0.000	0.000	0.000	0.000
10	A	27	ASN	0	0.017	0.021	18.185	0.813	0.813	0.000	0.000	0.000	0.000
11	A	28	ALA	0	0.049	0.015	16.337	-0.054	-0.054	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.852	-0.907	17.728	-12.913	-12.913	0.000	0.000	0.000	0.000
13	A	30	LYS	1	0.796	0.884	21.012	13.010	13.010	0.000	0.000	0.000	0.000
14	A	31	GLY	0	0.010	0.030	17.331	0.167	0.167	0.000	0.000	0.000	0.000
15	A	32	PHE	0	-0.008	-0.015	16.889	-0.267	-0.267	0.000	0.000	0.000	0.000
16	A	33	GLY	0	0.009	0.001	16.071	0.021	0.021	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.019	0.008	15.725	-0.196	-0.196	0.000	0.000	0.000	0.000
18	A	35	ILE	0	0.014	0.005	9.950	-0.087	-0.087	0.000	0.000	0.000	0.000
19	A	36	THR	0	0.014	-0.016	13.418	1.383	1.383	0.000	0.000	0.000	0.000
20	A	37	PRO	0	-0.034	-0.025	8.503	-1.792	-1.792	0.000	0.000	0.000	0.000
21	A	38	ASP	-1	-0.763	-0.830	7.669	-34.509	-34.509	0.000	0.000	0.000	0.000
22	A	39	ASP	-1	-0.904	-0.933	7.441	-29.872	-29.872	0.000	0.000	0.000	0.000
23	A	40	GLY	0	-0.045	-0.023	9.965	0.062	0.062	0.000	0.000	0.000	0.000
24	A	41	SER	0	-0.022	-0.027	12.726	0.472	0.472	0.000	0.000	0.000	0.000
25	A	42	LYS	1	0.918	0.951	13.811	18.260	18.260	0.000	0.000	0.000	0.000
26	A	43	ASP	-1	-0.722	-0.807	13.515	-20.216	-20.216	0.000	0.000	0.000	0.000
27	A	44	VAL	0	-0.039	-0.027	10.270	0.521	0.521	0.000	0.000	0.000	0.000
28	A	45	PHE	0	0.023	0.009	13.744	-0.308	-0.308	0.000	0.000	0.000	0.000
29	A	46	VAL	0	-0.046	-0.023	10.825	-0.811	-0.811	0.000	0.000	0.000	0.000
30	A	47	HIS	0	0.031	0.001	14.006	0.711	0.711	0.000	0.000	0.000	0.000
31	A	48	PHE	0	-0.046	-0.014	13.482	-1.098	-1.098	0.000	0.000	0.000	0.000
32	A	49	SER	0	0.030	0.007	15.569	0.893	0.893	0.000	0.000	0.000	0.000
33	A	50	ALA	0	0.013	0.015	16.358	-0.877	-0.877	0.000	0.000	0.000	0.000
34	A	51	GLY	0	0.026	0.007	17.554	0.831	0.831	0.000	0.000	0.000	0.000
35	A	52	SER	0	-0.067	-0.039	16.749	-0.106	-0.106	0.000	0.000	0.000	0.000
36	A	53	SER	0	0.000	-0.004	12.324	0.597	0.597	0.000	0.000	0.000	0.000
37	A	54	GLY	0	0.032	0.019	14.949	-0.442	-0.442	0.000	0.000	0.000	0.000
38	A	55	ALA	0	-0.030	0.000	13.762	0.615	0.615	0.000	0.000	0.000	0.000
39	A	56	ALA	0	0.014	0.006	15.718	0.530	0.530	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.014	0.006	16.496	-1.105	-1.105	0.000	0.000	0.000	0.000
41	A	58	ARG	1	0.820	0.907	11.629	23.807	23.807	0.000	0.000	0.000	0.000
42	A	59	GLY	0	0.017	0.006	17.325	0.342	0.342	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.026	-0.010	17.233	-1.698	-1.698	0.000	0.000	0.000	0.000
44	A	61	PRO	0	-0.036	0.001	13.944	0.635	0.635	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.007	-0.015	16.318	1.207	1.207	0.000	0.000	0.000	0.000
46	A	63	GLN	0	-0.056	-0.038	16.951	-0.794	-0.794	0.000	0.000	0.000	0.000
47	A	64	GLY	0	0.024	0.010	16.453	0.792	0.792	0.000	0.000	0.000	0.000
48	A	65	ASP	-1	-0.802	-0.878	13.315	-21.637	-21.637	0.000	0.000	0.000	0.000
49	A	66	ARG	1	0.785	0.846	7.635	34.213	34.213	0.000	0.000	0.000	0.000
50	A	67	VAL	0	-0.043	-0.015	8.462	0.698	0.698	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.770	-0.881	1.711	-150.719	-155.029	23.776	-11.746	-7.719	-0.144
52	A	69	GLY	0	0.029	0.028	3.080	10.300	10.768	0.018	-0.131	-0.356	0.000
53	A	70	LYS	1	0.920	0.944	2.385	11.327	16.276	5.373	-4.444	-5.877	-0.025
54	A	71	ILE	0	0.047	0.040	3.382	4.764	4.961	0.032	0.133	-0.363	-0.001
55	A	72	LYS	1	0.948	0.959	4.337	22.563	22.722	-0.001	-0.021	-0.137	0.000
56	A	73	SER	0	0.024	0.014	7.068	0.024	0.024	0.000	0.000	0.000	0.000
57	A	74	ILE	0	-0.007	0.001	10.051	0.094	0.094	0.000	0.000	0.000	0.000
58	A	75	THR	0	-0.035	-0.048	13.021	0.227	0.227	0.000	0.000	0.000	0.000
59	A	76	ASP	-1	-0.858	-0.882	15.234	-13.781	-13.781	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.030	-0.027	17.495	-0.392	-0.392	0.000	0.000	0.000	0.000
61	A	78	GLY	0	0.038	0.026	19.597	0.474	0.474	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.028	-0.026	21.883	-0.432	-0.432	0.000	0.000	0.000	0.000
63	A	80	PHE	0	-0.028	-0.005	24.685	0.344	0.344	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.035	-0.024	27.925	-0.185	-0.185	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.064	0.061	30.553	0.178	0.178	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.063	-0.058	33.447	0.124	0.124	0.000	0.000	0.000	0.000
67	A	84	ASP	-1	-0.910	-0.947	34.950	-8.235	-8.235	0.000	0.000	0.000	0.000
68	A	85	GLY	0	-0.040	-0.016	33.912	0.071	0.071	0.000	0.000	0.000	0.000
69	A	86	GLY	0	-0.009	0.004	31.565	-0.210	-0.210	0.000	0.000	0.000	0.000
70	A	87	ILE	0	-0.034	-0.031	24.735	-0.097	-0.097	0.000	0.000	0.000	0.000
71	A	88	ASP	-1	-0.856	-0.933	27.337	-9.462	-9.462	0.000	0.000	0.000	0.000
72	A	89	GLY	0	-0.025	-0.018	24.807	-0.083	-0.083	0.000	0.000	0.000	0.000
73	A	90	LEU	0	-0.043	-0.015	17.811	0.094	0.094	0.000	0.000	0.000	0.000
74	A	91	VAL	0	-0.015	-0.001	20.157	-0.323	-0.323	0.000	0.000	0.000	0.000
75	A	92	HIS	0	-0.034	-0.017	16.654	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	93	LEU	0	-0.034	-0.007	18.556	0.463	0.463	0.000	0.000	0.000	0.000
77	A	94	SER	0	-0.033	-0.041	18.934	-0.104	-0.104	0.000	0.000	0.000	0.000
78	A	95	ASP	-1	-0.907	-0.952	20.374	-10.723	-10.723	0.000	0.000	0.000	0.000
79	A	96	ILE	0	0.012	0.009	23.352	0.093	0.093	0.000	0.000	0.000	0.000
80	A	97	SER	0	-0.025	-0.010	26.110	0.123	0.123	0.000	0.000	0.000	0.000
81	A	98	TRP	0	-0.051	-0.023	27.408	0.119	0.119	0.000	0.000	0.000	0.000
82	A	99	ALA	0	0.011	0.008	32.807	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	100	GLN	0	-0.041	-0.022	34.891	-0.163	-0.163	0.000	0.000	0.000	0.000
84	A	101	ALA	0	0.032	0.015	36.320	0.175	0.175	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.990	-0.987	39.369	-6.698	-6.698	0.000	0.000	0.000	0.000

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