FMO DATABASE

FMODB ID: R84J8

Calculation Name: 1B34-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: A

ChEMBL ID:

UniProt ID: P62314

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:

Apendix: None

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-515728.100458
FMO2-HF: Nuclear repulsion	484113.576022
FMO2-HF: Total energy	-31614.524436
FMO2-MP2: Total energy	-31706.723302

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.
46.052	50.62	2.192	-2.502	-4.258	0.01

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 : 0.964

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	4	VAL	0	0.055	0.029	2.683	2.301	4.866	1.973	-1.788	-2.750	0.004
4	A	5	ARG	1	0.959	0.955	3.209	33.749	35.593	0.220	-0.681	-1.383	0.006
5	A	6	PHE	0	0.001	0.017	4.627	1.486	1.645	-0.001	-0.033	-0.125	0.000
6	A	7	LEU	0	0.053	0.020	6.583	2.056	2.056	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.064	-0.017	6.019	1.409	1.409	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.880	0.954	6.627	27.864	27.864	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.004	0.010	10.844	0.735	0.735	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.029	-0.013	13.462	0.695	0.695	0.000	0.000	0.000	0.000
11	A	12	HIS	0	-0.011	-0.025	16.132	0.368	0.368	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.929	-0.940	15.827	-14.218	-14.218	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.034	0.005	18.752	0.436	0.436	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.004	0.009	16.336	-0.452	-0.452	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.010	-0.005	19.793	0.849	0.849	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.010	-0.007	17.074	-0.620	-0.620	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.836	-0.886	19.148	-11.450	-11.450	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.025	0.008	19.227	-0.667	-0.667	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.903	0.951	16.774	14.953	14.953	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.008	0.015	21.845	0.002	0.002	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.023	-0.022	24.097	0.425	0.425	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.056	-0.042	25.326	0.433	0.433	0.000	0.000	0.000	0.000
23	A	24	GLN	0	0.014	0.011	23.950	-0.571	-0.571	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.003	-0.007	21.915	0.459	0.459	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.025	0.002	22.325	-0.331	-0.331	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.084	0.045	22.746	0.461	0.461	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.018	-0.003	21.433	-0.261	-0.261	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.006	0.000	14.882	0.260	0.260	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.069	-0.039	18.582	0.216	0.216	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.042	0.014	15.469	-0.105	-0.105	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.007	-0.002	10.405	0.279	0.279	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.755	-0.847	11.656	-17.099	-17.099	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.058	0.015	7.124	-0.627	-0.627	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.090	-0.043	8.213	-1.131	-1.131	0.000	0.000	0.000	0.000
35	A	36	MET	0	-0.060	-0.048	8.685	-0.199	-0.199	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.058	-0.046	11.083	1.064	1.064	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.013	-0.007	14.193	-0.749	-0.749	0.000	0.000	0.000	0.000
38	A	39	HIS	0	0.050	0.042	16.021	0.995	0.995	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.009	0.003	18.875	-0.396	-0.396	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.989	0.986	21.378	11.175	11.175	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.042	-0.021	24.754	-0.182	-0.182	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.004	-0.005	24.392	-0.236	-0.236	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.973	0.989	26.731	9.820	9.820	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.024	-0.009	26.900	-0.439	-0.439	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.009	-0.015	27.772	0.433	0.433	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.019	0.003	28.562	-0.281	-0.281	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.981	0.984	27.583	10.318	10.318	0.000	0.000	0.000	0.000
48	A	49	ASN	0	-0.040	-0.012	31.407	0.151	0.151	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.962	0.976	34.162	8.241	8.241	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.915	-0.935	34.257	-7.619	-7.619	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.076	-0.047	32.056	-0.123	-0.123	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.031	0.018	31.359	0.234	0.234	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.013	0.006	30.869	-0.477	-0.477	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.010	-0.012	28.127	0.135	0.135	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.894	-0.927	29.032	-8.756	-8.756	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.025	-0.021	25.035	-0.326	-0.326	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.006	0.007	23.432	0.253	0.253	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.010	-0.004	20.239	-0.394	-0.394	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.012	-0.016	18.306	0.402	0.402	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.986	0.997	17.435	11.357	11.357	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.138	0.084	13.691	0.110	0.110	0.000	0.000	0.000	0.000
62	A	63	ASN	0	0.001	-0.005	14.580	-0.240	-0.240	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.038	-0.036	16.118	0.376	0.376	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.005	0.012	14.441	0.604	0.604	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.807	0.891	16.074	12.515	12.515	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.044	-0.032	15.009	-0.989	-0.989	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.039	0.014	12.553	0.764	0.764	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.017	-0.018	15.690	-0.627	-0.627	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.018	-0.013	12.312	0.229	0.229	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.047	0.022	16.605	0.514	0.514	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.873	-0.937	18.472	-13.189	-13.189	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.037	-0.019	20.467	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.050	-0.024	13.384	-0.272	-0.272	0.000	0.000	0.000	0.000
74	A	75	PRO	0	0.024	0.025	14.931	-0.255	-0.255	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.033	0.006	12.064	-1.416	-1.416	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.866	-0.944	11.100	-21.853	-21.853	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.013	-0.018	11.197	-1.209	-1.209	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.039	0.011	9.025	-1.201	-1.201	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.137	-0.080	5.740	-3.426	-3.426	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.001	0.013	7.562	-0.638	-0.638	0.000	0.000	0.000	0.000

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