FMO DATABASE

FMODB ID: 2NG1R

Calculation Name: 1B34-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: B

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:

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467574.744417
FMO2-HF: Nuclear repulsion	437492.77537
FMO2-HF: Total energy	-30081.969047
FMO2-MP2: Total energy	-30167.254134

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(B:26:THR)

Summations of interaction energy for fragment #1(B:26:THR)

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.
-9.965	-7.316	10.733	-4.837	-8.545	0.003

Interaction energy analysis for fragmet #1(B:26:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.027

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	B	28	PRO	0	0.058	0.031	3.501	-0.941	0.494	0.024	-0.497	-0.962	0.001
4	B	29	LEU	0	0.021	0.000	2.170	-0.233	0.218	3.157	-1.084	-2.524	-0.002
5	B	30	SER	0	0.006	-0.012	1.888	-2.561	-1.630	7.506	-3.642	-4.794	0.004
6	B	31	VAL	0	0.039	0.017	3.282	-0.536	-0.704	0.046	0.386	-0.265	0.000
7	B	32	LEU	0	0.049	0.037	5.879	0.068	0.068	0.000	0.000	0.000	0.000
8	B	33	THR	0	-0.062	-0.002	5.296	-0.336	-0.336	0.000	0.000	0.000	0.000
9	B	34	GLN	0	0.006	-0.001	7.236	-0.606	-0.606	0.000	0.000	0.000	0.000
10	B	35	SER	0	-0.050	-0.048	9.219	-0.303	-0.303	0.000	0.000	0.000	0.000
11	B	36	VAL	0	-0.014	-0.008	10.792	-0.107	-0.107	0.000	0.000	0.000	0.000
12	B	37	LYS	1	0.927	0.980	11.649	-0.842	-0.842	0.000	0.000	0.000	0.000
13	B	38	ASN	0	0.002	-0.005	13.166	-0.055	-0.055	0.000	0.000	0.000	0.000
14	B	39	ASN	0	0.038	0.030	15.260	-0.059	-0.059	0.000	0.000	0.000	0.000
15	B	40	THR	0	0.008	0.033	13.723	-0.067	-0.067	0.000	0.000	0.000	0.000
16	B	41	GLN	0	-0.083	-0.050	15.019	0.023	0.023	0.000	0.000	0.000	0.000
17	B	42	VAL	0	0.016	0.014	11.366	-0.047	-0.047	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.026	0.006	14.377	0.023	0.023	0.000	0.000	0.000	0.000
19	B	44	ILE	0	0.009	0.001	13.078	-0.082	-0.082	0.000	0.000	0.000	0.000
20	B	45	ASN	0	0.001	0.002	14.040	0.054	0.054	0.000	0.000	0.000	0.000
21	B	46	CYS	0	-0.024	-0.026	14.412	-0.015	-0.015	0.000	0.000	0.000	0.000
22	B	47	ARG	1	1.010	0.996	15.602	0.132	0.132	0.000	0.000	0.000	0.000
23	B	48	ASN	0	-0.011	-0.004	18.223	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	49	ASN	0	0.060	0.040	20.535	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	50	LYS	1	0.911	0.969	20.161	0.051	0.051	0.000	0.000	0.000	0.000
26	B	51	LYS	1	0.928	0.954	18.779	0.220	0.220	0.000	0.000	0.000	0.000
27	B	52	LEU	0	0.025	0.027	17.717	0.028	0.028	0.000	0.000	0.000	0.000
28	B	53	LEU	0	-0.019	0.007	17.534	-0.018	-0.018	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.063	0.029	17.610	0.010	0.010	0.000	0.000	0.000	0.000
30	B	55	ARG	1	0.850	0.915	16.610	-0.171	-0.171	0.000	0.000	0.000	0.000
31	B	56	VAL	0	0.028	0.011	11.608	-0.016	-0.016	0.000	0.000	0.000	0.000
32	B	57	LYS	1	0.926	0.989	14.703	-0.351	-0.351	0.000	0.000	0.000	0.000
33	B	58	ALA	0	0.029	0.005	14.008	0.086	0.086	0.000	0.000	0.000	0.000
34	B	59	PHE	0	-0.017	-0.013	6.689	-0.080	-0.080	0.000	0.000	0.000	0.000
35	B	60	ASP	-1	-0.731	-0.846	10.355	0.947	0.947	0.000	0.000	0.000	0.000
36	B	61	ARG	1	0.944	0.945	4.806	-3.730	-3.730	0.000	0.000	0.000	0.000
37	B	62	HIS	0	0.015	0.012	7.418	-0.053	-0.053	0.000	0.000	0.000	0.000
38	B	63	CYS	0	-0.056	-0.023	7.274	-0.217	-0.217	0.000	0.000	0.000	0.000
39	B	64	ASN	0	0.008	0.008	9.689	-0.234	-0.234	0.000	0.000	0.000	0.000
40	B	65	MET	0	-0.040	-0.014	10.574	0.134	0.134	0.000	0.000	0.000	0.000
41	B	66	VAL	0	-0.005	0.005	14.341	-0.078	-0.078	0.000	0.000	0.000	0.000
42	B	67	LEU	0	-0.019	-0.024	14.843	0.040	0.040	0.000	0.000	0.000	0.000
43	B	68	GLU	-1	-0.850	-0.938	18.311	0.261	0.261	0.000	0.000	0.000	0.000
44	B	69	ASN	0	-0.082	-0.049	20.708	-0.023	-0.023	0.000	0.000	0.000	0.000
45	B	70	VAL	0	-0.009	-0.023	19.956	-0.014	-0.014	0.000	0.000	0.000	0.000
46	B	71	LYS	1	0.928	0.980	22.147	-0.029	-0.029	0.000	0.000	0.000	0.000
47	B	72	GLU	-1	-0.860	-0.934	22.440	0.015	0.015	0.000	0.000	0.000	0.000
48	B	73	MET	0	0.018	0.004	21.547	-0.011	-0.011	0.000	0.000	0.000	0.000
49	B	93	ASP	-1	-0.929	-0.965	28.127	-0.013	-0.013	0.000	0.000	0.000	0.000
50	B	94	ARG	1	0.879	0.928	26.895	-0.037	-0.037	0.000	0.000	0.000	0.000
51	B	95	TYR	0	-0.015	-0.005	25.948	0.003	0.003	0.000	0.000	0.000	0.000
52	B	96	ILE	0	0.001	-0.009	24.235	0.006	0.006	0.000	0.000	0.000	0.000
53	B	97	SER	0	-0.006	0.019	24.569	0.016	0.016	0.000	0.000	0.000	0.000
54	B	98	LYS	1	0.990	0.974	23.043	-0.182	-0.182	0.000	0.000	0.000	0.000
55	B	99	MET	0	0.005	0.020	20.081	-0.015	-0.015	0.000	0.000	0.000	0.000
56	B	100	PHE	0	0.015	0.015	17.292	0.040	0.040	0.000	0.000	0.000	0.000
57	B	101	LEU	0	-0.012	-0.008	14.740	-0.044	-0.044	0.000	0.000	0.000	0.000
58	B	102	ARG	1	0.930	0.939	15.930	-0.131	-0.131	0.000	0.000	0.000	0.000
59	B	103	GLY	0	0.051	0.014	12.335	-0.052	-0.052	0.000	0.000	0.000	0.000
60	B	104	ASP	-1	-0.866	-0.915	12.611	0.049	0.049	0.000	0.000	0.000	0.000
61	B	105	SER	0	-0.040	-0.026	14.525	-0.067	-0.067	0.000	0.000	0.000	0.000
62	B	106	VAL	0	-0.040	-0.027	10.401	-0.070	-0.070	0.000	0.000	0.000	0.000
63	B	107	ILE	0	-0.022	0.003	11.806	-0.029	-0.029	0.000	0.000	0.000	0.000
64	B	108	VAL	0	0.029	0.005	10.072	-0.164	-0.164	0.000	0.000	0.000	0.000
65	B	109	VAL	0	-0.035	-0.005	8.922	0.167	0.167	0.000	0.000	0.000	0.000
66	B	110	LEU	0	0.006	0.001	9.897	-0.221	-0.221	0.000	0.000	0.000	0.000
67	B	111	ARG	1	0.965	0.976	9.852	0.460	0.460	0.000	0.000	0.000	0.000
68	B	112	ASN	0	-0.004	0.001	12.988	-0.085	-0.085	0.000	0.000	0.000	0.000
69	B	113	PRO	0	-0.028	-0.008	15.601	0.055	0.055	0.000	0.000	0.000	0.000
70	B	114	LEU	0	0.043	0.015	17.959	-0.023	-0.023	0.000	0.000	0.000	0.000
71	B	115	ILE	0	-0.018	-0.010	18.265	0.016	0.016	0.000	0.000	0.000	0.000
72	B	116	ALA	0	0.017	0.017	22.322	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	117	GLY	0	0.012	0.002	25.004	-0.010	-0.010	0.000	0.000	0.000	0.000
74	B	118	LYS	1	0.996	1.004	24.630	0.105	0.105	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:THR)