FMO DATABASE

FMODB ID: JQ729

Calculation Name: 3BID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BID

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DDI1

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-288177.120985
FMO2-HF: Nuclear repulsion	264810.356772
FMO2-HF: Total energy	-23366.764213
FMO2-MP2: Total energy	-23434.657829

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-7.118	-1.46	8.15	-5.244	-8.563	-0.042

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.021

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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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	3	PHE	0	0.044	0.015	3.875	-0.597	1.205	-0.021	-0.859	-0.922	0.001
4	A	4	GLU	-1	-0.890	-0.955	6.269	0.321	0.321	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.003	-0.010	9.564	0.095	0.095	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.017	-0.011	12.750	0.059	0.059	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.938	0.972	15.986	0.046	0.046	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.860	-0.928	19.426	0.013	0.013	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.004	-0.023	20.850	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.949	0.981	23.942	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.020	0.003	24.290	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.965	-0.967	21.550	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.042	-0.047	17.890	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.936	0.970	15.199	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.059	0.032	8.217	-0.070	-0.070	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.887	0.938	8.773	0.031	0.031	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.012	0.006	2.635	-0.932	-0.921	3.119	-0.623	-2.507	-0.001
18	A	18	LYS	1	0.896	0.973	4.426	-0.137	0.248	-0.001	-0.089	-0.295	0.000
19	A	19	ALA	0	0.060	0.014	2.390	-6.558	-4.022	4.186	-3.493	-3.229	-0.040
20	A	20	ALA	0	0.013	0.001	3.503	0.704	0.807	0.000	0.119	-0.221	0.000
21	A	21	ASN	0	0.003	0.018	5.187	-0.108	-0.084	-0.001	-0.003	-0.020	0.000
22	A	22	HIS	0	-0.028	-0.040	7.146	-0.126	-0.126	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.903	-0.939	6.899	0.534	0.534	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.076	-0.048	6.254	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.011	0.023	2.729	-0.840	-0.043	0.868	-0.296	-1.369	-0.002
26	A	26	ALA	0	0.019	0.003	6.815	-0.083	-0.083	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.029	0.000	8.601	-0.186	-0.186	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.013	-0.008	11.379	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.890	-0.942	13.479	0.049	0.049	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.041	-0.018	17.238	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.044	0.017	15.800	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.041	0.007	20.443	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.019	0.006	21.674	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.969	0.993	18.064	0.199	0.199	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.014	0.009	18.311	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.007	-0.017	19.032	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.018	0.023	14.087	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.028	-0.018	14.214	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.054	0.036	14.464	-0.083	-0.083	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.014	0.014	14.662	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.019	-0.009	8.972	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.891	-0.964	10.213	-0.874	-0.874	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.022	-0.010	12.036	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.010	0.019	8.674	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.910	0.991	7.284	1.447	1.447	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.109	-0.038	8.297	-0.053	-0.053	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.047	-0.040	9.499	0.106	0.106	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.032	0.007	9.385	-0.159	-0.159	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.024	0.005	9.876	0.078	0.078	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.029	-0.013	10.993	0.076	0.076	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.033	-0.019	12.609	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.017	-0.009	14.156	0.024	0.024	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.045	0.024	13.132	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.917	0.954	16.225	0.053	0.053	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.929	-0.959	18.605	0.097	0.097	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.049	-0.019	20.440	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.012	-0.021	22.437	0.012	0.012	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.957	-0.960	25.570	0.065	0.065	0.000	0.000	0.000	0.000

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