FMO DATABASE

FMODB ID: ZV1NN

Calculation Name: 3BDU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDU

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D8G1

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	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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-261864.148443
FMO2-HF: Nuclear repulsion	240789.668847
FMO2-HF: Total energy	-21074.479597
FMO2-MP2: Total energy	-21134.935067

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-5.815	-2.296	0.226	-1.573	-2.174	-0.004

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.017

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	4	ASN	0	0.033	0.014	3.084	-5.465	-3.335	0.027	-1.028	-1.129	0.000
4	A	5	TYR	0	-0.009	-0.011	5.246	1.377	1.460	-0.001	-0.005	-0.077	0.000
5	A	6	VAL	0	-0.005	0.008	8.424	-0.093	-0.093	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.001	0.011	11.359	0.115	0.115	0.000	0.000	0.000	0.000
7	A	8	HIS	0	0.017	0.001	14.196	0.022	0.022	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.011	-0.031	17.907	0.020	0.020	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.031	-0.037	20.485	0.011	0.011	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.803	-0.816	22.830	-0.309	-0.309	0.000	0.000	0.000	0.000
11	A	12	GLY	0	-0.001	0.012	23.821	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.819	0.874	19.684	0.360	0.360	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.010	0.002	16.534	0.007	0.007	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.035	-0.015	12.899	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.010	-0.003	8.329	-0.076	-0.076	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.007	0.001	8.258	0.206	0.206	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.873	-0.926	3.383	-4.581	-4.195	0.009	-0.136	-0.259	0.000
18	A	19	GLY	0	0.013	0.006	2.997	0.285	1.175	0.176	-0.417	-0.650	-0.004
19	A	20	LYS	1	0.894	0.947	3.603	0.807	0.837	0.015	0.013	-0.059	0.000
20	A	21	PRO	0	0.022	0.011	7.315	0.224	0.224	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.850	0.919	8.278	0.553	0.553	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.017	0.010	12.841	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.811	-0.896	15.844	-0.158	-0.158	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.922	-0.967	17.545	-0.096	-0.096	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.976	-0.972	20.270	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.053	-0.048	19.344	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.020	0.003	21.500	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.058	-0.035	19.195	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.032	-0.017	13.901	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.019	0.014	13.768	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.022	-0.043	9.275	-0.054	-0.054	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.059	0.044	7.211	0.170	0.170	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.755	-0.872	8.257	-1.051	-1.051	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.002	-0.016	7.659	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.044	-0.010	8.745	0.065	0.065	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.007	0.009	8.689	0.158	0.158	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.068	-0.033	9.651	0.168	0.168	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.023	-0.016	11.292	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.047	-0.031	12.772	0.073	0.073	0.000	0.000	0.000	0.000
40	A	41	GLN	0	-0.008	-0.011	13.948	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.034	-0.006	16.079	0.008	0.008	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.048	-0.003	18.542	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.943	0.972	19.518	0.170	0.170	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.840	-0.897	20.915	-0.203	-0.203	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.062	-0.046	21.954	0.004	0.004	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.025	-0.016	16.318	-0.042	-0.042	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.874	0.953	19.494	0.306	0.306	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.863	-0.927	18.493	-0.316	-0.316	0.000	0.000	0.000	0.000
49	A	50	MET	0	-0.026	-0.022	12.076	-0.093	-0.093	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.002	0.020	13.317	0.079	0.079	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.900	0.947	6.928	0.541	0.541	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.029	0.020	8.804	0.255	0.255	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.936	0.963	9.877	0.995	0.995	0.000	0.000	0.000	0.000

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