FMO DATABASE

FMODB ID: 7GYZK

Calculation Name: 1B35-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B35

Chain ID: D

ChEMBL ID:

UniProt ID: P13418

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-206513.517177
FMO2-HF: Nuclear repulsion	186200.285391
FMO2-HF: Total energy	-20313.231786
FMO2-MP2: Total energy	-20373.912283

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(D:1:ALA)

Summations of interaction energy for fragment #1(D:1:ALA)

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.
-26.535	-19.28	6.3	-6.593	-6.96	-0.056

Interaction energy analysis for fragmet #1(D:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.019

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	D	3	SER	0	-0.008	-0.011	3.420	-4.429	-2.287	0.032	-1.045	-1.128	0.006
4	D	4	GLU	-1	-0.808	-0.913	2.065	-20.274	-16.609	6.247	-5.127	-4.784	-0.062
5	D	5	LEU	0	-0.020	-0.015	3.446	0.531	1.331	0.018	-0.299	-0.520	0.000
6	D	6	LYS	1	0.872	0.932	5.867	0.472	0.472	0.000	0.000	0.000	0.000
7	D	7	GLN	0	0.013	-0.006	7.313	-0.161	-0.161	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.013	0.004	8.242	0.149	0.149	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.892	-0.926	9.915	0.002	0.002	0.000	0.000	0.000	0.000
10	D	10	THR	0	-0.076	-0.043	12.283	0.105	0.105	0.000	0.000	0.000	0.000
11	D	11	ASN	0	-0.014	-0.004	12.375	0.119	0.119	0.000	0.000	0.000	0.000
12	D	12	ASN	0	-0.033	-0.014	14.157	0.042	0.042	0.000	0.000	0.000	0.000
13	D	13	SER	0	0.020	-0.002	13.150	0.015	0.015	0.000	0.000	0.000	0.000
14	D	14	PRO	0	0.009	0.003	10.210	-0.033	-0.033	0.000	0.000	0.000	0.000
15	D	15	SER	0	-0.042	-0.011	11.274	-0.040	-0.040	0.000	0.000	0.000	0.000
16	D	16	THR	0	-0.009	-0.009	11.369	0.015	0.015	0.000	0.000	0.000	0.000
17	D	17	ALA	0	-0.015	-0.007	13.701	0.071	0.071	0.000	0.000	0.000	0.000
18	D	18	LEU	0	0.001	0.015	17.368	-0.015	-0.015	0.000	0.000	0.000	0.000
19	D	19	GLY	0	0.010	0.005	20.664	-0.014	-0.014	0.000	0.000	0.000	0.000
20	D	20	GLN	0	-0.021	-0.019	22.302	0.026	0.026	0.000	0.000	0.000	0.000
21	D	21	ILE	0	-0.003	0.003	24.591	-0.011	-0.011	0.000	0.000	0.000	0.000
22	D	22	SER	0	0.036	-0.006	26.043	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	23	GLU	-1	-0.915	-0.952	27.025	-0.168	-0.168	0.000	0.000	0.000	0.000
24	D	24	GLY	0	-0.036	-0.006	29.080	0.008	0.008	0.000	0.000	0.000	0.000
25	D	25	LEU	0	-0.003	0.011	21.612	-0.001	-0.001	0.000	0.000	0.000	0.000
26	D	26	THR	0	-0.036	-0.026	25.399	0.002	0.002	0.000	0.000	0.000	0.000
27	D	27	THR	0	0.022	0.002	20.066	0.002	0.002	0.000	0.000	0.000	0.000
28	D	28	LEU	0	-0.018	-0.008	22.723	-0.011	-0.011	0.000	0.000	0.000	0.000
29	D	29	SER	0	0.005	0.001	25.280	-0.003	-0.003	0.000	0.000	0.000	0.000
30	D	30	HIS	0	-0.015	0.001	16.107	0.041	0.041	0.000	0.000	0.000	0.000
31	D	31	ILE	0	0.024	0.011	20.417	-0.012	-0.012	0.000	0.000	0.000	0.000
32	D	32	PRO	0	-0.047	-0.005	15.183	0.010	0.010	0.000	0.000	0.000	0.000
33	D	33	VAL	0	0.025	0.006	15.134	0.029	0.029	0.000	0.000	0.000	0.000
34	D	34	LEU	0	0.046	0.014	12.952	-0.049	-0.049	0.000	0.000	0.000	0.000
35	D	35	GLY	0	-0.001	0.023	11.286	-0.037	-0.037	0.000	0.000	0.000	0.000
36	D	36	ASN	0	-0.072	-0.061	9.183	-0.127	-0.127	0.000	0.000	0.000	0.000
37	D	37	ILE	0	0.023	0.002	7.210	0.188	0.188	0.000	0.000	0.000	0.000
38	D	38	PHE	0	0.003	0.000	3.366	0.480	0.737	0.005	-0.054	-0.208	0.000
39	D	39	SER	0	-0.009	0.002	4.305	-0.717	-0.601	-0.001	-0.014	-0.101	0.000
40	D	40	THR	0	-0.015	-0.003	6.483	-0.078	-0.078	0.000	0.000	0.000	0.000
41	D	41	PRO	0	0.008	0.012	4.174	1.150	1.333	0.000	-0.043	-0.139	0.000
42	D	42	ALA	0	0.026	-0.012	4.716	-1.476	-1.384	-0.001	-0.011	-0.080	0.000
43	D	43	TRP	0	0.004	0.008	5.586	-0.756	-0.756	0.000	0.000	0.000	0.000
44	D	44	ILE	0	-0.023	0.005	8.272	-0.450	-0.450	0.000	0.000	0.000	0.000
45	D	45	SER	0	-0.057	-0.036	10.685	-0.116	-0.116	0.000	0.000	0.000	0.000
46	D	46	ALA	0	0.054	0.010	13.287	-0.043	-0.043	0.000	0.000	0.000	0.000
47	D	47	LYS	1	0.936	0.983	13.038	-1.013	-1.013	0.000	0.000	0.000	0.000
48	D	48	ALA	0	0.053	0.016	17.240	0.022	0.022	0.000	0.000	0.000	0.000
49	D	49	ALA	0	0.016	-0.002	16.675	-0.004	-0.004	0.000	0.000	0.000	0.000
50	D	50	ASP	-1	-0.810	-0.904	12.973	1.024	1.024	0.000	0.000	0.000	0.000
51	D	51	LEU	0	0.028	0.023	14.879	0.005	0.005	0.000	0.000	0.000	0.000
52	D	52	ALA	0	0.018	0.015	17.450	-0.033	-0.033	0.000	0.000	0.000	0.000
53	D	53	LYS	1	0.875	0.923	12.597	-0.833	-0.833	0.000	0.000	0.000	0.000
54	D	54	LEU	0	-0.028	0.001	13.558	-0.018	-0.018	0.000	0.000	0.000	0.000
55	D	55	PHE	0	-0.058	-0.035	15.849	-0.034	-0.034	0.000	0.000	0.000	0.000
56	D	56	GLY	0	0.007	0.013	18.139	-0.041	-0.041	0.000	0.000	0.000	0.000
57	D	57	PHE	0	-0.068	-0.016	19.191	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:ALA)