FMO DATABASE

FMODB ID: M3R2Z

Calculation Name: 1B35-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	57
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-206182.141698
FMO2-HF: Nuclear repulsion	185869.246003
FMO2-HF: Total energy	-20312.895695
FMO2-MP2: Total energy	-20373.581073

3D Structure Molmil

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.
-10.668	-5.744	0.416	-1.825	-3.51	0.002

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 : 0.068 / q_NPA : 0.032

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	-0.006	-0.016	3.361	-3.826	-1.828	0.032	-0.941	-1.089	0.005
4	D	4	GLU	-1	-0.879	-0.941	2.723	-5.319	-3.936	0.304	-0.452	-1.234	-0.002
5	D	5	LEU	0	-0.012	-0.006	2.984	0.191	1.059	0.074	-0.297	-0.645	-0.001
6	D	6	LYS	1	0.955	0.985	5.851	0.497	0.497	0.000	0.000	0.000	0.000
7	D	7	GLN	0	-0.006	-0.018	7.679	-0.065	-0.065	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.014	0.004	8.231	0.131	0.131	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.971	-0.977	9.908	-0.105	-0.105	0.000	0.000	0.000	0.000
10	D	10	THR	0	-0.080	-0.040	12.271	0.096	0.096	0.000	0.000	0.000	0.000
11	D	11	ASN	0	-0.006	0.001	12.528	0.103	0.103	0.000	0.000	0.000	0.000
12	D	12	ASN	0	-0.022	-0.003	14.167	0.033	0.033	0.000	0.000	0.000	0.000
13	D	13	SER	0	0.011	-0.018	13.151	0.016	0.016	0.000	0.000	0.000	0.000
14	D	14	PRO	0	0.009	0.005	10.325	-0.025	-0.025	0.000	0.000	0.000	0.000
15	D	15	SER	0	-0.045	-0.013	11.277	-0.012	-0.012	0.000	0.000	0.000	0.000
16	D	16	THR	0	0.008	0.003	11.360	0.015	0.015	0.000	0.000	0.000	0.000
17	D	17	ALA	0	-0.018	-0.012	13.696	0.055	0.055	0.000	0.000	0.000	0.000
18	D	18	LEU	0	0.007	0.015	17.358	-0.014	-0.014	0.000	0.000	0.000	0.000
19	D	19	GLY	0	-0.003	0.002	20.670	-0.008	-0.008	0.000	0.000	0.000	0.000
20	D	20	GLN	0	-0.008	-0.013	22.322	0.024	0.024	0.000	0.000	0.000	0.000
21	D	21	ILE	0	0.000	0.006	24.613	-0.009	-0.009	0.000	0.000	0.000	0.000
22	D	22	SER	0	0.024	-0.002	26.115	0.000	0.000	0.000	0.000	0.000	0.000
23	D	23	GLU	-1	-0.908	-0.960	27.076	-0.115	-0.115	0.000	0.000	0.000	0.000
24	D	24	GLY	0	-0.049	-0.013	29.106	0.006	0.006	0.000	0.000	0.000	0.000
25	D	25	LEU	0	-0.001	0.010	21.506	0.000	0.000	0.000	0.000	0.000	0.000
26	D	26	THR	0	-0.026	-0.019	25.475	0.000	0.000	0.000	0.000	0.000	0.000
27	D	27	THR	0	-0.018	-0.012	20.099	0.008	0.008	0.000	0.000	0.000	0.000
28	D	28	LEU	0	0.019	0.003	22.782	-0.006	-0.006	0.000	0.000	0.000	0.000
29	D	29	SER	0	-0.013	-0.007	25.327	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	30	HIS	0	-0.007	0.004	16.058	0.029	0.029	0.000	0.000	0.000	0.000
31	D	31	ILE	0	0.023	0.012	20.360	-0.011	-0.011	0.000	0.000	0.000	0.000
32	D	32	PRO	0	-0.054	-0.008	15.270	0.011	0.011	0.000	0.000	0.000	0.000
33	D	33	VAL	0	0.042	0.016	14.912	0.017	0.017	0.000	0.000	0.000	0.000
34	D	34	LEU	0	0.049	0.022	12.939	-0.028	-0.028	0.000	0.000	0.000	0.000
35	D	35	GLY	0	0.016	0.036	11.278	-0.012	-0.012	0.000	0.000	0.000	0.000
36	D	36	ASN	0	-0.078	-0.078	9.171	-0.113	-0.113	0.000	0.000	0.000	0.000
37	D	37	ILE	0	0.026	0.007	7.119	0.158	0.158	0.000	0.000	0.000	0.000
38	D	38	PHE	0	0.008	0.001	3.309	0.197	0.497	0.008	-0.070	-0.237	0.000
39	D	39	SER	0	-0.022	-0.013	4.296	-0.553	-0.437	-0.001	-0.015	-0.099	0.000
40	D	40	THR	0	-0.018	0.002	6.388	-0.106	-0.106	0.000	0.000	0.000	0.000
41	D	41	PRO	0	-0.014	-0.003	4.148	1.057	1.228	0.000	-0.040	-0.130	0.000
42	D	42	ALA	0	0.033	-0.011	4.722	-1.311	-1.223	-0.001	-0.010	-0.076	0.000
43	D	43	TRP	0	0.011	0.016	5.628	-0.618	-0.618	0.000	0.000	0.000	0.000
44	D	44	ILE	0	-0.022	0.007	8.258	-0.391	-0.391	0.000	0.000	0.000	0.000
45	D	45	SER	0	-0.060	-0.033	10.693	-0.079	-0.079	0.000	0.000	0.000	0.000
46	D	46	ALA	0	0.061	0.020	13.279	-0.047	-0.047	0.000	0.000	0.000	0.000
47	D	47	LYS	1	0.944	0.982	13.923	-0.760	-0.760	0.000	0.000	0.000	0.000
48	D	48	ALA	0	0.049	0.016	17.207	0.013	0.013	0.000	0.000	0.000	0.000
49	D	49	ALA	0	-0.001	-0.011	16.585	-0.008	-0.008	0.000	0.000	0.000	0.000
50	D	50	ASP	-1	-0.862	-0.932	12.322	0.863	0.863	0.000	0.000	0.000	0.000
51	D	51	LEU	0	0.014	0.008	14.840	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	52	ALA	0	0.013	0.016	17.420	-0.031	-0.031	0.000	0.000	0.000	0.000
53	D	53	LYS	1	0.962	0.965	13.500	-0.492	-0.492	0.000	0.000	0.000	0.000
54	D	54	LEU	0	-0.022	0.010	13.726	-0.020	-0.020	0.000	0.000	0.000	0.000
55	D	55	PHE	0	-0.068	-0.042	15.818	-0.029	-0.029	0.000	0.000	0.000	0.000
56	D	56	GLY	0	0.008	0.013	18.101	-0.033	-0.033	0.000	0.000	0.000	0.000
57	D	57	PHE	0	-0.072	-0.019	19.146	-0.034	-0.034	0.000	0.000	0.000	0.000

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