FMO DATABASE

FMODB ID: 8962Y

Calculation Name: 1KRL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KRL

Chain ID: B

ChEMBL ID:

UniProt ID: P02881

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	48
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-215968.435256
FMO2-HF: Nuclear repulsion	196319.828545
FMO2-HF: Total energy	-19648.606711
FMO2-MP2: Total energy	-19705.542323

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:101:GLY)

Summations of interaction energy for fragment #1(B:101:GLY)

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.
-1.249	2.841	1.025	-2.458	-2.655	-0.017

Interaction energy analysis for fragmet #1(B:101:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.005

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	B	103	TRP	0	0.009	-0.012	3.757	1.602	2.581	0.007	-0.490	-0.497	0.000
4	B	104	GLU	-1	-0.846	-0.902	2.657	-5.528	-2.727	1.021	-1.932	-1.890	-0.017
5	B	105	ILE	0	-0.019	-0.012	4.689	0.661	0.703	-0.001	-0.007	-0.034	0.000
6	B	106	ILE	0	0.036	0.026	7.646	0.078	0.078	0.000	0.000	0.000	0.000
7	B	107	ASP	-1	-0.876	-0.940	9.785	-0.208	-0.208	0.000	0.000	0.000	0.000
8	B	108	ILE	0	-0.004	-0.006	13.426	-0.037	-0.037	0.000	0.000	0.000	0.000
9	B	109	GLY	0	0.056	0.038	16.331	0.033	0.033	0.000	0.000	0.000	0.000
10	B	110	PRO	0	0.028	-0.013	18.030	-0.022	-0.022	0.000	0.000	0.000	0.000
11	B	111	PHE	0	0.036	0.036	11.877	0.010	0.010	0.000	0.000	0.000	0.000
12	B	112	THR	0	0.044	0.005	13.779	-0.010	-0.010	0.000	0.000	0.000	0.000
13	B	113	GLN	0	-0.036	-0.023	15.957	0.002	0.002	0.000	0.000	0.000	0.000
14	B	114	ASN	0	-0.005	-0.010	19.599	0.009	0.009	0.000	0.000	0.000	0.000
15	B	115	LEU	0	-0.009	0.013	13.732	0.005	0.005	0.000	0.000	0.000	0.000
16	B	116	GLY	0	0.028	0.010	18.104	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	117	LYS	1	0.767	0.863	20.146	0.135	0.135	0.000	0.000	0.000	0.000
18	B	118	PHE	0	0.027	0.008	19.487	0.008	0.008	0.000	0.000	0.000	0.000
19	B	119	ALA	0	0.031	0.014	20.043	0.008	0.008	0.000	0.000	0.000	0.000
20	B	120	VAL	0	0.005	-0.001	22.108	0.010	0.010	0.000	0.000	0.000	0.000
21	B	121	ASP	-1	-0.783	-0.864	25.371	-0.114	-0.114	0.000	0.000	0.000	0.000
22	B	122	GLU	-1	-0.861	-0.897	23.857	-0.132	-0.132	0.000	0.000	0.000	0.000
23	B	123	GLU	-1	-0.760	-0.868	26.003	-0.149	-0.149	0.000	0.000	0.000	0.000
24	B	124	ASN	0	-0.095	-0.069	27.705	0.018	0.018	0.000	0.000	0.000	0.000
25	B	125	LYS	1	0.771	0.858	27.477	0.140	0.140	0.000	0.000	0.000	0.000
26	B	126	ILE	0	-0.021	0.005	26.547	0.005	0.005	0.000	0.000	0.000	0.000
27	B	127	GLY	0	-0.009	-0.002	31.002	0.007	0.007	0.000	0.000	0.000	0.000
28	B	128	GLN	0	-0.027	-0.014	27.315	0.005	0.005	0.000	0.000	0.000	0.000
29	B	129	TYR	0	-0.073	-0.042	27.300	0.002	0.002	0.000	0.000	0.000	0.000
30	B	130	GLY	0	-0.001	0.006	32.313	0.003	0.003	0.000	0.000	0.000	0.000
31	B	131	ARG	1	0.796	0.879	33.676	0.103	0.103	0.000	0.000	0.000	0.000
32	B	132	LEU	0	0.016	0.017	28.132	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	133	THR	0	0.028	0.022	30.576	0.002	0.002	0.000	0.000	0.000	0.000
34	B	134	PHE	0	0.021	0.009	22.454	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	135	ASN	0	-0.045	-0.024	26.299	0.015	0.015	0.000	0.000	0.000	0.000
36	B	136	LYS	1	0.957	0.975	23.329	0.160	0.160	0.000	0.000	0.000	0.000
37	B	137	VAL	0	-0.003	0.015	17.205	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	138	ILE	0	-0.005	-0.012	19.389	0.025	0.025	0.000	0.000	0.000	0.000
39	B	139	ARG	1	0.906	0.957	13.013	0.320	0.320	0.000	0.000	0.000	0.000
40	B	140	PRO	0	0.014	0.004	13.168	0.038	0.038	0.000	0.000	0.000	0.000
41	B	141	CYS	0	0.005	0.001	12.998	0.018	0.018	0.000	0.000	0.000	0.000
42	B	142	MET	0	-0.015	-0.016	9.096	-0.096	-0.096	0.000	0.000	0.000	0.000
43	B	143	LYS	1	0.863	0.930	4.593	0.755	0.809	-0.001	-0.005	-0.047	0.000
44	B	144	LYS	1	0.851	0.914	5.730	0.729	0.729	0.000	0.000	0.000	0.000
45	B	145	THR	0	-0.066	-0.026	3.951	0.589	0.761	0.000	-0.021	-0.150	0.000
46	B	146	ILE	0	-0.034	-0.024	6.469	-0.059	-0.059	0.000	0.000	0.000	0.000
47	B	147	TYR	0	0.013	0.004	4.734	-0.258	-0.216	-0.001	-0.003	-0.037	0.000
48	B	148	GLU	-1	-0.931	-0.956	11.189	-0.116	-0.116	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:101:GLY)