FMO DATABASE

FMODB ID: NN71Q

Calculation Name: 1KRL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KRL

Chain ID: A

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	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	44
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-200133.586293
FMO2-HF: Nuclear repulsion	182159.973536
FMO2-HF: Total energy	-17973.612757
FMO2-MP2: Total energy	-18027.757619

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:101:ARG)

Summations of interaction energy for fragment #1(A:101:ARG)

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.
46.139	46.369	-0.001	-0.056	-0.173	0

Interaction energy analysis for fragmet #1(A:101:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.014 / q_NPA : 1.008

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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Graph Options

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].
3	A	103	ILE	0	0.426	0.406	4.466	-4.759	-4.529	-0.001	-0.056	-0.173
4	A	104	LYS	1	0.945	0.943	5.425	28.302	28.302	0.000	0.000	0.000
5	A	105	GLY	0	-0.014	-0.039	8.009	3.093	3.093	0.000	0.000	0.000
6	A	106	TYR	0	-0.024	0.003	9.116	-2.313	-2.313	0.000	0.000	0.000
7	A	107	GLU	-1	-0.882	-0.968	11.895	-19.177	-19.177	0.000	0.000	0.000
8	A	108	TYR	0	-0.111	-0.033	14.390	-0.680	-0.680	0.000	0.000	0.000
9	A	109	GLN	0	0.000	0.002	16.724	0.821	0.821	0.000	0.000	0.000
10	A	110	LEU	0	0.003	-0.011	19.115	0.057	0.057	0.000	0.000	0.000
11	A	111	TYR	0	0.060	0.033	22.358	0.049	0.049	0.000	0.000	0.000
12	A	112	VAL	0	-0.012	-0.017	25.585	0.003	0.003	0.000	0.000	0.000
13	A	113	TYR	0	0.050	0.021	28.295	0.100	0.100	0.000	0.000	0.000
14	A	114	ALA	0	0.015	0.004	32.025	-0.023	-0.023	0.000	0.000	0.000
15	A	115	SER	0	-0.038	-0.031	34.189	0.150	0.150	0.000	0.000	0.000
16	A	116	ASP	-1	-0.857	-0.922	37.092	-7.988	-7.988	0.000	0.000	0.000
17	A	117	LYS	1	0.879	0.951	35.492	8.491	8.491	0.000	0.000	0.000
18	A	118	LEU	0	-0.018	0.012	29.005	-0.225	-0.225	0.000	0.000	0.000
19	A	119	PHE	0	-0.003	0.009	29.217	0.162	0.162	0.000	0.000	0.000
20	A	120	ARG	1	0.802	0.887	20.696	13.937	13.937	0.000	0.000	0.000
21	A	121	ALA	0	-0.006	-0.003	24.132	0.222	0.222	0.000	0.000	0.000
22	A	122	ASP	-1	-0.751	-0.855	18.941	-15.814	-15.814	0.000	0.000	0.000
23	A	123	ILE	0	-0.012	-0.015	19.125	0.640	0.640	0.000	0.000	0.000
24	A	124	SER	0	0.019	0.034	15.446	-0.884	-0.884	0.000	0.000	0.000
25	A	125	GLU	-1	-0.806	-0.926	14.713	-17.162	-17.162	0.000	0.000	0.000
26	A	126	ASP	-1	-0.867	-0.916	13.358	-21.736	-21.736	0.000	0.000	0.000
27	A	127	TYR	0	0.030	0.017	10.040	0.816	0.816	0.000	0.000	0.000
28	A	128	LYS	1	0.975	0.992	12.173	17.392	17.392	0.000	0.000	0.000
29	A	129	THR	0	-0.091	-0.082	14.531	1.124	1.124	0.000	0.000	0.000
30	A	130	ARG	1	0.955	0.999	16.314	18.777	18.777	0.000	0.000	0.000
31	A	131	GLY	0	0.015	0.015	17.702	0.810	0.810	0.000	0.000	0.000
32	A	132	ARG	1	0.867	0.923	17.834	14.433	14.433	0.000	0.000	0.000
33	A	133	LYS	1	0.943	0.980	19.581	14.080	14.080	0.000	0.000	0.000
34	A	134	LEU	0	-0.007	0.008	20.526	-0.538	-0.538	0.000	0.000	0.000
35	A	135	LEU	0	-0.050	-0.033	16.783	0.417	0.417	0.000	0.000	0.000
36	A	136	ARG	1	0.897	0.951	20.929	14.024	14.024	0.000	0.000	0.000
37	A	137	PHE	0	0.035	0.011	23.779	-0.277	-0.277	0.000	0.000	0.000
38	A	138	ASN	0	-0.022	-0.006	26.280	-0.043	-0.043	0.000	0.000	0.000
39	A	139	GLY	0	0.029	0.017	28.699	-0.259	-0.259	0.000	0.000	0.000
40	A	140	PRO	0	-0.023	-0.025	31.496	0.169	0.169	0.000	0.000	0.000
41	A	141	VAL	0	-0.025	-0.005	27.822	-0.051	-0.051	0.000	0.000	0.000
42	A	142	PRO	0	0.005	0.004	29.796	0.176	0.176	0.000	0.000	0.000
43	A	143	PRO	0	0.018	-0.008	29.774	-0.337	-0.337	0.000	0.000	0.000
44	A	144	PRO	0	0.012	0.012	25.843	0.160	0.160	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:101:ARG)