FMO DATABASE

FMODB ID: GNZY1

Calculation Name: 1K78-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K78

Chain ID: I

ChEMBL ID:

UniProt ID: P27577

Base Structure: X-ray

Registration Date: 2023-06-19

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-314137.152801
FMO2-HF: Nuclear repulsion	291034.679192
FMO2-HF: Total energy	-23102.473609
FMO2-MP2: Total energy	-23169.69894

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(I:84:GLY)

Summations of interaction energy for fragment #1(I:84: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.
0.13	2.309	-0.014	-1.316	-0.849	0.002

Interaction energy analysis for fragmet #1(I:84:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.029

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

Sort

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	I	86	SER	0	-0.023	-0.010	3.855	-0.240	1.939	-0.014	-1.316	-0.849	0.002
4	I	87	LYS	1	0.979	0.985	5.996	-0.370	-0.370	0.000	0.000	0.000	0.000
5	I	88	PRO	0	-0.008	-0.007	8.791	-0.119	-0.119	0.000	0.000	0.000	0.000
6	I	89	LYS	1	0.991	0.993	12.337	0.437	0.437	0.000	0.000	0.000	0.000
7	I	90	VAL	0	0.048	0.031	15.078	0.010	0.010	0.000	0.000	0.000	0.000
8	I	91	ALA	0	0.000	0.012	14.860	0.023	0.023	0.000	0.000	0.000	0.000
9	I	92	THR	0	0.012	0.003	15.756	0.038	0.038	0.000	0.000	0.000	0.000
10	I	93	PRO	0	0.059	0.010	15.834	-0.014	-0.014	0.000	0.000	0.000	0.000
11	I	94	LYS	1	1.033	1.017	18.427	-0.104	-0.104	0.000	0.000	0.000	0.000
12	I	95	VAL	0	0.020	0.025	20.129	-0.009	-0.009	0.000	0.000	0.000	0.000
13	I	96	VAL	0	-0.030	-0.022	17.253	-0.014	-0.014	0.000	0.000	0.000	0.000
14	I	97	GLU	-1	-0.933	-0.958	20.690	0.093	0.093	0.000	0.000	0.000	0.000
15	I	98	LYS	1	0.808	0.881	23.415	-0.028	-0.028	0.000	0.000	0.000	0.000
16	I	99	ILE	0	-0.009	-0.006	21.889	-0.010	-0.010	0.000	0.000	0.000	0.000
17	I	100	ALA	0	-0.010	-0.004	24.077	-0.005	-0.005	0.000	0.000	0.000	0.000
18	I	101	GLU	-1	-0.865	-0.925	25.946	0.027	0.027	0.000	0.000	0.000	0.000
19	I	102	TYR	0	-0.054	-0.068	28.704	-0.005	-0.005	0.000	0.000	0.000	0.000
20	I	103	LYS	1	0.835	0.902	27.696	0.041	0.041	0.000	0.000	0.000	0.000
21	I	104	ARG	1	0.927	0.970	29.998	-0.049	-0.049	0.000	0.000	0.000	0.000
22	I	105	GLN	0	0.023	0.026	31.730	-0.001	-0.001	0.000	0.000	0.000	0.000
23	I	106	ASN	0	0.012	-0.008	33.885	0.002	0.002	0.000	0.000	0.000	0.000
24	I	107	PRO	0	0.044	0.023	32.209	-0.006	-0.006	0.000	0.000	0.000	0.000
25	I	108	THR	0	-0.014	-0.007	32.705	-0.006	-0.006	0.000	0.000	0.000	0.000
26	I	109	MET	0	-0.005	0.054	31.907	-0.002	-0.002	0.000	0.000	0.000	0.000
27	I	110	PHE	0	0.029	0.014	31.727	-0.006	-0.006	0.000	0.000	0.000	0.000
28	I	111	ALA	0	-0.010	-0.026	26.999	0.002	0.002	0.000	0.000	0.000	0.000
29	I	112	TRP	0	-0.002	-0.005	28.477	-0.004	-0.004	0.000	0.000	0.000	0.000
30	I	113	GLU	-1	-0.769	-0.876	30.874	-0.040	-0.040	0.000	0.000	0.000	0.000
31	I	114	ILE	0	-0.036	-0.014	26.582	0.005	0.005	0.000	0.000	0.000	0.000
32	I	115	ARG	1	0.868	0.921	25.552	0.109	0.109	0.000	0.000	0.000	0.000
33	I	116	ASP	-1	-0.863	-0.932	28.545	-0.057	-0.057	0.000	0.000	0.000	0.000
34	I	117	ARG	1	0.819	0.880	31.643	0.013	0.013	0.000	0.000	0.000	0.000
35	I	118	LEU	0	-0.017	0.003	24.027	0.005	0.005	0.000	0.000	0.000	0.000
36	I	119	LEU	0	-0.008	-0.002	28.678	0.004	0.004	0.000	0.000	0.000	0.000
37	I	120	ALA	0	-0.012	-0.008	30.334	0.005	0.005	0.000	0.000	0.000	0.000
38	I	121	GLU	-1	-0.814	-0.887	31.268	0.007	0.007	0.000	0.000	0.000	0.000
39	I	122	ARG	1	0.905	0.953	30.541	0.015	0.015	0.000	0.000	0.000	0.000
40	I	123	VAL	0	-0.007	0.013	25.101	0.007	0.007	0.000	0.000	0.000	0.000
41	I	124	CYS	0	-0.093	-0.045	24.015	-0.003	-0.003	0.000	0.000	0.000	0.000
42	I	125	ASP	-1	-0.772	-0.861	25.550	-0.031	-0.031	0.000	0.000	0.000	0.000
43	I	126	ASN	0	-0.033	-0.046	26.684	-0.008	-0.008	0.000	0.000	0.000	0.000
44	I	127	ASP	-1	-0.896	-0.938	25.065	-0.105	-0.105	0.000	0.000	0.000	0.000
45	I	128	THR	0	-0.077	-0.058	21.430	-0.022	-0.022	0.000	0.000	0.000	0.000
46	I	129	VAL	0	-0.003	0.007	22.386	-0.001	-0.001	0.000	0.000	0.000	0.000
47	I	130	PRO	0	-0.015	0.001	20.577	-0.023	-0.023	0.000	0.000	0.000	0.000
48	I	131	SER	0	0.053	0.040	21.370	0.009	0.009	0.000	0.000	0.000	0.000
49	I	132	VAL	0	0.130	0.049	23.081	-0.001	-0.001	0.000	0.000	0.000	0.000
50	I	133	SER	0	0.010	0.000	21.989	0.013	0.013	0.000	0.000	0.000	0.000
51	I	134	SER	0	-0.046	-0.037	19.006	-0.029	-0.029	0.000	0.000	0.000	0.000
52	I	135	ILE	0	0.039	0.036	20.192	0.007	0.007	0.000	0.000	0.000	0.000
53	I	136	ASN	0	-0.013	-0.025	22.772	0.020	0.020	0.000	0.000	0.000	0.000
54	I	137	ARG	1	0.885	0.958	15.332	0.330	0.330	0.000	0.000	0.000	0.000
55	I	138	ILE	0	0.004	0.010	17.662	0.004	0.004	0.000	0.000	0.000	0.000
56	I	139	ILE	0	0.017	0.015	19.824	0.018	0.018	0.000	0.000	0.000	0.000
57	I	140	ARG	1	0.907	0.959	20.260	0.189	0.189	0.000	0.000	0.000	0.000
58	I	141	THR	0	-0.060	-0.024	15.205	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(I:84:GLY)