FMO DATABASE

FMODB ID: 9GZ32

Calculation Name: 3KJL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KJL

Chain ID: A

ChEMBL ID:

UniProt ID: Q03067

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-529979.0821
FMO2-HF: Nuclear repulsion	495027.919867
FMO2-HF: Total energy	-34951.162232
FMO2-MP2: Total energy	-35053.494701

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:7:GLN)

Summations of interaction energy for fragment #1(A:7:GLN)

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.
-0.006999999999999	2.425	-0.035	-1.249	-1.147	-0.001

Interaction energy analysis for fragmet #1(A:7:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.020

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	9	LYS	1	0.992	0.987	3.809	-1.981	0.451	-0.035	-1.249	-1.147	-0.001
4	A	10	SER	0	0.003	-0.009	5.876	-0.208	-0.208	0.000	0.000	0.000	0.000
5	A	11	GLN	0	0.071	0.045	6.543	0.781	0.781	0.000	0.000	0.000	0.000
6	A	12	ILE	0	-0.002	-0.003	6.441	-0.115	-0.115	0.000	0.000	0.000	0.000
7	A	13	GLN	0	-0.039	-0.019	9.549	-0.217	-0.217	0.000	0.000	0.000	0.000
8	A	14	GLN	0	0.030	0.007	11.400	0.002	0.002	0.000	0.000	0.000	0.000
9	A	15	TYR	0	0.084	0.041	10.602	0.046	0.046	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.032	-0.015	14.537	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.027	-0.002	16.713	-0.088	-0.088	0.000	0.000	0.000	0.000
12	A	18	GLU	-1	-0.862	-0.931	15.989	0.800	0.800	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.012	-0.018	18.534	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.008	0.005	20.256	-0.050	-0.050	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.003	0.001	22.005	-0.069	-0.069	0.000	0.000	0.000	0.000
16	A	22	TYR	0	0.000	0.002	22.881	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.977	-0.993	24.147	0.447	0.447	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.022	0.012	26.196	-0.037	-0.037	0.000	0.000	0.000	0.000
19	A	25	ILE	0	-0.044	-0.016	26.173	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.056	-0.025	28.833	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	27	ASN	0	-0.066	-0.045	29.618	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.802	-0.893	32.409	0.210	0.210	0.000	0.000	0.000	0.000
23	A	29	LEU	0	0.009	0.004	33.615	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.921	0.953	32.801	-0.292	-0.292	0.000	0.000	0.000	0.000
25	A	31	ALA	0	0.000	0.008	37.029	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.903	0.958	36.805	-0.200	-0.200	0.000	0.000	0.000	0.000
27	A	33	LEU	0	0.051	0.034	38.467	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.040	-0.027	41.213	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	35	GLN	0	-0.054	-0.030	42.167	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.843	-0.914	43.334	0.148	0.148	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.000	0.012	46.206	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	38	TRP	0	-0.010	-0.010	40.638	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.002	-0.017	42.010	0.000	0.000	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.966	-0.988	44.762	0.123	0.123	0.000	0.000	0.000	0.000
35	A	41	LYS	1	1.026	1.019	48.343	-0.126	-0.126	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.014	0.020	43.697	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.901	0.947	45.580	-0.148	-0.148	0.000	0.000	0.000	0.000
38	A	44	ASP	-1	-0.905	-0.951	48.269	0.114	0.114	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.053	-0.022	47.265	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	46	THR	0	0.004	-0.008	46.768	0.000	0.000	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.953	0.963	49.034	-0.122	-0.122	0.000	0.000	0.000	0.000
42	A	48	SER	0	0.000	0.008	52.366	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	49	GLU	-1	-0.874	-0.957	49.635	0.108	0.108	0.000	0.000	0.000	0.000
44	A	50	MET	0	-0.115	-0.056	48.334	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	51	ASN	0	-0.041	-0.008	52.911	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.049	-0.007	54.823	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	53	ASN	0	-0.025	-0.015	51.263	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.908	-0.941	54.780	0.087	0.087	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.086	-0.030	50.807	0.002	0.002	0.000	0.000	0.000	0.000
50	A	56	THR	0	0.058	0.018	50.646	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.029	-0.026	45.067	0.007	0.007	0.000	0.000	0.000	0.000
52	A	58	PHE	0	0.077	0.025	38.300	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	59	THR	0	0.034	0.011	41.322	0.005	0.005	0.000	0.000	0.000	0.000
54	A	60	GLN	0	-0.013	-0.020	43.030	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	61	ILE	0	0.018	0.024	46.325	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.016	0.000	38.716	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	63	SER	0	-0.040	-0.022	43.102	0.000	0.000	0.000	0.000	0.000	0.000
58	A	64	THR	0	-0.028	-0.003	44.082	0.000	0.000	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.012	0.008	44.444	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.946	-0.969	38.074	0.202	0.202	0.000	0.000	0.000	0.000
61	A	67	PRO	0	-0.004	-0.013	42.359	0.003	0.003	0.000	0.000	0.000	0.000
62	A	68	LYS	1	1.006	1.003	43.324	-0.115	-0.115	0.000	0.000	0.000	0.000
63	A	69	ALA	0	0.025	0.005	42.602	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.039	-0.025	37.804	0.004	0.004	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.939	-0.967	41.302	0.142	0.142	0.000	0.000	0.000	0.000
66	A	72	MET	0	-0.128	-0.057	44.182	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	73	VAL	0	-0.089	-0.021	39.651	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	74	SER	0	0.022	0.007	42.909	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.843	-0.938	42.441	0.134	0.134	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.007	-0.013	41.819	0.004	0.004	0.000	0.000	0.000	0.000
71	A	77	THR	0	-0.067	-0.036	38.509	0.008	0.008	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.956	0.988	37.343	-0.171	-0.171	0.000	0.000	0.000	0.000
73	A	79	GLU	-1	-0.822	-0.920	36.527	0.173	0.173	0.000	0.000	0.000	0.000
74	A	80	THR	0	-0.098	-0.047	36.193	0.005	0.005	0.000	0.000	0.000	0.000
75	A	81	VAL	0	0.026	0.004	32.541	0.010	0.010	0.000	0.000	0.000	0.000
76	A	82	LEU	0	-0.006	-0.001	32.157	0.019	0.019	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.889	0.930	31.544	-0.197	-0.197	0.000	0.000	0.000	0.000
78	A	84	GLN	0	-0.011	0.000	29.724	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.021	-0.023	27.292	0.020	0.020	0.000	0.000	0.000	0.000
80	A	86	ARG	1	0.911	0.979	26.810	-0.188	-0.188	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.894	-0.937	26.533	0.256	0.256	0.000	0.000	0.000	0.000
82	A	88	PHE	0	-0.030	-0.012	20.977	0.013	0.013	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.045	-0.036	22.288	0.034	0.034	0.000	0.000	0.000	0.000
84	A	90	GLU	-1	-0.978	-0.993	21.947	0.265	0.265	0.000	0.000	0.000	0.000
85	A	91	GLU	-1	-0.955	-0.961	19.049	0.513	0.513	0.000	0.000	0.000	0.000
86	A	92	ILE	0	-0.104	-0.037	16.694	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLN)