FMO DATABASE

FMODB ID: M345Z

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	OptHSide
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	-529503.967111
FMO2-HF: Nuclear repulsion	494552.082174
FMO2-HF: Total energy	-34951.884937
FMO2-MP2: Total energy	-35054.125626

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.
0.227	2.655	-0.034	-1.235	-1.16	-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 : -0.024 / q_NPA : -0.025

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	0.993	0.993	3.809	-1.573	0.855	-0.034	-1.235	-1.160	-0.001
4	A	10	SER	0	0.009	-0.001	5.813	-0.162	-0.162	0.000	0.000	0.000	0.000
5	A	11	GLN	0	0.060	0.032	6.713	0.598	0.598	0.000	0.000	0.000	0.000
6	A	12	ILE	0	-0.011	-0.007	6.544	-0.083	-0.083	0.000	0.000	0.000	0.000
7	A	13	GLN	0	-0.037	-0.020	9.634	-0.194	-0.194	0.000	0.000	0.000	0.000
8	A	14	GLN	0	0.023	0.005	11.507	0.007	0.007	0.000	0.000	0.000	0.000
9	A	15	TYR	0	0.086	0.046	11.155	0.030	0.030	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.045	-0.018	14.591	-0.079	-0.079	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.027	-0.005	16.793	-0.077	-0.077	0.000	0.000	0.000	0.000
12	A	18	GLU	-1	-0.854	-0.929	15.564	0.790	0.790	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.030	-0.023	18.587	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	20	GLY	0	0.010	0.007	20.313	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.036	-0.029	22.150	-0.066	-0.066	0.000	0.000	0.000	0.000
16	A	22	TYR	0	-0.016	0.002	22.912	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.958	-0.983	24.384	0.407	0.407	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.007	0.012	26.251	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	25	ILE	0	-0.015	-0.007	26.215	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.045	-0.025	28.878	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	27	ASN	0	-0.081	-0.053	30.281	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.771	-0.857	32.459	0.184	0.184	0.000	0.000	0.000	0.000
23	A	29	LEU	0	0.019	0.010	33.609	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.916	0.954	32.097	-0.281	-0.281	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.002	0.007	37.080	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.882	0.933	36.885	-0.183	-0.183	0.000	0.000	0.000	0.000
27	A	33	LEU	0	0.047	0.032	38.433	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.026	-0.028	41.259	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	35	GLN	0	-0.042	-0.020	41.609	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.826	-0.856	43.515	0.138	0.138	0.000	0.000	0.000	0.000
31	A	37	GLY	0	-0.003	0.006	46.256	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	38	TRP	0	-0.032	-0.027	40.771	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.022	-0.001	42.030	0.000	0.000	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.831	-0.911	44.800	0.122	0.122	0.000	0.000	0.000	0.000
35	A	41	LYS	1	0.955	0.984	48.332	-0.124	-0.124	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.026	0.025	43.678	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.841	0.919	46.147	-0.135	-0.135	0.000	0.000	0.000	0.000
38	A	44	ASP	-1	-0.858	-0.925	48.302	0.107	0.107	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.014	-0.006	47.540	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	46	THR	0	-0.001	-0.016	47.000	0.001	0.001	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.871	0.919	49.310	-0.114	-0.114	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.013	-0.002	52.619	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	49	GLU	-1	-0.880	-0.932	50.029	0.108	0.108	0.000	0.000	0.000	0.000
44	A	50	MET	0	-0.084	-0.044	48.529	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	51	ASN	0	-0.045	-0.007	53.255	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.046	-0.010	55.220	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	53	ASN	0	-0.031	-0.013	51.317	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.907	-0.943	55.106	0.086	0.086	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.087	-0.055	50.804	0.002	0.002	0.000	0.000	0.000	0.000
50	A	56	THR	0	0.065	0.023	50.966	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.020	-0.017	45.264	0.008	0.008	0.000	0.000	0.000	0.000
52	A	58	PHE	0	0.065	0.024	38.636	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	59	THR	0	0.036	0.006	41.319	0.003	0.003	0.000	0.000	0.000	0.000
54	A	60	GLN	0	-0.001	0.005	43.338	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	61	ILE	0	0.021	0.024	46.671	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.020	0.002	38.997	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	63	SER	0	-0.057	-0.029	43.436	0.001	0.001	0.000	0.000	0.000	0.000
58	A	64	THR	0	-0.031	-0.033	44.400	0.000	0.000	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.018	-0.004	44.986	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.940	-0.974	38.790	0.199	0.199	0.000	0.000	0.000	0.000
61	A	67	PRO	0	0.004	-0.003	42.676	0.002	0.002	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.977	0.993	43.660	-0.114	-0.114	0.000	0.000	0.000	0.000
63	A	69	ALA	0	0.026	0.005	42.933	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.024	-0.016	38.118	0.003	0.003	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.936	-0.961	41.556	0.144	0.144	0.000	0.000	0.000	0.000
66	A	72	MET	0	-0.100	-0.041	44.411	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	73	VAL	0	-0.104	-0.029	39.572	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.005	-0.033	42.921	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.848	-0.938	42.452	0.130	0.130	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.012	-0.008	41.930	0.003	0.003	0.000	0.000	0.000	0.000
71	A	77	THR	0	-0.061	-0.050	38.564	0.008	0.008	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.939	0.972	37.736	-0.162	-0.162	0.000	0.000	0.000	0.000
73	A	79	GLU	-1	-0.838	-0.924	36.634	0.166	0.166	0.000	0.000	0.000	0.000
74	A	80	THR	0	-0.097	-0.052	36.367	0.004	0.004	0.000	0.000	0.000	0.000
75	A	81	VAL	0	0.037	0.007	32.727	0.008	0.008	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.002	0.007	32.193	0.019	0.019	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.775	0.879	31.756	-0.187	-0.187	0.000	0.000	0.000	0.000
78	A	84	GLN	0	-0.027	-0.022	29.771	0.004	0.004	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.003	-0.013	27.586	0.019	0.019	0.000	0.000	0.000	0.000
80	A	86	ARG	1	0.942	0.978	26.992	-0.178	-0.178	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.827	-0.893	26.740	0.227	0.227	0.000	0.000	0.000	0.000
82	A	88	PHE	0	-0.007	-0.004	20.987	0.010	0.010	0.000	0.000	0.000	0.000
83	A	89	LEU	0	-0.029	-0.019	22.453	0.031	0.031	0.000	0.000	0.000	0.000
84	A	90	GLU	-1	-0.969	-0.990	22.148	0.250	0.250	0.000	0.000	0.000	0.000
85	A	91	GLU	-1	-0.938	-0.943	19.479	0.441	0.441	0.000	0.000	0.000	0.000
86	A	92	ILE	0	-0.112	-0.048	17.004	0.009	0.009	0.000	0.000	0.000	0.000

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