FMO DATABASE

FMODB ID: VQ3G1

Calculation Name: 1KLX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KLX

Chain ID: A

ChEMBL ID:

UniProt ID: O25103

Base Structure: X-ray

Registration Date: 2023-09-24

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1120024.644505
FMO2-HF: Nuclear repulsion	1067069.633621
FMO2-HF: Total energy	-52955.010884
FMO2-MP2: Total energy	-53104.906511

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:3:GLY)

Summations of interaction energy for fragment #1(A:3: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.
2.443	2.557	4.499	-2.452	-2.16	0

Interaction energy analysis for fragmet #1(A:3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.012

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	5	GLY	0	0.002	-0.019	3.480	-0.711	0.943	-0.010	-0.796	-0.847
4	A	6	THR	0	-0.023	0.010	2.093	1.144	-0.409	4.510	-1.652	-1.305
5	A	7	VAL	0	0.185	0.092	5.128	0.073	0.086	-0.001	-0.004	-0.008
6	A	8	LYS	1	0.940	0.971	6.163	0.473	0.473	0.000	0.000	0.000
7	A	9	LYS	1	0.930	0.968	5.540	0.364	0.364	0.000	0.000	0.000
8	A	10	ASP	-1	-0.852	-0.928	7.373	-0.117	-0.117	0.000	0.000	0.000
9	A	11	LEU	0	-0.004	-0.007	10.337	0.056	0.056	0.000	0.000	0.000
10	A	12	LYS	1	0.883	0.936	8.176	0.610	0.610	0.000	0.000	0.000
11	A	13	LYS	1	0.960	0.985	11.614	0.125	0.125	0.000	0.000	0.000
12	A	14	ALA	0	0.019	0.012	13.443	0.039	0.039	0.000	0.000	0.000
13	A	15	ILE	0	-0.045	-0.010	14.568	0.025	0.025	0.000	0.000	0.000
14	A	16	GLN	0	0.084	0.034	17.478	0.025	0.025	0.000	0.000	0.000
15	A	17	TYR	0	-0.014	-0.002	19.143	0.012	0.012	0.000	0.000	0.000
16	A	18	TYR	0	0.048	0.007	18.836	0.011	0.011	0.000	0.000	0.000
17	A	19	VAL	0	-0.063	-0.018	21.149	0.006	0.006	0.000	0.000	0.000
18	A	20	LYS	1	0.887	0.929	23.460	0.060	0.060	0.000	0.000	0.000
19	A	21	ALA	0	0.120	0.076	24.885	0.004	0.004	0.000	0.000	0.000
20	A	22	CYS	0	-0.155	-0.062	24.274	-0.004	-0.004	0.000	0.000	0.000
21	A	23	GLU	-1	-0.845	-0.938	27.398	-0.053	-0.053	0.000	0.000	0.000
22	A	24	LEU	0	-0.013	0.002	29.481	0.004	0.004	0.000	0.000	0.000
23	A	25	ASN	0	-0.023	-0.015	30.685	0.000	0.000	0.000	0.000	0.000
24	A	26	GLU	-1	-0.872	-0.919	28.408	-0.040	-0.040	0.000	0.000	0.000
25	A	27	MET	0	0.026	-0.003	29.337	-0.004	-0.004	0.000	0.000	0.000
26	A	28	PHE	0	0.037	0.013	25.995	-0.003	-0.003	0.000	0.000	0.000
27	A	29	GLY	0	0.079	0.064	25.077	-0.009	-0.009	0.000	0.000	0.000
28	A	31	LEU	0	0.078	0.044	24.734	-0.007	-0.007	0.000	0.000	0.000
29	A	32	SER	0	-0.007	-0.020	20.774	-0.010	-0.010	0.000	0.000	0.000
30	A	33	LEU	0	-0.060	-0.028	20.083	-0.017	-0.017	0.000	0.000	0.000
31	A	34	VAL	0	-0.024	-0.017	20.487	-0.013	-0.013	0.000	0.000	0.000
32	A	35	SER	0	-0.060	-0.013	20.062	-0.003	-0.003	0.000	0.000	0.000
33	A	36	ASN	0	0.003	0.006	14.826	-0.039	-0.039	0.000	0.000	0.000
34	A	37	SER	0	0.017	-0.017	13.419	-0.012	-0.012	0.000	0.000	0.000
35	A	38	GLN	0	-0.090	-0.043	10.225	-0.067	-0.067	0.000	0.000	0.000
36	A	39	ILE	0	-0.033	0.008	13.479	0.001	0.001	0.000	0.000	0.000
37	A	40	ASN	0	0.038	0.032	17.009	0.021	0.021	0.000	0.000	0.000
38	A	41	LYS	1	0.992	0.960	18.770	0.133	0.133	0.000	0.000	0.000
39	A	42	GLN	0	0.044	0.040	22.359	0.014	0.014	0.000	0.000	0.000
40	A	43	LYS	1	0.885	0.932	19.377	0.112	0.112	0.000	0.000	0.000
41	A	44	LEU	0	0.037	0.025	21.853	0.006	0.006	0.000	0.000	0.000
42	A	45	PHE	0	0.030	0.043	23.193	0.006	0.006	0.000	0.000	0.000
43	A	46	GLN	0	0.062	0.036	24.853	0.001	0.001	0.000	0.000	0.000
44	A	47	TYR	0	-0.009	-0.017	19.119	0.005	0.005	0.000	0.000	0.000
45	A	48	LEU	0	0.008	-0.013	25.732	0.004	0.004	0.000	0.000	0.000
46	A	49	SER	0	-0.036	-0.023	28.253	0.007	0.007	0.000	0.000	0.000
47	A	50	LYS	1	0.972	1.000	28.320	0.056	0.056	0.000	0.000	0.000
48	A	51	ALA	0	0.018	0.019	28.741	0.004	0.004	0.000	0.000	0.000
49	A	52	CYS	0	-0.144	-0.079	30.769	0.003	0.003	0.000	0.000	0.000
50	A	53	GLU	-1	-0.937	-0.981	33.449	-0.040	-0.040	0.000	0.000	0.000
51	A	54	LEU	0	-0.079	-0.028	31.106	0.003	0.003	0.000	0.000	0.000
52	A	55	ASN	0	-0.049	-0.024	35.030	0.001	0.001	0.000	0.000	0.000
53	A	56	SER	0	0.038	0.029	31.076	0.001	0.001	0.000	0.000	0.000
54	A	57	GLY	0	0.063	0.010	34.106	-0.001	-0.001	0.000	0.000	0.000
55	A	58	ASN	0	-0.022	-0.036	30.455	-0.003	-0.003	0.000	0.000	0.000
56	A	59	GLY	0	0.028	-0.002	30.084	-0.003	-0.003	0.000	0.000	0.000
57	A	61	ARG	1	0.924	0.963	31.950	0.053	0.053	0.000	0.000	0.000
58	A	62	PHE	0	-0.025	-0.020	28.427	-0.001	-0.001	0.000	0.000	0.000
59	A	63	LEU	0	-0.026	0.000	30.332	-0.003	-0.003	0.000	0.000	0.000
60	A	64	GLY	0	0.028	0.006	31.428	0.000	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.778	-0.867	30.545	-0.056	-0.056	0.000	0.000	0.000
62	A	66	PHE	0	-0.063	-0.036	25.406	-0.002	-0.002	0.000	0.000	0.000
63	A	67	TYR	0	0.000	-0.003	31.027	0.001	0.001	0.000	0.000	0.000
64	A	68	GLU	-1	-0.785	-0.897	34.713	-0.038	-0.038	0.000	0.000	0.000
65	A	69	ASN	0	-0.041	-0.045	29.965	0.005	0.005	0.000	0.000	0.000
66	A	70	GLY	0	-0.039	-0.017	33.170	0.001	0.001	0.000	0.000	0.000
67	A	71	LYS	1	0.906	0.968	25.399	0.082	0.082	0.000	0.000	0.000
68	A	72	TYR	0	-0.007	-0.028	24.051	-0.006	-0.006	0.000	0.000	0.000
69	A	73	VAL	0	0.025	0.031	28.465	-0.001	-0.001	0.000	0.000	0.000
70	A	74	LYS	1	0.971	1.000	31.783	0.037	0.037	0.000	0.000	0.000
71	A	75	LYS	1	1.020	0.989	35.211	0.042	0.042	0.000	0.000	0.000
72	A	76	ASP	-1	-0.915	-0.949	36.713	-0.034	-0.034	0.000	0.000	0.000
73	A	77	LEU	0	0.028	0.010	39.024	0.000	0.000	0.000	0.000	0.000
74	A	78	ARG	1	0.978	1.003	40.818	0.028	0.028	0.000	0.000	0.000
75	A	79	LYS	1	0.899	0.968	37.583	0.038	0.038	0.000	0.000	0.000
76	A	80	ALA	0	-0.005	-0.012	37.201	-0.001	-0.001	0.000	0.000	0.000
77	A	81	ALA	0	0.058	0.033	38.156	0.000	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.040	-0.022	40.683	0.000	0.000	0.000	0.000	0.000
79	A	83	TYR	0	-0.001	-0.001	36.110	0.001	0.001	0.000	0.000	0.000
80	A	84	TYR	0	-0.008	-0.022	34.556	0.001	0.001	0.000	0.000	0.000
81	A	85	SER	0	-0.020	-0.003	38.993	0.001	0.001	0.000	0.000	0.000
82	A	86	LYS	1	0.922	0.968	37.839	0.036	0.036	0.000	0.000	0.000
83	A	87	ALA	0	0.010	0.002	36.764	0.001	0.001	0.000	0.000	0.000
84	A	88	CYS	0	-0.069	-0.019	38.411	0.003	0.003	0.000	0.000	0.000
85	A	89	GLY	0	-0.039	-0.038	41.540	0.002	0.002	0.000	0.000	0.000
86	A	90	LEU	0	-0.082	-0.040	37.660	0.001	0.001	0.000	0.000	0.000
87	A	91	ASN	0	-0.031	-0.009	39.799	0.000	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.824	-0.909	35.173	-0.043	-0.043	0.000	0.000	0.000
89	A	93	GLN	0	0.049	0.012	37.434	0.000	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.821	-0.901	33.755	-0.045	-0.045	0.000	0.000	0.000
91	A	95	GLY	0	-0.002	-0.014	37.175	0.000	0.000	0.000	0.000	0.000
92	A	97	LEU	0	0.077	0.053	38.698	0.001	0.001	0.000	0.000	0.000
93	A	98	ILE	0	-0.014	-0.018	35.512	0.001	0.001	0.000	0.000	0.000
94	A	99	LEU	0	-0.036	-0.011	40.067	0.001	0.001	0.000	0.000	0.000
95	A	100	GLY	0	0.036	0.003	42.705	0.001	0.001	0.000	0.000	0.000
96	A	101	TYR	0	0.039	0.024	42.242	0.001	0.001	0.000	0.000	0.000
97	A	102	LYS	1	0.788	0.902	38.697	0.039	0.039	0.000	0.000	0.000
98	A	103	GLN	0	0.069	0.043	44.454	0.001	0.001	0.000	0.000	0.000
99	A	104	TYR	0	0.077	0.054	47.626	0.001	0.001	0.000	0.000	0.000
100	A	105	ALA	0	-0.042	-0.036	46.167	0.001	0.001	0.000	0.000	0.000
101	A	106	GLY	0	0.038	0.026	48.281	0.001	0.001	0.000	0.000	0.000
102	A	107	LYS	1	0.848	0.937	41.016	0.035	0.035	0.000	0.000	0.000
103	A	108	GLY	0	-0.017	-0.032	43.495	-0.001	-0.001	0.000	0.000	0.000
104	A	109	VAL	0	-0.001	0.008	44.520	0.000	0.000	0.000	0.000	0.000
105	A	110	VAL	0	-0.007	-0.003	47.383	0.000	0.000	0.000	0.000	0.000
106	A	111	LYS	1	0.977	0.986	50.675	0.022	0.022	0.000	0.000	0.000
107	A	112	ASN	0	-0.042	-0.026	51.354	0.001	0.001	0.000	0.000	0.000
108	A	113	GLU	-1	-0.840	-0.914	52.210	-0.021	-0.021	0.000	0.000	0.000
109	A	114	LYS	1	0.984	1.001	53.254	0.016	0.016	0.000	0.000	0.000
110	A	115	GLN	0	-0.052	-0.038	50.284	0.000	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.027	0.007	48.999	0.000	0.000	0.000	0.000	0.000
112	A	117	VAL	0	0.046	0.025	49.277	-0.001	-0.001	0.000	0.000	0.000
113	A	118	LYS	1	0.977	1.005	51.067	0.018	0.018	0.000	0.000	0.000
114	A	119	THR	0	-0.116	-0.089	45.432	0.000	0.000	0.000	0.000	0.000
115	A	120	PHE	0	0.026	0.004	44.208	-0.001	-0.001	0.000	0.000	0.000
116	A	121	GLU	-1	-0.843	-0.923	47.277	-0.019	-0.019	0.000	0.000	0.000
117	A	122	LYS	1	0.831	0.923	44.606	0.026	0.026	0.000	0.000	0.000
118	A	123	ALA	0	0.008	0.002	42.978	0.000	0.000	0.000	0.000	0.000
119	A	124	CYS	0	-0.067	-0.033	43.601	0.001	0.001	0.000	0.000	0.000
120	A	125	ARG	1	0.967	0.974	45.626	0.020	0.020	0.000	0.000	0.000
121	A	126	LEU	0	-0.112	-0.052	41.511	0.000	0.000	0.000	0.000	0.000
122	A	127	GLY	0	0.026	0.013	41.283	-0.001	-0.001	0.000	0.000	0.000
123	A	128	SER	0	-0.036	-0.003	40.535	-0.001	-0.001	0.000	0.000	0.000
124	A	129	GLU	-1	-0.844	-0.943	40.708	-0.027	-0.027	0.000	0.000	0.000
125	A	130	ASP	-1	-0.870	-0.933	40.458	-0.032	-0.032	0.000	0.000	0.000
126	A	131	ALA	0	-0.077	-0.040	43.213	0.001	0.001	0.000	0.000	0.000
127	A	133	GLY	0	0.017	0.008	46.415	0.001	0.001	0.000	0.000	0.000
128	A	134	ILE	0	-0.099	-0.038	44.728	0.001	0.001	0.000	0.000	0.000
129	A	135	LEU	0	-0.060	-0.009	48.703	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLY)