FMO DATABASE

FMODB ID: 1N1LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1120859.399724
FMO2-HF: Nuclear repulsion	1067902.756048
FMO2-HF: Total energy	-52956.643675
FMO2-MP2: Total energy	-53106.438451

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.
2.94	4.27	2.16	-1.611	-1.879	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 : 0.065 / q_NPA : 0.015

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].
3	A	5	GLY	0	0.022	-0.013	3.306	-0.331	1.292	-0.009	-0.764	-0.850
4	A	6	THR	0	-0.019	0.010	2.296	0.634	0.325	2.170	-0.842	-1.019
5	A	7	VAL	0	0.149	0.067	5.089	0.122	0.138	-0.001	-0.005	-0.010
6	A	8	LYS	1	0.943	0.974	6.106	0.492	0.492	0.000	0.000	0.000
7	A	9	LYS	1	0.893	0.940	5.554	0.786	0.786	0.000	0.000	0.000
8	A	10	ASP	-1	-0.763	-0.867	7.353	-0.233	-0.233	0.000	0.000	0.000
9	A	11	LEU	0	-0.002	0.002	10.302	0.078	0.078	0.000	0.000	0.000
10	A	12	LYS	1	0.864	0.915	8.374	0.615	0.615	0.000	0.000	0.000
11	A	13	LYS	1	0.899	0.947	11.592	0.303	0.303	0.000	0.000	0.000
12	A	14	ALA	0	0.021	0.017	13.423	0.047	0.047	0.000	0.000	0.000
13	A	15	ILE	0	-0.050	-0.016	14.428	0.034	0.034	0.000	0.000	0.000
14	A	16	GLN	0	0.079	0.030	17.464	0.029	0.029	0.000	0.000	0.000
15	A	17	TYR	0	0.009	0.013	19.124	0.013	0.013	0.000	0.000	0.000
16	A	18	TYR	0	0.056	0.008	18.701	0.007	0.007	0.000	0.000	0.000
17	A	19	VAL	0	-0.072	-0.024	21.175	0.009	0.009	0.000	0.000	0.000
18	A	20	LYS	1	0.878	0.913	23.447	0.082	0.082	0.000	0.000	0.000
19	A	21	ALA	0	0.119	0.079	24.862	0.006	0.006	0.000	0.000	0.000
20	A	22	CYS	0	-0.160	-0.070	24.255	-0.002	-0.002	0.000	0.000	0.000
21	A	23	GLU	-1	-0.800	-0.887	27.381	-0.064	-0.064	0.000	0.000	0.000
22	A	24	LEU	0	-0.004	0.010	29.317	0.005	0.005	0.000	0.000	0.000
23	A	25	ASN	0	-0.033	-0.020	30.673	0.001	0.001	0.000	0.000	0.000
24	A	26	GLU	-1	-0.850	-0.913	27.944	-0.065	-0.065	0.000	0.000	0.000
25	A	27	MET	0	0.012	-0.006	29.314	-0.005	-0.005	0.000	0.000	0.000
26	A	28	PHE	0	0.052	0.017	25.952	-0.005	-0.005	0.000	0.000	0.000
27	A	29	GLY	0	0.071	0.061	25.051	-0.011	-0.011	0.000	0.000	0.000
28	A	31	LEU	0	0.087	0.053	24.719	-0.007	-0.007	0.000	0.000	0.000
29	A	32	SER	0	-0.004	-0.008	20.767	-0.012	-0.012	0.000	0.000	0.000
30	A	33	LEU	0	-0.060	-0.027	20.065	-0.020	-0.020	0.000	0.000	0.000
31	A	34	VAL	0	-0.026	-0.022	20.476	-0.012	-0.012	0.000	0.000	0.000
32	A	35	SER	0	-0.073	-0.030	20.212	-0.001	-0.001	0.000	0.000	0.000
33	A	36	ASN	0	0.017	0.018	14.897	-0.043	-0.043	0.000	0.000	0.000
34	A	37	SER	0	0.021	-0.015	13.376	-0.010	-0.010	0.000	0.000	0.000
35	A	38	GLN	0	-0.072	-0.024	9.985	-0.064	-0.064	0.000	0.000	0.000
36	A	39	ILE	0	-0.017	0.022	13.477	0.004	0.004	0.000	0.000	0.000
37	A	40	ASN	0	0.041	0.024	17.009	0.022	0.022	0.000	0.000	0.000
38	A	41	LYS	1	0.947	0.946	18.778	0.154	0.154	0.000	0.000	0.000
39	A	42	GLN	0	0.061	0.040	22.398	0.011	0.011	0.000	0.000	0.000
40	A	43	LYS	1	0.892	0.939	19.333	0.117	0.117	0.000	0.000	0.000
41	A	44	LEU	0	0.032	0.020	21.776	0.004	0.004	0.000	0.000	0.000
42	A	45	PHE	0	0.034	0.044	23.192	0.006	0.006	0.000	0.000	0.000
43	A	46	GLN	0	0.064	0.042	24.674	-0.002	-0.002	0.000	0.000	0.000
44	A	47	TYR	0	-0.006	-0.020	19.148	0.007	0.007	0.000	0.000	0.000
45	A	48	LEU	0	0.006	-0.013	25.728	0.004	0.004	0.000	0.000	0.000
46	A	49	SER	0	-0.013	-0.012	28.248	0.007	0.007	0.000	0.000	0.000
47	A	50	LYS	1	0.913	0.960	28.328	0.066	0.066	0.000	0.000	0.000
48	A	51	ALA	0	0.015	0.016	28.769	0.004	0.004	0.000	0.000	0.000
49	A	52	CYS	0	-0.133	-0.072	30.760	0.004	0.004	0.000	0.000	0.000
50	A	53	GLU	-1	-0.891	-0.948	33.552	-0.045	-0.045	0.000	0.000	0.000
51	A	54	LEU	0	-0.093	-0.037	31.194	0.003	0.003	0.000	0.000	0.000
52	A	55	ASN	0	-0.028	-0.016	35.021	0.001	0.001	0.000	0.000	0.000
53	A	56	SER	0	0.036	0.023	31.029	0.001	0.001	0.000	0.000	0.000
54	A	57	GLY	0	0.057	0.013	34.092	-0.001	-0.001	0.000	0.000	0.000
55	A	58	ASN	0	0.001	-0.032	30.443	-0.004	-0.004	0.000	0.000	0.000
56	A	59	GLY	0	0.016	-0.002	30.073	-0.003	-0.003	0.000	0.000	0.000
57	A	61	ARG	1	0.862	0.911	32.125	0.064	0.064	0.000	0.000	0.000
58	A	62	PHE	0	-0.017	-0.024	28.469	-0.001	-0.001	0.000	0.000	0.000
59	A	63	LEU	0	-0.030	0.000	30.326	-0.002	-0.002	0.000	0.000	0.000
60	A	64	GLY	0	0.041	0.015	31.424	0.001	0.001	0.000	0.000	0.000
61	A	65	ASP	-1	-0.759	-0.849	30.604	-0.063	-0.063	0.000	0.000	0.000
62	A	66	PHE	0	-0.046	-0.022	25.134	-0.001	-0.001	0.000	0.000	0.000
63	A	67	TYR	0	0.029	0.011	31.028	0.002	0.002	0.000	0.000	0.000
64	A	68	GLU	-1	-0.749	-0.851	34.715	-0.042	-0.042	0.000	0.000	0.000
65	A	69	ASN	0	-0.049	-0.034	31.199	0.003	0.003	0.000	0.000	0.000
66	A	70	GLY	0	-0.041	-0.021	33.137	0.002	0.002	0.000	0.000	0.000
67	A	71	LYS	1	0.909	0.965	25.299	0.085	0.085	0.000	0.000	0.000
68	A	72	TYR	0	0.004	-0.013	24.466	-0.003	-0.003	0.000	0.000	0.000
69	A	73	VAL	0	0.024	0.029	28.475	0.000	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.976	1.002	31.793	0.037	0.037	0.000	0.000	0.000
71	A	75	LYS	1	0.911	0.924	35.221	0.049	0.049	0.000	0.000	0.000
72	A	76	ASP	-1	-0.898	-0.944	36.720	-0.035	-0.035	0.000	0.000	0.000
73	A	77	LEU	0	0.029	0.011	39.026	-0.001	-0.001	0.000	0.000	0.000
74	A	78	ARG	1	0.995	1.003	40.819	0.029	0.029	0.000	0.000	0.000
75	A	79	LYS	1	0.879	0.963	37.678	0.040	0.040	0.000	0.000	0.000
76	A	80	ALA	0	0.000	-0.016	37.194	-0.001	-0.001	0.000	0.000	0.000
77	A	81	ALA	0	0.053	0.031	38.154	-0.001	-0.001	0.000	0.000	0.000
78	A	82	GLN	0	-0.021	-0.010	40.703	0.000	0.000	0.000	0.000	0.000
79	A	83	TYR	0	0.006	0.005	36.090	0.001	0.001	0.000	0.000	0.000
80	A	84	TYR	0	0.001	-0.036	34.699	0.001	0.001	0.000	0.000	0.000
81	A	85	SER	0	-0.010	0.003	38.984	0.001	0.001	0.000	0.000	0.000
82	A	86	LYS	1	0.838	0.915	37.586	0.043	0.043	0.000	0.000	0.000
83	A	87	ALA	0	0.002	-0.004	36.863	0.000	0.000	0.000	0.000	0.000
84	A	88	CYS	0	-0.075	-0.024	38.397	0.003	0.003	0.000	0.000	0.000
85	A	89	GLY	0	0.003	-0.001	41.526	0.002	0.002	0.000	0.000	0.000
86	A	90	LEU	0	-0.081	-0.043	37.661	0.001	0.001	0.000	0.000	0.000
87	A	91	ASN	0	-0.014	0.001	39.781	0.000	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.811	-0.896	35.042	-0.055	-0.055	0.000	0.000	0.000
89	A	93	GLN	0	0.024	-0.004	37.531	0.000	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.772	-0.862	33.921	-0.057	-0.057	0.000	0.000	0.000
91	A	95	GLY	0	-0.003	-0.011	37.158	0.001	0.001	0.000	0.000	0.000
92	A	97	LEU	0	0.083	0.052	38.723	0.002	0.002	0.000	0.000	0.000
93	A	98	ILE	0	-0.029	-0.025	35.481	0.002	0.002	0.000	0.000	0.000
94	A	99	LEU	0	-0.038	-0.019	40.055	0.001	0.001	0.000	0.000	0.000
95	A	100	GLY	0	0.024	0.010	42.694	0.002	0.002	0.000	0.000	0.000
96	A	101	TYR	0	0.061	0.025	41.537	0.002	0.002	0.000	0.000	0.000
97	A	102	LYS	1	0.800	0.919	38.094	0.046	0.046	0.000	0.000	0.000
98	A	103	GLN	0	0.051	0.034	44.447	0.001	0.001	0.000	0.000	0.000
99	A	104	TYR	0	0.033	0.015	47.604	0.001	0.001	0.000	0.000	0.000
100	A	105	ALA	0	-0.033	-0.023	46.129	0.001	0.001	0.000	0.000	0.000
101	A	106	GLY	0	0.046	0.032	48.275	0.001	0.001	0.000	0.000	0.000
102	A	107	LYS	1	0.808	0.903	39.524	0.042	0.042	0.000	0.000	0.000
103	A	108	GLY	0	-0.026	-0.036	43.493	-0.001	-0.001	0.000	0.000	0.000
104	A	109	VAL	0	-0.012	-0.009	44.520	0.000	0.000	0.000	0.000	0.000
105	A	110	VAL	0	0.001	0.004	47.380	0.000	0.000	0.000	0.000	0.000
106	A	111	LYS	1	0.880	0.921	50.670	0.025	0.025	0.000	0.000	0.000
107	A	112	ASN	0	-0.045	-0.028	51.344	0.002	0.002	0.000	0.000	0.000
108	A	113	GLU	-1	-0.737	-0.839	52.201	-0.025	-0.025	0.000	0.000	0.000
109	A	114	LYS	1	0.984	1.002	53.243	0.019	0.019	0.000	0.000	0.000
110	A	115	GLN	0	-0.042	-0.025	50.311	0.000	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.027	0.007	48.993	-0.001	-0.001	0.000	0.000	0.000
112	A	117	VAL	0	0.038	0.019	49.263	-0.001	-0.001	0.000	0.000	0.000
113	A	118	LYS	1	0.989	1.000	51.051	0.022	0.022	0.000	0.000	0.000
114	A	119	THR	0	-0.074	-0.062	45.292	0.000	0.000	0.000	0.000	0.000
115	A	120	PHE	0	0.020	-0.002	44.294	-0.001	-0.001	0.000	0.000	0.000
116	A	121	GLU	-1	-0.789	-0.878	47.258	-0.025	-0.025	0.000	0.000	0.000
117	A	122	LYS	1	0.779	0.881	44.565	0.033	0.033	0.000	0.000	0.000
118	A	123	ALA	0	0.014	0.003	42.805	-0.001	-0.001	0.000	0.000	0.000
119	A	124	CYS	0	-0.079	-0.026	43.580	0.001	0.001	0.000	0.000	0.000
120	A	125	ARG	1	0.880	0.923	45.602	0.026	0.026	0.000	0.000	0.000
121	A	126	LEU	0	-0.111	-0.050	41.472	0.000	0.000	0.000	0.000	0.000
122	A	127	GLY	0	0.031	0.017	41.259	-0.002	-0.002	0.000	0.000	0.000
123	A	128	SER	0	-0.033	-0.005	40.379	-0.001	-0.001	0.000	0.000	0.000
124	A	129	GLU	-1	-0.836	-0.937	40.822	-0.037	-0.037	0.000	0.000	0.000
125	A	130	ASP	-1	-0.871	-0.932	40.806	-0.041	-0.041	0.000	0.000	0.000
126	A	131	ALA	0	-0.061	-0.036	43.192	0.002	0.002	0.000	0.000	0.000
127	A	133	GLY	0	0.027	0.011	46.392	0.001	0.001	0.000	0.000	0.000
128	A	134	ILE	0	-0.091	-0.038	44.670	0.001	0.001	0.000	0.000	0.000
129	A	135	LEU	0	-0.093	-0.024	48.684	0.002	0.002	0.000	0.000	0.000

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