FMO DATABASE

FMODB ID: KRLL3

Calculation Name: 6WXD-A-Xray128

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6WXD

Chain ID: A

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2020-06-09

Reference: K. Kato Y. Handa, Y. Kawashima, K. Fukuzawa, C. Watanabe, T. Honma, , To be published

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Selected crystal waters in PDB
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-864801.026679
FMO2-HF: Nuclear repulsion	820002.163352
FMO2-HF: Total energy	-44798.863327
FMO2-MP2: Total energy	-44927.484146

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:1:ASN )

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

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.
-20.035	-14.955	1.611	-3.349	-3.342	-0.042

Interaction energy analysis for fragmet #1(A:1:ASN )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.901

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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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	3	GLU	-1	-0.838	-0.899	3.823	-52.620	-50.531	-0.012	-0.836	-1.241	-0.002
4	A	4	LEU	0	-0.009	-0.006	5.757	3.769	3.769	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.010	0.011	9.545	0.440	0.440	0.000	0.000	0.000	0.000
6	A	6	PRO	0	-0.046	-0.015	11.893	1.373	1.373	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.002	-0.017	14.932	0.570	0.570	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.007	0.013	18.635	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.006	0.000	21.767	0.214	0.214	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.908	0.948	23.633	12.927	12.927	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.020	0.004	27.669	0.090	0.090	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.046	-0.001	31.257	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.022	-0.013	34.083	-0.092	-0.092	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.094	-0.036	36.282	-0.188	-0.188	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.055	0.042	38.427	0.125	0.125	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.030	0.005	39.569	-0.233	-0.233	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.057	0.025	41.331	0.206	0.206	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.019	0.012	42.821	-0.173	-0.173	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.027	0.008	44.819	-0.054	-0.054	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.038	0.008	40.292	0.053	0.053	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.004	-0.008	43.955	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.015	0.009	46.821	0.062	0.062	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.072	-0.005	42.446	-0.114	-0.114	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.005	-0.018	44.624	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.830	-0.904	45.853	-6.687	-6.687	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.912	-0.930	41.233	-7.699	-7.699	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.013	0.010	42.670	-0.124	-0.124	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.004	-0.003	38.208	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.002	0.011	34.923	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.024	0.001	32.417	-0.118	-0.118	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.022	0.001	28.066	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.015	-0.035	27.081	-0.118	-0.118	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.080	0.039	21.286	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.024	-0.008	22.563	0.490	0.490	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.005	-0.004	20.726	-0.777	-0.777	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.984	0.980	19.780	14.464	14.464	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.015	0.013	21.948	0.472	0.472	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.042	0.037	24.409	0.069	0.069	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.866	0.920	25.185	9.742	9.742	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.016	0.012	23.553	0.281	0.281	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.029	0.014	25.909	-0.259	-0.259	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.032	-0.008	23.350	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.024	-0.005	27.597	0.099	0.099	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.004	0.001	30.993	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.000	0.010	33.441	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.002	-0.019	36.250	0.171	0.171	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.796	-0.885	40.057	-7.634	-7.634	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.038	0.025	43.038	0.149	0.149	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.024	0.029	42.572	-0.282	-0.282	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.893	-0.954	43.535	-7.030	-7.030	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.020	0.000	40.542	0.054	0.054	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.832	0.907	39.995	7.505	7.505	0.000	0.000	0.000	0.000
53	A	53	TRP	0	0.004	0.001	37.325	-0.266	-0.266	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.041	0.022	35.787	0.099	0.099	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.816	0.899	37.642	7.357	7.357	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.019	-0.017	34.110	-0.118	-0.118	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.018	0.022	37.062	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.836	0.897	32.470	8.777	8.777	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.005	-0.023	32.591	0.073	0.073	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.815	-0.895	34.911	-8.701	-8.701	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.017	0.022	37.324	0.170	0.170	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.063	-0.029	38.005	0.154	0.154	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.069	0.027	39.255	0.190	0.190	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.082	-0.033	39.053	-0.060	-0.060	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.019	-0.002	32.568	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.050	0.020	36.505	0.049	0.049	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.036	-0.022	31.747	-0.066	-0.066	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.791	-0.864	34.733	-8.143	-8.143	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.021	-0.013	34.007	-0.372	-0.372	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.789	-0.862	31.162	-9.942	-9.942	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.002	-0.007	35.152	0.146	0.146	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.018	0.012	36.512	-0.290	-0.290	0.000	0.000	0.000	0.000
73	A	73	CYS	0	-0.004	-0.003	35.086	0.070	0.070	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.941	0.973	37.059	7.429	7.429	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.012	-0.012	35.554	-0.134	-0.134	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.037	0.018	38.862	0.166	0.166	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.004	0.013	36.731	-0.178	-0.178	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.822	-0.896	39.101	-7.638	-7.638	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.067	-0.050	39.918	-0.123	-0.123	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.065	0.012	41.651	0.135	0.135	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.958	0.995	44.759	6.889	6.889	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.068	0.044	46.263	0.132	0.132	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.042	0.015	43.808	-0.130	-0.130	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.799	0.906	42.381	7.206	7.206	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.010	0.019	41.971	-0.202	-0.202	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.823	0.906	38.631	7.967	7.967	0.000	0.000	0.000	0.000
87	A	87	TYR	0	0.025	0.009	39.025	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.002	0.000	31.051	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	89	TYR	0	-0.037	-0.027	34.995	0.077	0.077	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.039	0.014	28.559	-0.268	-0.268	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.006	0.008	29.057	0.367	0.367	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.871	0.911	30.120	8.609	8.609	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.003	-0.003	28.725	-0.128	-0.128	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.102	-0.021	25.011	-0.539	-0.539	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.071	0.032	19.577	0.109	0.109	0.000	0.000	0.000	0.000
96	A	96	ASN	0	0.086	0.015	22.399	0.367	0.367	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.003	0.016	16.360	0.131	0.131	0.000	0.000	0.000	0.000
98	A	98	ASN	0	0.020	-0.011	20.511	-0.471	-0.471	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.784	0.864	22.543	11.337	11.337	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.008	0.005	23.028	0.373	0.373	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.010	0.001	17.532	0.259	0.259	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.010	-0.002	22.839	0.229	0.229	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.001	0.002	26.504	0.285	0.285	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.026	0.010	24.168	0.249	0.249	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.017	0.000	24.918	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.005	0.005	25.967	0.300	0.300	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.005	0.007	28.299	0.269	0.269	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.025	0.006	25.779	0.160	0.160	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.066	-0.047	27.565	0.182	0.182	0.000	0.000	0.000	0.000
110	A	110	VAL	0	-0.033	-0.006	30.154	0.411	0.411	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.904	0.951	33.198	8.630	8.630	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.008	-0.011	32.690	0.179	0.179	0.000	0.000	0.000	0.000
113	A	113	GLN	-1	-0.958	-0.980	36.846	-8.178	-8.178	0.000	0.000	0.000	0.000
114	A	301	HOH	0	-0.018	-0.024	34.332	-0.135	-0.135	0.000	0.000	0.000	0.000
115	A	302	HOH	0	-0.046	-0.030	33.177	0.110	0.110	0.000	0.000	0.000	0.000
116	A	303	HOH	0	0.013	0.004	23.268	-0.061	-0.061	0.000	0.000	0.000	0.000
117	A	304	HOH	0	-0.049	-0.035	44.530	0.067	0.067	0.000	0.000	0.000	0.000
118	A	305	HOH	0	-0.028	-0.024	40.525	0.047	0.047	0.000	0.000	0.000	0.000
119	A	306	HOH	0	-0.003	-0.010	2.289	-22.214	-19.223	1.623	-2.513	-2.101	-0.040
120	A	307	HOH	0	-0.020	-0.011	38.962	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	308	HOH	0	-0.006	-0.006	38.811	0.082	0.082	0.000	0.000	0.000	0.000
122	A	309	HOH	0	0.005	0.004	45.202	0.019	0.019	0.000	0.000	0.000	0.000
123	A	310	HOH	0	0.045	0.029	22.384	-0.051	-0.051	0.000	0.000	0.000	0.000
124	A	311	HOH	0	0.031	0.020	47.073	-0.036	-0.036	0.000	0.000	0.000	0.000
125	A	312	HOH	0	0.027	0.020	22.060	0.147	0.147	0.000	0.000	0.000	0.000
126	A	313	HOH	0	-0.009	-0.018	25.434	-0.175	-0.175	0.000	0.000	0.000	0.000

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