FMO DATABASE

FMODB ID: 9G3Z2

Calculation Name: 1WKA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WKA

Chain ID: A

ChEMBL ID:

UniProt ID: P96142

Base Structure: X-ray

Registration Date: 2023-06-20

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1364039.385729
FMO2-HF: Nuclear repulsion	1308410.139351
FMO2-HF: Total energy	-55629.246378
FMO2-MP2: Total energy	-55795.899702

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:195:GLY)

Summations of interaction energy for fragment #1(A:195: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.
-4.19	-1.228	0.101	-1.342	-1.722	-0.003

Interaction energy analysis for fragmet #1(A:195:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	197	LEU	0	-0.010	0.008	3.831	0.534	2.313	-0.024	-0.986	-0.769	-0.002
4	A	198	TYR	0	-0.005	-0.003	6.306	0.270	0.270	0.000	0.000	0.000	0.000
5	A	199	THR	0	0.002	0.003	9.819	0.001	0.001	0.000	0.000	0.000	0.000
6	A	200	LEU	0	-0.006	-0.010	13.280	0.025	0.025	0.000	0.000	0.000	0.000
7	A	201	ARG	1	0.919	0.968	15.822	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	202	TYR	0	-0.024	-0.048	16.671	0.033	0.033	0.000	0.000	0.000	0.000
9	A	203	GLU	-1	-0.869	-0.930	21.530	0.060	0.060	0.000	0.000	0.000	0.000
10	A	204	VAL	0	0.008	0.002	25.272	0.007	0.007	0.000	0.000	0.000	0.000
11	A	205	GLU	-1	-0.887	-0.948	27.446	0.037	0.037	0.000	0.000	0.000	0.000
12	A	206	GLY	0	-0.055	-0.032	30.851	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	207	GLY	0	-0.022	-0.004	31.113	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	208	GLY	0	-0.003	0.004	28.472	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	209	PHE	0	-0.001	-0.018	22.972	0.008	0.008	0.000	0.000	0.000	0.000
16	A	210	ILE	0	0.008	0.019	21.279	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	211	GLU	-1	-0.932	-0.972	17.824	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	212	ILE	0	0.005	0.034	14.556	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	213	ALA	0	0.043	0.026	11.358	0.014	0.014	0.000	0.000	0.000	0.000
20	A	214	THR	0	0.001	-0.001	9.863	0.055	0.055	0.000	0.000	0.000	0.000
21	A	215	VAL	0	0.082	0.037	4.308	-0.021	0.011	-0.001	-0.008	-0.023	0.000
22	A	216	ARG	1	0.780	0.896	5.997	0.462	0.462	0.000	0.000	0.000	0.000
23	A	217	PRO	0	0.050	0.032	8.037	-0.269	-0.269	0.000	0.000	0.000	0.000
24	A	218	GLU	-1	-0.635	-0.812	9.821	1.227	1.227	0.000	0.000	0.000	0.000
25	A	219	THR	0	-0.075	-0.053	12.168	-0.139	-0.139	0.000	0.000	0.000	0.000
26	A	220	VAL	0	0.025	0.030	13.643	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	221	PHE	0	0.056	0.017	15.910	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	222	ALA	0	-0.027	-0.002	17.861	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	223	ASP	-1	-0.747	-0.849	17.025	0.223	0.223	0.000	0.000	0.000	0.000
30	A	224	GLN	0	-0.026	-0.032	19.714	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	225	ALA	0	-0.014	-0.016	21.699	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	226	ILE	0	0.013	0.031	20.015	0.014	0.014	0.000	0.000	0.000	0.000
33	A	227	ALA	0	-0.027	-0.015	20.721	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	228	VAL	0	0.045	0.023	21.181	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	229	HIS	0	0.097	0.054	23.485	0.008	0.008	0.000	0.000	0.000	0.000
36	A	230	PRO	0	0.002	-0.006	25.372	0.001	0.001	0.000	0.000	0.000	0.000
37	A	231	GLU	-1	-0.935	-0.971	28.620	-0.046	-0.046	0.000	0.000	0.000	0.000
38	A	232	ASP	-1	-0.841	-0.903	23.647	-0.080	-0.080	0.000	0.000	0.000	0.000
39	A	233	GLU	-1	-0.877	-0.951	27.207	-0.053	-0.053	0.000	0.000	0.000	0.000
40	A	234	ARG	1	0.760	0.870	20.552	0.112	0.112	0.000	0.000	0.000	0.000
41	A	235	TYR	0	-0.008	-0.049	20.573	0.014	0.014	0.000	0.000	0.000	0.000
42	A	236	ARG	1	0.909	0.948	26.896	0.036	0.036	0.000	0.000	0.000	0.000
43	A	237	HIS	0	-0.030	-0.007	28.836	0.004	0.004	0.000	0.000	0.000	0.000
44	A	238	LEU	0	-0.030	-0.029	26.078	0.005	0.005	0.000	0.000	0.000	0.000
45	A	239	LEU	0	-0.016	0.010	27.909	0.007	0.007	0.000	0.000	0.000	0.000
46	A	240	GLY	0	-0.042	-0.017	30.078	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	241	LYS	1	0.910	0.978	29.917	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	242	ARG	1	0.940	0.961	28.128	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	243	ALA	0	0.028	0.016	23.605	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	244	ARG	1	0.872	0.928	24.919	-0.103	-0.103	0.000	0.000	0.000	0.000
51	A	245	ILE	0	-0.040	-0.007	19.713	0.004	0.004	0.000	0.000	0.000	0.000
52	A	246	PRO	0	0.006	0.014	18.523	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	247	LEU	0	-0.020	-0.020	18.607	0.027	0.027	0.000	0.000	0.000	0.000
54	A	248	THR	0	-0.037	-0.005	22.093	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	249	GLU	-1	-0.876	-0.949	24.789	0.083	0.083	0.000	0.000	0.000	0.000
56	A	250	VAL	0	-0.028	-0.020	24.789	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	251	TRP	0	-0.035	-0.012	25.667	0.002	0.002	0.000	0.000	0.000	0.000
58	A	252	ILE	0	-0.052	-0.017	21.702	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	253	PRO	0	-0.040	-0.022	26.162	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	254	ILE	0	0.059	0.052	24.874	0.005	0.005	0.000	0.000	0.000	0.000
61	A	255	LEU	0	-0.038	-0.034	24.918	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	256	ALA	0	0.043	0.008	25.769	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	257	ASP	-1	-0.786	-0.891	24.126	0.004	0.004	0.000	0.000	0.000	0.000
64	A	258	PRO	0	-0.002	-0.019	24.862	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	259	ALA	0	-0.005	0.013	22.335	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	260	VAL	0	-0.064	-0.011	19.850	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	261	GLU	-1	-0.862	-0.943	18.579	-0.140	-0.140	0.000	0.000	0.000	0.000
68	A	262	LYS	1	0.885	0.949	19.010	0.066	0.066	0.000	0.000	0.000	0.000
69	A	263	ASP	-1	-0.865	-0.925	19.016	-0.170	-0.170	0.000	0.000	0.000	0.000
70	A	264	PHE	0	-0.052	-0.009	10.924	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	265	GLY	0	0.010	0.001	13.287	0.043	0.043	0.000	0.000	0.000	0.000
72	A	266	THR	0	-0.028	-0.048	14.112	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	267	GLY	0	0.036	0.048	17.099	0.014	0.014	0.000	0.000	0.000	0.000
74	A	268	ALA	0	-0.056	-0.023	18.356	0.018	0.018	0.000	0.000	0.000	0.000
75	A	269	LEU	0	0.014	0.000	15.258	0.000	0.000	0.000	0.000	0.000	0.000
76	A	270	LYS	1	0.788	0.903	12.777	-0.321	-0.321	0.000	0.000	0.000	0.000
77	A	271	VAL	0	0.042	0.024	16.607	0.001	0.001	0.000	0.000	0.000	0.000
78	A	272	THR	0	-0.067	-0.055	16.005	0.029	0.029	0.000	0.000	0.000	0.000
79	A	273	PRO	0	0.029	-0.003	17.986	0.014	0.014	0.000	0.000	0.000	0.000
80	A	274	ALA	0	-0.022	-0.005	20.078	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	275	HIS	0	-0.068	-0.022	14.816	0.028	0.028	0.000	0.000	0.000	0.000
82	A	276	ASP	-1	-0.774	-0.888	13.718	0.149	0.149	0.000	0.000	0.000	0.000
83	A	277	PRO	0	0.004	0.000	15.278	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	278	LEU	0	0.059	0.043	16.226	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	279	ASP	-1	-0.787	-0.910	16.374	0.118	0.118	0.000	0.000	0.000	0.000
86	A	280	TYR	0	-0.100	-0.046	19.113	0.002	0.002	0.000	0.000	0.000	0.000
87	A	281	GLU	-1	-0.903	-0.936	21.704	0.001	0.001	0.000	0.000	0.000	0.000
88	A	282	ILE	0	-0.064	-0.024	20.054	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	283	GLY	0	0.001	-0.028	23.182	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	284	GLU	-1	-0.917	-0.955	24.853	0.037	0.037	0.000	0.000	0.000	0.000
91	A	285	ARG	1	0.813	0.890	23.705	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	286	HIS	1	0.770	0.880	26.227	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	287	GLY	0	0.014	0.030	29.117	0.002	0.002	0.000	0.000	0.000	0.000
94	A	288	LEU	0	-0.056	-0.017	23.805	0.004	0.004	0.000	0.000	0.000	0.000
95	A	289	LYS	1	0.948	0.967	27.268	-0.075	-0.075	0.000	0.000	0.000	0.000
96	A	290	PRO	0	0.069	0.034	23.573	0.010	0.010	0.000	0.000	0.000	0.000
97	A	291	VAL	0	0.001	0.005	22.688	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	292	SER	0	0.007	-0.005	20.428	0.025	0.025	0.000	0.000	0.000	0.000
99	A	293	VAL	0	0.012	0.001	17.252	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	294	ILE	0	-0.038	-0.019	13.974	0.055	0.055	0.000	0.000	0.000	0.000
101	A	295	ASN	0	0.011	0.012	18.376	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	296	LEU	0	0.059	0.006	19.375	0.026	0.026	0.000	0.000	0.000	0.000
103	A	297	GLU	-1	-0.970	-0.972	20.344	0.208	0.208	0.000	0.000	0.000	0.000
104	A	298	GLY	0	-0.036	-0.012	16.706	0.022	0.022	0.000	0.000	0.000	0.000
105	A	299	ARG	1	0.907	0.949	16.208	-0.199	-0.199	0.000	0.000	0.000	0.000
106	A	300	MET	0	-0.033	0.001	15.834	0.013	0.013	0.000	0.000	0.000	0.000
107	A	301	GLU	-1	-0.889	-0.956	18.815	0.177	0.177	0.000	0.000	0.000	0.000
108	A	302	GLY	0	0.048	0.016	22.304	0.002	0.002	0.000	0.000	0.000	0.000
109	A	303	GLU	-1	-0.956	-0.974	24.375	0.142	0.142	0.000	0.000	0.000	0.000
110	A	304	ARG	1	0.814	0.878	21.961	-0.174	-0.174	0.000	0.000	0.000	0.000
111	A	305	VAL	0	-0.025	0.016	19.277	0.015	0.015	0.000	0.000	0.000	0.000
112	A	306	PRO	0	0.021	0.004	19.410	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	307	GLU	-1	-0.915	-0.964	21.878	0.187	0.187	0.000	0.000	0.000	0.000
114	A	308	ALA	0	-0.009	-0.005	21.098	0.006	0.006	0.000	0.000	0.000	0.000
115	A	309	LEU	0	-0.025	-0.021	16.155	0.034	0.034	0.000	0.000	0.000	0.000
116	A	310	ARG	1	0.873	0.947	19.185	-0.179	-0.179	0.000	0.000	0.000	0.000
117	A	311	GLY	0	0.007	0.007	21.309	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	312	LEU	0	-0.017	0.003	16.711	0.005	0.005	0.000	0.000	0.000	0.000
119	A	313	ASP	-1	-0.819	-0.909	13.579	0.655	0.655	0.000	0.000	0.000	0.000
120	A	314	ARG	1	0.929	0.955	10.099	-0.802	-0.802	0.000	0.000	0.000	0.000
121	A	315	PHE	0	-0.065	-0.049	7.206	0.181	0.181	0.000	0.000	0.000	0.000
122	A	316	GLU	-1	-0.907	-0.961	10.224	0.681	0.681	0.000	0.000	0.000	0.000
123	A	317	ALA	0	0.028	0.004	12.844	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	318	ARG	1	0.806	0.890	5.037	-2.958	-2.958	0.000	0.000	0.000	0.000
125	A	319	ARG	1	0.932	0.966	8.631	-1.077	-1.077	0.000	0.000	0.000	0.000
126	A	320	LYS	1	0.942	0.971	10.553	-0.583	-0.583	0.000	0.000	0.000	0.000
127	A	321	ALA	0	0.025	0.016	12.647	-0.085	-0.085	0.000	0.000	0.000	0.000
128	A	322	VAL	0	-0.020	0.001	9.212	-0.083	-0.083	0.000	0.000	0.000	0.000
129	A	323	GLU	-1	-0.799	-0.882	12.570	0.253	0.253	0.000	0.000	0.000	0.000
130	A	324	LEU	0	0.028	0.026	15.131	-0.062	-0.062	0.000	0.000	0.000	0.000
131	A	325	PHE	0	-0.024	-0.027	13.657	-0.047	-0.047	0.000	0.000	0.000	0.000
132	A	326	ARG	1	0.705	0.824	11.685	-0.246	-0.246	0.000	0.000	0.000	0.000
133	A	327	GLU	-1	-0.965	-0.988	17.083	0.180	0.180	0.000	0.000	0.000	0.000
134	A	328	ALA	0	-0.028	0.003	20.117	-0.021	-0.021	0.000	0.000	0.000	0.000
135	A	329	GLY	0	0.012	0.018	20.662	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	330	HIS	0	-0.044	-0.038	18.387	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	331	LEU	0	-0.007	0.001	12.234	0.003	0.003	0.000	0.000	0.000	0.000
138	A	332	VAL	0	-0.070	-0.022	16.097	-0.027	-0.027	0.000	0.000	0.000	0.000
139	A	333	LYS	1	0.936	0.959	13.058	0.233	0.233	0.000	0.000	0.000	0.000
140	A	334	GLU	-1	-0.838	-0.925	9.015	0.147	0.147	0.000	0.000	0.000	0.000
141	A	335	GLU	-1	-0.925	-0.952	8.494	-0.627	-0.627	0.000	0.000	0.000	0.000
142	A	336	ASP	-1	-0.896	-0.953	5.244	-2.056	-2.046	-0.001	-0.015	0.006	0.000
143	A	337	TYR	0	-0.034	-0.014	2.941	0.059	1.200	0.127	-0.333	-0.936	-0.001

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:195:GLY)