FMO DATABASE

FMODB ID: M354Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1364414.478474
FMO2-HF: Nuclear repulsion	1308784.53677
FMO2-HF: Total energy	-55629.941704
FMO2-MP2: Total energy	-55796.573309

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.
-3.586	-0.771	0.081	-1.317	-1.577	-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 : 0.000 / q_NPA : -0.013

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	-0.022	-0.003	3.831	0.657	2.377	-0.023	-0.958	-0.739	-0.002
4	A	198	TYR	0	0.004	0.004	5.875	0.192	0.192	0.000	0.000	0.000	0.000
5	A	199	THR	0	0.004	0.010	9.832	-0.005	-0.005	0.000	0.000	0.000	0.000
6	A	200	LEU	0	0.016	0.001	13.260	0.023	0.023	0.000	0.000	0.000	0.000
7	A	201	ARG	1	0.926	0.982	15.836	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	202	TYR	0	-0.035	-0.045	16.577	0.029	0.029	0.000	0.000	0.000	0.000
9	A	203	GLU	-1	-0.852	-0.919	21.544	0.071	0.071	0.000	0.000	0.000	0.000
10	A	204	VAL	0	0.008	0.000	25.287	0.006	0.006	0.000	0.000	0.000	0.000
11	A	205	GLU	-1	-0.822	-0.904	27.460	0.042	0.042	0.000	0.000	0.000	0.000
12	A	206	GLY	0	-0.040	-0.025	30.865	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	207	GLY	0	-0.024	-0.005	31.126	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	208	GLY	0	-0.004	0.002	28.485	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	209	PHE	0	-0.001	-0.020	22.988	0.007	0.007	0.000	0.000	0.000	0.000
16	A	210	ILE	0	0.004	0.016	21.443	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	211	GLU	-1	-0.874	-0.957	17.915	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	212	ILE	0	0.010	0.036	14.444	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	213	ALA	0	0.030	0.022	11.419	0.011	0.011	0.000	0.000	0.000	0.000
20	A	214	THR	0	0.007	0.003	9.875	0.063	0.063	0.000	0.000	0.000	0.000
21	A	215	VAL	0	0.068	0.030	4.337	-0.042	-0.010	-0.001	-0.008	-0.023	0.000
22	A	216	ARG	1	0.720	0.838	6.008	0.580	0.580	0.000	0.000	0.000	0.000
23	A	217	PRO	0	0.062	0.034	7.969	-0.255	-0.255	0.000	0.000	0.000	0.000
24	A	218	GLU	-1	-0.670	-0.804	9.884	1.179	1.179	0.000	0.000	0.000	0.000
25	A	219	THR	0	-0.085	-0.062	12.184	-0.143	-0.143	0.000	0.000	0.000	0.000
26	A	220	VAL	0	0.041	0.035	13.612	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	221	PHE	0	0.063	0.024	15.923	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	222	ALA	0	-0.031	0.003	17.807	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	223	ASP	-1	-0.747	-0.860	17.051	0.227	0.227	0.000	0.000	0.000	0.000
30	A	224	GLN	0	-0.044	-0.038	19.725	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	225	ALA	0	-0.009	-0.011	21.710	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	226	ILE	0	0.010	0.027	20.051	0.014	0.014	0.000	0.000	0.000	0.000
33	A	227	ALA	0	-0.026	-0.011	20.733	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	228	VAL	0	0.039	0.016	21.191	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	229	HIS	0	0.086	0.054	23.494	0.009	0.009	0.000	0.000	0.000	0.000
36	A	230	PRO	0	0.003	-0.009	25.380	0.001	0.001	0.000	0.000	0.000	0.000
37	A	231	GLU	-1	-0.927	-0.969	28.584	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	232	ASP	-1	-0.831	-0.887	23.649	-0.073	-0.073	0.000	0.000	0.000	0.000
39	A	233	GLU	-1	-0.858	-0.954	27.216	-0.053	-0.053	0.000	0.000	0.000	0.000
40	A	234	ARG	1	0.754	0.859	20.675	0.105	0.105	0.000	0.000	0.000	0.000
41	A	235	TYR	0	0.004	-0.041	20.667	0.014	0.014	0.000	0.000	0.000	0.000
42	A	236	ARG	1	0.922	0.972	26.907	0.033	0.033	0.000	0.000	0.000	0.000
43	A	237	HIS	0	-0.014	0.004	28.826	0.005	0.005	0.000	0.000	0.000	0.000
44	A	238	LEU	0	-0.015	-0.019	26.104	0.005	0.005	0.000	0.000	0.000	0.000
45	A	239	LEU	0	-0.010	0.013	27.886	0.007	0.007	0.000	0.000	0.000	0.000
46	A	240	GLY	0	-0.041	-0.016	30.095	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	241	LYS	1	0.853	0.942	29.931	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	242	ARG	1	0.871	0.917	28.155	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	243	ALA	0	0.013	0.006	23.638	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	244	ARG	1	0.827	0.905	25.107	-0.100	-0.100	0.000	0.000	0.000	0.000
51	A	245	ILE	0	-0.035	-0.010	19.698	0.004	0.004	0.000	0.000	0.000	0.000
52	A	246	PRO	0	0.007	0.010	18.380	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	247	LEU	0	-0.022	-0.017	18.700	0.028	0.028	0.000	0.000	0.000	0.000
54	A	248	THR	0	-0.048	-0.017	22.040	0.000	0.000	0.000	0.000	0.000	0.000
55	A	249	GLU	-1	-0.794	-0.890	24.789	0.086	0.086	0.000	0.000	0.000	0.000
56	A	250	VAL	0	-0.038	-0.020	24.801	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	251	TRP	0	-0.045	-0.030	25.680	0.001	0.001	0.000	0.000	0.000	0.000
58	A	252	ILE	0	-0.044	-0.011	21.617	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	253	PRO	0	-0.026	-0.015	26.174	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	254	ILE	0	0.046	0.047	24.828	0.005	0.005	0.000	0.000	0.000	0.000
61	A	255	LEU	0	-0.041	-0.034	24.996	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	256	ALA	0	0.045	0.009	25.778	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	257	ASP	-1	-0.770	-0.874	24.116	0.009	0.009	0.000	0.000	0.000	0.000
64	A	258	PRO	0	-0.001	-0.017	24.869	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	259	ALA	0	-0.010	0.014	22.365	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	260	VAL	0	-0.072	-0.022	19.734	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	261	GLU	-1	-0.847	-0.933	18.514	-0.130	-0.130	0.000	0.000	0.000	0.000
68	A	262	LYS	1	0.862	0.940	19.017	0.063	0.063	0.000	0.000	0.000	0.000
69	A	263	ASP	-1	-0.853	-0.924	19.075	-0.161	-0.161	0.000	0.000	0.000	0.000
70	A	264	PHE	0	-0.066	-0.015	10.850	-0.052	-0.052	0.000	0.000	0.000	0.000
71	A	265	GLY	0	0.005	-0.001	13.295	0.042	0.042	0.000	0.000	0.000	0.000
72	A	266	THR	0	-0.034	-0.052	14.120	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	267	GLY	0	0.042	0.046	17.106	0.012	0.012	0.000	0.000	0.000	0.000
74	A	268	ALA	0	-0.071	-0.028	18.350	0.016	0.016	0.000	0.000	0.000	0.000
75	A	269	LEU	0	0.007	-0.002	15.248	0.001	0.001	0.000	0.000	0.000	0.000
76	A	270	LYS	1	0.829	0.923	12.895	-0.324	-0.324	0.000	0.000	0.000	0.000
77	A	271	VAL	0	0.025	0.015	16.617	0.001	0.001	0.000	0.000	0.000	0.000
78	A	272	THR	0	-0.084	-0.058	15.885	0.027	0.027	0.000	0.000	0.000	0.000
79	A	273	PRO	0	0.026	-0.009	17.994	0.014	0.014	0.000	0.000	0.000	0.000
80	A	274	ALA	0	-0.018	-0.003	20.050	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	275	HIS	0	-0.037	-0.015	14.852	0.033	0.033	0.000	0.000	0.000	0.000
82	A	276	ASP	-1	-0.753	-0.877	13.237	0.190	0.190	0.000	0.000	0.000	0.000
83	A	277	PRO	0	0.010	0.016	15.301	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	278	LEU	0	0.058	0.042	16.334	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	279	ASP	-1	-0.782	-0.891	16.365	0.138	0.138	0.000	0.000	0.000	0.000
86	A	280	TYR	0	-0.144	-0.084	19.120	0.002	0.002	0.000	0.000	0.000	0.000
87	A	281	GLU	-1	-0.823	-0.886	21.700	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	282	ILE	0	-0.035	-0.011	19.943	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	283	GLY	0	0.000	-0.022	23.187	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	284	GLU	-1	-0.866	-0.913	24.861	0.044	0.044	0.000	0.000	0.000	0.000
91	A	285	ARG	1	0.738	0.842	23.651	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	286	HIS	1	0.763	0.860	26.056	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	287	GLY	0	0.011	0.028	29.125	0.002	0.002	0.000	0.000	0.000	0.000
94	A	288	LEU	0	-0.052	-0.016	23.818	0.004	0.004	0.000	0.000	0.000	0.000
95	A	289	LYS	1	0.957	0.972	27.277	-0.076	-0.076	0.000	0.000	0.000	0.000
96	A	290	PRO	0	0.060	0.037	23.579	0.010	0.010	0.000	0.000	0.000	0.000
97	A	291	VAL	0	0.002	0.001	22.701	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	292	SER	0	0.003	-0.005	20.433	0.025	0.025	0.000	0.000	0.000	0.000
99	A	293	VAL	0	0.005	-0.002	17.291	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	294	ILE	0	-0.029	-0.013	14.108	0.048	0.048	0.000	0.000	0.000	0.000
101	A	295	ASN	0	0.004	-0.005	18.366	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	296	LEU	0	0.056	0.011	19.367	0.026	0.026	0.000	0.000	0.000	0.000
103	A	297	GLU	-1	-0.970	-0.978	20.336	0.207	0.207	0.000	0.000	0.000	0.000
104	A	298	GLY	0	-0.029	-0.008	16.697	0.020	0.020	0.000	0.000	0.000	0.000
105	A	299	ARG	1	0.902	0.946	16.196	-0.192	-0.192	0.000	0.000	0.000	0.000
106	A	300	MET	0	-0.029	0.005	15.613	0.014	0.014	0.000	0.000	0.000	0.000
107	A	301	GLU	-1	-0.904	-0.946	18.801	0.176	0.176	0.000	0.000	0.000	0.000
108	A	302	GLY	0	0.054	0.014	22.304	0.003	0.003	0.000	0.000	0.000	0.000
109	A	303	GLU	-1	-0.960	-0.978	24.375	0.140	0.140	0.000	0.000	0.000	0.000
110	A	304	ARG	1	0.814	0.866	21.887	-0.177	-0.177	0.000	0.000	0.000	0.000
111	A	305	VAL	0	-0.022	0.017	19.141	0.015	0.015	0.000	0.000	0.000	0.000
112	A	306	PRO	0	0.033	0.012	19.452	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	307	GLU	-1	-0.857	-0.927	21.878	0.183	0.183	0.000	0.000	0.000	0.000
114	A	308	ALA	0	-0.015	-0.009	21.133	0.006	0.006	0.000	0.000	0.000	0.000
115	A	309	LEU	0	-0.020	-0.021	16.150	0.032	0.032	0.000	0.000	0.000	0.000
116	A	310	ARG	1	0.824	0.918	19.169	-0.175	-0.175	0.000	0.000	0.000	0.000
117	A	311	GLY	0	0.011	0.010	21.293	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	312	LEU	0	-0.041	-0.006	16.703	0.006	0.006	0.000	0.000	0.000	0.000
119	A	313	ASP	-1	-0.824	-0.921	13.395	0.655	0.655	0.000	0.000	0.000	0.000
120	A	314	ARG	1	0.925	0.947	10.136	-0.793	-0.793	0.000	0.000	0.000	0.000
121	A	315	PHE	0	-0.056	-0.043	7.513	0.161	0.161	0.000	0.000	0.000	0.000
122	A	316	GLU	-1	-0.792	-0.879	10.207	0.759	0.759	0.000	0.000	0.000	0.000
123	A	317	ALA	0	0.006	-0.005	12.827	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	318	ARG	1	0.814	0.888	5.017	-2.993	-2.956	-0.001	-0.003	-0.032	0.000
125	A	319	ARG	1	0.862	0.926	8.660	-0.962	-0.962	0.000	0.000	0.000	0.000
126	A	320	LYS	1	0.924	0.949	10.550	-0.568	-0.568	0.000	0.000	0.000	0.000
127	A	321	ALA	0	0.012	0.010	12.665	-0.085	-0.085	0.000	0.000	0.000	0.000
128	A	322	VAL	0	-0.017	0.004	9.183	-0.078	-0.078	0.000	0.000	0.000	0.000
129	A	323	GLU	-1	-0.792	-0.865	12.508	0.243	0.243	0.000	0.000	0.000	0.000
130	A	324	LEU	0	0.023	0.020	15.128	-0.061	-0.061	0.000	0.000	0.000	0.000
131	A	325	PHE	0	-0.017	-0.025	13.695	-0.045	-0.045	0.000	0.000	0.000	0.000
132	A	326	ARG	1	0.678	0.774	11.392	-0.252	-0.252	0.000	0.000	0.000	0.000
133	A	327	GLU	-1	-0.971	-0.989	17.080	0.163	0.163	0.000	0.000	0.000	0.000
134	A	328	ALA	0	-0.035	-0.003	20.106	-0.021	-0.021	0.000	0.000	0.000	0.000
135	A	329	GLY	0	0.002	0.014	20.653	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	330	HIS	0	-0.052	-0.042	18.441	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	331	LEU	0	-0.016	-0.003	12.186	0.004	0.004	0.000	0.000	0.000	0.000
138	A	332	VAL	0	-0.092	-0.026	16.102	-0.027	-0.027	0.000	0.000	0.000	0.000
139	A	333	LYS	1	0.843	0.888	13.296	0.286	0.286	0.000	0.000	0.000	0.000
140	A	334	GLU	-1	-0.816	-0.886	8.968	0.195	0.195	0.000	0.000	0.000	0.000
141	A	335	GLU	-1	-0.854	-0.905	8.507	-0.485	-0.485	0.000	0.000	0.000	0.000
142	A	336	ASP	-1	-0.877	-0.925	5.235	-2.125	-2.121	-0.001	-0.015	0.012	0.000
143	A	337	TYR	0	-0.026	-0.002	2.953	0.144	1.166	0.107	-0.333	-0.795	-0.001

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