FMO DATABASE

FMODB ID: ZYM1N

Calculation Name: 2DWK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DWK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D394

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1603465.139686
FMO2-HF: Nuclear repulsion	1538490.717269
FMO2-HF: Total energy	-64974.422417
FMO2-MP2: Total energy	-65157.691778

3D Structure Molmil

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:83:MET)

Summations of interaction energy for fragment #1(A:83:MET)

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.
-14.743	-5.276	12.118	-7.08	-14.502	-0.042

Interaction energy analysis for fragmet #1(A:83:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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	85	ASN	0	0.023	0.007	3.193	-2.610	-0.374	0.004	-0.970	-1.271	0.002
4	A	86	GLU	-1	-0.892	-0.948	2.415	-9.199	-6.944	3.011	-1.943	-3.323	-0.026
5	A	87	ARG	1	0.900	0.979	2.781	-0.420	1.187	0.301	-0.446	-1.462	0.000
6	A	88	MET	0	0.062	0.032	5.410	0.366	0.366	0.000	0.000	0.000	0.000
7	A	89	ASN	0	-0.052	-0.032	7.317	0.351	0.351	0.000	0.000	0.000	0.000
8	A	90	LEU	0	0.023	0.013	6.477	0.195	0.195	0.000	0.000	0.000	0.000
9	A	91	MET	0	0.036	0.034	9.501	0.159	0.159	0.000	0.000	0.000	0.000
10	A	92	ASN	0	-0.032	-0.015	11.411	0.117	0.117	0.000	0.000	0.000	0.000
11	A	93	MET	0	-0.014	-0.002	11.483	0.041	0.041	0.000	0.000	0.000	0.000
12	A	94	ALA	0	0.027	0.002	13.599	0.046	0.046	0.000	0.000	0.000	0.000
13	A	95	LYS	1	0.913	0.953	15.039	0.107	0.107	0.000	0.000	0.000	0.000
14	A	96	LEU	0	-0.039	-0.018	17.445	0.029	0.029	0.000	0.000	0.000	0.000
15	A	97	SER	0	0.027	-0.020	18.173	0.006	0.006	0.000	0.000	0.000	0.000
16	A	98	ILE	0	-0.042	-0.016	17.796	0.016	0.016	0.000	0.000	0.000	0.000
17	A	99	LYS	1	0.968	0.987	21.134	0.110	0.110	0.000	0.000	0.000	0.000
18	A	100	GLY	0	0.031	0.021	22.939	0.009	0.009	0.000	0.000	0.000	0.000
19	A	101	LEU	0	-0.016	-0.007	23.681	0.008	0.008	0.000	0.000	0.000	0.000
20	A	102	ILE	0	0.002	-0.005	24.451	0.009	0.009	0.000	0.000	0.000	0.000
21	A	103	GLU	-1	-0.948	-0.975	27.278	-0.068	-0.068	0.000	0.000	0.000	0.000
22	A	104	SER	0	-0.057	-0.028	27.916	0.004	0.004	0.000	0.000	0.000	0.000
23	A	105	ALA	0	-0.003	-0.009	29.484	0.004	0.004	0.000	0.000	0.000	0.000
24	A	106	LEU	0	-0.033	-0.010	31.157	0.005	0.005	0.000	0.000	0.000	0.000
25	A	107	ASN	0	-0.031	-0.008	33.182	0.008	0.008	0.000	0.000	0.000	0.000
26	A	108	LEU	0	-0.113	-0.046	33.459	0.002	0.002	0.000	0.000	0.000	0.000
27	A	109	GLY	0	0.022	0.005	35.316	0.003	0.003	0.000	0.000	0.000	0.000
28	A	110	ARG	1	0.930	0.982	34.733	0.070	0.070	0.000	0.000	0.000	0.000
29	A	111	THR	0	0.010	-0.021	35.089	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	112	LEU	0	-0.100	-0.049	29.279	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	113	ASP	-1	-0.725	-0.861	31.617	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	114	SER	0	-0.030	-0.035	28.695	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	115	ASP	-1	-0.907	-0.916	28.639	-0.105	-0.105	0.000	0.000	0.000	0.000
34	A	116	TYR	0	-0.019	-0.019	28.177	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	117	ALA	0	0.083	0.033	26.406	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	118	PRO	0	-0.018	-0.009	24.608	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	119	LEU	0	0.042	0.025	23.519	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	120	GLN	0	-0.070	-0.059	23.015	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	121	GLN	0	0.018	0.040	19.264	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	122	PHE	0	0.053	0.025	18.690	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	123	PHE	0	-0.010	-0.013	18.279	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	124	VAL	0	-0.010	0.008	15.862	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	125	VAL	0	0.020	0.014	13.589	-0.046	-0.046	0.000	0.000	0.000	0.000
44	A	126	MET	0	0.001	0.005	13.351	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	127	GLU	-1	-0.780	-0.879	13.963	-0.251	-0.251	0.000	0.000	0.000	0.000
46	A	128	HIS	0	-0.007	-0.020	10.274	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	129	CYS	0	-0.056	-0.020	9.234	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	130	LEU	0	-0.007	-0.004	9.654	0.114	0.114	0.000	0.000	0.000	0.000
49	A	131	LYS	1	0.902	0.960	9.323	0.454	0.454	0.000	0.000	0.000	0.000
50	A	132	HIS	0	0.012	0.026	1.866	1.338	0.423	6.000	-1.427	-3.657	0.003
51	A	133	GLY	0	0.045	0.010	4.201	0.494	0.813	0.033	-0.081	-0.271	0.000
52	A	134	LEU	0	-0.045	-0.006	4.813	-0.344	-0.308	0.004	-0.008	-0.031	0.000
53	A	135	LYS	1	0.879	0.963	8.107	-0.413	-0.413	0.000	0.000	0.000	0.000
54	A	136	ALA	0	-0.036	-0.012	9.850	-0.103	-0.103	0.000	0.000	0.000	0.000
55	A	144	ASN	0	0.050	0.013	14.075	0.029	0.029	0.000	0.000	0.000	0.000
56	A	145	LYS	1	0.859	0.903	17.795	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	146	SER	0	0.049	0.033	13.106	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	147	PHE	0	0.055	0.011	13.020	0.027	0.027	0.000	0.000	0.000	0.000
59	A	148	TRP	0	-0.010	-0.016	14.503	0.012	0.012	0.000	0.000	0.000	0.000
60	A	149	GLY	0	-0.019	-0.004	16.892	0.009	0.009	0.000	0.000	0.000	0.000
61	A	150	PRO	0	0.035	0.012	13.405	0.003	0.003	0.000	0.000	0.000	0.000
62	A	151	LEU	0	-0.029	-0.011	16.528	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	152	GLU	-1	-0.851	-0.900	19.201	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	153	LEU	0	-0.033	-0.018	17.746	0.000	0.000	0.000	0.000	0.000	0.000
65	A	154	VAL	0	0.017	0.010	20.324	0.003	0.003	0.000	0.000	0.000	0.000
66	A	155	GLU	-1	-0.892	-0.941	22.670	0.001	0.001	0.000	0.000	0.000	0.000
67	A	156	LYS	1	0.903	0.954	23.655	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	157	LEU	0	-0.101	-0.043	20.628	0.006	0.006	0.000	0.000	0.000	0.000
69	A	158	VAL	0	0.001	-0.005	24.501	0.001	0.001	0.000	0.000	0.000	0.000
70	A	159	PRO	0	0.034	0.014	27.158	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	160	GLU	-1	-0.830	-0.915	30.020	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	161	ALA	0	0.003	0.016	26.120	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	162	ALA	0	-0.004	0.013	28.078	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	163	GLU	-1	-0.879	-0.946	30.344	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	164	ILE	0	0.015	0.019	26.141	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	165	THR	0	-0.032	-0.039	25.959	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	166	ALA	0	-0.036	-0.024	27.765	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	167	SER	0	0.042	0.012	30.598	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	168	VAL	0	-0.064	-0.034	25.392	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	169	LYS	1	0.795	0.902	27.028	0.014	0.014	0.000	0.000	0.000	0.000
81	A	170	ASP	-1	-0.864	-0.916	29.436	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	171	LEU	0	-0.032	-0.009	28.542	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	172	PRO	0	0.033	-0.005	31.574	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	173	GLY	0	-0.023	-0.010	31.907	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	174	LEU	0	-0.024	0.011	25.615	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	175	LYS	1	0.943	0.962	27.186	0.077	0.077	0.000	0.000	0.000	0.000
87	A	176	THR	0	0.003	0.008	21.738	0.002	0.002	0.000	0.000	0.000	0.000
88	A	177	PRO	0	0.027	0.010	19.094	0.002	0.002	0.000	0.000	0.000	0.000
89	A	178	VAL	0	0.050	0.034	16.375	0.004	0.004	0.000	0.000	0.000	0.000
90	A	179	GLY	0	-0.003	0.006	18.970	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	180	ARG	1	0.986	0.984	22.440	0.071	0.071	0.000	0.000	0.000	0.000
92	A	181	GLY	0	0.024	0.017	19.143	0.008	0.008	0.000	0.000	0.000	0.000
93	A	182	ARG	1	0.798	0.865	17.292	0.223	0.223	0.000	0.000	0.000	0.000
94	A	183	ALA	0	0.007	0.006	21.257	0.002	0.002	0.000	0.000	0.000	0.000
95	A	184	TRP	0	0.077	0.037	20.934	0.001	0.001	0.000	0.000	0.000	0.000
96	A	185	LEU	0	-0.002	-0.009	17.731	0.004	0.004	0.000	0.000	0.000	0.000
97	A	186	ARG	1	0.884	0.948	21.622	0.137	0.137	0.000	0.000	0.000	0.000
98	A	187	LEU	0	0.069	0.029	25.431	0.004	0.004	0.000	0.000	0.000	0.000
99	A	188	ALA	0	0.037	0.026	23.910	0.005	0.005	0.000	0.000	0.000	0.000
100	A	189	LEU	0	-0.058	-0.032	23.773	0.003	0.003	0.000	0.000	0.000	0.000
101	A	190	MET	0	-0.027	0.009	26.130	0.002	0.002	0.000	0.000	0.000	0.000
102	A	191	GLN	0	0.023	0.027	28.734	0.003	0.003	0.000	0.000	0.000	0.000
103	A	192	LYS	1	0.844	0.939	27.861	0.045	0.045	0.000	0.000	0.000	0.000
104	A	193	LYS	1	0.925	0.966	26.522	0.014	0.014	0.000	0.000	0.000	0.000
105	A	194	LEU	0	-0.003	-0.001	20.238	0.005	0.005	0.000	0.000	0.000	0.000
106	A	195	SER	0	0.048	0.016	20.865	0.004	0.004	0.000	0.000	0.000	0.000
107	A	196	GLU	-1	-0.928	-0.958	21.340	0.011	0.011	0.000	0.000	0.000	0.000
108	A	197	TYR	0	0.020	-0.014	21.899	0.011	0.011	0.000	0.000	0.000	0.000
109	A	198	MET	0	-0.013	-0.007	16.963	0.009	0.009	0.000	0.000	0.000	0.000
110	A	199	LYS	1	0.985	0.985	17.581	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	200	ALA	0	0.011	0.010	19.529	0.015	0.015	0.000	0.000	0.000	0.000
112	A	201	LEU	0	0.006	0.000	16.320	0.011	0.011	0.000	0.000	0.000	0.000
113	A	202	ILE	0	0.011	0.023	13.612	0.021	0.021	0.000	0.000	0.000	0.000
114	A	203	ASN	0	-0.129	-0.059	15.434	0.026	0.026	0.000	0.000	0.000	0.000
115	A	204	LYS	1	0.933	0.960	17.121	-0.076	-0.076	0.000	0.000	0.000	0.000
116	A	205	LYS	1	0.971	0.975	11.144	-0.198	-0.198	0.000	0.000	0.000	0.000
117	A	206	GLU	-1	-0.910	-0.934	14.264	0.158	0.158	0.000	0.000	0.000	0.000
118	A	207	LEU	0	0.013	0.028	16.766	0.004	0.004	0.000	0.000	0.000	0.000
119	A	208	LEU	0	0.008	-0.003	12.754	0.001	0.001	0.000	0.000	0.000	0.000
120	A	209	SER	0	-0.049	-0.038	11.940	0.027	0.027	0.000	0.000	0.000	0.000
121	A	210	GLU	-1	-0.968	-0.977	13.021	0.124	0.124	0.000	0.000	0.000	0.000
122	A	211	PHE	0	-0.021	-0.037	12.952	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	212	TYR	0	-0.092	-0.065	8.026	-0.030	-0.030	0.000	0.000	0.000	0.000
124	A	213	GLU	-1	-0.861	-0.936	5.207	0.583	0.641	-0.001	-0.014	-0.042	0.000
125	A	214	VAL	0	-0.006	-0.021	6.297	-0.074	-0.074	0.000	0.000	0.000	0.000
126	A	215	ASN	0	-0.005	0.008	2.494	-2.168	0.074	1.344	-0.994	-2.592	-0.006
127	A	216	ALA	0	0.028	0.013	2.550	-3.095	-1.525	1.423	-1.189	-1.803	-0.015
128	A	217	LEU	0	0.014	-0.005	4.896	-0.657	-0.598	-0.001	-0.008	-0.050	0.000
129	A	218	MET	0	-0.046	-0.024	6.471	-0.093	-0.093	0.000	0.000	0.000	0.000
130	A	219	MET	0	-0.043	-0.004	7.359	-0.059	-0.059	0.000	0.000	0.000	0.000
131	A	220	GLU	-1	-0.932	-0.967	5.315	0.201	0.201	0.000	0.000	0.000	0.000
132	A	221	GLU	-1	-0.949	-0.976	8.643	0.149	0.149	0.000	0.000	0.000	0.000
133	A	222	GLU	-1	-0.821	-0.939	7.429	-0.154	-0.154	0.000	0.000	0.000	0.000
134	A	223	GLY	0	0.032	0.013	9.794	-0.014	-0.014	0.000	0.000	0.000	0.000
135	A	224	ALA	0	-0.007	-0.019	11.365	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	225	ILE	0	-0.032	-0.003	13.650	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	226	ILE	0	0.005	-0.009	11.343	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	227	ALA	0	0.000	-0.003	15.230	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	228	GLY	0	-0.001	0.000	17.513	0.001	0.001	0.000	0.000	0.000	0.000
140	A	229	LEU	0	-0.019	-0.026	16.573	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	230	LEU	0	-0.012	-0.006	17.681	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	231	VAL	0	-0.007	0.008	20.947	0.001	0.001	0.000	0.000	0.000	0.000
143	A	232	GLY	0	-0.001	0.008	23.737	0.002	0.002	0.000	0.000	0.000	0.000
144	A	233	LEU	0	-0.001	-0.016	21.553	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	234	ASN	0	0.002	0.010	25.551	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	235	VAL	0	-0.025	-0.009	28.180	0.003	0.003	0.000	0.000	0.000	0.000
147	A	236	ILE	0	-0.046	-0.026	26.823	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	237	ASP	-1	-0.849	-0.879	30.022	-0.044	-0.044	0.000	0.000	0.000	0.000
149	A	238	ALA	0	0.015	0.005	29.668	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	239	ASN	0	0.053	0.013	31.708	0.002	0.002	0.000	0.000	0.000	0.000
151	A	240	PHE	0	-0.055	-0.060	27.241	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	241	CYS	0	-0.048	-0.021	32.111	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	242	MET	0	0.009	0.004	35.341	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	243	LYS	1	0.899	0.941	35.991	0.063	0.063	0.000	0.000	0.000	0.000
155	A	244	GLY	0	0.029	0.010	40.147	0.001	0.001	0.000	0.000	0.000	0.000
156	A	245	GLU	-1	-0.905	-0.963	40.709	-0.044	-0.044	0.000	0.000	0.000	0.000
157	A	246	ASP	-1	-0.946	-0.969	41.185	-0.050	-0.050	0.000	0.000	0.000	0.000
158	A	247	LEU	0	-0.124	-0.065	43.957	0.000	0.000	0.000	0.000	0.000	0.000
159	A	248	ASP	-1	-0.933	-0.948	46.978	-0.028	-0.028	0.000	0.000	0.000	0.000
160	A	249	SER	0	-0.024	-0.027	49.318	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	250	GLN	0	-0.035	-0.002	52.815	0.002	0.002	0.000	0.000	0.000	0.000
162	A	251	VAL	0	-0.025	-0.008	55.650	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:83:MET)