FMO DATABASE

FMODB ID: KGKQ3

Calculation Name: 2X29-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X29

Chain ID: A

ChEMBL ID:

UniProt ID: P41273

Base Structure: X-ray

Registration Date: 2023-09-22

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1508507.850583
FMO2-HF: Nuclear repulsion	1447390.749404
FMO2-HF: Total energy	-61117.101179
FMO2-MP2: Total energy	-61298.162748

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:80:ASP)

Summations of interaction energy for fragment #1(A:80:ASP)

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.
-116.735	-139.018	55.83	-19.924	-13.624	0.192

Interaction energy analysis for fragmet #1(A:80:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.813 / q_NPA : -0.904

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	82	ALA	0	-0.025	-0.003	2.022	-23.491	-20.706	5.979	-4.112	-4.651	0.048
4	A	83	GLY	0	0.047	0.040	3.748	-5.524	-5.471	0.010	0.031	-0.094	0.002
5	A	84	LEU	0	-0.039	-0.036	6.896	1.854	1.854	0.000	0.000	0.000	0.000
6	A	85	LEU	0	0.018	0.003	8.372	-3.942	-3.942	0.000	0.000	0.000	0.000
7	A	86	ASP	-1	-0.918	-0.960	11.777	21.815	21.815	0.000	0.000	0.000	0.000
8	A	87	LEU	0	0.012	0.013	13.709	-1.435	-1.435	0.000	0.000	0.000	0.000
9	A	88	ARG	1	0.975	0.983	17.193	-14.663	-14.663	0.000	0.000	0.000	0.000
10	A	89	GLN	0	0.033	-0.018	20.280	0.065	0.065	0.000	0.000	0.000	0.000
11	A	90	GLY	0	-0.012	0.002	22.846	-0.363	-0.363	0.000	0.000	0.000	0.000
12	A	91	MET	0	-0.068	-0.019	20.657	-0.518	-0.518	0.000	0.000	0.000	0.000
13	A	92	PHE	0	0.007	-0.005	20.948	0.330	0.330	0.000	0.000	0.000	0.000
14	A	93	ALA	0	0.039	0.018	16.428	0.016	0.016	0.000	0.000	0.000	0.000
15	A	94	GLN	0	-0.031	-0.014	18.235	-0.288	-0.288	0.000	0.000	0.000	0.000
16	A	95	LEU	0	-0.026	-0.004	12.439	0.395	0.395	0.000	0.000	0.000	0.000
17	A	96	VAL	0	0.040	0.022	16.669	-0.749	-0.749	0.000	0.000	0.000	0.000
18	A	97	ALA	0	-0.032	-0.021	16.994	1.087	1.087	0.000	0.000	0.000	0.000
19	A	98	GLN	0	-0.042	-0.039	16.658	-2.093	-2.093	0.000	0.000	0.000	0.000
20	A	99	ASN	0	-0.010	-0.006	17.024	-0.292	-0.292	0.000	0.000	0.000	0.000
21	A	100	VAL	0	0.068	0.041	20.228	-0.367	-0.367	0.000	0.000	0.000	0.000
22	A	101	LEU	0	0.002	0.005	23.735	-0.429	-0.429	0.000	0.000	0.000	0.000
23	A	102	LEU	0	-0.019	0.003	22.980	0.653	0.653	0.000	0.000	0.000	0.000
24	A	103	ILE	0	-0.044	-0.029	20.764	-0.486	-0.486	0.000	0.000	0.000	0.000
25	A	104	ASP	-1	-0.816	-0.911	20.798	14.160	14.160	0.000	0.000	0.000	0.000
26	A	105	GLY	0	-0.009	-0.001	17.485	0.345	0.345	0.000	0.000	0.000	0.000
27	A	106	PRO	0	-0.051	-0.024	12.365	-0.376	-0.376	0.000	0.000	0.000	0.000
28	A	107	LEU	0	0.005	0.004	14.555	-0.671	-0.671	0.000	0.000	0.000	0.000
29	A	108	SER	0	-0.046	-0.027	12.699	2.458	2.458	0.000	0.000	0.000	0.000
30	A	109	TRP	0	-0.013	-0.011	11.848	-2.627	-2.627	0.000	0.000	0.000	0.000
31	A	110	TYR	0	0.066	0.046	12.578	1.577	1.577	0.000	0.000	0.000	0.000
32	A	111	SER	0	0.036	0.023	14.599	-0.287	-0.287	0.000	0.000	0.000	0.000
33	A	112	ASP	-1	-0.853	-0.942	16.335	13.725	13.725	0.000	0.000	0.000	0.000
34	A	113	PRO	0	-0.019	-0.019	19.122	-0.250	-0.250	0.000	0.000	0.000	0.000
35	A	114	GLY	0	-0.008	0.011	21.429	-0.527	-0.527	0.000	0.000	0.000	0.000
36	A	115	LEU	0	-0.060	-0.020	21.799	-0.516	-0.516	0.000	0.000	0.000	0.000
37	A	116	ALA	0	-0.007	-0.008	23.030	0.254	0.254	0.000	0.000	0.000	0.000
38	A	117	GLY	0	0.023	0.001	21.053	0.429	0.429	0.000	0.000	0.000	0.000
39	A	118	VAL	0	-0.061	-0.031	16.055	-0.247	-0.247	0.000	0.000	0.000	0.000
40	A	119	SER	0	-0.007	-0.012	14.398	0.244	0.244	0.000	0.000	0.000	0.000
41	A	120	LEU	0	-0.032	-0.005	9.723	0.597	0.597	0.000	0.000	0.000	0.000
42	A	121	THR	0	0.011	-0.002	9.503	-1.708	-1.708	0.000	0.000	0.000	0.000
43	A	122	GLY	0	-0.029	-0.025	6.331	2.634	2.634	0.000	0.000	0.000	0.000
44	A	123	GLY	0	-0.018	-0.006	5.643	2.559	2.559	0.000	0.000	0.000	0.000
45	A	124	LEU	0	0.009	0.029	7.121	-1.036	-1.036	0.000	0.000	0.000	0.000
46	A	125	SER	0	-0.012	-0.006	9.358	-2.282	-2.282	0.000	0.000	0.000	0.000
47	A	126	TYR	0	-0.002	-0.027	12.800	0.238	0.238	0.000	0.000	0.000	0.000
48	A	127	LYS	1	0.870	0.940	16.109	-14.571	-14.571	0.000	0.000	0.000	0.000
49	A	128	GLU	-1	-0.846	-0.896	9.370	26.301	26.301	0.000	0.000	0.000	0.000
50	A	129	ASP	-1	-0.903	-0.964	12.533	22.194	22.194	0.000	0.000	0.000	0.000
51	A	130	THR	0	0.034	0.003	6.440	1.482	1.482	0.000	0.000	0.000	0.000
52	A	131	LYS	1	0.938	0.971	8.702	-26.551	-26.551	0.000	0.000	0.000	0.000
53	A	132	GLU	-1	-0.894	-0.915	4.485	63.110	63.319	-0.001	-0.008	-0.200	0.000
54	A	133	LEU	0	0.025	0.017	6.575	1.159	1.159	0.000	0.000	0.000	0.000
55	A	134	VAL	0	0.012	0.006	3.920	-0.937	-0.530	0.002	-0.135	-0.275	0.001
56	A	135	VAL	0	-0.011	0.007	7.422	-2.746	-2.746	0.000	0.000	0.000	0.000
57	A	136	ALA	0	0.042	0.017	10.050	0.596	0.596	0.000	0.000	0.000	0.000
58	A	137	LYS	1	0.896	0.946	10.931	-20.508	-20.508	0.000	0.000	0.000	0.000
59	A	138	ALA	0	0.028	0.024	14.568	0.137	0.137	0.000	0.000	0.000	0.000
60	A	139	GLY	0	-0.009	-0.006	16.310	-0.970	-0.970	0.000	0.000	0.000	0.000
61	A	140	VAL	0	0.015	0.011	18.799	0.583	0.583	0.000	0.000	0.000	0.000
62	A	141	TYR	0	-0.017	-0.042	15.704	-0.433	-0.433	0.000	0.000	0.000	0.000
63	A	142	TYR	0	0.006	0.005	20.599	-0.203	-0.203	0.000	0.000	0.000	0.000
64	A	143	VAL	0	-0.013	-0.013	17.438	0.414	0.414	0.000	0.000	0.000	0.000
65	A	144	PHE	0	0.036	0.005	20.522	-0.659	-0.659	0.000	0.000	0.000	0.000
66	A	145	PHE	0	-0.003	0.004	17.561	0.848	0.848	0.000	0.000	0.000	0.000
67	A	146	GLN	0	-0.012	-0.012	21.944	-1.000	-1.000	0.000	0.000	0.000	0.000
68	A	147	MET	0	-0.024	-0.017	23.372	0.677	0.677	0.000	0.000	0.000	0.000
69	A	148	GLU	-1	-0.855	-0.908	25.397	9.827	9.827	0.000	0.000	0.000	0.000
70	A	149	LEU	0	-0.022	0.006	27.075	0.326	0.326	0.000	0.000	0.000	0.000
71	A	150	ARG	1	0.975	0.965	29.514	-10.491	-10.491	0.000	0.000	0.000	0.000
72	A	151	ARG	1	0.774	0.875	32.124	-8.265	-8.265	0.000	0.000	0.000	0.000
73	A	152	VAL	0	-0.068	-0.039	31.978	-0.173	-0.173	0.000	0.000	0.000	0.000
74	A	153	VAL	0	-0.023	0.014	34.880	-0.167	-0.167	0.000	0.000	0.000	0.000
75	A	154	ALA	0	-0.009	-0.019	37.304	-0.032	-0.032	0.000	0.000	0.000	0.000
76	A	155	GLY	0	0.015	0.010	40.647	-0.067	-0.067	0.000	0.000	0.000	0.000
77	A	156	GLU	-1	-0.910	-0.947	38.333	8.042	8.042	0.000	0.000	0.000	0.000
78	A	157	GLY	0	0.029	0.005	35.740	0.177	0.177	0.000	0.000	0.000	0.000
79	A	158	SER	0	-0.044	-0.035	35.449	-0.135	-0.135	0.000	0.000	0.000	0.000
80	A	159	GLY	0	0.021	0.014	33.373	0.146	0.146	0.000	0.000	0.000	0.000
81	A	160	SER	0	0.045	0.024	30.295	-0.175	-0.175	0.000	0.000	0.000	0.000
82	A	161	VAL	0	-0.033	0.017	25.152	0.225	0.225	0.000	0.000	0.000	0.000
83	A	162	SER	0	0.025	0.028	24.516	-0.266	-0.266	0.000	0.000	0.000	0.000
84	A	163	LEU	0	0.002	0.006	19.806	0.492	0.492	0.000	0.000	0.000	0.000
85	A	164	ALA	0	-0.004	-0.015	19.333	-0.657	-0.657	0.000	0.000	0.000	0.000
86	A	165	LEU	0	-0.007	0.013	14.225	0.911	0.911	0.000	0.000	0.000	0.000
87	A	166	HIS	0	-0.017	-0.019	14.296	-0.648	-0.648	0.000	0.000	0.000	0.000
88	A	167	LEU	0	0.034	0.013	12.885	1.989	1.989	0.000	0.000	0.000	0.000
89	A	168	MET	0	-0.027	0.010	7.826	-1.789	-1.789	0.000	0.000	0.000	0.000
90	A	169	PRO	0	0.039	-0.003	9.280	1.174	1.174	0.000	0.000	0.000	0.000
91	A	170	LEU	0	0.038	0.024	11.383	-1.344	-1.344	0.000	0.000	0.000	0.000
92	A	171	ARG	1	0.907	0.936	13.056	-24.313	-24.313	0.000	0.000	0.000	0.000
93	A	172	SER	0	-0.004	-0.010	15.402	-1.229	-1.229	0.000	0.000	0.000	0.000
94	A	173	ALA	0	0.018	0.008	18.061	-0.578	-0.578	0.000	0.000	0.000	0.000
95	A	174	ALA	0	-0.003	-0.013	21.021	-0.695	-0.695	0.000	0.000	0.000	0.000
96	A	175	GLY	0	0.010	0.015	23.790	-0.457	-0.457	0.000	0.000	0.000	0.000
97	A	176	ALA	0	-0.054	-0.017	21.100	-0.438	-0.438	0.000	0.000	0.000	0.000
98	A	177	ALA	0	-0.019	-0.009	19.638	0.362	0.362	0.000	0.000	0.000	0.000
99	A	178	ALA	0	0.018	0.026	18.078	-0.693	-0.693	0.000	0.000	0.000	0.000
100	A	179	LEU	0	-0.011	-0.014	19.766	-0.889	-0.889	0.000	0.000	0.000	0.000
101	A	180	ALA	0	0.019	0.006	20.658	0.684	0.684	0.000	0.000	0.000	0.000
102	A	181	LEU	0	-0.031	-0.010	23.181	-0.483	-0.483	0.000	0.000	0.000	0.000
103	A	182	THR	0	0.006	-0.009	25.080	0.402	0.402	0.000	0.000	0.000	0.000
104	A	183	VAL	0	-0.002	0.003	27.739	-0.284	-0.284	0.000	0.000	0.000	0.000
105	A	184	ASP	-1	-0.845	-0.907	30.003	9.708	9.708	0.000	0.000	0.000	0.000
106	A	185	LEU	0	-0.063	-0.045	30.688	-0.043	-0.043	0.000	0.000	0.000	0.000
107	A	186	PRO	0	0.006	0.012	34.561	-0.167	-0.167	0.000	0.000	0.000	0.000
108	A	187	PRO	0	0.021	0.001	38.143	0.079	0.079	0.000	0.000	0.000	0.000
109	A	188	ALA	0	0.056	0.009	40.259	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	189	SER	0	0.021	0.009	42.763	-0.079	-0.079	0.000	0.000	0.000	0.000
111	A	190	SER	0	-0.064	-0.049	41.149	-0.020	-0.020	0.000	0.000	0.000	0.000
112	A	191	GLU	-1	-0.889	-0.901	40.997	7.309	7.309	0.000	0.000	0.000	0.000
113	A	192	ALA	0	-0.032	-0.019	42.625	0.040	0.040	0.000	0.000	0.000	0.000
114	A	193	ARG	1	0.914	0.944	38.735	-7.942	-7.942	0.000	0.000	0.000	0.000
115	A	194	ASN	0	0.058	0.052	37.791	0.106	0.106	0.000	0.000	0.000	0.000
116	A	195	SER	0	0.045	0.034	34.203	0.112	0.112	0.000	0.000	0.000	0.000
117	A	196	ALA	0	-0.019	-0.013	31.902	-0.260	-0.260	0.000	0.000	0.000	0.000
118	A	197	PHE	0	0.002	0.000	29.101	0.241	0.241	0.000	0.000	0.000	0.000
119	A	198	GLY	0	0.036	0.021	28.860	-0.296	-0.296	0.000	0.000	0.000	0.000
120	A	199	PHE	0	0.009	0.001	26.126	0.424	0.424	0.000	0.000	0.000	0.000
121	A	200	GLN	0	0.003	0.013	25.043	-0.577	-0.577	0.000	0.000	0.000	0.000
122	A	201	GLY	0	0.052	0.014	23.896	0.658	0.658	0.000	0.000	0.000	0.000
123	A	202	ARG	1	0.860	0.938	23.165	-13.818	-13.818	0.000	0.000	0.000	0.000
124	A	203	LEU	0	0.002	0.009	22.904	0.593	0.593	0.000	0.000	0.000	0.000
125	A	204	LEU	0	-0.014	-0.006	18.346	-0.123	-0.123	0.000	0.000	0.000	0.000
126	A	205	HIS	0	-0.005	-0.004	19.281	0.204	0.204	0.000	0.000	0.000	0.000
127	A	206	LEU	0	-0.006	0.000	14.317	0.674	0.674	0.000	0.000	0.000	0.000
128	A	207	SER	0	0.041	0.020	14.002	-0.996	-0.996	0.000	0.000	0.000	0.000
129	A	208	ALA	0	0.015	0.002	12.532	1.174	1.174	0.000	0.000	0.000	0.000
130	A	209	GLY	0	0.013	0.004	8.159	0.266	0.266	0.000	0.000	0.000	0.000
131	A	210	GLN	0	-0.093	-0.033	7.853	1.684	1.684	0.000	0.000	0.000	0.000
132	A	211	ARG	1	0.748	0.829	1.495	-121.182	-146.919	49.840	-15.700	-8.404	0.141
133	A	212	LEU	0	-0.012	-0.010	8.197	-4.831	-4.831	0.000	0.000	0.000	0.000
134	A	213	GLY	0	0.080	0.036	9.195	3.275	3.275	0.000	0.000	0.000	0.000
135	A	214	VAL	0	-0.033	-0.007	11.426	-1.843	-1.843	0.000	0.000	0.000	0.000
136	A	215	HIS	0	0.002	0.010	13.323	0.395	0.395	0.000	0.000	0.000	0.000
137	A	216	LEU	0	0.019	0.016	17.160	-0.788	-0.788	0.000	0.000	0.000	0.000
138	A	217	HIS	0	-0.079	-0.053	20.429	0.700	0.700	0.000	0.000	0.000	0.000
139	A	218	THR	0	-0.005	-0.050	23.559	-0.500	-0.500	0.000	0.000	0.000	0.000
140	A	219	GLU	-1	-0.895	-0.936	26.986	10.266	10.266	0.000	0.000	0.000	0.000
141	A	220	ALA	0	-0.047	-0.037	29.803	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	221	ARG	1	0.970	0.977	31.663	-8.631	-8.631	0.000	0.000	0.000	0.000
143	A	222	ALA	0	0.046	0.036	30.500	-0.184	-0.184	0.000	0.000	0.000	0.000
144	A	223	ARG	1	0.945	0.970	26.375	-11.611	-11.611	0.000	0.000	0.000	0.000
145	A	224	HIS	0	-0.028	-0.017	29.492	0.224	0.224	0.000	0.000	0.000	0.000
146	A	225	ALA	0	0.034	0.022	32.469	-0.228	-0.228	0.000	0.000	0.000	0.000
147	A	226	TRP	0	-0.026	0.000	30.749	-0.108	-0.108	0.000	0.000	0.000	0.000
148	A	227	GLN	0	-0.011	-0.014	27.746	0.276	0.276	0.000	0.000	0.000	0.000
149	A	228	LEU	0	-0.019	-0.013	22.145	-0.263	-0.263	0.000	0.000	0.000	0.000
150	A	229	THR	0	-0.083	-0.073	26.151	-0.090	-0.090	0.000	0.000	0.000	0.000
151	A	230	GLN	0	0.000	-0.014	23.929	0.009	0.009	0.000	0.000	0.000	0.000
152	A	231	GLY	0	0.037	0.025	22.977	-0.326	-0.326	0.000	0.000	0.000	0.000
153	A	232	ALA	0	-0.004	0.004	24.012	0.034	0.034	0.000	0.000	0.000	0.000
154	A	233	THR	0	0.002	-0.003	20.048	-0.209	-0.209	0.000	0.000	0.000	0.000
155	A	234	VAL	0	-0.026	-0.003	19.934	0.678	0.678	0.000	0.000	0.000	0.000
156	A	235	LEU	0	0.004	0.015	14.262	-0.285	-0.285	0.000	0.000	0.000	0.000
157	A	236	GLY	0	0.006	0.007	17.946	0.434	0.434	0.000	0.000	0.000	0.000
158	A	237	LEU	0	-0.021	-0.019	14.797	0.110	0.110	0.000	0.000	0.000	0.000
159	A	238	PHE	0	0.019	0.014	18.846	-0.118	-0.118	0.000	0.000	0.000	0.000
160	A	239	ARG	1	0.783	0.883	18.307	-16.527	-16.527	0.000	0.000	0.000	0.000
161	A	240	VAL	0	0.019	0.014	21.149	-0.633	-0.633	0.000	0.000	0.000	0.000
162	A	241	THR	0	0.033	0.027	21.707	-0.467	-0.467	0.000	0.000	0.000	0.000
163	A	242	PRO	0	-0.027	-0.005	22.560	0.629	0.629	0.000	0.000	0.000	0.000
164	A	243	GLU	-1	-0.848	-0.916	19.305	17.001	17.001	0.000	0.000	0.000	0.000
165	A	244	ILE	0	-0.015	-0.010	22.221	-0.605	-0.605	0.000	0.000	0.000	0.000
166	A	245	PRO	0	0.004	0.002	24.831	0.196	0.196	0.000	0.000	0.000	0.000
167	A	246	ALA	0	0.018	0.018	26.518	-0.114	-0.114	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:80:ASP)