FMO DATABASE

FMODB ID: 5JRGZ

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	OptAll
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	-1510209.920562
FMO2-HF: Nuclear repulsion	1449091.414609
FMO2-HF: Total energy	-61118.505953
FMO2-MP2: Total energy	-61299.448252

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.
-140.69	-152.883	43.111	-17.327	-13.592	0.201

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 : -0.802 / q_NPA : -0.874

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	-0.018	0.013	1.879	-24.966	-24.963	9.368	-4.604	-4.767	0.045
4	A	83	GLY	0	0.035	0.014	3.685	-5.656	-5.562	0.017	0.034	-0.145	0.002
5	A	84	LEU	0	-0.058	-0.021	6.432	-0.058	-0.058	0.000	0.000	0.000	0.000
6	A	85	LEU	0	0.036	0.006	7.932	-3.977	-3.977	0.000	0.000	0.000	0.000
7	A	86	ASP	-1	-0.832	-0.914	11.485	20.823	20.823	0.000	0.000	0.000	0.000
8	A	87	LEU	0	0.000	0.005	13.815	-1.123	-1.123	0.000	0.000	0.000	0.000
9	A	88	ARG	1	0.983	0.984	17.355	-14.424	-14.424	0.000	0.000	0.000	0.000
10	A	89	GLN	0	0.018	-0.018	20.457	0.058	0.058	0.000	0.000	0.000	0.000
11	A	90	GLY	0	-0.015	-0.003	23.031	-0.324	-0.324	0.000	0.000	0.000	0.000
12	A	91	MET	0	-0.053	-0.002	20.404	-0.472	-0.472	0.000	0.000	0.000	0.000
13	A	92	PHE	0	0.006	-0.010	20.904	0.271	0.271	0.000	0.000	0.000	0.000
14	A	93	ALA	0	0.028	0.021	16.424	0.043	0.043	0.000	0.000	0.000	0.000
15	A	94	GLN	0	-0.027	-0.022	18.165	-0.321	-0.321	0.000	0.000	0.000	0.000
16	A	95	LEU	0	-0.027	-0.008	12.764	0.622	0.622	0.000	0.000	0.000	0.000
17	A	96	VAL	0	0.041	0.024	16.659	-0.690	-0.690	0.000	0.000	0.000	0.000
18	A	97	ALA	0	-0.013	-0.013	16.955	1.096	1.096	0.000	0.000	0.000	0.000
19	A	98	GLN	0	-0.032	-0.037	16.460	-1.796	-1.796	0.000	0.000	0.000	0.000
20	A	99	ASN	0	-0.038	-0.017	17.287	0.050	0.050	0.000	0.000	0.000	0.000
21	A	100	VAL	0	0.083	0.034	20.047	-0.382	-0.382	0.000	0.000	0.000	0.000
22	A	101	LEU	0	0.003	0.009	23.322	-0.549	-0.549	0.000	0.000	0.000	0.000
23	A	102	LEU	0	0.001	0.013	22.623	0.717	0.717	0.000	0.000	0.000	0.000
24	A	103	ILE	0	-0.042	-0.037	20.468	-0.365	-0.365	0.000	0.000	0.000	0.000
25	A	104	ASP	-1	-0.790	-0.876	20.372	14.188	14.188	0.000	0.000	0.000	0.000
26	A	105	GLY	0	0.009	0.010	17.225	0.354	0.354	0.000	0.000	0.000	0.000
27	A	106	PRO	0	-0.021	-0.019	11.994	-0.479	-0.479	0.000	0.000	0.000	0.000
28	A	107	LEU	0	0.007	0.014	14.126	-0.332	-0.332	0.000	0.000	0.000	0.000
29	A	108	SER	0	-0.024	-0.032	12.633	2.180	2.180	0.000	0.000	0.000	0.000
30	A	109	TRP	0	-0.046	-0.021	12.073	-2.715	-2.715	0.000	0.000	0.000	0.000
31	A	110	TYR	0	0.022	0.005	12.293	1.864	1.864	0.000	0.000	0.000	0.000
32	A	111	SER	0	0.042	0.027	14.452	-0.388	-0.388	0.000	0.000	0.000	0.000
33	A	112	ASP	-1	-0.744	-0.869	16.310	14.168	14.168	0.000	0.000	0.000	0.000
34	A	113	PRO	0	-0.006	-0.016	18.894	-0.402	-0.402	0.000	0.000	0.000	0.000
35	A	114	GLY	0	-0.031	0.006	21.508	-0.551	-0.551	0.000	0.000	0.000	0.000
36	A	115	LEU	0	-0.050	-0.022	21.656	-0.523	-0.523	0.000	0.000	0.000	0.000
37	A	116	ALA	0	0.000	0.004	22.884	0.360	0.360	0.000	0.000	0.000	0.000
38	A	117	GLY	0	0.017	-0.001	20.721	0.174	0.174	0.000	0.000	0.000	0.000
39	A	118	VAL	0	-0.064	-0.033	15.739	-0.344	-0.344	0.000	0.000	0.000	0.000
40	A	119	SER	0	-0.015	-0.017	14.152	0.073	0.073	0.000	0.000	0.000	0.000
41	A	120	LEU	0	-0.002	0.001	10.015	0.782	0.782	0.000	0.000	0.000	0.000
42	A	121	THR	0	-0.011	0.002	10.116	-2.344	-2.344	0.000	0.000	0.000	0.000
43	A	122	GLY	0	0.001	-0.017	6.389	3.141	3.141	0.000	0.000	0.000	0.000
44	A	123	GLY	0	-0.021	-0.010	6.305	1.227	1.227	0.000	0.000	0.000	0.000
45	A	124	LEU	0	-0.025	0.015	7.116	-1.719	-1.719	0.000	0.000	0.000	0.000
46	A	125	SER	0	0.002	-0.017	9.480	-1.940	-1.940	0.000	0.000	0.000	0.000
47	A	126	TYR	0	-0.022	-0.028	12.955	0.224	0.224	0.000	0.000	0.000	0.000
48	A	127	LYS	1	0.789	0.890	16.308	-14.726	-14.726	0.000	0.000	0.000	0.000
49	A	128	GLU	-1	-0.825	-0.873	9.532	25.778	25.778	0.000	0.000	0.000	0.000
50	A	129	ASP	-1	-0.880	-0.913	12.368	22.632	22.632	0.000	0.000	0.000	0.000
51	A	130	THR	0	0.017	-0.016	6.203	0.988	0.988	0.000	0.000	0.000	0.000
52	A	131	LYS	1	0.884	0.928	8.278	-25.580	-25.580	0.000	0.000	0.000	0.000
53	A	132	GLU	-1	-0.884	-0.923	5.094	56.276	56.419	-0.001	-0.001	-0.141	0.000
54	A	133	LEU	0	0.016	0.011	6.628	0.695	0.695	0.000	0.000	0.000	0.000
55	A	134	VAL	0	0.014	-0.002	3.805	2.056	2.469	0.005	-0.128	-0.291	0.001
56	A	135	VAL	0	0.010	0.017	7.118	-2.959	-2.959	0.000	0.000	0.000	0.000
57	A	136	ALA	0	0.021	0.002	10.038	0.260	0.260	0.000	0.000	0.000	0.000
58	A	137	LYS	1	0.813	0.894	10.932	-20.464	-20.464	0.000	0.000	0.000	0.000
59	A	138	ALA	0	0.005	0.012	14.444	0.189	0.189	0.000	0.000	0.000	0.000
60	A	139	GLY	0	0.005	0.000	16.565	-0.880	-0.880	0.000	0.000	0.000	0.000
61	A	140	VAL	0	0.003	0.002	18.879	0.597	0.597	0.000	0.000	0.000	0.000
62	A	141	TYR	0	-0.003	-0.024	15.687	-0.284	-0.284	0.000	0.000	0.000	0.000
63	A	142	TYR	0	0.002	0.008	20.542	-0.227	-0.227	0.000	0.000	0.000	0.000
64	A	143	VAL	0	-0.010	-0.012	17.570	0.572	0.572	0.000	0.000	0.000	0.000
65	A	144	PHE	0	0.027	-0.003	20.465	-0.640	-0.640	0.000	0.000	0.000	0.000
66	A	145	PHE	0	0.012	0.005	17.009	0.887	0.887	0.000	0.000	0.000	0.000
67	A	146	GLN	0	-0.022	-0.024	21.765	-0.970	-0.970	0.000	0.000	0.000	0.000
68	A	147	MET	0	-0.010	0.001	22.950	0.813	0.813	0.000	0.000	0.000	0.000
69	A	148	GLU	-1	-0.843	-0.894	25.063	10.153	10.153	0.000	0.000	0.000	0.000
70	A	149	LEU	0	-0.019	-0.004	26.839	0.390	0.390	0.000	0.000	0.000	0.000
71	A	150	ARG	1	0.909	0.944	28.777	-11.036	-11.036	0.000	0.000	0.000	0.000
72	A	151	ARG	1	0.779	0.878	31.924	-8.280	-8.280	0.000	0.000	0.000	0.000
73	A	152	VAL	0	-0.072	-0.044	31.680	-0.062	-0.062	0.000	0.000	0.000	0.000
74	A	153	VAL	0	0.018	0.029	34.720	-0.119	-0.119	0.000	0.000	0.000	0.000
75	A	154	ALA	0	-0.002	-0.013	37.348	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	155	GLY	0	0.016	0.009	40.606	-0.098	-0.098	0.000	0.000	0.000	0.000
77	A	156	GLU	-1	-0.931	-0.955	38.251	8.207	8.207	0.000	0.000	0.000	0.000
78	A	157	GLY	0	0.039	0.010	35.622	0.149	0.149	0.000	0.000	0.000	0.000
79	A	158	SER	0	-0.046	-0.034	35.380	-0.112	-0.112	0.000	0.000	0.000	0.000
80	A	159	GLY	0	0.005	0.003	33.111	0.114	0.114	0.000	0.000	0.000	0.000
81	A	160	SER	0	0.025	-0.008	30.452	-0.182	-0.182	0.000	0.000	0.000	0.000
82	A	161	VAL	0	-0.031	0.007	24.964	0.253	0.253	0.000	0.000	0.000	0.000
83	A	162	SER	0	-0.006	-0.018	24.541	-0.282	-0.282	0.000	0.000	0.000	0.000
84	A	163	LEU	0	-0.001	0.002	19.738	0.525	0.525	0.000	0.000	0.000	0.000
85	A	164	ALA	0	-0.010	-0.018	19.212	-0.660	-0.660	0.000	0.000	0.000	0.000
86	A	165	LEU	0	-0.021	0.005	14.600	1.066	1.066	0.000	0.000	0.000	0.000
87	A	166	HIS	0	0.016	-0.003	13.783	-0.835	-0.835	0.000	0.000	0.000	0.000
88	A	167	LEU	0	0.033	0.017	12.623	2.048	2.048	0.000	0.000	0.000	0.000
89	A	168	MET	0	-0.040	0.009	8.098	-1.610	-1.610	0.000	0.000	0.000	0.000
90	A	169	PRO	0	0.045	-0.002	9.069	1.156	1.156	0.000	0.000	0.000	0.000
91	A	170	LEU	0	0.028	0.020	11.167	-1.409	-1.409	0.000	0.000	0.000	0.000
92	A	171	ARG	1	0.924	0.944	12.885	-24.291	-24.291	0.000	0.000	0.000	0.000
93	A	172	SER	0	-0.019	-0.018	15.141	-1.355	-1.355	0.000	0.000	0.000	0.000
94	A	173	ALA	0	0.007	-0.001	17.744	-0.694	-0.694	0.000	0.000	0.000	0.000
95	A	174	ALA	0	-0.003	-0.005	20.542	-0.703	-0.703	0.000	0.000	0.000	0.000
96	A	175	GLY	0	0.004	0.010	23.251	-0.532	-0.532	0.000	0.000	0.000	0.000
97	A	176	ALA	0	-0.053	-0.015	20.530	-0.479	-0.479	0.000	0.000	0.000	0.000
98	A	177	ALA	0	-0.007	0.004	19.296	0.572	0.572	0.000	0.000	0.000	0.000
99	A	178	ALA	0	0.021	0.023	17.928	-0.750	-0.750	0.000	0.000	0.000	0.000
100	A	179	LEU	0	-0.011	-0.012	19.656	-0.893	-0.893	0.000	0.000	0.000	0.000
101	A	180	ALA	0	0.025	0.013	20.461	0.716	0.716	0.000	0.000	0.000	0.000
102	A	181	LEU	0	-0.024	-0.004	22.947	-0.408	-0.408	0.000	0.000	0.000	0.000
103	A	182	THR	0	0.019	0.022	24.913	0.585	0.585	0.000	0.000	0.000	0.000
104	A	183	VAL	0	-0.003	0.007	27.599	-0.274	-0.274	0.000	0.000	0.000	0.000
105	A	184	ASP	-1	-0.844	-0.894	29.851	10.053	10.053	0.000	0.000	0.000	0.000
106	A	185	LEU	0	-0.028	-0.020	30.355	-0.056	-0.056	0.000	0.000	0.000	0.000
107	A	186	PRO	0	-0.007	0.003	34.336	-0.150	-0.150	0.000	0.000	0.000	0.000
108	A	187	PRO	0	-0.012	-0.003	38.171	0.033	0.033	0.000	0.000	0.000	0.000
109	A	188	ALA	0	0.090	0.031	40.119	-0.035	-0.035	0.000	0.000	0.000	0.000
110	A	189	SER	0	0.006	-0.001	42.083	-0.065	-0.065	0.000	0.000	0.000	0.000
111	A	190	SER	0	-0.050	-0.049	40.622	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	191	GLU	-1	-0.865	-0.910	40.755	7.326	7.326	0.000	0.000	0.000	0.000
113	A	192	ALA	0	-0.048	-0.023	42.452	0.039	0.039	0.000	0.000	0.000	0.000
114	A	193	ARG	1	0.907	0.955	38.281	-8.005	-8.005	0.000	0.000	0.000	0.000
115	A	194	ASN	0	0.047	0.034	37.496	0.082	0.082	0.000	0.000	0.000	0.000
116	A	195	SER	0	0.029	0.015	33.948	0.113	0.113	0.000	0.000	0.000	0.000
117	A	196	ALA	0	-0.011	-0.001	31.952	-0.292	-0.292	0.000	0.000	0.000	0.000
118	A	197	PHE	0	0.006	-0.002	29.037	0.298	0.298	0.000	0.000	0.000	0.000
119	A	198	GLY	0	0.037	0.021	28.729	-0.327	-0.327	0.000	0.000	0.000	0.000
120	A	199	PHE	0	0.000	-0.005	25.739	0.431	0.431	0.000	0.000	0.000	0.000
121	A	200	GLN	0	-0.018	-0.002	25.289	-0.695	-0.695	0.000	0.000	0.000	0.000
122	A	201	GLY	0	0.067	0.026	23.685	0.753	0.753	0.000	0.000	0.000	0.000
123	A	202	ARG	1	0.826	0.923	22.402	-14.442	-14.442	0.000	0.000	0.000	0.000
124	A	203	LEU	0	0.023	0.015	23.217	0.515	0.515	0.000	0.000	0.000	0.000
125	A	204	LEU	0	-0.015	-0.011	18.176	-0.108	-0.108	0.000	0.000	0.000	0.000
126	A	205	HIS	0	0.003	0.008	17.697	-0.551	-0.551	0.000	0.000	0.000	0.000
127	A	206	LEU	0	-0.021	-0.010	14.283	0.695	0.695	0.000	0.000	0.000	0.000
128	A	207	SER	0	0.047	0.009	13.789	-1.136	-1.136	0.000	0.000	0.000	0.000
129	A	208	ALA	0	0.024	0.016	12.582	1.230	1.230	0.000	0.000	0.000	0.000
130	A	209	GLY	0	0.010	0.009	8.217	-0.157	-0.157	0.000	0.000	0.000	0.000
131	A	210	GLN	0	-0.103	-0.053	7.937	1.874	1.874	0.000	0.000	0.000	0.000
132	A	211	ARG	1	0.761	0.836	1.687	-134.987	-147.833	33.722	-12.628	-8.248	0.153
133	A	212	LEU	0	-0.009	-0.003	7.794	-5.530	-5.530	0.000	0.000	0.000	0.000
134	A	213	GLY	0	0.089	0.041	8.753	4.179	4.179	0.000	0.000	0.000	0.000
135	A	214	VAL	0	-0.031	-0.010	11.062	-2.070	-2.070	0.000	0.000	0.000	0.000
136	A	215	HIS	0	-0.008	0.008	13.396	0.617	0.617	0.000	0.000	0.000	0.000
137	A	216	LEU	0	0.027	0.021	16.843	-0.778	-0.778	0.000	0.000	0.000	0.000
138	A	217	HIS	0	-0.052	-0.051	20.160	0.924	0.924	0.000	0.000	0.000	0.000
139	A	218	THR	0	0.013	-0.016	23.132	-0.526	-0.526	0.000	0.000	0.000	0.000
140	A	219	GLU	-1	-0.903	-0.944	26.756	10.166	10.166	0.000	0.000	0.000	0.000
141	A	220	ALA	0	-0.013	-0.020	29.669	0.018	0.018	0.000	0.000	0.000	0.000
142	A	221	ARG	1	0.928	0.981	31.309	-8.809	-8.809	0.000	0.000	0.000	0.000
143	A	222	ALA	0	0.056	0.036	30.033	-0.232	-0.232	0.000	0.000	0.000	0.000
144	A	223	ARG	1	0.843	0.892	25.575	-12.160	-12.160	0.000	0.000	0.000	0.000
145	A	224	HIS	0	-0.001	0.000	28.980	0.358	0.358	0.000	0.000	0.000	0.000
146	A	225	ALA	0	0.025	0.024	31.873	-0.210	-0.210	0.000	0.000	0.000	0.000
147	A	226	TRP	0	-0.043	-0.018	30.657	-0.175	-0.175	0.000	0.000	0.000	0.000
148	A	227	GLN	0	0.018	0.006	27.598	0.288	0.288	0.000	0.000	0.000	0.000
149	A	228	LEU	0	-0.002	-0.001	21.951	-0.273	-0.273	0.000	0.000	0.000	0.000
150	A	229	THR	0	-0.078	-0.074	26.114	-0.172	-0.172	0.000	0.000	0.000	0.000
151	A	230	GLN	0	0.019	0.006	22.998	-0.045	-0.045	0.000	0.000	0.000	0.000
152	A	231	GLY	0	0.012	0.007	23.035	-0.424	-0.424	0.000	0.000	0.000	0.000
153	A	232	ALA	0	0.013	0.012	23.845	0.157	0.157	0.000	0.000	0.000	0.000
154	A	233	THR	0	-0.013	0.001	20.399	-0.221	-0.221	0.000	0.000	0.000	0.000
155	A	234	VAL	0	-0.017	-0.009	19.874	0.633	0.633	0.000	0.000	0.000	0.000
156	A	235	LEU	0	-0.007	0.010	14.223	-0.256	-0.256	0.000	0.000	0.000	0.000
157	A	236	GLY	0	-0.002	0.001	17.994	0.352	0.352	0.000	0.000	0.000	0.000
158	A	237	LEU	0	-0.008	-0.013	14.761	0.063	0.063	0.000	0.000	0.000	0.000
159	A	238	PHE	0	0.012	0.009	18.877	-0.122	-0.122	0.000	0.000	0.000	0.000
160	A	239	ARG	1	0.757	0.865	18.178	-16.476	-16.476	0.000	0.000	0.000	0.000
161	A	240	VAL	0	0.005	0.000	20.970	-0.644	-0.644	0.000	0.000	0.000	0.000
162	A	241	THR	0	0.026	0.024	21.824	-0.520	-0.520	0.000	0.000	0.000	0.000
163	A	242	PRO	0	-0.005	0.004	22.459	0.598	0.598	0.000	0.000	0.000	0.000
164	A	243	GLU	-1	-0.785	-0.870	18.858	17.365	17.365	0.000	0.000	0.000	0.000
165	A	244	ILE	0	-0.014	-0.015	22.367	-0.591	-0.591	0.000	0.000	0.000	0.000
166	A	245	PRO	0	-0.029	-0.015	24.480	0.148	0.148	0.000	0.000	0.000	0.000
167	A	246	ALA	0	0.024	0.025	26.380	-0.181	-0.181	0.000	0.000	0.000	0.000

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