FMO DATABASE

FMODB ID: 72ZRK

Calculation Name: 5OOO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5OOO

Chain ID: A

ChEMBL ID:

UniProt ID: P21698

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1706594.185705
FMO2-HF: Nuclear repulsion	1639739.337404
FMO2-HF: Total energy	-66854.848301
FMO2-MP2: Total energy	-67043.578142

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:79:GLY)

Summations of interaction energy for fragment #1(A:79: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.
-4.502	-0.479	3.004	-2.724	-4.302	-0.01

Interaction energy analysis for fragmet #1(A:79:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.028

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	81	MET	0	0.009	-0.002	3.753	-0.503	1.454	-0.020	-1.077	-0.860	0.006
4	A	82	VAL	0	-0.003	0.001	6.583	0.401	0.401	0.000	0.000	0.000	0.000
5	A	83	ALA	0	0.009	0.002	9.211	0.248	0.248	0.000	0.000	0.000	0.000
6	A	84	LYS	1	0.855	0.923	9.286	1.541	1.541	0.000	0.000	0.000	0.000
7	A	85	PRO	0	-0.027	-0.021	13.238	0.108	0.108	0.000	0.000	0.000	0.000
8	A	86	PHE	0	0.093	0.046	16.428	0.070	0.070	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.068	-0.035	14.464	-0.082	-0.082	0.000	0.000	0.000	0.000
10	A	88	ARG	1	0.963	0.969	17.399	0.491	0.491	0.000	0.000	0.000	0.000
11	A	89	LEU	0	0.058	0.038	21.081	0.032	0.032	0.000	0.000	0.000	0.000
12	A	90	ILE	0	0.030	0.003	16.410	0.032	0.032	0.000	0.000	0.000	0.000
13	A	91	ASP	-1	-0.851	-0.910	19.161	-0.529	-0.529	0.000	0.000	0.000	0.000
14	A	92	LEU	0	-0.054	-0.016	21.539	0.036	0.036	0.000	0.000	0.000	0.000
15	A	93	ILE	0	0.014	-0.012	23.179	0.027	0.027	0.000	0.000	0.000	0.000
16	A	94	GLY	0	0.004	0.006	22.670	0.020	0.020	0.000	0.000	0.000	0.000
17	A	95	HIS	0	-0.085	-0.038	23.516	0.015	0.015	0.000	0.000	0.000	0.000
18	A	96	MET	0	-0.040	0.020	26.862	0.022	0.022	0.000	0.000	0.000	0.000
19	A	97	THR	0	0.045	0.017	28.449	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	98	LEU	0	0.064	0.027	28.160	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	99	SER	0	0.007	0.000	30.593	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	100	ASP	-1	-0.862	-0.936	31.599	-0.171	-0.171	0.000	0.000	0.000	0.000
23	A	101	PHE	0	0.053	0.012	27.459	0.000	0.000	0.000	0.000	0.000	0.000
24	A	102	THR	0	-0.029	-0.034	31.817	0.007	0.007	0.000	0.000	0.000	0.000
25	A	103	ARG	1	0.824	0.915	33.839	0.161	0.161	0.000	0.000	0.000	0.000
26	A	104	PHE	0	-0.015	0.008	34.081	0.008	0.008	0.000	0.000	0.000	0.000
27	A	105	PRO	0	0.029	0.017	34.507	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	106	ASN	0	0.055	0.010	32.797	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	107	LEU	0	0.039	0.016	30.063	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	108	LYS	1	0.908	0.967	29.543	0.124	0.124	0.000	0.000	0.000	0.000
31	A	109	GLU	-1	-0.850	-0.903	29.188	-0.192	-0.192	0.000	0.000	0.000	0.000
32	A	110	ALA	0	-0.004	0.013	26.552	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	111	ILE	0	-0.012	-0.001	24.746	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	112	SER	0	-0.016	-0.028	25.808	0.002	0.002	0.000	0.000	0.000	0.000
35	A	113	TRP	0	-0.033	0.030	17.723	0.008	0.008	0.000	0.000	0.000	0.000
36	A	114	PRO	0	0.012	-0.011	19.450	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.015	-0.038	21.955	0.020	0.020	0.000	0.000	0.000	0.000
38	A	116	GLY	0	-0.017	0.007	24.765	0.019	0.019	0.000	0.000	0.000	0.000
39	A	117	GLU	-1	-0.872	-0.916	27.424	-0.153	-0.153	0.000	0.000	0.000	0.000
40	A	118	PRO	0	-0.028	-0.017	27.168	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	119	SER	0	0.004	-0.002	24.202	0.001	0.001	0.000	0.000	0.000	0.000
42	A	120	LEU	0	0.047	0.019	23.565	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	121	ALA	0	0.037	0.027	21.457	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	122	PHE	0	0.064	0.009	16.595	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	123	PHE	0	0.018	0.016	17.319	-0.082	-0.082	0.000	0.000	0.000	0.000
46	A	124	ASP	-1	-0.867	-0.930	19.087	-0.363	-0.363	0.000	0.000	0.000	0.000
47	A	125	LEU	0	-0.049	-0.015	15.633	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	126	SER	0	0.007	0.002	14.434	-0.121	-0.121	0.000	0.000	0.000	0.000
49	A	127	SER	0	-0.010	0.016	15.446	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	128	THR	0	-0.084	-0.061	15.890	0.012	0.012	0.000	0.000	0.000	0.000
51	A	129	ARG	1	0.927	0.964	18.122	0.365	0.365	0.000	0.000	0.000	0.000
52	A	130	VAL	0	-0.011	0.005	20.330	0.038	0.038	0.000	0.000	0.000	0.000
53	A	131	HIS	0	-0.020	0.002	20.378	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	132	ARG	1	0.859	0.905	16.289	0.518	0.518	0.000	0.000	0.000	0.000
55	A	133	ASN	0	-0.025	-0.036	20.808	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	134	ASP	-1	-0.875	-0.954	15.094	-0.427	-0.427	0.000	0.000	0.000	0.000
57	A	135	ASP	-1	-0.912	-0.936	17.015	-0.123	-0.123	0.000	0.000	0.000	0.000
58	A	136	ILE	0	0.016	0.004	19.232	0.015	0.015	0.000	0.000	0.000	0.000
59	A	137	ARG	1	0.894	0.950	11.355	0.748	0.748	0.000	0.000	0.000	0.000
60	A	138	ARG	1	0.977	0.984	12.174	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	139	ASP	-1	-0.862	-0.934	15.615	-0.099	-0.099	0.000	0.000	0.000	0.000
62	A	140	GLN	0	-0.014	-0.010	18.534	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	141	ILE	0	0.018	-0.004	12.272	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.035	0.031	16.073	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	143	THR	0	-0.039	-0.030	17.340	0.021	0.021	0.000	0.000	0.000	0.000
66	A	144	LEU	0	-0.025	-0.013	17.967	0.016	0.016	0.000	0.000	0.000	0.000
67	A	145	ALA	0	0.035	0.034	15.757	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	146	MET	0	-0.009	0.010	17.819	0.029	0.029	0.000	0.000	0.000	0.000
69	A	147	ARG	1	0.825	0.899	20.944	0.186	0.186	0.000	0.000	0.000	0.000
70	A	148	SER	0	-0.032	-0.014	19.551	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	149	CYS	0	-0.050	-0.035	19.335	0.021	0.021	0.000	0.000	0.000	0.000
72	A	150	LYS	1	0.806	0.908	21.556	0.171	0.171	0.000	0.000	0.000	0.000
73	A	151	ILE	0	0.033	0.034	19.834	0.015	0.015	0.000	0.000	0.000	0.000
74	A	152	THR	0	0.019	-0.031	21.574	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	153	ASN	0	-0.044	-0.022	23.558	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	154	ASP	-1	-0.801	-0.905	18.509	0.154	0.154	0.000	0.000	0.000	0.000
77	A	155	LEU	0	-0.005	0.005	15.437	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	156	GLU	-1	-0.882	-0.934	11.536	0.197	0.197	0.000	0.000	0.000	0.000
79	A	157	ASP	-1	-0.894	-0.948	14.923	0.070	0.070	0.000	0.000	0.000	0.000
80	A	158	SER	0	-0.115	-0.062	16.812	-0.057	-0.057	0.000	0.000	0.000	0.000
81	A	159	PHE	0	0.018	-0.006	11.816	-0.101	-0.101	0.000	0.000	0.000	0.000
82	A	160	VAL	0	0.043	0.031	13.080	-0.089	-0.089	0.000	0.000	0.000	0.000
83	A	161	GLY	0	-0.010	-0.012	14.198	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	162	LEU	0	-0.025	-0.028	14.167	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	163	HIS	0	-0.003	-0.008	10.126	0.092	0.092	0.000	0.000	0.000	0.000
86	A	164	ARG	1	0.952	0.973	13.364	0.024	0.024	0.000	0.000	0.000	0.000
87	A	165	MET	0	-0.059	0.005	16.463	0.003	0.003	0.000	0.000	0.000	0.000
88	A	166	ILE	0	0.011	0.011	12.932	0.014	0.014	0.000	0.000	0.000	0.000
89	A	167	ALA	0	0.027	0.014	14.665	0.006	0.006	0.000	0.000	0.000	0.000
90	A	168	THR	0	-0.036	-0.032	16.309	0.034	0.034	0.000	0.000	0.000	0.000
91	A	169	GLU	-1	-0.776	-0.862	19.660	-0.242	-0.242	0.000	0.000	0.000	0.000
92	A	170	ALA	0	0.013	-0.001	16.919	0.012	0.012	0.000	0.000	0.000	0.000
93	A	171	ILE	0	0.009	0.015	18.724	0.019	0.019	0.000	0.000	0.000	0.000
94	A	172	LEU	0	-0.015	0.011	20.819	0.020	0.020	0.000	0.000	0.000	0.000
95	A	173	ARG	1	0.858	0.894	21.441	0.258	0.258	0.000	0.000	0.000	0.000
96	A	174	GLY	0	-0.047	-0.011	22.386	0.004	0.004	0.000	0.000	0.000	0.000
97	A	175	ILE	0	-0.023	-0.008	16.455	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	176	ASP	-1	-0.822	-0.911	15.999	-0.463	-0.463	0.000	0.000	0.000	0.000
99	A	177	LEU	0	0.025	0.000	13.916	-0.089	-0.089	0.000	0.000	0.000	0.000
100	A	178	CYS	0	-0.077	-0.033	11.598	-0.073	-0.073	0.000	0.000	0.000	0.000
101	A	179	LEU	0	-0.053	-0.033	10.438	-0.206	-0.206	0.000	0.000	0.000	0.000
102	A	180	LEU	0	-0.069	-0.028	10.042	-0.193	-0.193	0.000	0.000	0.000	0.000
103	A	181	PRO	0	-0.008	0.002	5.510	0.232	0.232	0.000	0.000	0.000	0.000
104	A	182	GLY	0	0.045	0.012	6.695	0.224	0.224	0.000	0.000	0.000	0.000
105	A	183	PHE	0	-0.077	-0.033	2.694	-4.790	-2.801	3.025	-1.641	-3.373	-0.016
106	A	184	ASP	-1	-0.798	-0.900	4.791	-1.269	-1.192	-0.001	-0.006	-0.069	0.000
107	A	185	LEU	0	0.054	0.019	7.748	0.244	0.244	0.000	0.000	0.000	0.000
108	A	186	MET	0	-0.031	0.001	10.820	0.193	0.193	0.000	0.000	0.000	0.000
109	A	187	TYR	0	0.050	0.007	10.788	0.093	0.093	0.000	0.000	0.000	0.000
110	A	188	GLU	-1	-0.802	-0.918	8.390	-1.562	-1.562	0.000	0.000	0.000	0.000
111	A	189	VAL	0	-0.006	0.008	12.843	0.118	0.118	0.000	0.000	0.000	0.000
112	A	190	ALA	0	0.048	0.025	15.879	0.073	0.073	0.000	0.000	0.000	0.000
113	A	191	HIS	0	0.063	0.056	14.954	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	192	VAL	0	-0.005	-0.012	16.151	0.070	0.070	0.000	0.000	0.000	0.000
115	A	193	GLN	0	-0.014	-0.024	18.621	0.030	0.030	0.000	0.000	0.000	0.000
116	A	194	CYS	0	-0.040	-0.007	19.945	0.043	0.043	0.000	0.000	0.000	0.000
117	A	195	VAL	0	-0.013	0.007	20.070	0.039	0.039	0.000	0.000	0.000	0.000
118	A	196	ARG	1	0.725	0.832	22.602	0.291	0.291	0.000	0.000	0.000	0.000
119	A	197	LEU	0	0.000	-0.003	24.257	0.030	0.030	0.000	0.000	0.000	0.000
120	A	198	LEU	0	-0.026	-0.004	23.685	0.024	0.024	0.000	0.000	0.000	0.000
121	A	199	GLN	0	-0.023	-0.016	26.431	0.044	0.044	0.000	0.000	0.000	0.000
122	A	200	ALA	0	0.027	0.014	28.634	0.018	0.018	0.000	0.000	0.000	0.000
123	A	201	ALA	0	0.001	-0.013	30.259	0.016	0.016	0.000	0.000	0.000	0.000
124	A	202	LYS	1	0.806	0.907	30.417	0.210	0.210	0.000	0.000	0.000	0.000
125	A	203	GLU	-1	-0.823	-0.902	34.008	-0.121	-0.121	0.000	0.000	0.000	0.000
126	A	204	ASP	-1	-0.760	-0.880	34.471	-0.151	-0.151	0.000	0.000	0.000	0.000
127	A	205	ILE	0	-0.026	-0.016	34.622	0.007	0.007	0.000	0.000	0.000	0.000
128	A	206	SER	0	-0.076	-0.027	38.073	0.009	0.009	0.000	0.000	0.000	0.000
129	A	207	ASN	0	-0.077	-0.049	39.216	0.013	0.013	0.000	0.000	0.000	0.000
130	A	208	ALA	0	-0.054	-0.020	41.478	0.004	0.004	0.000	0.000	0.000	0.000
131	A	209	VAL	0	-0.010	0.005	37.470	0.003	0.003	0.000	0.000	0.000	0.000
132	A	210	VAL	0	-0.002	-0.007	40.953	0.000	0.000	0.000	0.000	0.000	0.000
133	A	211	PRO	0	-0.007	-0.010	37.803	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	212	ASN	0	0.009	0.012	34.129	0.002	0.002	0.000	0.000	0.000	0.000
135	A	213	SER	0	0.009	-0.005	33.511	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	214	ALA	0	0.050	0.017	30.539	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	215	LEU	0	0.017	0.010	30.800	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	216	ILE	0	0.012	-0.006	32.644	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	217	VAL	0	0.015	0.015	27.527	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	218	LEU	0	-0.002	0.008	26.512	-0.015	-0.015	0.000	0.000	0.000	0.000
141	A	219	MET	0	-0.052	-0.022	29.215	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	220	GLU	-1	-0.975	-0.993	29.517	-0.243	-0.243	0.000	0.000	0.000	0.000
143	A	221	GLU	-1	-0.785	-0.894	22.916	-0.394	-0.394	0.000	0.000	0.000	0.000
144	A	222	SER	0	-0.061	-0.059	27.114	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	223	LEU	0	-0.043	-0.023	28.819	0.007	0.007	0.000	0.000	0.000	0.000
146	A	224	MET	0	0.008	0.031	23.714	0.008	0.008	0.000	0.000	0.000	0.000
147	A	225	LEU	0	0.038	-0.006	22.686	0.004	0.004	0.000	0.000	0.000	0.000
148	A	226	ARG	1	0.881	0.933	26.679	0.201	0.201	0.000	0.000	0.000	0.000
149	A	227	SER	0	-0.012	0.002	29.778	0.015	0.015	0.000	0.000	0.000	0.000
150	A	228	SER	0	-0.081	-0.016	24.549	0.006	0.006	0.000	0.000	0.000	0.000
151	A	229	LEU	0	0.015	-0.007	20.331	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	230	PRO	0	0.045	0.024	24.201	-0.023	-0.023	0.000	0.000	0.000	0.000
153	A	231	SER	0	-0.016	-0.009	22.627	-0.006	-0.006	0.000	0.000	0.000	0.000
154	A	232	MET	0	-0.002	0.011	17.406	-0.034	-0.034	0.000	0.000	0.000	0.000
155	A	233	MET	0	-0.037	-0.015	21.342	-0.016	-0.016	0.000	0.000	0.000	0.000
156	A	234	GLY	0	0.040	0.049	23.341	0.009	0.009	0.000	0.000	0.000	0.000
157	A	235	ARG	1	0.799	0.881	23.900	0.229	0.229	0.000	0.000	0.000	0.000
158	A	236	ASN	0	-0.027	-0.017	27.014	-0.014	-0.014	0.000	0.000	0.000	0.000
159	A	237	ASN	0	-0.018	-0.013	27.120	0.003	0.003	0.000	0.000	0.000	0.000
160	A	238	TRP	0	0.000	0.000	27.264	-0.006	-0.006	0.000	0.000	0.000	0.000
161	A	239	ILE	0	-0.001	-0.002	30.900	0.010	0.010	0.000	0.000	0.000	0.000
162	A	240	PRO	0	0.007	0.011	33.601	-0.005	-0.005	0.000	0.000	0.000	0.000
163	A	241	VAL	0	-0.034	-0.011	34.011	0.006	0.006	0.000	0.000	0.000	0.000
164	A	242	ILE	0	-0.005	-0.005	36.493	0.004	0.004	0.000	0.000	0.000	0.000
165	A	243	PRO	0	-0.023	-0.017	40.147	0.000	0.000	0.000	0.000	0.000	0.000
166	A	244	PRO	0	0.002	0.018	40.707	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:79:GLY)