FMO DATABASE

FMODB ID: MV27Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1705084.391981
FMO2-HF: Nuclear repulsion	1638230.139232
FMO2-HF: Total energy	-66854.252749
FMO2-MP2: Total energy	-67042.971962

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.
-4.376	-0.449	3.291	-2.782	-4.436	-0.008

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 : 0.041 / q_NPA : 0.029

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	0.004	-0.004	3.753	-0.526	1.450	-0.021	-1.090	-0.865	0.007
4	A	82	VAL	0	0.002	0.003	6.621	0.398	0.398	0.000	0.000	0.000	0.000
5	A	83	ALA	0	0.012	0.005	9.210	0.251	0.251	0.000	0.000	0.000	0.000
6	A	84	LYS	1	0.907	0.956	9.143	1.605	1.605	0.000	0.000	0.000	0.000
7	A	85	PRO	0	-0.033	-0.019	13.286	0.107	0.107	0.000	0.000	0.000	0.000
8	A	86	PHE	0	0.108	0.049	16.486	0.071	0.071	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.072	-0.034	14.427	-0.085	-0.085	0.000	0.000	0.000	0.000
10	A	88	ARG	1	0.967	0.967	17.350	0.464	0.464	0.000	0.000	0.000	0.000
11	A	89	LEU	0	0.073	0.041	21.033	0.031	0.031	0.000	0.000	0.000	0.000
12	A	90	ILE	0	0.027	0.006	16.340	0.031	0.031	0.000	0.000	0.000	0.000
13	A	91	ASP	-1	-0.854	-0.891	19.046	-0.519	-0.519	0.000	0.000	0.000	0.000
14	A	92	LEU	0	-0.061	-0.025	21.498	0.036	0.036	0.000	0.000	0.000	0.000
15	A	93	ILE	0	0.013	-0.009	23.152	0.026	0.026	0.000	0.000	0.000	0.000
16	A	94	GLY	0	-0.015	-0.006	22.632	0.020	0.020	0.000	0.000	0.000	0.000
17	A	95	HIS	0	-0.066	-0.024	23.478	0.012	0.012	0.000	0.000	0.000	0.000
18	A	96	MET	0	-0.051	0.013	26.826	0.021	0.021	0.000	0.000	0.000	0.000
19	A	97	THR	0	0.021	0.002	28.412	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	98	LEU	0	0.063	0.026	28.099	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	99	SER	0	-0.012	-0.010	30.554	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	100	ASP	-1	-0.870	-0.928	31.435	-0.176	-0.176	0.000	0.000	0.000	0.000
23	A	101	PHE	0	0.048	0.007	27.436	0.000	0.000	0.000	0.000	0.000	0.000
24	A	102	THR	0	-0.024	-0.030	31.771	0.007	0.007	0.000	0.000	0.000	0.000
25	A	103	ARG	1	0.881	0.942	33.795	0.155	0.155	0.000	0.000	0.000	0.000
26	A	104	PHE	0	-0.023	0.004	33.920	0.008	0.008	0.000	0.000	0.000	0.000
27	A	105	PRO	0	0.022	0.010	34.554	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	106	ASN	0	0.047	0.017	32.845	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	107	LEU	0	0.037	0.015	30.181	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	108	LYS	1	0.912	0.969	29.589	0.125	0.125	0.000	0.000	0.000	0.000
31	A	109	GLU	-1	-0.896	-0.921	29.822	-0.177	-0.177	0.000	0.000	0.000	0.000
32	A	110	ALA	0	-0.021	0.000	26.526	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	111	ILE	0	-0.015	0.000	24.592	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	112	SER	0	-0.016	-0.031	25.765	0.002	0.002	0.000	0.000	0.000	0.000
35	A	113	TRP	0	-0.040	0.032	17.799	0.008	0.008	0.000	0.000	0.000	0.000
36	A	114	PRO	0	0.010	-0.014	19.507	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.020	-0.039	21.794	0.020	0.020	0.000	0.000	0.000	0.000
38	A	116	GLY	0	-0.008	0.010	24.731	0.019	0.019	0.000	0.000	0.000	0.000
39	A	117	GLU	-1	-0.924	-0.970	27.448	-0.142	-0.142	0.000	0.000	0.000	0.000
40	A	118	PRO	0	-0.019	-0.006	27.130	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	119	SER	0	-0.003	0.000	23.792	0.003	0.003	0.000	0.000	0.000	0.000
42	A	120	LEU	0	0.058	0.023	23.546	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	121	ALA	0	0.027	0.011	21.376	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	122	PHE	0	0.058	0.007	16.363	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	123	PHE	0	0.022	0.015	17.282	-0.076	-0.076	0.000	0.000	0.000	0.000
46	A	124	ASP	-1	-0.869	-0.928	19.051	-0.353	-0.353	0.000	0.000	0.000	0.000
47	A	125	LEU	0	-0.081	-0.031	15.561	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	126	SER	0	0.031	0.016	14.390	-0.119	-0.119	0.000	0.000	0.000	0.000
49	A	127	SER	0	0.005	0.014	15.411	-0.059	-0.059	0.000	0.000	0.000	0.000
50	A	128	THR	0	-0.108	-0.085	15.886	0.009	0.009	0.000	0.000	0.000	0.000
51	A	129	ARG	1	0.928	0.960	18.093	0.363	0.363	0.000	0.000	0.000	0.000
52	A	130	VAL	0	-0.013	0.004	20.320	0.039	0.039	0.000	0.000	0.000	0.000
53	A	131	HIS	0	-0.024	0.000	20.361	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	132	ARG	1	0.888	0.929	16.106	0.498	0.498	0.000	0.000	0.000	0.000
55	A	133	ASN	0	0.021	0.005	20.815	0.005	0.005	0.000	0.000	0.000	0.000
56	A	134	ASP	-1	-0.877	-0.955	15.475	-0.371	-0.371	0.000	0.000	0.000	0.000
57	A	135	ASP	-1	-0.935	-0.961	17.028	-0.108	-0.108	0.000	0.000	0.000	0.000
58	A	136	ILE	0	-0.002	-0.001	19.248	0.014	0.014	0.000	0.000	0.000	0.000
59	A	137	ARG	1	0.880	0.946	11.661	0.708	0.708	0.000	0.000	0.000	0.000
60	A	138	ARG	1	0.972	0.979	12.158	-0.063	-0.063	0.000	0.000	0.000	0.000
61	A	139	ASP	-1	-0.857	-0.928	15.623	-0.089	-0.089	0.000	0.000	0.000	0.000
62	A	140	GLN	0	-0.028	-0.027	18.528	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	141	ILE	0	0.015	-0.006	12.158	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.038	0.035	16.062	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	143	THR	0	-0.024	-0.015	17.338	0.018	0.018	0.000	0.000	0.000	0.000
66	A	144	LEU	0	-0.039	-0.021	17.952	0.015	0.015	0.000	0.000	0.000	0.000
67	A	145	ALA	0	0.035	0.026	15.757	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	146	MET	0	-0.011	0.003	17.801	0.028	0.028	0.000	0.000	0.000	0.000
69	A	147	ARG	1	0.844	0.923	20.932	0.190	0.190	0.000	0.000	0.000	0.000
70	A	148	SER	0	-0.044	-0.014	19.513	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	149	CYS	0	-0.046	-0.016	19.393	0.020	0.020	0.000	0.000	0.000	0.000
72	A	150	LYS	1	0.880	0.948	21.575	0.149	0.149	0.000	0.000	0.000	0.000
73	A	151	ILE	0	0.031	0.032	20.043	0.015	0.015	0.000	0.000	0.000	0.000
74	A	152	THR	0	0.015	-0.032	21.568	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	153	ASN	0	-0.052	-0.031	23.557	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	154	ASP	-1	-0.750	-0.857	18.414	0.155	0.155	0.000	0.000	0.000	0.000
77	A	155	LEU	0	-0.015	-0.007	15.504	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	156	GLU	-1	-0.908	-0.951	11.722	0.205	0.205	0.000	0.000	0.000	0.000
79	A	157	ASP	-1	-0.896	-0.957	14.925	0.072	0.072	0.000	0.000	0.000	0.000
80	A	158	SER	0	-0.118	-0.061	17.121	-0.058	-0.058	0.000	0.000	0.000	0.000
81	A	159	PHE	0	0.021	0.000	11.779	-0.101	-0.101	0.000	0.000	0.000	0.000
82	A	160	VAL	0	0.047	0.034	13.177	-0.093	-0.093	0.000	0.000	0.000	0.000
83	A	161	GLY	0	-0.017	-0.020	14.199	-0.047	-0.047	0.000	0.000	0.000	0.000
84	A	162	LEU	0	-0.018	-0.028	14.097	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	163	HIS	0	-0.002	-0.005	9.474	0.069	0.069	0.000	0.000	0.000	0.000
86	A	164	ARG	1	0.937	0.962	13.379	0.043	0.043	0.000	0.000	0.000	0.000
87	A	165	MET	0	-0.057	-0.009	16.470	0.004	0.004	0.000	0.000	0.000	0.000
88	A	166	ILE	0	0.005	0.010	12.769	0.020	0.020	0.000	0.000	0.000	0.000
89	A	167	ALA	0	0.015	0.010	14.679	0.007	0.007	0.000	0.000	0.000	0.000
90	A	168	THR	0	-0.023	-0.009	16.321	0.034	0.034	0.000	0.000	0.000	0.000
91	A	169	GLU	-1	-0.788	-0.873	19.678	-0.247	-0.247	0.000	0.000	0.000	0.000
92	A	170	ALA	0	0.022	0.001	16.938	0.013	0.013	0.000	0.000	0.000	0.000
93	A	171	ILE	0	0.003	0.008	18.716	0.020	0.020	0.000	0.000	0.000	0.000
94	A	172	LEU	0	-0.032	-0.005	20.831	0.020	0.020	0.000	0.000	0.000	0.000
95	A	173	ARG	1	0.855	0.893	21.466	0.266	0.266	0.000	0.000	0.000	0.000
96	A	174	GLY	0	-0.054	-0.010	22.403	0.004	0.004	0.000	0.000	0.000	0.000
97	A	175	ILE	0	-0.015	-0.004	16.396	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	176	ASP	-1	-0.859	-0.932	15.808	-0.455	-0.455	0.000	0.000	0.000	0.000
99	A	177	LEU	0	0.031	-0.001	13.900	-0.089	-0.089	0.000	0.000	0.000	0.000
100	A	178	CYS	0	-0.042	-0.010	11.588	-0.078	-0.078	0.000	0.000	0.000	0.000
101	A	179	LEU	0	-0.062	-0.039	10.450	-0.208	-0.208	0.000	0.000	0.000	0.000
102	A	180	LEU	0	-0.079	-0.030	10.088	-0.188	-0.188	0.000	0.000	0.000	0.000
103	A	181	PRO	0	-0.006	0.001	5.460	0.219	0.219	0.000	0.000	0.000	0.000
104	A	182	GLY	0	0.041	0.005	6.696	0.185	0.185	0.000	0.000	0.000	0.000
105	A	183	PHE	0	-0.070	-0.031	2.671	-4.741	-2.865	3.313	-1.686	-3.504	-0.015
106	A	184	ASP	-1	-0.838	-0.933	4.831	-1.294	-1.219	-0.001	-0.006	-0.067	0.000
107	A	185	LEU	0	0.063	0.021	7.708	0.243	0.243	0.000	0.000	0.000	0.000
108	A	186	MET	0	-0.040	-0.003	10.782	0.192	0.192	0.000	0.000	0.000	0.000
109	A	187	TYR	0	0.052	0.008	10.699	0.107	0.107	0.000	0.000	0.000	0.000
110	A	188	GLU	-1	-0.800	-0.912	8.714	-1.435	-1.435	0.000	0.000	0.000	0.000
111	A	189	VAL	0	-0.013	0.006	12.887	0.119	0.119	0.000	0.000	0.000	0.000
112	A	190	ALA	0	0.049	0.024	15.832	0.072	0.072	0.000	0.000	0.000	0.000
113	A	191	HIS	0	0.057	0.052	15.053	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	192	VAL	0	-0.005	-0.010	16.216	0.071	0.071	0.000	0.000	0.000	0.000
115	A	193	GLN	0	-0.015	-0.030	18.661	0.031	0.031	0.000	0.000	0.000	0.000
116	A	194	CYS	0	-0.027	0.001	19.996	0.044	0.044	0.000	0.000	0.000	0.000
117	A	195	VAL	0	-0.013	0.008	20.108	0.038	0.038	0.000	0.000	0.000	0.000
118	A	196	ARG	1	0.764	0.856	22.642	0.299	0.299	0.000	0.000	0.000	0.000
119	A	197	LEU	0	0.001	-0.003	24.278	0.029	0.029	0.000	0.000	0.000	0.000
120	A	198	LEU	0	-0.026	-0.007	23.782	0.024	0.024	0.000	0.000	0.000	0.000
121	A	199	GLN	0	-0.015	-0.010	26.574	0.041	0.041	0.000	0.000	0.000	0.000
122	A	200	ALA	0	0.018	0.012	28.675	0.018	0.018	0.000	0.000	0.000	0.000
123	A	201	ALA	0	0.003	-0.010	30.301	0.016	0.016	0.000	0.000	0.000	0.000
124	A	202	LYS	1	0.816	0.909	30.428	0.213	0.213	0.000	0.000	0.000	0.000
125	A	203	GLU	-1	-0.863	-0.923	34.049	-0.123	-0.123	0.000	0.000	0.000	0.000
126	A	204	ASP	-1	-0.770	-0.900	34.380	-0.153	-0.153	0.000	0.000	0.000	0.000
127	A	205	ILE	0	-0.028	-0.018	34.752	0.007	0.007	0.000	0.000	0.000	0.000
128	A	206	SER	0	-0.070	-0.024	38.118	0.010	0.010	0.000	0.000	0.000	0.000
129	A	207	ASN	0	-0.010	-0.001	39.497	0.011	0.011	0.000	0.000	0.000	0.000
130	A	208	ALA	0	-0.057	-0.025	41.524	0.004	0.004	0.000	0.000	0.000	0.000
131	A	209	VAL	0	-0.022	-0.001	37.527	0.003	0.003	0.000	0.000	0.000	0.000
132	A	210	VAL	0	-0.001	-0.009	41.002	0.000	0.000	0.000	0.000	0.000	0.000
133	A	211	PRO	0	-0.001	-0.007	37.889	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	212	ASN	0	0.022	0.013	34.373	0.002	0.002	0.000	0.000	0.000	0.000
135	A	213	SER	0	-0.008	-0.018	33.274	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	214	ALA	0	0.087	0.037	30.519	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	215	LEU	0	0.009	0.007	30.748	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	216	ILE	0	0.010	-0.007	32.695	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	217	VAL	0	0.011	0.013	27.523	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	218	LEU	0	-0.005	0.006	26.674	-0.015	-0.015	0.000	0.000	0.000	0.000
141	A	219	MET	0	-0.050	-0.029	29.266	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	220	GLU	-1	-0.979	-0.992	29.206	-0.249	-0.249	0.000	0.000	0.000	0.000
143	A	221	GLU	-1	-0.812	-0.901	23.053	-0.391	-0.391	0.000	0.000	0.000	0.000
144	A	222	SER	0	-0.046	-0.045	27.159	-0.007	-0.007	0.000	0.000	0.000	0.000
145	A	223	LEU	0	-0.061	-0.029	28.863	0.007	0.007	0.000	0.000	0.000	0.000
146	A	224	MET	0	0.009	0.028	23.738	0.009	0.009	0.000	0.000	0.000	0.000
147	A	225	LEU	0	0.036	-0.004	22.819	0.004	0.004	0.000	0.000	0.000	0.000
148	A	226	ARG	1	0.888	0.929	26.718	0.202	0.202	0.000	0.000	0.000	0.000
149	A	227	SER	0	-0.047	-0.016	29.814	0.010	0.010	0.000	0.000	0.000	0.000
150	A	228	SER	0	-0.035	0.010	24.252	0.002	0.002	0.000	0.000	0.000	0.000
151	A	229	LEU	0	0.016	-0.009	20.442	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	230	PRO	0	0.042	0.024	24.233	-0.023	-0.023	0.000	0.000	0.000	0.000
153	A	231	SER	0	-0.016	-0.008	22.688	-0.006	-0.006	0.000	0.000	0.000	0.000
154	A	232	MET	0	0.003	0.016	17.543	-0.035	-0.035	0.000	0.000	0.000	0.000
155	A	233	MET	0	-0.043	-0.023	21.377	-0.016	-0.016	0.000	0.000	0.000	0.000
156	A	234	GLY	0	0.033	0.040	23.366	0.009	0.009	0.000	0.000	0.000	0.000
157	A	235	ARG	1	0.843	0.914	23.927	0.231	0.231	0.000	0.000	0.000	0.000
158	A	236	ASN	0	-0.029	-0.012	27.038	-0.018	-0.018	0.000	0.000	0.000	0.000
159	A	237	ASN	0	-0.015	-0.010	27.113	0.004	0.004	0.000	0.000	0.000	0.000
160	A	238	TRP	0	-0.008	-0.008	27.236	-0.007	-0.007	0.000	0.000	0.000	0.000
161	A	239	ILE	0	-0.002	-0.003	30.931	0.010	0.010	0.000	0.000	0.000	0.000
162	A	240	PRO	0	0.015	0.016	33.634	-0.005	-0.005	0.000	0.000	0.000	0.000
163	A	241	VAL	0	-0.025	-0.004	34.026	0.006	0.006	0.000	0.000	0.000	0.000
164	A	242	ILE	0	-0.011	-0.011	36.529	0.004	0.004	0.000	0.000	0.000	0.000
165	A	243	PRO	0	-0.023	-0.020	40.183	0.000	0.000	0.000	0.000	0.000	0.000
166	A	244	PRO	0	0.000	0.018	40.736	0.006	0.006	0.000	0.000	0.000	0.000

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