FMO DATABASE

FMODB ID: 944V2

Calculation Name: 5B0U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5B0U

Chain ID: A

ChEMBL ID:

UniProt ID: Q9GV45

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	OptHSide
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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1738339.390143
FMO2-HF: Nuclear repulsion	1672426.852817
FMO2-HF: Total energy	-65912.537326
FMO2-MP2: Total energy	-66108.123065

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:-1:GLU)

Summations of interaction energy for fragment #1(A:-1:GLU)

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.
-24.748	-25.384	18.846	-10.208	-8.002	0.11

Interaction energy analysis for fragmet #1(A:-1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.871 / q_NPA : -0.932

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	1	PHE	0	-0.006	0.005	3.810	-4.244	-2.469	-0.022	-0.785	-0.968	0.001
4	A	2	THR	0	-0.034	-0.032	6.587	-1.037	-1.037	0.000	0.000	0.000	0.000
5	A	3	LEU	0	0.053	0.007	9.933	0.219	0.219	0.000	0.000	0.000	0.000
6	A	4	GLU	-1	-0.897	-0.952	13.002	15.298	15.298	0.000	0.000	0.000	0.000
7	A	5	ASP	-1	-0.836	-0.898	9.013	23.418	23.418	0.000	0.000	0.000	0.000
8	A	6	PHE	0	-0.038	-0.040	10.243	0.033	0.033	0.000	0.000	0.000	0.000
9	A	7	VAL	0	-0.024	0.006	13.987	-1.037	-1.037	0.000	0.000	0.000	0.000
10	A	8	GLY	0	-0.011	-0.013	16.534	0.416	0.416	0.000	0.000	0.000	0.000
11	A	9	ASP	-1	-0.795	-0.845	18.997	11.798	11.798	0.000	0.000	0.000	0.000
12	A	10	TRP	0	-0.039	-0.026	13.255	0.182	0.182	0.000	0.000	0.000	0.000
13	A	11	ARG	1	0.908	0.939	20.093	-13.366	-13.366	0.000	0.000	0.000	0.000
14	A	12	GLN	0	0.053	0.026	20.601	0.324	0.324	0.000	0.000	0.000	0.000
15	A	13	THR	0	-0.057	-0.027	18.879	-0.513	-0.513	0.000	0.000	0.000	0.000
16	A	14	ALA	0	0.040	0.017	19.846	-0.371	-0.371	0.000	0.000	0.000	0.000
17	A	15	GLY	0	-0.014	-0.016	21.088	0.375	0.375	0.000	0.000	0.000	0.000
18	A	16	TYR	0	-0.038	-0.002	22.262	-0.514	-0.514	0.000	0.000	0.000	0.000
19	A	17	ASN	0	0.018	-0.003	23.616	0.010	0.010	0.000	0.000	0.000	0.000
20	A	18	LEU	0	0.018	0.017	23.069	-0.118	-0.118	0.000	0.000	0.000	0.000
21	A	19	ASP	-1	-0.858	-0.927	25.953	10.385	10.385	0.000	0.000	0.000	0.000
22	A	20	GLN	0	0.073	0.033	29.378	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	21	VAL	0	-0.048	-0.009	25.165	-0.201	-0.201	0.000	0.000	0.000	0.000
24	A	22	LEU	0	0.029	0.007	26.667	-0.118	-0.118	0.000	0.000	0.000	0.000
25	A	23	GLU	-1	-0.948	-0.969	29.856	8.760	8.760	0.000	0.000	0.000	0.000
26	A	24	GLN	0	-0.068	-0.040	29.326	-0.416	-0.416	0.000	0.000	0.000	0.000
27	A	25	GLY	0	-0.004	0.006	30.747	-0.074	-0.074	0.000	0.000	0.000	0.000
28	A	26	GLY	0	-0.037	-0.027	31.739	-0.054	-0.054	0.000	0.000	0.000	0.000
29	A	27	VAL	0	-0.056	-0.033	29.740	-0.210	-0.210	0.000	0.000	0.000	0.000
30	A	28	SER	0	0.035	0.024	31.987	0.205	0.205	0.000	0.000	0.000	0.000
31	A	29	SER	0	0.005	0.007	31.889	-0.248	-0.248	0.000	0.000	0.000	0.000
32	A	30	LEU	0	0.023	0.002	33.931	-0.137	-0.137	0.000	0.000	0.000	0.000
33	A	31	PHE	0	0.030	-0.005	33.113	-0.139	-0.139	0.000	0.000	0.000	0.000
34	A	32	GLN	0	0.022	0.008	32.188	0.022	0.022	0.000	0.000	0.000	0.000
35	A	33	ASN	0	-0.026	-0.013	34.910	-0.089	-0.089	0.000	0.000	0.000	0.000
36	A	34	LEU	0	-0.066	-0.020	38.338	-0.232	-0.232	0.000	0.000	0.000	0.000
37	A	35	GLY	0	0.004	0.014	37.762	-0.161	-0.161	0.000	0.000	0.000	0.000
38	A	36	VAL	0	-0.018	-0.004	36.718	-0.075	-0.075	0.000	0.000	0.000	0.000
39	A	37	SER	0	-0.007	0.000	34.142	0.220	0.220	0.000	0.000	0.000	0.000
40	A	38	VAL	0	-0.006	-0.011	30.655	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	39	THR	0	-0.020	-0.014	27.540	0.361	0.361	0.000	0.000	0.000	0.000
42	A	40	PRO	0	-0.053	-0.012	25.411	-0.110	-0.110	0.000	0.000	0.000	0.000
43	A	41	ILE	0	0.019	0.006	23.977	0.437	0.437	0.000	0.000	0.000	0.000
44	A	42	GLN	0	0.005	0.008	19.600	-0.281	-0.281	0.000	0.000	0.000	0.000
45	A	43	ARG	1	0.822	0.872	21.361	-10.869	-10.869	0.000	0.000	0.000	0.000
46	A	44	ILE	0	-0.025	-0.004	17.214	-0.262	-0.262	0.000	0.000	0.000	0.000
47	A	45	VAL	0	0.019	0.004	20.140	0.129	0.129	0.000	0.000	0.000	0.000
48	A	46	LEU	0	0.061	0.029	16.478	0.152	0.152	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.069	-0.030	20.438	-0.841	-0.841	0.000	0.000	0.000	0.000
50	A	48	GLY	0	-0.002	-0.005	21.982	0.280	0.280	0.000	0.000	0.000	0.000
51	A	49	GLU	-1	-0.957	-0.982	18.940	14.583	14.583	0.000	0.000	0.000	0.000
52	A	50	ASN	0	0.032	0.020	18.028	0.356	0.356	0.000	0.000	0.000	0.000
53	A	51	GLY	0	0.089	0.032	19.057	0.215	0.215	0.000	0.000	0.000	0.000
54	A	52	LEU	0	-0.057	-0.021	16.130	0.303	0.303	0.000	0.000	0.000	0.000
55	A	53	LYS	1	0.824	0.917	20.691	-11.128	-11.128	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.006	-0.001	19.321	0.231	0.231	0.000	0.000	0.000	0.000
57	A	55	ASP	-1	-0.823	-0.886	23.455	10.486	10.486	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.012	-0.005	23.866	0.366	0.366	0.000	0.000	0.000	0.000
59	A	57	HIS	0	0.035	0.027	26.792	-0.791	-0.791	0.000	0.000	0.000	0.000
60	A	58	VAL	0	0.003	-0.002	28.623	0.284	0.284	0.000	0.000	0.000	0.000
61	A	59	ILE	0	0.007	-0.003	29.963	-0.343	-0.343	0.000	0.000	0.000	0.000
62	A	60	ILE	0	-0.003	-0.011	32.569	0.166	0.166	0.000	0.000	0.000	0.000
63	A	61	PRO	0	0.046	0.028	35.449	-0.121	-0.121	0.000	0.000	0.000	0.000
64	A	62	TYR	0	-0.033	-0.017	38.301	-0.079	-0.079	0.000	0.000	0.000	0.000
65	A	63	GLU	-1	-0.893	-0.946	41.563	6.884	6.884	0.000	0.000	0.000	0.000
66	A	64	GLY	0	-0.048	-0.021	41.399	0.177	0.177	0.000	0.000	0.000	0.000
67	A	65	LEU	0	-0.049	-0.013	40.458	0.075	0.075	0.000	0.000	0.000	0.000
68	A	66	SER	0	-0.012	-0.011	43.612	-0.130	-0.130	0.000	0.000	0.000	0.000
69	A	67	GLY	0	0.037	0.009	46.095	0.078	0.078	0.000	0.000	0.000	0.000
70	A	68	ASP	-1	-0.933	-0.978	48.019	6.347	6.347	0.000	0.000	0.000	0.000
71	A	69	GLN	0	0.031	0.001	42.560	0.000	0.000	0.000	0.000	0.000	0.000
72	A	70	MET	0	0.029	0.039	42.517	0.206	0.206	0.000	0.000	0.000	0.000
73	A	71	GLY	0	0.058	0.034	43.979	0.062	0.062	0.000	0.000	0.000	0.000
74	A	72	GLN	0	-0.075	-0.043	43.645	0.097	0.097	0.000	0.000	0.000	0.000
75	A	73	ILE	0	0.036	0.030	38.646	0.125	0.125	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.912	-0.950	40.648	7.064	7.064	0.000	0.000	0.000	0.000
77	A	75	LYS	1	0.883	0.940	42.866	-6.502	-6.502	0.000	0.000	0.000	0.000
78	A	76	ILE	0	-0.059	-0.033	38.407	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	77	PHE	0	0.005	-0.015	35.116	0.140	0.140	0.000	0.000	0.000	0.000
80	A	78	LYS	1	0.920	0.983	38.657	-7.351	-7.351	0.000	0.000	0.000	0.000
81	A	79	VAL	0	-0.050	-0.032	38.267	-0.183	-0.183	0.000	0.000	0.000	0.000
82	A	80	VAL	0	0.032	0.023	38.313	0.247	0.247	0.000	0.000	0.000	0.000
83	A	81	TYR	0	-0.058	-0.036	35.764	-0.130	-0.130	0.000	0.000	0.000	0.000
84	A	82	PRO	0	0.044	0.023	38.141	0.117	0.117	0.000	0.000	0.000	0.000
85	A	83	VAL	0	-0.073	-0.037	34.179	0.177	0.177	0.000	0.000	0.000	0.000
86	A	84	ASP	-1	-0.820	-0.904	36.511	8.329	8.329	0.000	0.000	0.000	0.000
87	A	85	ASP	-1	-0.909	-0.961	39.259	7.095	7.095	0.000	0.000	0.000	0.000
88	A	86	HIS	0	-0.055	-0.030	38.942	-0.136	-0.136	0.000	0.000	0.000	0.000
89	A	87	HIS	0	-0.072	-0.043	35.987	0.120	0.120	0.000	0.000	0.000	0.000
90	A	88	PHE	0	0.028	0.014	37.754	-0.093	-0.093	0.000	0.000	0.000	0.000
91	A	89	LYS	1	0.884	0.933	31.152	-9.282	-9.282	0.000	0.000	0.000	0.000
92	A	90	VAL	0	0.025	0.022	33.668	-0.250	-0.250	0.000	0.000	0.000	0.000
93	A	91	ILE	0	-0.042	-0.026	29.890	0.291	0.291	0.000	0.000	0.000	0.000
94	A	92	LEU	0	-0.013	0.007	29.456	-0.220	-0.220	0.000	0.000	0.000	0.000
95	A	93	HIS	0	-0.032	-0.015	27.175	0.386	0.386	0.000	0.000	0.000	0.000
96	A	94	TYR	0	-0.057	-0.066	21.938	0.002	0.002	0.000	0.000	0.000	0.000
97	A	95	GLY	0	0.107	0.040	25.871	-0.141	-0.141	0.000	0.000	0.000	0.000
98	A	96	THR	0	-0.063	-0.036	24.842	0.316	0.316	0.000	0.000	0.000	0.000
99	A	97	LEU	0	-0.053	-0.027	19.778	-0.161	-0.161	0.000	0.000	0.000	0.000
100	A	98	VAL	0	0.042	0.016	22.338	0.148	0.148	0.000	0.000	0.000	0.000
101	A	99	ILE	0	-0.065	-0.035	16.414	0.057	0.057	0.000	0.000	0.000	0.000
102	A	100	ASP	-1	-0.741	-0.844	18.292	14.073	14.073	0.000	0.000	0.000	0.000
103	A	101	GLY	0	-0.057	-0.031	20.370	-0.052	-0.052	0.000	0.000	0.000	0.000
104	A	102	VAL	0	-0.099	-0.052	20.987	-0.373	-0.373	0.000	0.000	0.000	0.000
105	A	103	THR	0	-0.043	-0.053	24.565	-0.750	-0.750	0.000	0.000	0.000	0.000
106	A	104	PRO	0	-0.042	-0.019	25.576	0.388	0.388	0.000	0.000	0.000	0.000
107	A	105	ASN	0	-0.016	0.010	23.682	-0.331	-0.331	0.000	0.000	0.000	0.000
108	A	106	MET	0	-0.003	0.005	27.053	0.023	0.023	0.000	0.000	0.000	0.000
109	A	107	ILE	0	-0.043	-0.016	24.442	0.196	0.196	0.000	0.000	0.000	0.000
110	A	108	ASP	-1	-0.822	-0.943	27.901	9.636	9.636	0.000	0.000	0.000	0.000
111	A	109	TYR	0	-0.071	-0.038	24.199	-0.217	-0.217	0.000	0.000	0.000	0.000
112	A	110	PHE	0	0.014	-0.001	26.173	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	111	GLY	0	-0.015	0.010	31.449	-0.271	-0.271	0.000	0.000	0.000	0.000
114	A	112	ARG	1	0.864	0.926	34.586	-8.650	-8.650	0.000	0.000	0.000	0.000
115	A	113	PRO	0	0.043	0.026	32.057	0.216	0.216	0.000	0.000	0.000	0.000
116	A	114	TYR	0	-0.055	-0.025	24.815	-0.276	-0.276	0.000	0.000	0.000	0.000
117	A	115	GLU	-1	-0.882	-0.937	29.195	10.220	10.220	0.000	0.000	0.000	0.000
118	A	116	GLY	0	-0.027	-0.023	24.997	0.135	0.135	0.000	0.000	0.000	0.000
119	A	117	ILE	0	-0.007	0.006	21.946	0.032	0.032	0.000	0.000	0.000	0.000
120	A	118	ALA	0	0.022	0.007	19.311	0.494	0.494	0.000	0.000	0.000	0.000
121	A	119	VAL	0	0.015	0.004	15.175	-0.160	-0.160	0.000	0.000	0.000	0.000
122	A	120	PHE	0	0.028	0.003	9.081	0.508	0.508	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.834	-0.905	9.410	30.899	30.899	0.000	0.000	0.000	0.000
124	A	122	GLY	0	-0.001	0.001	7.573	2.673	2.673	0.000	0.000	0.000	0.000
125	A	123	LYS	1	0.793	0.868	1.722	-111.911	-114.459	18.869	-9.419	-6.903	0.109
126	A	124	LYS	1	0.817	0.889	6.904	-26.465	-26.465	0.000	0.000	0.000	0.000
127	A	125	ILE	0	-0.008	0.011	10.304	-0.718	-0.718	0.000	0.000	0.000	0.000
128	A	126	THR	0	-0.035	-0.023	13.881	-0.058	-0.058	0.000	0.000	0.000	0.000
129	A	127	VAL	0	0.023	0.017	16.557	-0.337	-0.337	0.000	0.000	0.000	0.000
130	A	128	THR	0	-0.041	-0.025	20.255	-0.148	-0.148	0.000	0.000	0.000	0.000
131	A	129	GLY	0	0.054	0.026	22.759	-0.246	-0.246	0.000	0.000	0.000	0.000
132	A	130	THR	0	-0.067	-0.027	26.512	0.295	0.295	0.000	0.000	0.000	0.000
133	A	131	LEU	0	0.043	0.033	28.959	-0.197	-0.197	0.000	0.000	0.000	0.000
134	A	132	TRP	0	0.085	0.034	31.540	-0.204	-0.204	0.000	0.000	0.000	0.000
135	A	133	ASN	0	-0.109	-0.062	33.785	-0.061	-0.061	0.000	0.000	0.000	0.000
136	A	134	GLY	0	0.020	0.010	34.500	-0.163	-0.163	0.000	0.000	0.000	0.000
137	A	135	ASN	0	-0.031	0.002	30.841	0.039	0.039	0.000	0.000	0.000	0.000
138	A	136	LYS	1	0.924	0.975	23.842	-12.943	-12.943	0.000	0.000	0.000	0.000
139	A	137	ILE	0	0.013	-0.004	24.446	0.062	0.062	0.000	0.000	0.000	0.000
140	A	138	ILE	0	-0.027	-0.022	19.240	0.098	0.098	0.000	0.000	0.000	0.000
141	A	139	ASP	-1	-0.804	-0.860	19.817	14.840	14.840	0.000	0.000	0.000	0.000
142	A	140	GLU	-1	-0.774	-0.872	14.418	21.693	21.693	0.000	0.000	0.000	0.000
143	A	141	ARG	1	0.826	0.907	14.134	-16.596	-16.596	0.000	0.000	0.000	0.000
144	A	142	LEU	0	0.001	0.001	7.522	0.715	0.715	0.000	0.000	0.000	0.000
145	A	143	ILE	0	0.032	0.036	7.707	-1.949	-1.949	0.000	0.000	0.000	0.000
146	A	144	ASN	0	-0.058	-0.036	6.729	5.922	5.922	0.000	0.000	0.000	0.000
147	A	145	PRO	0	0.026	-0.004	4.932	-1.256	-1.119	-0.001	-0.004	-0.131	0.000
148	A	146	ASP	-1	-0.855	-0.897	6.709	23.018	23.018	0.000	0.000	0.000	0.000
149	A	147	GLY	0	-0.010	0.004	9.254	-2.139	-2.139	0.000	0.000	0.000	0.000
150	A	148	SER	0	-0.061	-0.044	10.782	-1.571	-1.571	0.000	0.000	0.000	0.000
151	A	149	LEU	0	0.009	0.008	11.178	1.764	1.764	0.000	0.000	0.000	0.000
152	A	150	LEU	0	-0.056	-0.024	12.454	-1.565	-1.565	0.000	0.000	0.000	0.000
153	A	151	PHE	0	-0.023	-0.015	14.234	0.378	0.378	0.000	0.000	0.000	0.000
154	A	152	ARG	1	0.865	0.914	13.716	-21.710	-21.710	0.000	0.000	0.000	0.000
155	A	153	VAL	0	0.031	0.012	18.427	0.103	0.103	0.000	0.000	0.000	0.000
156	A	154	THR	0	0.009	0.008	20.612	-0.150	-0.150	0.000	0.000	0.000	0.000
157	A	155	ILE	0	0.025	0.014	23.270	-0.056	-0.056	0.000	0.000	0.000	0.000
158	A	156	ASN	0	-0.016	-0.004	26.896	-0.039	-0.039	0.000	0.000	0.000	0.000
159	A	157	GLY	0	-0.012	-0.006	25.160	-0.156	-0.156	0.000	0.000	0.000	0.000
160	A	158	VAL	0	-0.015	0.014	25.497	0.309	0.309	0.000	0.000	0.000	0.000
161	A	159	THR	0	0.031	-0.011	20.134	0.083	0.083	0.000	0.000	0.000	0.000
162	A	160	GLY	0	-0.004	0.006	22.577	-0.419	-0.419	0.000	0.000	0.000	0.000
163	A	161	TRP	0	-0.037	-0.031	18.356	0.623	0.623	0.000	0.000	0.000	0.000
164	A	162	ARG	1	0.927	0.952	19.453	-13.232	-13.232	0.000	0.000	0.000	0.000
165	A	163	LEU	0	-0.005	0.005	14.229	0.780	0.780	0.000	0.000	0.000	0.000
166	A	164	CYS	0	-0.043	-0.027	16.393	-1.446	-1.446	0.000	0.000	0.000	0.000
167	A	165	GLU	-1	-0.782	-0.878	16.024	15.536	15.536	0.000	0.000	0.000	0.000
168	A	166	ARG	1	0.906	0.961	12.432	-19.245	-19.245	0.000	0.000	0.000	0.000
169	A	167	ILE	0	-0.019	-0.012	18.272	-0.262	-0.262	0.000	0.000	0.000	0.000
170	A	168	LEU	0	-0.008	0.005	19.961	0.169	0.169	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:GLU)