FMO DATABASE

FMODB ID: 22V4R

Calculation Name: 3RBW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: A

ChEMBL ID:

UniProt ID: Q08AE8

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1538259.125329
FMO2-HF: Nuclear repulsion	1475081.261073
FMO2-HF: Total energy	-63177.864256
FMO2-MP2: Total energy	-63356.895962

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:38:ASP)

Summations of interaction energy for fragment #1(A:38: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.
-104.888	-108.907	30.863	-14.897	-11.947	0.142

Interaction energy analysis for fragmet #1(A:38:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.811 / q_NPA : -0.892

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	40	LEU	0	-0.004	0.023	3.864	-3.957	-2.071	-0.013	-0.987	-0.887	0.002
4	A	41	SER	0	-0.068	-0.079	5.847	-1.122	-1.122	0.000	0.000	0.000	0.000
5	A	42	LEU	0	0.033	0.005	9.329	-0.285	-0.285	0.000	0.000	0.000	0.000
6	A	43	GLU	-1	-0.846	-0.920	12.072	14.985	14.985	0.000	0.000	0.000	0.000
7	A	44	GLU	-1	-0.845	-0.878	7.477	25.152	25.152	0.000	0.000	0.000	0.000
8	A	45	ILE	0	0.000	-0.004	8.981	-0.577	-0.577	0.000	0.000	0.000	0.000
9	A	46	LEU	0	-0.027	-0.010	11.521	-0.814	-0.814	0.000	0.000	0.000	0.000
10	A	47	ARG	1	0.841	0.914	13.939	-16.047	-16.047	0.000	0.000	0.000	0.000
11	A	48	LEU	0	-0.052	-0.019	9.617	-0.655	-0.655	0.000	0.000	0.000	0.000
12	A	49	TYR	0	0.012	0.005	13.014	-0.865	-0.865	0.000	0.000	0.000	0.000
13	A	50	ASN	0	-0.030	0.010	16.283	-0.777	-0.777	0.000	0.000	0.000	0.000
14	A	51	GLN	0	-0.062	-0.042	18.351	-0.865	-0.865	0.000	0.000	0.000	0.000
15	A	52	PRO	0	0.005	0.020	18.674	0.699	0.699	0.000	0.000	0.000	0.000
16	A	53	ILE	0	0.010	0.013	16.148	0.304	0.304	0.000	0.000	0.000	0.000
17	A	54	ASN	0	-0.006	-0.009	18.796	-0.811	-0.811	0.000	0.000	0.000	0.000
18	A	55	GLU	-1	-0.717	-0.847	20.907	11.412	11.412	0.000	0.000	0.000	0.000
19	A	56	GLU	-1	-0.797	-0.860	20.809	13.491	13.491	0.000	0.000	0.000	0.000
20	A	57	GLN	0	0.062	0.017	16.385	0.012	0.012	0.000	0.000	0.000	0.000
21	A	58	ALA	0	0.052	0.041	18.016	0.760	0.760	0.000	0.000	0.000	0.000
22	A	59	TRP	0	0.020	0.012	20.223	0.419	0.419	0.000	0.000	0.000	0.000
23	A	60	ALA	0	-0.009	-0.022	16.802	0.175	0.175	0.000	0.000	0.000	0.000
24	A	61	VAL	0	0.028	0.008	14.549	0.458	0.458	0.000	0.000	0.000	0.000
25	A	62	CYS	0	0.003	0.007	16.798	0.216	0.216	0.000	0.000	0.000	0.000
26	A	63	TYR	0	0.012	0.017	18.495	-0.595	-0.595	0.000	0.000	0.000	0.000
27	A	64	GLN	0	-0.031	-0.047	13.345	-1.349	-1.349	0.000	0.000	0.000	0.000
28	A	65	CYS	0	0.025	0.031	15.682	0.400	0.400	0.000	0.000	0.000	0.000
29	A	66	CYS	0	-0.016	-0.006	16.661	-0.351	-0.351	0.000	0.000	0.000	0.000
30	A	67	GLY	0	-0.013	-0.016	18.048	-0.379	-0.379	0.000	0.000	0.000	0.000
31	A	68	SER	0	-0.036	-0.036	13.693	0.262	0.262	0.000	0.000	0.000	0.000
32	A	69	LEU	0	-0.004	-0.002	16.056	-0.262	-0.262	0.000	0.000	0.000	0.000
33	A	70	ARG	1	0.814	0.886	18.933	-13.767	-13.767	0.000	0.000	0.000	0.000
34	A	71	ALA	0	-0.069	-0.049	17.171	-0.743	-0.743	0.000	0.000	0.000	0.000
35	A	72	ALA	0	0.046	0.038	17.168	0.167	0.167	0.000	0.000	0.000	0.000
36	A	73	ALA	0	0.041	0.020	18.946	-0.499	-0.499	0.000	0.000	0.000	0.000
37	A	74	ARG	1	0.897	0.945	20.066	-15.068	-15.068	0.000	0.000	0.000	0.000
38	A	75	ARG	1	0.919	0.954	19.015	-14.663	-14.663	0.000	0.000	0.000	0.000
39	A	76	ARG	1	0.887	0.951	22.014	-11.085	-11.085	0.000	0.000	0.000	0.000
40	A	77	GLN	0	0.061	0.040	17.419	-0.717	-0.717	0.000	0.000	0.000	0.000
41	A	78	PRO	0	-0.013	-0.003	20.874	-0.312	-0.312	0.000	0.000	0.000	0.000
42	A	79	ARG	1	0.895	0.953	21.203	-10.945	-10.945	0.000	0.000	0.000	0.000
43	A	80	HIS	0	0.039	0.026	18.858	-0.541	-0.541	0.000	0.000	0.000	0.000
44	A	81	ARG	1	0.880	0.904	21.398	-10.717	-10.717	0.000	0.000	0.000	0.000
45	A	82	VAL	0	-0.012	-0.010	18.464	0.592	0.592	0.000	0.000	0.000	0.000
46	A	83	ARG	1	0.856	0.915	20.343	-12.480	-12.480	0.000	0.000	0.000	0.000
47	A	84	SER	0	0.067	0.023	18.243	-0.262	-0.262	0.000	0.000	0.000	0.000
48	A	85	ALA	0	0.039	0.015	15.887	0.546	0.546	0.000	0.000	0.000	0.000
49	A	86	ALA	0	0.042	0.024	13.465	1.067	1.067	0.000	0.000	0.000	0.000
50	A	87	GLN	0	-0.076	-0.061	12.442	0.777	0.777	0.000	0.000	0.000	0.000
51	A	88	ILE	0	0.054	0.034	13.005	0.680	0.680	0.000	0.000	0.000	0.000
52	A	89	ARG	1	0.946	0.975	7.908	-22.991	-22.991	0.000	0.000	0.000	0.000
53	A	90	VAL	0	0.035	0.019	8.440	-0.738	-0.738	0.000	0.000	0.000	0.000
54	A	91	TRP	0	-0.034	-0.017	3.392	0.418	1.723	0.040	-0.560	-0.784	0.004
55	A	92	ARG	1	0.880	0.923	1.725	-137.983	-146.205	30.444	-12.921	-9.301	0.137
56	A	93	ASP	-1	-0.905	-0.977	5.110	31.106	31.252	-0.001	-0.004	-0.141	0.000
57	A	94	GLY	0	0.029	0.020	7.644	-4.776	-4.776	0.000	0.000	0.000	0.000
58	A	95	ALA	0	0.006	0.022	8.822	-3.730	-3.730	0.000	0.000	0.000	0.000
59	A	96	VAL	0	0.029	-0.001	10.216	0.885	0.885	0.000	0.000	0.000	0.000
60	A	97	THR	0	-0.020	0.015	10.401	-0.735	-0.735	0.000	0.000	0.000	0.000
61	A	98	LEU	0	0.003	0.010	12.166	0.609	0.609	0.000	0.000	0.000	0.000
62	A	99	ALA	0	-0.063	-0.025	11.892	0.308	0.308	0.000	0.000	0.000	0.000
63	A	100	PRO	0	0.021	0.012	13.780	-0.954	-0.954	0.000	0.000	0.000	0.000
64	A	101	ALA	0	0.001	0.002	16.093	0.571	0.571	0.000	0.000	0.000	0.000
65	A	102	ALA	0	0.002	-0.003	18.520	0.212	0.212	0.000	0.000	0.000	0.000
66	A	103	ASP	-1	-0.876	-0.911	19.401	12.145	12.145	0.000	0.000	0.000	0.000
67	A	119	GLN	0	0.020	0.013	29.951	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	120	CYS	0	-0.042	-0.035	26.865	0.124	0.124	0.000	0.000	0.000	0.000
69	A	121	MET	0	-0.043	-0.014	28.283	0.183	0.183	0.000	0.000	0.000	0.000
70	A	122	GLU	-1	-0.830	-0.944	25.886	12.013	12.013	0.000	0.000	0.000	0.000
71	A	123	THR	0	0.039	0.000	26.806	0.389	0.389	0.000	0.000	0.000	0.000
72	A	124	GLU	-1	-0.702	-0.812	28.064	10.199	10.199	0.000	0.000	0.000	0.000
73	A	125	VAL	0	-0.046	-0.007	21.706	0.224	0.224	0.000	0.000	0.000	0.000
74	A	126	ILE	0	-0.021	-0.005	23.920	0.412	0.412	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.856	-0.903	25.162	10.630	10.630	0.000	0.000	0.000	0.000
76	A	128	SER	0	-0.056	-0.034	23.998	0.333	0.333	0.000	0.000	0.000	0.000
77	A	129	LEU	0	-0.004	-0.027	18.803	0.448	0.448	0.000	0.000	0.000	0.000
78	A	130	GLY	0	0.017	0.005	22.065	0.267	0.267	0.000	0.000	0.000	0.000
79	A	131	ILE	0	0.038	0.026	24.481	0.025	0.025	0.000	0.000	0.000	0.000
80	A	132	ILE	0	-0.064	-0.014	18.048	0.109	0.109	0.000	0.000	0.000	0.000
81	A	133	ILE	0	-0.011	-0.007	18.739	0.311	0.311	0.000	0.000	0.000	0.000
82	A	134	TYR	0	0.020	0.008	21.219	0.319	0.319	0.000	0.000	0.000	0.000
83	A	135	LYS	1	0.972	0.960	22.070	-11.264	-11.264	0.000	0.000	0.000	0.000
84	A	136	ALA	0	-0.025	-0.017	18.172	0.050	0.050	0.000	0.000	0.000	0.000
85	A	137	LEU	0	-0.093	-0.047	20.018	0.160	0.160	0.000	0.000	0.000	0.000
86	A	138	ASP	-1	-0.875	-0.938	22.455	10.482	10.482	0.000	0.000	0.000	0.000
87	A	139	TYR	0	-0.066	-0.026	18.727	-0.106	-0.106	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.009	0.003	22.360	-0.066	-0.066	0.000	0.000	0.000	0.000
89	A	141	LEU	0	-0.005	0.032	24.676	-0.330	-0.330	0.000	0.000	0.000	0.000
90	A	142	LYS	1	0.716	0.829	28.005	-9.600	-9.600	0.000	0.000	0.000	0.000
91	A	143	GLU	-1	-0.911	-0.957	30.850	8.571	8.571	0.000	0.000	0.000	0.000
92	A	144	ASN	0	-0.086	-0.049	33.169	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	145	GLU	-1	-0.852	-0.904	30.986	9.006	9.006	0.000	0.000	0.000	0.000
94	A	146	GLU	-1	-0.816	-0.905	30.865	9.258	9.258	0.000	0.000	0.000	0.000
95	A	147	ARG	1	0.820	0.897	22.926	-11.898	-11.898	0.000	0.000	0.000	0.000
96	A	148	GLU	-1	-0.929	-0.961	30.059	8.537	8.537	0.000	0.000	0.000	0.000
97	A	149	LEU	0	-0.042	-0.016	26.679	0.433	0.433	0.000	0.000	0.000	0.000
98	A	150	SER	0	-0.050	-0.058	28.981	-0.385	-0.385	0.000	0.000	0.000	0.000
99	A	151	PRO	0	0.093	0.032	30.897	0.226	0.226	0.000	0.000	0.000	0.000
100	A	152	PRO	0	-0.052	-0.029	30.820	0.036	0.036	0.000	0.000	0.000	0.000
101	A	153	LEU	0	-0.025	-0.022	24.999	0.273	0.273	0.000	0.000	0.000	0.000
102	A	154	GLU	-1	-0.868	-0.926	28.984	9.313	9.313	0.000	0.000	0.000	0.000
103	A	155	GLN	0	0.006	0.004	30.936	0.171	0.171	0.000	0.000	0.000	0.000
104	A	156	LEU	0	-0.025	-0.012	25.152	0.012	0.012	0.000	0.000	0.000	0.000
105	A	157	ILE	0	-0.016	-0.025	24.654	0.161	0.161	0.000	0.000	0.000	0.000
106	A	158	ASP	-1	-0.814	-0.903	28.316	9.310	9.310	0.000	0.000	0.000	0.000
107	A	159	HIS	0	-0.087	-0.047	31.370	-0.170	-0.170	0.000	0.000	0.000	0.000
108	A	160	MET	0	-0.151	-0.089	23.265	0.078	0.078	0.000	0.000	0.000	0.000
109	A	161	ALA	0	0.015	-0.008	28.356	0.087	0.087	0.000	0.000	0.000	0.000
110	A	162	ASN	0	-0.140	-0.041	30.081	-0.290	-0.290	0.000	0.000	0.000	0.000
111	A	163	THR	0	-0.005	-0.012	33.201	-0.171	-0.171	0.000	0.000	0.000	0.000
112	A	164	VAL	0	0.010	0.010	35.025	0.051	0.051	0.000	0.000	0.000	0.000
113	A	165	GLU	-1	-0.982	-0.975	37.750	7.134	7.134	0.000	0.000	0.000	0.000
114	A	192	ALA	0	0.049	0.025	35.684	-0.116	-0.116	0.000	0.000	0.000	0.000
115	A	193	ILE	0	-0.025	-0.029	29.044	0.178	0.178	0.000	0.000	0.000	0.000
116	A	194	ARG	1	0.848	0.903	31.189	-9.251	-9.251	0.000	0.000	0.000	0.000
117	A	195	SER	0	-0.033	-0.044	28.152	0.070	0.070	0.000	0.000	0.000	0.000
118	A	196	TYR	0	0.083	0.030	22.887	0.052	0.052	0.000	0.000	0.000	0.000
119	A	197	ARG	1	0.864	0.924	24.963	-10.454	-10.454	0.000	0.000	0.000	0.000
120	A	198	ASP	-1	-0.793	-0.850	26.209	10.221	10.221	0.000	0.000	0.000	0.000
121	A	199	VAL	0	0.107	0.052	24.112	-0.149	-0.149	0.000	0.000	0.000	0.000
122	A	200	MET	0	0.044	0.063	20.175	-0.049	-0.049	0.000	0.000	0.000	0.000
123	A	201	LYS	1	0.942	0.967	24.523	-9.956	-9.956	0.000	0.000	0.000	0.000
124	A	202	LEU	0	0.064	0.045	27.802	-0.221	-0.221	0.000	0.000	0.000	0.000
125	A	203	CYS	0	-0.019	-0.005	23.245	0.026	0.026	0.000	0.000	0.000	0.000
126	A	204	ALA	0	-0.037	-0.012	25.046	0.148	0.148	0.000	0.000	0.000	0.000
127	A	205	ALA	0	0.019	0.023	26.085	-0.147	-0.147	0.000	0.000	0.000	0.000
128	A	206	HIS	1	0.789	0.885	25.028	-12.192	-12.192	0.000	0.000	0.000	0.000
129	A	207	LEU	0	-0.017	0.006	23.559	0.111	0.111	0.000	0.000	0.000	0.000
130	A	208	PRO	0	-0.002	-0.004	27.987	-0.295	-0.295	0.000	0.000	0.000	0.000
131	A	209	THR	0	-0.005	-0.018	28.752	-0.557	-0.557	0.000	0.000	0.000	0.000
132	A	210	GLU	-1	-0.938	-0.960	27.884	10.902	10.902	0.000	0.000	0.000	0.000
133	A	211	SER	0	-0.057	-0.045	26.715	0.302	0.302	0.000	0.000	0.000	0.000
134	A	212	ASP	-1	-0.849	-0.906	24.481	12.591	12.591	0.000	0.000	0.000	0.000
135	A	213	ALA	0	0.023	0.008	22.474	0.764	0.764	0.000	0.000	0.000	0.000
136	A	214	PRO	0	-0.072	-0.041	19.192	0.732	0.732	0.000	0.000	0.000	0.000
137	A	215	ASN	0	-0.009	-0.002	17.635	1.768	1.768	0.000	0.000	0.000	0.000
138	A	216	HIS	0	-0.056	-0.022	18.106	1.238	1.238	0.000	0.000	0.000	0.000
139	A	217	TYR	0	0.046	-0.027	17.989	0.685	0.685	0.000	0.000	0.000	0.000
140	A	218	GLN	0	0.023	0.044	11.653	-0.062	-0.062	0.000	0.000	0.000	0.000
141	A	219	ALA	0	0.005	0.007	13.978	1.145	1.145	0.000	0.000	0.000	0.000
142	A	220	VAL	0	0.035	0.015	13.991	1.152	1.152	0.000	0.000	0.000	0.000
143	A	221	CYS	0	-0.038	-0.008	11.765	-0.082	-0.082	0.000	0.000	0.000	0.000
144	A	222	ARG	1	0.895	0.928	9.654	-24.222	-24.222	0.000	0.000	0.000	0.000
145	A	223	ALA	0	-0.043	-0.010	9.865	2.176	2.176	0.000	0.000	0.000	0.000
146	A	224	LEU	0	0.089	0.051	11.644	0.153	0.153	0.000	0.000	0.000	0.000
147	A	225	PHE	0	-0.045	0.005	2.658	1.755	2.509	0.393	-0.381	-0.766	-0.001
148	A	226	ALA	0	-0.022	-0.026	8.300	0.708	0.708	0.000	0.000	0.000	0.000
149	A	227	GLU	-1	-0.894	-0.961	9.491	18.364	18.364	0.000	0.000	0.000	0.000
150	A	228	THR	0	-0.012	-0.028	8.779	-1.500	-1.500	0.000	0.000	0.000	0.000
151	A	229	MET	0	-0.048	-0.030	4.715	1.797	1.909	0.000	-0.044	-0.068	0.000
152	A	230	GLU	-1	-0.981	-0.976	8.230	20.204	20.204	0.000	0.000	0.000	0.000
153	A	231	LEU	0	-0.017	0.001	11.810	-1.220	-1.220	0.000	0.000	0.000	0.000
154	A	232	HIS	1	0.807	0.917	9.551	-22.094	-22.094	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:ASP)