FMO DATABASE

FMODB ID: 9G1L2

Calculation Name: 3RBW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: B

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	-1537521.113383
FMO2-HF: Nuclear repulsion	1474343.771346
FMO2-HF: Total energy	-63177.342036
FMO2-MP2: Total energy	-63356.368904

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(B:38:ASP)

Summations of interaction energy for fragment #1(B: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.
-82.567	-86.778	31.164	-14.95	-12.001	0.141

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.814 / q_NPA : -0.894

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	B	40	LEU	0	0.003	0.025	3.873	-3.998	-2.089	-0.013	-1.019	-0.876	0.002
4	B	41	SER	0	-0.079	-0.080	5.866	-1.184	-1.184	0.000	0.000	0.000	0.000
5	B	42	LEU	0	0.035	0.004	9.357	-0.299	-0.299	0.000	0.000	0.000	0.000
6	B	43	GLU	-1	-0.844	-0.922	12.117	14.950	14.950	0.000	0.000	0.000	0.000
7	B	44	GLU	-1	-0.851	-0.882	7.558	24.937	24.937	0.000	0.000	0.000	0.000
8	B	45	ILE	0	0.006	0.001	9.009	-0.588	-0.588	0.000	0.000	0.000	0.000
9	B	46	LEU	0	-0.029	-0.010	11.535	-0.818	-0.818	0.000	0.000	0.000	0.000
10	B	47	ARG	1	0.831	0.907	13.901	-16.059	-16.059	0.000	0.000	0.000	0.000
11	B	48	LEU	0	-0.046	-0.013	9.621	-0.633	-0.633	0.000	0.000	0.000	0.000
12	B	49	TYR	0	0.018	-0.004	12.713	-1.021	-1.021	0.000	0.000	0.000	0.000
13	B	50	ASN	0	-0.030	0.012	16.298	-0.793	-0.793	0.000	0.000	0.000	0.000
14	B	51	GLN	0	-0.069	-0.047	18.366	-0.843	-0.843	0.000	0.000	0.000	0.000
15	B	52	PRO	0	0.005	0.019	18.693	0.691	0.691	0.000	0.000	0.000	0.000
16	B	53	ILE	0	0.014	0.018	16.210	0.271	0.271	0.000	0.000	0.000	0.000
17	B	54	ASN	0	-0.001	-0.009	18.849	-0.809	-0.809	0.000	0.000	0.000	0.000
18	B	55	GLU	-1	-0.727	-0.848	20.960	11.357	11.357	0.000	0.000	0.000	0.000
19	B	56	GLU	-1	-0.793	-0.861	20.816	13.478	13.478	0.000	0.000	0.000	0.000
20	B	57	GLN	0	0.061	0.019	16.361	-0.040	-0.040	0.000	0.000	0.000	0.000
21	B	58	ALA	0	0.064	0.044	18.084	0.726	0.726	0.000	0.000	0.000	0.000
22	B	59	TRP	0	0.015	0.011	20.322	0.351	0.351	0.000	0.000	0.000	0.000
23	B	60	ALA	0	-0.010	-0.020	16.867	0.199	0.199	0.000	0.000	0.000	0.000
24	B	61	VAL	0	0.021	0.001	14.610	0.458	0.458	0.000	0.000	0.000	0.000
25	B	62	CYS	0	-0.004	0.007	16.887	0.237	0.237	0.000	0.000	0.000	0.000
26	B	63	TYR	0	0.023	0.012	18.523	-0.551	-0.551	0.000	0.000	0.000	0.000
27	B	64	GLN	0	-0.026	-0.039	13.423	-1.324	-1.324	0.000	0.000	0.000	0.000
28	B	65	CYS	0	0.020	0.032	15.729	0.586	0.586	0.000	0.000	0.000	0.000
29	B	66	CYS	0	-0.029	-0.010	16.711	-0.383	-0.383	0.000	0.000	0.000	0.000
30	B	67	GLY	0	-0.005	-0.015	18.090	-0.368	-0.368	0.000	0.000	0.000	0.000
31	B	68	SER	0	-0.023	-0.029	13.681	0.226	0.226	0.000	0.000	0.000	0.000
32	B	69	LEU	0	-0.007	-0.003	16.041	-0.288	-0.288	0.000	0.000	0.000	0.000
33	B	70	ARG	1	0.825	0.888	18.962	-13.745	-13.745	0.000	0.000	0.000	0.000
34	B	71	ALA	0	-0.086	-0.055	17.183	-0.754	-0.754	0.000	0.000	0.000	0.000
35	B	72	ALA	0	0.046	0.038	17.186	0.156	0.156	0.000	0.000	0.000	0.000
36	B	73	ALA	0	0.046	0.022	18.988	-0.504	-0.504	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.897	0.948	20.109	-15.008	-15.008	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.914	0.953	19.017	-14.683	-14.683	0.000	0.000	0.000	0.000
39	B	76	ARG	1	0.885	0.946	22.027	-11.071	-11.071	0.000	0.000	0.000	0.000
40	B	77	GLN	0	0.055	0.040	17.423	-0.715	-0.715	0.000	0.000	0.000	0.000
41	B	78	PRO	0	-0.011	-0.004	20.878	-0.326	-0.326	0.000	0.000	0.000	0.000
42	B	79	ARG	1	0.893	0.952	21.231	-10.939	-10.939	0.000	0.000	0.000	0.000
43	B	80	HIS	0	0.045	0.027	18.897	-0.536	-0.536	0.000	0.000	0.000	0.000
44	B	81	ARG	1	0.872	0.900	21.440	-10.712	-10.712	0.000	0.000	0.000	0.000
45	B	82	VAL	0	-0.007	-0.005	18.558	0.568	0.568	0.000	0.000	0.000	0.000
46	B	83	ARG	1	0.848	0.912	20.465	-12.463	-12.463	0.000	0.000	0.000	0.000
47	B	84	SER	0	0.072	0.026	18.277	-0.263	-0.263	0.000	0.000	0.000	0.000
48	B	85	ALA	0	0.049	0.016	15.865	0.541	0.541	0.000	0.000	0.000	0.000
49	B	86	ALA	0	0.041	0.027	13.496	1.076	1.076	0.000	0.000	0.000	0.000
50	B	87	GLN	0	-0.079	-0.062	12.541	0.750	0.750	0.000	0.000	0.000	0.000
51	B	88	ILE	0	0.043	0.034	12.977	0.690	0.690	0.000	0.000	0.000	0.000
52	B	89	ARG	1	0.953	0.977	7.975	-23.031	-23.031	0.000	0.000	0.000	0.000
53	B	90	VAL	0	0.029	0.011	8.418	-0.729	-0.729	0.000	0.000	0.000	0.000
54	B	91	TRP	0	-0.043	-0.024	3.332	0.291	1.664	0.047	-0.598	-0.822	0.004
55	B	92	ARG	1	0.880	0.926	1.727	-137.231	-145.740	30.792	-12.916	-9.367	0.136
56	B	93	ASP	-1	-0.888	-0.975	5.076	30.524	30.669	-0.001	-0.004	-0.139	0.000
57	B	94	GLY	0	0.036	0.025	7.665	-4.739	-4.739	0.000	0.000	0.000	0.000
58	B	95	ALA	0	-0.007	0.019	8.837	-3.833	-3.833	0.000	0.000	0.000	0.000
59	B	96	VAL	0	0.037	0.008	9.994	1.222	1.222	0.000	0.000	0.000	0.000
60	B	97	THR	0	-0.028	0.007	10.463	-0.754	-0.754	0.000	0.000	0.000	0.000
61	B	98	LEU	0	0.002	0.012	12.133	0.664	0.664	0.000	0.000	0.000	0.000
62	B	99	ALA	0	-0.061	-0.025	11.874	0.262	0.262	0.000	0.000	0.000	0.000
63	B	100	PRO	0	0.024	0.010	13.788	-0.944	-0.944	0.000	0.000	0.000	0.000
64	B	101	ALA	0	-0.002	0.001	16.101	0.564	0.564	0.000	0.000	0.000	0.000
65	B	102	ALA	0	0.003	-0.007	18.512	0.233	0.233	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.874	-0.908	19.456	12.123	12.123	0.000	0.000	0.000	0.000
67	B	119	GLN	0	0.020	0.014	30.023	-0.022	-0.022	0.000	0.000	0.000	0.000
68	B	120	CYS	0	-0.040	-0.033	26.893	0.126	0.126	0.000	0.000	0.000	0.000
69	B	121	MET	0	-0.045	-0.015	28.330	0.180	0.180	0.000	0.000	0.000	0.000
70	B	122	GLU	-1	-0.835	-0.945	25.858	11.996	11.996	0.000	0.000	0.000	0.000
71	B	123	THR	0	0.043	0.002	26.873	0.381	0.381	0.000	0.000	0.000	0.000
72	B	124	GLU	-1	-0.694	-0.810	28.089	10.192	10.192	0.000	0.000	0.000	0.000
73	B	125	VAL	0	-0.064	-0.014	21.787	0.247	0.247	0.000	0.000	0.000	0.000
74	B	126	ILE	0	-0.015	-0.007	23.903	0.416	0.416	0.000	0.000	0.000	0.000
75	B	127	GLU	-1	-0.870	-0.911	25.070	10.666	10.666	0.000	0.000	0.000	0.000
76	B	128	SER	0	-0.045	-0.028	24.034	0.349	0.349	0.000	0.000	0.000	0.000
77	B	129	LEU	0	-0.013	-0.027	18.776	0.416	0.416	0.000	0.000	0.000	0.000
78	B	130	GLY	0	0.029	0.013	21.965	0.309	0.309	0.000	0.000	0.000	0.000
79	B	131	ILE	0	0.054	0.033	24.362	0.051	0.051	0.000	0.000	0.000	0.000
80	B	132	ILE	0	-0.078	-0.020	18.080	0.123	0.123	0.000	0.000	0.000	0.000
81	B	133	ILE	0	-0.004	-0.010	18.667	0.281	0.281	0.000	0.000	0.000	0.000
82	B	134	TYR	0	0.007	-0.002	21.235	0.300	0.300	0.000	0.000	0.000	0.000
83	B	135	LYS	1	0.978	0.961	22.093	-11.252	-11.252	0.000	0.000	0.000	0.000
84	B	136	ALA	0	-0.023	-0.010	18.157	0.039	0.039	0.000	0.000	0.000	0.000
85	B	137	LEU	0	-0.088	-0.040	20.023	0.194	0.194	0.000	0.000	0.000	0.000
86	B	138	ASP	-1	-0.887	-0.947	22.462	10.460	10.460	0.000	0.000	0.000	0.000
87	B	139	TYR	0	-0.057	-0.023	18.752	-0.126	-0.126	0.000	0.000	0.000	0.000
88	B	140	GLY	0	0.009	0.005	22.399	-0.069	-0.069	0.000	0.000	0.000	0.000
89	B	141	LEU	0	-0.002	0.033	24.705	-0.334	-0.334	0.000	0.000	0.000	0.000
90	B	142	LYS	1	0.714	0.827	28.024	-9.579	-9.579	0.000	0.000	0.000	0.000
91	B	143	GLU	-1	-0.911	-0.957	30.874	8.558	8.558	0.000	0.000	0.000	0.000
92	B	144	ASN	0	-0.088	-0.050	33.183	-0.015	-0.015	0.000	0.000	0.000	0.000
93	B	145	GLU	-1	-0.853	-0.904	31.005	8.988	8.988	0.000	0.000	0.000	0.000
94	B	146	GLU	-1	-0.817	-0.905	30.856	9.241	9.241	0.000	0.000	0.000	0.000
95	B	147	ARG	1	0.819	0.897	22.943	-11.892	-11.892	0.000	0.000	0.000	0.000
96	B	148	GLU	-1	-0.931	-0.964	30.070	8.522	8.522	0.000	0.000	0.000	0.000
97	B	149	LEU	0	-0.042	-0.014	26.733	0.401	0.401	0.000	0.000	0.000	0.000
98	B	150	SER	0	-0.043	-0.056	29.033	-0.384	-0.384	0.000	0.000	0.000	0.000
99	B	151	PRO	0	0.083	0.028	30.966	0.220	0.220	0.000	0.000	0.000	0.000
100	B	152	PRO	0	-0.055	-0.031	30.820	0.041	0.041	0.000	0.000	0.000	0.000
101	B	153	LEU	0	-0.016	-0.016	25.042	0.272	0.272	0.000	0.000	0.000	0.000
102	B	154	GLU	-1	-0.875	-0.932	29.003	9.321	9.321	0.000	0.000	0.000	0.000
103	B	155	GLN	0	0.031	0.015	30.967	0.147	0.147	0.000	0.000	0.000	0.000
104	B	156	LEU	0	-0.041	-0.019	25.195	0.025	0.025	0.000	0.000	0.000	0.000
105	B	157	ILE	0	-0.021	-0.027	24.642	0.159	0.159	0.000	0.000	0.000	0.000
106	B	158	ASP	-1	-0.816	-0.906	28.346	9.293	9.293	0.000	0.000	0.000	0.000
107	B	159	HIS	0	-0.081	-0.048	31.523	-0.146	-0.146	0.000	0.000	0.000	0.000
108	B	160	MET	0	-0.148	-0.088	23.281	0.094	0.094	0.000	0.000	0.000	0.000
109	B	161	ALA	0	0.007	-0.007	28.408	0.087	0.087	0.000	0.000	0.000	0.000
110	B	162	ASN	0	-0.134	-0.040	30.107	-0.300	-0.300	0.000	0.000	0.000	0.000
111	B	163	THR	0	-0.006	-0.008	33.202	-0.142	-0.142	0.000	0.000	0.000	0.000
112	B	164	VAL	0	0.006	0.009	35.055	0.062	0.062	0.000	0.000	0.000	0.000
113	B	165	GLU	-1	-0.978	-0.974	37.747	7.127	7.127	0.000	0.000	0.000	0.000
114	B	192	ALA	0	0.045	0.024	35.729	-0.118	-0.118	0.000	0.000	0.000	0.000
115	B	193	ILE	0	-0.023	-0.029	29.087	0.176	0.176	0.000	0.000	0.000	0.000
116	B	194	ARG	1	0.844	0.900	31.351	-9.275	-9.275	0.000	0.000	0.000	0.000
117	B	195	SER	0	-0.022	-0.034	28.211	0.054	0.054	0.000	0.000	0.000	0.000
118	B	196	TYR	0	0.077	0.031	22.946	0.034	0.034	0.000	0.000	0.000	0.000
119	B	197	ARG	1	0.853	0.918	25.017	-10.439	-10.439	0.000	0.000	0.000	0.000
120	B	198	ASP	-1	-0.789	-0.852	26.252	10.236	10.236	0.000	0.000	0.000	0.000
121	B	199	VAL	0	0.116	0.054	24.145	-0.154	-0.154	0.000	0.000	0.000	0.000
122	B	200	MET	0	0.027	0.059	20.250	-0.034	-0.034	0.000	0.000	0.000	0.000
123	B	201	LYS	1	0.954	0.970	24.607	-9.905	-9.905	0.000	0.000	0.000	0.000
124	B	202	LEU	0	0.059	0.037	27.902	-0.229	-0.229	0.000	0.000	0.000	0.000
125	B	203	CYS	0	-0.026	0.004	23.205	0.044	0.044	0.000	0.000	0.000	0.000
126	B	204	ALA	0	-0.022	-0.006	25.114	0.133	0.133	0.000	0.000	0.000	0.000
127	B	205	ALA	0	0.013	0.015	26.108	-0.138	-0.138	0.000	0.000	0.000	0.000
128	B	206	HIS	1	0.802	0.895	25.024	-12.175	-12.175	0.000	0.000	0.000	0.000
129	B	207	LEU	0	-0.026	0.002	23.561	0.091	0.091	0.000	0.000	0.000	0.000
130	B	208	PRO	0	0.003	-0.002	27.983	-0.293	-0.293	0.000	0.000	0.000	0.000
131	B	209	THR	0	-0.008	-0.019	28.813	-0.557	-0.557	0.000	0.000	0.000	0.000
132	B	210	GLU	-1	-0.936	-0.959	27.947	10.883	10.883	0.000	0.000	0.000	0.000
133	B	211	SER	0	-0.062	-0.047	26.764	0.303	0.303	0.000	0.000	0.000	0.000
134	B	212	ASP	-1	-0.844	-0.904	24.534	12.564	12.564	0.000	0.000	0.000	0.000
135	B	213	ALA	0	0.004	0.001	22.498	0.762	0.762	0.000	0.000	0.000	0.000
136	B	214	PRO	0	-0.064	-0.036	19.302	0.709	0.709	0.000	0.000	0.000	0.000
137	B	215	ASN	0	0.003	0.002	17.710	1.748	1.748	0.000	0.000	0.000	0.000
138	B	216	HIS	0	-0.063	-0.024	18.075	1.282	1.282	0.000	0.000	0.000	0.000
139	B	217	TYR	0	0.042	-0.032	18.012	0.646	0.646	0.000	0.000	0.000	0.000
140	B	218	GLN	0	0.035	0.050	11.644	-0.145	-0.145	0.000	0.000	0.000	0.000
141	B	219	ALA	0	-0.016	-0.001	13.953	1.142	1.142	0.000	0.000	0.000	0.000
142	B	220	VAL	0	0.036	0.016	14.082	1.014	1.014	0.000	0.000	0.000	0.000
143	B	221	CYS	0	-0.037	-0.010	11.798	-0.064	-0.064	0.000	0.000	0.000	0.000
144	B	222	ARG	1	0.892	0.926	9.678	-24.192	-24.192	0.000	0.000	0.000	0.000
145	B	223	ALA	0	-0.042	-0.010	9.867	2.124	2.124	0.000	0.000	0.000	0.000
146	B	224	LEU	0	0.083	0.047	11.651	0.274	0.274	0.000	0.000	0.000	0.000
147	B	225	PHE	0	-0.037	0.012	2.700	1.729	2.478	0.338	-0.360	-0.727	-0.001
148	B	226	ALA	0	-0.016	-0.020	8.486	0.416	0.416	0.000	0.000	0.000	0.000
149	B	227	GLU	-1	-0.872	-0.956	9.509	18.381	18.381	0.000	0.000	0.000	0.000
150	B	228	THR	0	-0.044	-0.041	8.808	-1.676	-1.676	0.000	0.000	0.000	0.000
151	B	229	MET	0	-0.075	-0.043	4.665	2.300	2.422	0.001	-0.053	-0.070	0.000
152	B	230	GLU	-1	-0.946	-0.960	8.218	20.259	20.259	0.000	0.000	0.000	0.000
153	B	231	LEU	0	-0.092	-0.018	11.575	-1.421	-1.421	0.000	0.000	0.000	0.000
154	B	232	HIS	0	-0.087	-0.043	9.000	0.769	0.769	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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