FMO DATABASE

FMODB ID: GN381

Calculation Name: 3RBW-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RBW

Chain ID: D

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1467122.588186
FMO2-HF: Nuclear repulsion	1405721.886937
FMO2-HF: Total energy	-61400.70125
FMO2-MP2: Total energy	-61574.487259

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(D:37:ARG)

Summations of interaction energy for fragment #1(D:37:ARG)

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.
-129.763	-130.568	27.458	-13.442	-13.212	-0.121

Interaction energy analysis for fragmet #1(D:37:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.900 / q_NPA : 0.943

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	D	39	ALA	0	-0.030	-0.013	2.689	2.431	7.471	0.054	-2.724	-2.370	0.003
4	D	40	LEU	0	0.018	0.020	2.406	-17.810	-17.342	3.803	-1.377	-2.894	-0.011
5	D	41	SER	0	-0.085	-0.038	4.799	11.460	11.539	-0.001	-0.006	-0.072	0.000
6	D	42	LEU	0	0.058	0.017	6.871	-1.859	-1.859	0.000	0.000	0.000	0.000
7	D	43	GLU	-1	-0.806	-0.900	8.274	-24.498	-24.498	0.000	0.000	0.000	0.000
8	D	44	GLU	-1	-0.811	-0.888	1.726	-120.314	-128.735	23.485	-8.698	-6.366	-0.109
9	D	45	ILE	0	0.010	0.009	5.795	0.983	0.983	0.000	0.000	0.000	0.000
10	D	46	LEU	0	-0.009	0.011	7.977	2.154	2.154	0.000	0.000	0.000	0.000
11	D	47	ARG	1	0.848	0.909	7.981	29.724	29.724	0.000	0.000	0.000	0.000
12	D	48	LEU	0	-0.027	-0.002	4.876	2.057	2.057	0.000	0.000	0.000	0.000
13	D	49	TYR	0	0.011	-0.010	9.197	2.751	2.751	0.000	0.000	0.000	0.000
14	D	50	ASN	0	-0.027	0.009	11.817	1.644	1.644	0.000	0.000	0.000	0.000
15	D	51	GLN	0	-0.065	-0.042	13.804	2.271	2.271	0.000	0.000	0.000	0.000
16	D	52	PRO	0	-0.018	0.012	14.532	-1.394	-1.394	0.000	0.000	0.000	0.000
17	D	53	ILE	0	0.015	0.024	13.765	-0.192	-0.192	0.000	0.000	0.000	0.000
18	D	54	ASN	0	0.069	0.019	16.269	1.437	1.437	0.000	0.000	0.000	0.000
19	D	55	GLU	-1	-0.732	-0.869	19.399	-12.467	-12.467	0.000	0.000	0.000	0.000
20	D	56	GLU	-1	-0.840	-0.922	21.413	-13.505	-13.505	0.000	0.000	0.000	0.000
21	D	57	GLN	0	0.029	-0.002	15.438	-0.216	-0.216	0.000	0.000	0.000	0.000
22	D	58	ALA	0	0.015	0.007	17.599	-0.742	-0.742	0.000	0.000	0.000	0.000
23	D	59	TRP	0	-0.009	0.000	19.370	-0.036	-0.036	0.000	0.000	0.000	0.000
24	D	60	ALA	0	-0.001	-0.006	17.996	-0.154	-0.154	0.000	0.000	0.000	0.000
25	D	61	VAL	0	0.033	0.003	14.220	-0.258	-0.258	0.000	0.000	0.000	0.000
26	D	62	CYS	0	0.044	0.027	16.817	-0.139	-0.139	0.000	0.000	0.000	0.000
27	D	63	TYR	0	-0.007	-0.005	19.702	0.770	0.770	0.000	0.000	0.000	0.000
28	D	64	GLN	0	-0.025	-0.032	15.920	1.187	1.187	0.000	0.000	0.000	0.000
29	D	65	CYS	0	0.004	0.023	17.123	-0.394	-0.394	0.000	0.000	0.000	0.000
30	D	66	CYS	0	-0.052	-0.024	18.041	0.430	0.430	0.000	0.000	0.000	0.000
31	D	67	GLY	0	0.014	0.002	20.622	0.659	0.659	0.000	0.000	0.000	0.000
32	D	68	SER	0	-0.025	-0.033	16.222	0.458	0.458	0.000	0.000	0.000	0.000
33	D	69	LEU	0	-0.003	0.013	18.623	0.360	0.360	0.000	0.000	0.000	0.000
34	D	70	ARG	0	0.106	0.067	21.219	1.068	1.068	0.000	0.000	0.000	0.000
35	D	71	ALA	0	-0.037	-0.017	20.721	0.473	0.473	0.000	0.000	0.000	0.000
36	D	72	ALA	0	0.023	0.013	20.320	0.127	0.127	0.000	0.000	0.000	0.000
37	D	73	ALA	0	0.019	0.007	22.450	0.364	0.364	0.000	0.000	0.000	0.000
38	D	74	ARG	1	0.819	0.875	25.828	11.314	11.314	0.000	0.000	0.000	0.000
39	D	75	ARG	1	0.864	0.938	20.225	14.280	14.280	0.000	0.000	0.000	0.000
40	D	76	ARG	1	0.899	0.957	25.467	10.094	10.094	0.000	0.000	0.000	0.000
41	D	77	GLN	0	0.033	0.029	20.298	0.471	0.471	0.000	0.000	0.000	0.000
42	D	78	PRO	0	-0.022	-0.009	22.345	0.155	0.155	0.000	0.000	0.000	0.000
43	D	79	ARG	1	0.879	0.933	22.605	10.796	10.796	0.000	0.000	0.000	0.000
44	D	80	HIS	0	0.010	0.011	18.936	0.147	0.147	0.000	0.000	0.000	0.000
45	D	81	ARG	1	0.839	0.895	20.936	12.144	12.144	0.000	0.000	0.000	0.000
46	D	82	VAL	0	0.005	-0.001	16.311	-0.707	-0.707	0.000	0.000	0.000	0.000
47	D	83	ARG	1	0.914	0.962	16.713	15.008	15.008	0.000	0.000	0.000	0.000
48	D	84	SER	0	0.066	0.011	12.860	0.584	0.584	0.000	0.000	0.000	0.000
49	D	85	ALA	0	0.048	0.026	12.341	-0.504	-0.504	0.000	0.000	0.000	0.000
50	D	86	ALA	0	0.044	0.031	9.125	-2.326	-2.326	0.000	0.000	0.000	0.000
51	D	87	GLN	0	-0.058	-0.052	9.150	-2.573	-2.573	0.000	0.000	0.000	0.000
52	D	88	ILE	0	0.039	0.032	11.850	0.287	0.287	0.000	0.000	0.000	0.000
53	D	89	ARG	1	0.833	0.912	7.608	31.040	31.040	0.000	0.000	0.000	0.000
54	D	90	VAL	0	0.049	0.013	8.658	3.238	3.238	0.000	0.000	0.000	0.000
55	D	91	TRP	0	-0.041	-0.055	6.859	-5.678	-5.678	0.000	0.000	0.000	0.000
56	D	92	ARG	1	0.908	0.930	3.070	41.585	42.256	0.012	-0.253	-0.430	0.000
57	D	93	ASP	-1	-0.916	-0.964	7.905	-21.421	-21.421	0.000	0.000	0.000	0.000
58	D	94	GLY	0	0.057	0.028	10.880	2.059	2.059	0.000	0.000	0.000	0.000
59	D	95	ALA	0	-0.037	0.005	11.829	1.477	1.477	0.000	0.000	0.000	0.000
60	D	96	VAL	0	0.035	0.019	11.476	-2.111	-2.111	0.000	0.000	0.000	0.000
61	D	97	THR	0	0.036	0.041	12.161	1.211	1.211	0.000	0.000	0.000	0.000
62	D	98	LEU	0	-0.014	-0.017	13.406	-1.185	-1.185	0.000	0.000	0.000	0.000
63	D	99	ALA	0	-0.032	-0.001	11.569	1.037	1.037	0.000	0.000	0.000	0.000
64	D	100	PRO	0	0.020	0.022	13.676	0.962	0.962	0.000	0.000	0.000	0.000
65	D	101	ALA	0	0.007	0.006	14.116	-1.164	-1.164	0.000	0.000	0.000	0.000
66	D	119	GLN	0	-0.012	-0.018	28.814	0.005	0.005	0.000	0.000	0.000	0.000
67	D	120	CYS	0	-0.029	-0.019	26.753	-0.267	-0.267	0.000	0.000	0.000	0.000
68	D	121	MET	0	-0.008	0.006	28.834	0.067	0.067	0.000	0.000	0.000	0.000
69	D	122	GLU	-1	-0.863	-0.949	27.481	-11.513	-11.513	0.000	0.000	0.000	0.000
70	D	123	THR	0	0.055	0.005	27.395	-0.356	-0.356	0.000	0.000	0.000	0.000
71	D	124	GLU	-1	-0.722	-0.837	26.937	-11.129	-11.129	0.000	0.000	0.000	0.000
72	D	125	VAL	0	-0.055	-0.011	21.816	-0.375	-0.375	0.000	0.000	0.000	0.000
73	D	126	ILE	0	0.004	0.001	23.177	-0.517	-0.517	0.000	0.000	0.000	0.000
74	D	127	GLU	-1	-0.895	-0.935	24.349	-12.459	-12.459	0.000	0.000	0.000	0.000
75	D	128	SER	0	-0.017	-0.013	21.489	-0.496	-0.496	0.000	0.000	0.000	0.000
76	D	129	LEU	0	-0.027	-0.034	18.111	-0.610	-0.610	0.000	0.000	0.000	0.000
77	D	130	GLY	0	0.073	0.057	20.461	-0.529	-0.529	0.000	0.000	0.000	0.000
78	D	131	ILE	0	0.037	0.025	21.609	-0.432	-0.432	0.000	0.000	0.000	0.000
79	D	132	ILE	0	-0.100	-0.052	15.741	-0.446	-0.446	0.000	0.000	0.000	0.000
80	D	133	ILE	0	0.013	-0.005	16.963	-0.936	-0.936	0.000	0.000	0.000	0.000
81	D	134	TYR	0	0.069	0.047	19.114	-0.319	-0.319	0.000	0.000	0.000	0.000
82	D	135	LYS	1	0.949	0.967	18.319	15.262	15.262	0.000	0.000	0.000	0.000
83	D	136	ALA	0	-0.059	-0.023	15.402	-0.511	-0.511	0.000	0.000	0.000	0.000
84	D	137	LEU	0	-0.047	-0.031	16.681	-0.508	-0.508	0.000	0.000	0.000	0.000
85	D	138	ASP	-1	-0.881	-0.944	19.512	-13.014	-13.014	0.000	0.000	0.000	0.000
86	D	139	TYR	0	-0.038	-0.014	13.863	-0.433	-0.433	0.000	0.000	0.000	0.000
87	D	140	GLY	0	-0.002	-0.011	18.205	0.226	0.226	0.000	0.000	0.000	0.000
88	D	141	LEU	0	-0.027	0.012	19.651	0.497	0.497	0.000	0.000	0.000	0.000
89	D	142	LYS	1	0.726	0.834	23.108	12.392	12.392	0.000	0.000	0.000	0.000
90	D	143	GLU	-1	-0.911	-0.957	25.723	-10.869	-10.869	0.000	0.000	0.000	0.000
91	D	144	ASN	0	-0.085	-0.052	28.184	0.035	0.035	0.000	0.000	0.000	0.000
92	D	145	GLU	-1	-0.851	-0.899	26.145	-11.351	-11.351	0.000	0.000	0.000	0.000
93	D	146	GLU	-1	-0.862	-0.919	27.189	-10.455	-10.455	0.000	0.000	0.000	0.000
94	D	147	ARG	1	0.786	0.875	19.790	14.523	14.523	0.000	0.000	0.000	0.000
95	D	148	GLU	-1	-0.922	-0.952	26.744	-9.579	-9.579	0.000	0.000	0.000	0.000
96	D	149	LEU	0	-0.054	-0.031	24.486	-0.407	-0.407	0.000	0.000	0.000	0.000
97	D	150	SER	0	-0.031	-0.035	27.997	0.499	0.499	0.000	0.000	0.000	0.000
98	D	151	PRO	0	0.096	0.031	30.416	-0.118	-0.118	0.000	0.000	0.000	0.000
99	D	152	PRO	0	-0.061	-0.027	29.978	0.000	0.000	0.000	0.000	0.000	0.000
100	D	153	LEU	0	-0.009	-0.013	23.651	-0.171	-0.171	0.000	0.000	0.000	0.000
101	D	154	GLU	-1	-0.905	-0.947	27.558	-10.002	-10.002	0.000	0.000	0.000	0.000
102	D	155	GLN	0	-0.023	-0.021	29.553	0.138	0.138	0.000	0.000	0.000	0.000
103	D	156	LEU	0	-0.027	-0.005	24.533	-0.005	-0.005	0.000	0.000	0.000	0.000
104	D	157	ILE	0	0.012	-0.004	23.327	-0.319	-0.319	0.000	0.000	0.000	0.000
105	D	158	ASP	-1	-0.866	-0.923	26.893	-10.326	-10.326	0.000	0.000	0.000	0.000
106	D	159	HIS	0	-0.052	-0.045	30.115	0.031	0.031	0.000	0.000	0.000	0.000
107	D	160	MET	0	-0.157	-0.067	22.866	0.030	0.030	0.000	0.000	0.000	0.000
108	D	161	ALA	0	0.092	0.050	26.812	-0.432	-0.432	0.000	0.000	0.000	0.000
109	D	162	ASN	0	-0.119	-0.050	29.096	0.460	0.460	0.000	0.000	0.000	0.000
110	D	192	ALA	0	0.002	-0.011	35.785	-0.053	-0.053	0.000	0.000	0.000	0.000
111	D	193	ILE	0	0.014	0.016	29.183	0.057	0.057	0.000	0.000	0.000	0.000
112	D	194	ARG	1	0.913	0.945	31.666	8.804	8.804	0.000	0.000	0.000	0.000
113	D	195	SER	0	-0.036	-0.020	29.978	-0.033	-0.033	0.000	0.000	0.000	0.000
114	D	196	TYR	0	0.092	0.026	24.189	0.010	0.010	0.000	0.000	0.000	0.000
115	D	197	ARG	1	0.874	0.926	26.376	9.725	9.725	0.000	0.000	0.000	0.000
116	D	198	ASP	-1	-0.825	-0.894	28.562	-9.837	-9.837	0.000	0.000	0.000	0.000
117	D	199	VAL	0	0.134	0.061	24.674	0.181	0.181	0.000	0.000	0.000	0.000
118	D	200	MET	0	-0.051	-0.012	23.219	-0.049	-0.049	0.000	0.000	0.000	0.000
119	D	201	LYS	1	0.932	0.962	26.254	9.678	9.678	0.000	0.000	0.000	0.000
120	D	202	LEU	0	0.054	0.038	28.623	0.254	0.254	0.000	0.000	0.000	0.000
121	D	203	CYS	0	-0.019	-0.002	24.463	-0.110	-0.110	0.000	0.000	0.000	0.000
122	D	204	ALA	0	-0.030	0.000	26.525	-0.172	-0.172	0.000	0.000	0.000	0.000
123	D	205	ALA	0	0.051	0.031	27.990	0.142	0.142	0.000	0.000	0.000	0.000
124	D	206	HIS	1	0.804	0.914	25.253	12.510	12.510	0.000	0.000	0.000	0.000
125	D	207	LEU	0	-0.026	0.000	25.623	-0.169	-0.169	0.000	0.000	0.000	0.000
126	D	208	PRO	0	0.009	0.000	29.824	0.284	0.284	0.000	0.000	0.000	0.000
127	D	209	THR	0	-0.013	-0.002	31.253	0.475	0.475	0.000	0.000	0.000	0.000
128	D	210	GLU	-1	-0.933	-0.962	30.320	-10.019	-10.019	0.000	0.000	0.000	0.000
129	D	211	SER	0	-0.053	-0.036	29.553	-0.233	-0.233	0.000	0.000	0.000	0.000
130	D	212	ASP	-1	-0.902	-0.957	26.765	-11.075	-11.075	0.000	0.000	0.000	0.000
131	D	213	ALA	0	0.064	0.036	24.805	-0.492	-0.492	0.000	0.000	0.000	0.000
132	D	214	PRO	0	-0.062	-0.035	22.083	-0.658	-0.658	0.000	0.000	0.000	0.000
133	D	215	ASN	0	0.007	-0.008	20.726	-1.042	-1.042	0.000	0.000	0.000	0.000
134	D	216	HIS	0	-0.005	0.004	20.882	-0.656	-0.656	0.000	0.000	0.000	0.000
135	D	217	TYR	0	0.034	-0.016	19.554	-0.728	-0.728	0.000	0.000	0.000	0.000
136	D	218	GLN	0	-0.013	0.013	15.093	-0.734	-0.734	0.000	0.000	0.000	0.000
137	D	219	ALA	0	0.010	-0.004	15.741	-1.433	-1.433	0.000	0.000	0.000	0.000
138	D	220	VAL	0	0.002	0.020	16.745	-0.743	-0.743	0.000	0.000	0.000	0.000
139	D	221	CYS	0	-0.049	-0.010	13.321	-0.924	-0.924	0.000	0.000	0.000	0.000
140	D	222	ARG	1	0.879	0.921	12.112	17.211	17.211	0.000	0.000	0.000	0.000
141	D	223	ALA	0	-0.032	0.005	12.181	-1.391	-1.391	0.000	0.000	0.000	0.000
142	D	224	LEU	0	0.062	0.032	11.197	-1.211	-1.211	0.000	0.000	0.000	0.000
143	D	225	PHE	0	-0.059	0.001	4.392	-3.515	-3.299	-0.001	-0.024	-0.192	0.000
144	D	226	ALA	0	0.020	-0.004	8.082	-3.135	-3.135	0.000	0.000	0.000	0.000
145	D	227	GLU	-1	-0.871	-0.940	10.063	-21.380	-21.380	0.000	0.000	0.000	0.000
146	D	228	THR	0	-0.046	-0.042	6.103	0.652	0.652	0.000	0.000	0.000	0.000
147	D	229	MET	0	-0.092	-0.053	3.126	-9.916	-8.774	0.106	-0.360	-0.888	-0.004
148	D	230	GLU	-1	-0.987	-0.960	6.851	-22.810	-22.810	0.000	0.000	0.000	0.000
149	D	231	LEU	0	-0.076	-0.026	6.841	-1.559	-1.559	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:37:ARG)