FMO DATABASE

FMODB ID: 53ZRZ

Calculation Name: 3RBW-D-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1486940.940782
FMO2-HF: Nuclear repulsion	1425028.530744
FMO2-HF: Total energy	-61912.410038
FMO2-MP2: Total energy	-62087.842827

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:36:ACE )

Summations of interaction energy for fragment #1(D:36:ACE )

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.
0.249	1.113	-0.004	-0.337	-0.522	0

Interaction energy analysis for fragmet #1(D:36:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.001

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].
3	D	38	ASP	-1	-0.849	-0.931	3.860	0.409	1.273	-0.004	-0.337	-0.522
4	D	39	ALA	0	-0.050	-0.020	6.683	0.369	0.369	0.000	0.000	0.000
5	D	40	LEU	0	0.054	0.030	9.475	-0.196	-0.196	0.000	0.000	0.000
6	D	41	SER	0	-0.082	-0.003	12.262	0.102	0.102	0.000	0.000	0.000
7	D	42	LEU	0	0.052	0.015	15.758	-0.004	-0.004	0.000	0.000	0.000
8	D	43	GLU	-1	-0.951	-0.986	18.206	-0.208	-0.208	0.000	0.000	0.000
9	D	44	GLU	-1	-0.876	-0.959	12.363	-0.669	-0.669	0.000	0.000	0.000
10	D	45	ILE	0	0.007	0.013	15.736	0.013	0.013	0.000	0.000	0.000
11	D	46	LEU	0	0.003	0.017	17.502	0.024	0.024	0.000	0.000	0.000
12	D	47	ARG	1	0.905	0.956	18.552	0.234	0.234	0.000	0.000	0.000
13	D	48	LEU	0	-0.024	0.000	13.898	0.020	0.020	0.000	0.000	0.000
14	D	49	TYR	0	0.035	0.011	17.885	0.017	0.017	0.000	0.000	0.000
15	D	50	ASN	0	-0.036	-0.008	20.900	0.010	0.010	0.000	0.000	0.000
16	D	51	GLN	0	-0.062	-0.037	23.547	0.017	0.017	0.000	0.000	0.000
17	D	52	PRO	0	-0.021	0.004	23.978	-0.014	-0.014	0.000	0.000	0.000
18	D	53	ILE	0	0.007	0.023	22.105	0.000	0.000	0.000	0.000	0.000
19	D	54	ASN	0	0.077	0.023	24.664	0.007	0.007	0.000	0.000	0.000
20	D	55	GLU	-1	-0.775	-0.896	26.745	-0.065	-0.065	0.000	0.000	0.000
21	D	56	GLU	-1	-0.862	-0.941	26.497	-0.062	-0.062	0.000	0.000	0.000
22	D	57	GLN	0	0.044	0.004	21.496	-0.004	-0.004	0.000	0.000	0.000
23	D	58	ALA	0	-0.004	0.003	24.128	-0.010	-0.010	0.000	0.000	0.000
24	D	59	TRP	0	0.000	0.005	26.584	-0.002	-0.002	0.000	0.000	0.000
25	D	60	ALA	0	-0.004	-0.009	22.881	-0.003	-0.003	0.000	0.000	0.000
26	D	61	VAL	0	0.040	0.010	20.478	-0.005	-0.005	0.000	0.000	0.000
27	D	62	CYS	0	0.027	0.013	22.812	-0.005	-0.005	0.000	0.000	0.000
28	D	63	TYR	0	0.017	0.000	24.377	0.007	0.007	0.000	0.000	0.000
29	D	64	GLN	0	-0.033	-0.033	19.447	0.011	0.011	0.000	0.000	0.000
30	D	65	CYS	0	-0.003	0.024	21.919	-0.008	-0.008	0.000	0.000	0.000
31	D	66	CYS	0	-0.056	-0.035	22.945	0.002	0.002	0.000	0.000	0.000
32	D	67	GLY	0	0.024	0.010	24.251	0.008	0.008	0.000	0.000	0.000
33	D	68	SER	0	-0.050	-0.052	20.345	0.007	0.007	0.000	0.000	0.000
34	D	69	LEU	0	-0.007	0.012	22.272	0.004	0.004	0.000	0.000	0.000
35	D	70	ARG	0	0.112	0.067	25.272	0.013	0.013	0.000	0.000	0.000
36	D	71	ALA	0	-0.068	-0.032	23.571	0.006	0.006	0.000	0.000	0.000
37	D	72	ALA	0	-0.010	-0.004	23.345	0.003	0.003	0.000	0.000	0.000
38	D	73	ALA	0	0.011	0.007	25.316	0.004	0.004	0.000	0.000	0.000
39	D	74	ARG	1	0.827	0.870	28.665	0.050	0.050	0.000	0.000	0.000
40	D	75	ARG	1	0.937	0.978	22.549	0.075	0.075	0.000	0.000	0.000
41	D	76	ARG	1	0.900	0.961	27.670	0.046	0.046	0.000	0.000	0.000
42	D	77	GLN	0	0.022	0.019	23.208	0.009	0.009	0.000	0.000	0.000
43	D	78	PRO	0	-0.014	-0.013	26.147	0.001	0.001	0.000	0.000	0.000
44	D	79	ARG	1	0.901	0.962	26.784	0.059	0.059	0.000	0.000	0.000
45	D	80	HIS	0	0.031	0.017	23.691	0.003	0.003	0.000	0.000	0.000
46	D	81	ARG	1	0.940	0.971	27.072	0.086	0.086	0.000	0.000	0.000
47	D	82	VAL	0	0.003	0.000	24.191	-0.010	-0.010	0.000	0.000	0.000
48	D	83	ARG	1	0.911	0.965	25.713	0.119	0.119	0.000	0.000	0.000
49	D	84	SER	0	0.096	0.033	23.489	0.006	0.006	0.000	0.000	0.000
50	D	85	ALA	0	0.057	0.030	21.663	-0.009	-0.009	0.000	0.000	0.000
51	D	86	ALA	0	0.071	0.042	18.973	-0.025	-0.025	0.000	0.000	0.000
52	D	87	GLN	0	-0.062	-0.056	17.950	-0.037	-0.037	0.000	0.000	0.000
53	D	88	ILE	0	0.029	0.029	19.079	-0.005	-0.005	0.000	0.000	0.000
54	D	89	ARG	1	0.827	0.908	13.919	0.361	0.361	0.000	0.000	0.000
55	D	90	VAL	0	0.054	0.013	14.820	0.043	0.043	0.000	0.000	0.000
56	D	91	TRP	0	-0.010	-0.054	9.506	-0.105	-0.105	0.000	0.000	0.000
57	D	92	ARG	1	0.951	0.984	5.728	0.470	0.470	0.000	0.000	0.000
58	D	93	ASP	-1	-0.924	-0.969	10.534	-0.073	-0.073	0.000	0.000	0.000
59	D	94	GLY	0	0.042	0.018	13.532	0.031	0.031	0.000	0.000	0.000
60	D	95	ALA	0	-0.041	0.004	14.947	0.017	0.017	0.000	0.000	0.000
61	D	96	VAL	0	0.047	0.028	15.814	-0.040	-0.040	0.000	0.000	0.000
62	D	97	THR	0	0.004	0.049	15.936	0.012	0.012	0.000	0.000	0.000
63	D	98	LEU	0	0.002	-0.006	18.306	-0.016	-0.016	0.000	0.000	0.000
64	D	99	ALA	0	-0.037	-0.004	17.424	0.013	0.013	0.000	0.000	0.000
65	D	100	PRO	0	0.032	0.025	19.014	0.020	0.020	0.000	0.000	0.000
66	D	101	ALA	0	-0.015	-0.019	21.043	-0.017	-0.017	0.000	0.000	0.000
67	D	102	NME	0	0.017	0.021	22.321	-0.001	-0.001	0.000	0.000	0.000
68	D	118	ACE	0	-0.008	-0.018	32.868	-0.001	-0.001	0.000	0.000	0.000
69	D	119	GLN	0	0.011	-0.002	33.701	0.004	0.004	0.000	0.000	0.000
70	D	120	CYS	0	0.001	0.008	32.788	-0.004	-0.004	0.000	0.000	0.000
71	D	121	MET	0	-0.017	0.008	34.433	0.001	0.001	0.000	0.000	0.000
72	D	122	GLU	-1	-0.894	-0.973	32.295	-0.064	-0.064	0.000	0.000	0.000
73	D	123	THR	0	0.053	0.007	33.195	-0.003	-0.003	0.000	0.000	0.000
74	D	124	GLU	-1	-0.852	-0.936	34.620	-0.068	-0.068	0.000	0.000	0.000
75	D	125	VAL	0	-0.068	-0.013	28.271	-0.005	-0.005	0.000	0.000	0.000
76	D	126	ILE	0	0.013	0.017	30.435	-0.006	-0.006	0.000	0.000	0.000
77	D	127	GLU	-1	-0.907	-0.934	31.468	-0.081	-0.081	0.000	0.000	0.000
78	D	128	SER	0	-0.020	-0.029	29.725	-0.006	-0.006	0.000	0.000	0.000
79	D	129	LEU	0	-0.026	-0.037	24.977	-0.007	-0.007	0.000	0.000	0.000
80	D	130	GLY	0	0.078	0.056	28.546	-0.004	-0.004	0.000	0.000	0.000
81	D	131	ILE	0	0.051	0.031	30.836	-0.004	-0.004	0.000	0.000	0.000
82	D	132	ILE	0	-0.095	-0.056	24.781	-0.004	-0.004	0.000	0.000	0.000
83	D	133	ILE	0	0.014	-0.003	25.099	-0.009	-0.009	0.000	0.000	0.000
84	D	134	TYR	0	0.070	0.044	27.801	-0.001	-0.001	0.000	0.000	0.000
85	D	135	LYS	1	0.941	0.966	28.256	0.111	0.111	0.000	0.000	0.000
86	D	136	ALA	0	-0.050	-0.017	24.644	-0.004	-0.004	0.000	0.000	0.000
87	D	137	LEU	0	-0.044	-0.034	26.313	-0.002	-0.002	0.000	0.000	0.000
88	D	138	ASP	-1	-0.911	-0.961	28.820	-0.080	-0.080	0.000	0.000	0.000
89	D	139	TYR	0	-0.034	0.006	24.226	-0.006	-0.006	0.000	0.000	0.000
90	D	140	GLY	0	-0.022	-0.030	28.446	0.004	0.004	0.000	0.000	0.000
91	D	141	LEU	0	-0.003	0.021	29.977	0.005	0.005	0.000	0.000	0.000
92	D	142	LYS	1	0.826	0.902	33.475	0.068	0.068	0.000	0.000	0.000
93	D	143	GLU	-1	-0.924	-0.959	36.289	-0.063	-0.063	0.000	0.000	0.000
94	D	144	ASN	0	-0.055	-0.042	38.826	-0.001	-0.001	0.000	0.000	0.000
95	D	145	GLU	-1	-0.923	-0.942	36.184	-0.060	-0.060	0.000	0.000	0.000
96	D	146	GLU	-1	-0.882	-0.932	37.139	-0.056	-0.056	0.000	0.000	0.000
97	D	147	ARG	1	0.798	0.886	28.634	0.085	0.085	0.000	0.000	0.000
98	D	148	GLU	-1	-0.927	-0.954	36.094	-0.043	-0.043	0.000	0.000	0.000
99	D	149	LEU	0	-0.036	-0.025	32.818	-0.003	-0.003	0.000	0.000	0.000
100	D	150	SER	0	0.014	0.001	35.130	0.004	0.004	0.000	0.000	0.000
101	D	151	PRO	0	0.069	0.015	37.898	-0.001	-0.001	0.000	0.000	0.000
102	D	152	PRO	0	-0.057	-0.033	36.415	-0.001	-0.001	0.000	0.000	0.000
103	D	153	LEU	0	-0.016	-0.019	31.250	-0.002	-0.002	0.000	0.000	0.000
104	D	154	GLU	-1	-0.899	-0.942	35.135	-0.051	-0.051	0.000	0.000	0.000
105	D	155	GLN	0	0.006	0.000	37.569	-0.001	-0.001	0.000	0.000	0.000
106	D	156	LEU	0	-0.046	-0.017	31.271	-0.001	-0.001	0.000	0.000	0.000
107	D	157	ILE	0	0.035	0.008	31.540	-0.004	-0.004	0.000	0.000	0.000
108	D	158	ASP	-1	-0.877	-0.928	35.034	-0.056	-0.056	0.000	0.000	0.000
109	D	159	HIS	0	-0.066	-0.045	37.331	0.003	0.003	0.000	0.000	0.000
110	D	160	MET	0	-0.133	-0.056	29.922	0.001	0.001	0.000	0.000	0.000
111	D	161	ALA	0	0.089	0.038	34.762	-0.005	-0.005	0.000	0.000	0.000
112	D	162	ASN	0	-0.093	-0.026	37.350	0.000	0.000	0.000	0.000	0.000
113	D	163	NME	0	-0.012	-0.006	40.488	0.003	0.003	0.000	0.000	0.000
114	D	191	ACE	0	0.063	0.015	42.747	0.000	0.000	0.000	0.000	0.000
115	D	192	ALA	0	-0.060	-0.038	41.449	0.000	0.000	0.000	0.000	0.000
116	D	193	ILE	0	-0.008	0.015	34.987	0.001	0.001	0.000	0.000	0.000
117	D	194	ARG	1	0.903	0.939	37.198	0.038	0.038	0.000	0.000	0.000
118	D	195	SER	0	-0.006	0.004	34.421	0.000	0.000	0.000	0.000	0.000
119	D	196	TYR	0	0.075	0.018	28.987	0.001	0.001	0.000	0.000	0.000
120	D	197	ARG	1	0.907	0.949	30.778	0.042	0.042	0.000	0.000	0.000
121	D	198	ASP	-1	-0.853	-0.913	32.595	-0.044	-0.044	0.000	0.000	0.000
122	D	199	VAL	0	0.098	0.043	30.211	0.002	0.002	0.000	0.000	0.000
123	D	200	MET	0	-0.046	-0.029	27.628	-0.001	-0.001	0.000	0.000	0.000
124	D	201	LYS	1	0.919	0.957	30.636	0.039	0.039	0.000	0.000	0.000
125	D	202	LEU	0	0.064	0.044	33.625	0.003	0.003	0.000	0.000	0.000
126	D	203	CYS	0	-0.039	-0.002	29.219	-0.001	-0.001	0.000	0.000	0.000
127	D	204	ALA	0	-0.029	-0.016	31.223	0.000	0.000	0.000	0.000	0.000
128	D	205	ALA	0	0.059	0.038	32.065	0.003	0.003	0.000	0.000	0.000
129	D	206	HIS	1	0.805	0.922	30.753	0.056	0.056	0.000	0.000	0.000
130	D	207	LEU	0	-0.017	0.000	29.529	-0.001	-0.001	0.000	0.000	0.000
131	D	208	PRO	0	0.002	-0.002	33.586	0.002	0.002	0.000	0.000	0.000
132	D	209	THR	0	-0.014	0.000	34.210	0.003	0.003	0.000	0.000	0.000
133	D	210	GLU	-1	-0.907	-0.950	33.660	-0.035	-0.035	0.000	0.000	0.000
134	D	211	SER	0	-0.038	-0.039	32.850	-0.002	-0.002	0.000	0.000	0.000
135	D	212	ASP	-1	-0.924	-0.961	29.077	-0.025	-0.025	0.000	0.000	0.000
136	D	213	ALA	0	0.079	0.038	28.022	-0.003	-0.003	0.000	0.000	0.000
137	D	214	PRO	0	-0.080	-0.035	25.109	-0.006	-0.006	0.000	0.000	0.000
138	D	215	ASN	0	-0.003	-0.019	23.460	-0.002	-0.002	0.000	0.000	0.000
139	D	216	HIS	0	0.007	0.018	23.399	0.001	0.001	0.000	0.000	0.000
140	D	217	TYR	0	0.037	-0.005	23.589	-0.007	-0.007	0.000	0.000	0.000
141	D	218	GLN	0	-0.021	-0.003	17.285	-0.002	-0.002	0.000	0.000	0.000
142	D	219	ALA	0	0.005	-0.007	18.880	-0.015	-0.015	0.000	0.000	0.000
143	D	220	VAL	0	0.004	0.024	19.638	-0.006	-0.006	0.000	0.000	0.000
144	D	221	CYS	0	-0.044	-0.013	17.846	-0.013	-0.013	0.000	0.000	0.000
145	D	222	ARG	1	0.921	0.961	14.358	0.027	0.027	0.000	0.000	0.000
146	D	223	ALA	0	-0.028	0.008	14.965	-0.009	-0.009	0.000	0.000	0.000
147	D	224	LEU	0	0.050	0.025	16.217	-0.014	-0.014	0.000	0.000	0.000
148	D	225	PHE	0	-0.056	-0.012	7.861	-0.059	-0.059	0.000	0.000	0.000
149	D	226	ALA	0	0.017	-0.007	12.233	-0.041	-0.041	0.000	0.000	0.000
150	D	227	GLU	-1	-0.912	-0.962	13.297	-0.110	-0.110	0.000	0.000	0.000
151	D	228	THR	0	0.002	-0.018	13.392	0.007	0.007	0.000	0.000	0.000
152	D	229	MET	0	-0.119	-0.065	8.348	-0.185	-0.185	0.000	0.000	0.000
153	D	230	GLU	-1	-0.984	-0.959	11.011	-0.049	-0.049	0.000	0.000	0.000
154	D	231	LEU	0	-0.078	-0.032	13.276	0.021	0.021	0.000	0.000	0.000
155	D	232	NME	0	-0.011	0.003	11.579	-0.064	-0.064	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:36:ACE )