FMO DATABASE

FMODB ID: M3QRZ

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	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1542268.937771
FMO2-HF: Nuclear repulsion	1479090.729626
FMO2-HF: Total energy	-63178.208145
FMO2-MP2: Total energy	-63357.156923

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.
-86.3	-89.601	30.749	-15.032	-12.415	0.139

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 : -0.811 / q_NPA : -0.887

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	0.025	0.029	3.752	-4.099	-1.903	-0.010	-1.226	-0.959	0.002
4	B	41	SER	0	-0.091	-0.084	6.074	-0.833	-0.833	0.000	0.000	0.000	0.000
5	B	42	LEU	0	0.038	0.010	9.778	-0.112	-0.112	0.000	0.000	0.000	0.000
6	B	43	GLU	-1	-0.797	-0.897	12.588	14.355	14.355	0.000	0.000	0.000	0.000
7	B	44	GLU	-1	-0.850	-0.887	7.873	24.031	24.031	0.000	0.000	0.000	0.000
8	B	45	ILE	0	0.006	0.004	9.081	-0.546	-0.546	0.000	0.000	0.000	0.000
9	B	46	LEU	0	-0.020	-0.002	11.719	-0.671	-0.671	0.000	0.000	0.000	0.000
10	B	47	ARG	1	0.838	0.914	14.159	-15.841	-15.841	0.000	0.000	0.000	0.000
11	B	48	LEU	0	-0.046	-0.019	9.644	-0.568	-0.568	0.000	0.000	0.000	0.000
12	B	49	TYR	0	0.004	-0.021	13.225	-0.949	-0.949	0.000	0.000	0.000	0.000
13	B	50	ASN	0	-0.052	-0.002	16.367	-0.697	-0.697	0.000	0.000	0.000	0.000
14	B	51	GLN	0	-0.051	-0.028	18.735	-0.970	-0.970	0.000	0.000	0.000	0.000
15	B	52	PRO	0	0.006	0.019	18.981	0.721	0.721	0.000	0.000	0.000	0.000
16	B	53	ILE	0	-0.014	0.004	16.330	0.232	0.232	0.000	0.000	0.000	0.000
17	B	54	ASN	0	0.055	0.017	19.176	-0.830	-0.830	0.000	0.000	0.000	0.000
18	B	55	GLU	-1	-0.747	-0.863	21.051	11.386	11.386	0.000	0.000	0.000	0.000
19	B	56	GLU	-1	-0.785	-0.853	20.969	13.331	13.331	0.000	0.000	0.000	0.000
20	B	57	GLN	0	0.058	0.016	16.518	0.030	0.030	0.000	0.000	0.000	0.000
21	B	58	ALA	0	0.043	0.030	18.003	0.723	0.723	0.000	0.000	0.000	0.000
22	B	59	TRP	0	0.019	0.002	20.342	0.297	0.297	0.000	0.000	0.000	0.000
23	B	60	ALA	0	-0.016	-0.012	16.894	0.150	0.150	0.000	0.000	0.000	0.000
24	B	61	VAL	0	0.026	0.006	14.512	0.700	0.700	0.000	0.000	0.000	0.000
25	B	62	CYS	0	0.002	0.012	16.845	0.215	0.215	0.000	0.000	0.000	0.000
26	B	63	TYR	0	0.018	0.010	17.992	-0.403	-0.403	0.000	0.000	0.000	0.000
27	B	64	GLN	0	0.001	-0.023	12.808	-1.329	-1.329	0.000	0.000	0.000	0.000
28	B	65	CYS	0	-0.015	0.012	15.424	0.582	0.582	0.000	0.000	0.000	0.000
29	B	66	CYS	0	-0.036	-0.014	16.361	-0.497	-0.497	0.000	0.000	0.000	0.000
30	B	67	GLY	0	0.013	-0.017	17.537	-0.521	-0.521	0.000	0.000	0.000	0.000
31	B	68	SER	0	-0.013	-0.032	13.256	-0.174	-0.174	0.000	0.000	0.000	0.000
32	B	69	LEU	0	-0.008	0.003	15.771	-0.387	-0.387	0.000	0.000	0.000	0.000
33	B	70	ARG	1	0.848	0.902	18.834	-13.806	-13.806	0.000	0.000	0.000	0.000
34	B	71	ALA	0	-0.074	-0.044	16.782	-0.670	-0.670	0.000	0.000	0.000	0.000
35	B	72	ALA	0	0.038	0.022	17.321	-0.281	-0.281	0.000	0.000	0.000	0.000
36	B	73	ALA	0	0.056	0.030	18.997	-0.579	-0.579	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.871	0.944	19.643	-15.182	-15.182	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.892	0.926	19.109	-14.370	-14.370	0.000	0.000	0.000	0.000
39	B	76	ARG	1	0.900	0.955	21.978	-10.991	-10.991	0.000	0.000	0.000	0.000
40	B	77	GLN	0	0.067	0.045	18.096	-0.570	-0.570	0.000	0.000	0.000	0.000
41	B	78	PRO	0	-0.025	-0.004	20.564	-0.428	-0.428	0.000	0.000	0.000	0.000
42	B	79	ARG	1	0.840	0.911	20.997	-10.839	-10.839	0.000	0.000	0.000	0.000
43	B	80	HIS	0	0.050	0.032	18.861	-0.579	-0.579	0.000	0.000	0.000	0.000
44	B	81	ARG	1	0.872	0.901	21.204	-10.808	-10.808	0.000	0.000	0.000	0.000
45	B	82	VAL	0	-0.025	-0.007	18.652	0.485	0.485	0.000	0.000	0.000	0.000
46	B	83	ARG	1	0.836	0.891	20.305	-12.365	-12.365	0.000	0.000	0.000	0.000
47	B	84	SER	0	0.015	-0.005	17.658	-0.325	-0.325	0.000	0.000	0.000	0.000
48	B	85	ALA	0	0.082	0.030	15.673	0.532	0.532	0.000	0.000	0.000	0.000
49	B	86	ALA	0	0.010	0.010	13.290	1.193	1.193	0.000	0.000	0.000	0.000
50	B	87	GLN	0	-0.069	-0.046	12.539	0.602	0.602	0.000	0.000	0.000	0.000
51	B	88	ILE	0	0.006	0.012	13.224	0.989	0.989	0.000	0.000	0.000	0.000
52	B	89	ARG	1	0.943	0.980	8.049	-22.955	-22.955	0.000	0.000	0.000	0.000
53	B	90	VAL	0	0.032	0.014	8.390	-1.032	-1.032	0.000	0.000	0.000	0.000
54	B	91	TRP	0	-0.023	-0.027	3.322	0.321	1.621	0.043	-0.545	-0.798	0.004
55	B	92	ARG	1	0.887	0.925	1.725	-137.973	-145.701	30.467	-12.918	-9.821	0.134
56	B	93	ASP	-1	-0.842	-0.927	5.056	30.425	30.572	-0.001	-0.005	-0.141	0.000
57	B	94	GLY	0	0.043	0.034	7.415	-4.885	-4.885	0.000	0.000	0.000	0.000
58	B	95	ALA	0	-0.023	-0.001	8.332	-3.789	-3.789	0.000	0.000	0.000	0.000
59	B	96	VAL	0	0.025	0.003	9.519	1.329	1.329	0.000	0.000	0.000	0.000
60	B	97	THR	0	-0.048	-0.008	10.123	-0.593	-0.593	0.000	0.000	0.000	0.000
61	B	98	LEU	0	0.009	0.015	12.078	0.504	0.504	0.000	0.000	0.000	0.000
62	B	99	ALA	0	-0.025	-0.002	11.594	-0.019	-0.019	0.000	0.000	0.000	0.000
63	B	100	PRO	0	0.008	-0.005	13.529	-1.006	-1.006	0.000	0.000	0.000	0.000
64	B	101	ALA	0	0.026	0.022	15.938	0.582	0.582	0.000	0.000	0.000	0.000
65	B	102	ALA	0	-0.004	0.000	18.399	0.214	0.214	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.871	-0.907	19.395	11.974	11.974	0.000	0.000	0.000	0.000
67	B	119	GLN	0	0.033	0.018	29.586	0.048	0.048	0.000	0.000	0.000	0.000
68	B	120	CYS	0	-0.033	-0.021	26.513	0.120	0.120	0.000	0.000	0.000	0.000
69	B	121	MET	0	-0.013	0.000	27.949	0.186	0.186	0.000	0.000	0.000	0.000
70	B	122	GLU	-1	-0.841	-0.934	25.657	12.053	12.053	0.000	0.000	0.000	0.000
71	B	123	THR	0	0.047	0.009	26.629	0.327	0.327	0.000	0.000	0.000	0.000
72	B	124	GLU	-1	-0.693	-0.816	28.014	10.149	10.149	0.000	0.000	0.000	0.000
73	B	125	VAL	0	-0.054	-0.006	21.703	0.274	0.274	0.000	0.000	0.000	0.000
74	B	126	ILE	0	-0.043	-0.018	23.491	0.485	0.485	0.000	0.000	0.000	0.000
75	B	127	GLU	-1	-0.863	-0.923	25.358	10.756	10.756	0.000	0.000	0.000	0.000
76	B	128	SER	0	-0.004	-0.021	24.024	0.351	0.351	0.000	0.000	0.000	0.000
77	B	129	LEU	0	-0.036	-0.029	18.970	0.369	0.369	0.000	0.000	0.000	0.000
78	B	130	GLY	0	0.037	0.019	22.200	0.283	0.283	0.000	0.000	0.000	0.000
79	B	131	ILE	0	0.038	0.020	24.768	0.014	0.014	0.000	0.000	0.000	0.000
80	B	132	ILE	0	-0.063	-0.031	18.626	0.067	0.067	0.000	0.000	0.000	0.000
81	B	133	ILE	0	-0.015	-0.021	18.477	0.434	0.434	0.000	0.000	0.000	0.000
82	B	134	TYR	0	-0.011	-0.018	21.429	0.331	0.331	0.000	0.000	0.000	0.000
83	B	135	LYS	1	0.970	0.969	22.138	-11.147	-11.147	0.000	0.000	0.000	0.000
84	B	136	ALA	0	-0.038	-0.018	18.299	0.088	0.088	0.000	0.000	0.000	0.000
85	B	137	LEU	0	-0.043	-0.017	20.096	0.240	0.240	0.000	0.000	0.000	0.000
86	B	138	ASP	-1	-0.849	-0.923	22.902	10.365	10.365	0.000	0.000	0.000	0.000
87	B	139	TYR	0	-0.066	-0.037	18.976	-0.115	-0.115	0.000	0.000	0.000	0.000
88	B	140	GLY	0	0.027	0.011	22.655	0.103	0.103	0.000	0.000	0.000	0.000
89	B	141	LEU	0	-0.032	0.019	25.066	-0.357	-0.357	0.000	0.000	0.000	0.000
90	B	142	LYS	1	0.731	0.843	28.435	-9.505	-9.505	0.000	0.000	0.000	0.000
91	B	143	GLU	-1	-0.888	-0.954	31.402	8.479	8.479	0.000	0.000	0.000	0.000
92	B	144	ASN	0	-0.128	-0.064	33.620	-0.099	-0.099	0.000	0.000	0.000	0.000
93	B	145	GLU	-1	-0.851	-0.911	31.421	8.890	8.890	0.000	0.000	0.000	0.000
94	B	146	GLU	-1	-0.817	-0.889	30.942	9.227	9.227	0.000	0.000	0.000	0.000
95	B	147	ARG	1	0.783	0.874	23.071	-11.911	-11.911	0.000	0.000	0.000	0.000
96	B	148	GLU	-1	-0.922	-0.949	30.083	8.629	8.629	0.000	0.000	0.000	0.000
97	B	149	LEU	0	-0.033	-0.014	26.810	0.442	0.442	0.000	0.000	0.000	0.000
98	B	150	SER	0	-0.034	-0.048	28.929	-0.361	-0.361	0.000	0.000	0.000	0.000
99	B	151	PRO	0	0.066	0.019	31.116	0.191	0.191	0.000	0.000	0.000	0.000
100	B	152	PRO	0	-0.060	-0.031	30.721	0.004	0.004	0.000	0.000	0.000	0.000
101	B	153	LEU	0	-0.011	-0.012	24.818	0.249	0.249	0.000	0.000	0.000	0.000
102	B	154	GLU	-1	-0.883	-0.940	28.809	9.341	9.341	0.000	0.000	0.000	0.000
103	B	155	GLN	0	0.048	0.023	30.997	0.113	0.113	0.000	0.000	0.000	0.000
104	B	156	LEU	0	-0.058	-0.025	25.407	0.029	0.029	0.000	0.000	0.000	0.000
105	B	157	ILE	0	-0.003	-0.017	24.580	0.192	0.192	0.000	0.000	0.000	0.000
106	B	158	ASP	-1	-0.836	-0.905	28.446	9.303	9.303	0.000	0.000	0.000	0.000
107	B	159	HIS	0	-0.052	-0.036	31.568	-0.138	-0.138	0.000	0.000	0.000	0.000
108	B	160	MET	0	-0.131	-0.068	23.505	0.063	0.063	0.000	0.000	0.000	0.000
109	B	161	ALA	0	-0.012	-0.007	28.670	0.035	0.035	0.000	0.000	0.000	0.000
110	B	162	ASN	0	-0.125	-0.057	30.242	-0.371	-0.371	0.000	0.000	0.000	0.000
111	B	163	THR	0	-0.014	-0.007	33.300	-0.279	-0.279	0.000	0.000	0.000	0.000
112	B	164	VAL	0	0.001	0.001	35.188	0.052	0.052	0.000	0.000	0.000	0.000
113	B	165	GLU	-1	-0.990	-0.983	37.739	7.077	7.077	0.000	0.000	0.000	0.000
114	B	192	ALA	0	0.063	0.034	35.117	-0.116	-0.116	0.000	0.000	0.000	0.000
115	B	193	ILE	0	-0.049	-0.031	28.701	0.186	0.186	0.000	0.000	0.000	0.000
116	B	194	ARG	1	0.829	0.882	31.063	-9.583	-9.583	0.000	0.000	0.000	0.000
117	B	195	SER	0	-0.031	-0.024	27.940	0.030	0.030	0.000	0.000	0.000	0.000
118	B	196	TYR	0	0.087	0.022	22.460	0.003	0.003	0.000	0.000	0.000	0.000
119	B	197	ARG	1	0.836	0.906	24.323	-10.205	-10.205	0.000	0.000	0.000	0.000
120	B	198	ASP	-1	-0.738	-0.826	25.926	10.292	10.292	0.000	0.000	0.000	0.000
121	B	199	VAL	0	0.099	0.051	23.841	-0.157	-0.157	0.000	0.000	0.000	0.000
122	B	200	MET	0	0.031	0.072	19.702	-0.071	-0.071	0.000	0.000	0.000	0.000
123	B	201	LYS	1	0.912	0.968	23.953	-10.015	-10.015	0.000	0.000	0.000	0.000
124	B	202	LEU	0	0.050	0.023	27.295	-0.146	-0.146	0.000	0.000	0.000	0.000
125	B	203	CYS	0	-0.012	0.006	23.058	0.060	0.060	0.000	0.000	0.000	0.000
126	B	204	ALA	0	-0.033	-0.006	24.893	0.149	0.149	0.000	0.000	0.000	0.000
127	B	205	ALA	0	-0.002	-0.008	25.741	-0.077	-0.077	0.000	0.000	0.000	0.000
128	B	206	HIS	1	0.815	0.907	24.837	-12.248	-12.248	0.000	0.000	0.000	0.000
129	B	207	LEU	0	-0.022	0.000	23.431	-0.013	-0.013	0.000	0.000	0.000	0.000
130	B	208	PRO	0	-0.014	-0.012	28.022	-0.285	-0.285	0.000	0.000	0.000	0.000
131	B	209	THR	0	-0.002	-0.027	28.017	-0.496	-0.496	0.000	0.000	0.000	0.000
132	B	210	GLU	-1	-0.932	-0.962	27.252	10.943	10.943	0.000	0.000	0.000	0.000
133	B	211	SER	0	-0.046	-0.055	26.087	0.259	0.259	0.000	0.000	0.000	0.000
134	B	212	ASP	-1	-0.818	-0.873	23.754	12.673	12.673	0.000	0.000	0.000	0.000
135	B	213	ALA	0	0.002	0.010	21.760	0.784	0.784	0.000	0.000	0.000	0.000
136	B	214	PRO	0	-0.052	-0.027	18.521	0.720	0.720	0.000	0.000	0.000	0.000
137	B	215	ASN	0	-0.002	-0.003	17.097	1.668	1.668	0.000	0.000	0.000	0.000
138	B	216	HIS	0	-0.026	-0.022	17.400	1.340	1.340	0.000	0.000	0.000	0.000
139	B	217	TYR	0	0.021	-0.018	17.691	0.665	0.665	0.000	0.000	0.000	0.000
140	B	218	GLN	0	0.001	0.016	10.783	-0.530	-0.530	0.000	0.000	0.000	0.000
141	B	219	ALA	0	-0.016	-0.010	13.223	1.739	1.739	0.000	0.000	0.000	0.000
142	B	220	VAL	0	0.015	0.010	14.390	0.742	0.742	0.000	0.000	0.000	0.000
143	B	221	CYS	0	-0.061	-0.016	11.794	-0.081	-0.081	0.000	0.000	0.000	0.000
144	B	222	ARG	1	0.862	0.906	9.611	-24.700	-24.700	0.000	0.000	0.000	0.000
145	B	223	ALA	0	-0.039	-0.001	10.159	1.528	1.528	0.000	0.000	0.000	0.000
146	B	224	LEU	0	0.079	0.039	11.838	0.556	0.556	0.000	0.000	0.000	0.000
147	B	225	PHE	0	-0.024	0.001	2.754	1.485	2.176	0.250	-0.301	-0.641	-0.001
148	B	226	ALA	0	-0.007	-0.008	8.289	0.861	0.861	0.000	0.000	0.000	0.000
149	B	227	GLU	-1	-0.860	-0.944	9.531	18.173	18.173	0.000	0.000	0.000	0.000
150	B	228	THR	0	-0.034	-0.015	8.985	-1.826	-1.826	0.000	0.000	0.000	0.000
151	B	229	MET	0	-0.066	-0.037	4.817	2.103	2.196	0.000	-0.037	-0.055	0.000
152	B	230	GLU	-1	-0.948	-0.965	8.463	20.168	20.168	0.000	0.000	0.000	0.000
153	B	231	LEU	0	-0.072	-0.011	11.737	-1.470	-1.470	0.000	0.000	0.000	0.000
154	B	232	HIS	0	-0.105	-0.053	8.676	1.085	1.085	0.000	0.000	0.000	0.000

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