FMO DATABASE

FMODB ID: 1415Z

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	OptH
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	-1465531.661988
FMO2-HF: Nuclear repulsion	1404132.152611
FMO2-HF: Total energy	-61399.509377
FMO2-MP2: Total energy	-61573.32026

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.
-122.464	-129.093	30.597	-12.765	-11.203	-0.083

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 : 0.925 / q_NPA : 0.956

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	-0.056	-0.024	2.527	2.692	7.777	0.133	-2.777	-2.441	0.003
4	D	40	LEU	0	0.053	0.029	2.888	-17.104	-14.583	0.304	-1.082	-1.741	-0.009
5	D	41	SER	0	-0.084	-0.002	5.500	9.527	9.527	0.000	0.000	0.000	0.000
6	D	42	LEU	0	0.053	0.016	7.647	-1.637	-1.637	0.000	0.000	0.000	0.000
7	D	43	GLU	-1	-0.950	-0.986	8.086	-24.733	-24.733	0.000	0.000	0.000	0.000
8	D	44	GLU	-1	-0.878	-0.960	1.626	-103.035	-119.337	29.876	-8.240	-5.335	-0.072
9	D	45	ILE	0	0.012	0.015	6.334	0.468	0.468	0.000	0.000	0.000	0.000
10	D	46	LEU	0	0.001	0.016	9.058	1.809	1.809	0.000	0.000	0.000	0.000
11	D	47	ARG	1	0.903	0.956	8.004	29.051	29.051	0.000	0.000	0.000	0.000
12	D	48	LEU	0	-0.024	0.000	4.816	1.948	1.948	0.000	0.000	0.000	0.000
13	D	49	TYR	0	0.038	0.012	9.194	1.617	1.617	0.000	0.000	0.000	0.000
14	D	50	ASN	0	-0.040	-0.010	12.178	1.206	1.206	0.000	0.000	0.000	0.000
15	D	51	GLN	0	-0.061	-0.036	14.141	1.464	1.464	0.000	0.000	0.000	0.000
16	D	52	PRO	0	-0.020	0.005	15.381	-1.363	-1.363	0.000	0.000	0.000	0.000
17	D	53	ILE	0	0.007	0.023	15.001	-0.213	-0.213	0.000	0.000	0.000	0.000
18	D	54	ASN	0	0.076	0.022	17.440	0.900	0.900	0.000	0.000	0.000	0.000
19	D	55	GLU	-1	-0.775	-0.896	20.629	-12.448	-12.448	0.000	0.000	0.000	0.000
20	D	56	GLU	-1	-0.860	-0.941	21.805	-13.357	-13.357	0.000	0.000	0.000	0.000
21	D	57	GLN	0	0.039	0.002	15.965	-0.277	-0.277	0.000	0.000	0.000	0.000
22	D	58	ALA	0	0.000	0.005	18.447	-0.682	-0.682	0.000	0.000	0.000	0.000
23	D	59	TRP	0	-0.005	0.003	20.594	-0.019	-0.019	0.000	0.000	0.000	0.000
24	D	60	ALA	0	-0.003	-0.009	18.209	-0.144	-0.144	0.000	0.000	0.000	0.000
25	D	61	VAL	0	0.042	0.009	14.816	-0.243	-0.243	0.000	0.000	0.000	0.000
26	D	62	CYS	0	0.028	0.014	17.298	-0.065	-0.065	0.000	0.000	0.000	0.000
27	D	63	TYR	0	0.017	0.000	20.167	0.753	0.753	0.000	0.000	0.000	0.000
28	D	64	GLN	0	-0.025	-0.031	15.689	1.129	1.129	0.000	0.000	0.000	0.000
29	D	65	CYS	0	-0.011	0.020	17.044	-0.353	-0.353	0.000	0.000	0.000	0.000
30	D	66	CYS	0	-0.054	-0.034	17.947	0.419	0.419	0.000	0.000	0.000	0.000
31	D	67	GLY	0	0.024	0.010	20.495	0.652	0.652	0.000	0.000	0.000	0.000
32	D	68	SER	0	-0.050	-0.053	16.082	0.464	0.464	0.000	0.000	0.000	0.000
33	D	69	LEU	0	-0.005	0.013	18.484	0.384	0.384	0.000	0.000	0.000	0.000
34	D	70	ARG	0	0.106	0.066	21.089	1.050	1.050	0.000	0.000	0.000	0.000
35	D	71	ALA	0	-0.063	-0.031	20.566	0.479	0.479	0.000	0.000	0.000	0.000
36	D	72	ALA	0	-0.011	-0.004	20.177	0.102	0.102	0.000	0.000	0.000	0.000
37	D	73	ALA	0	0.012	0.007	22.291	0.362	0.362	0.000	0.000	0.000	0.000
38	D	74	ARG	1	0.825	0.869	25.677	11.165	11.165	0.000	0.000	0.000	0.000
39	D	75	ARG	1	0.936	0.978	20.472	13.985	13.985	0.000	0.000	0.000	0.000
40	D	76	ARG	1	0.900	0.961	25.456	9.965	9.965	0.000	0.000	0.000	0.000
41	D	77	GLN	0	0.020	0.018	20.617	0.609	0.609	0.000	0.000	0.000	0.000
42	D	78	PRO	0	-0.012	-0.010	22.778	0.128	0.128	0.000	0.000	0.000	0.000
43	D	79	ARG	1	0.913	0.967	22.675	10.566	10.566	0.000	0.000	0.000	0.000
44	D	80	HIS	0	0.025	0.015	18.966	0.350	0.350	0.000	0.000	0.000	0.000
45	D	81	ARG	1	0.940	0.971	21.136	12.212	12.212	0.000	0.000	0.000	0.000
46	D	82	VAL	0	0.001	-0.001	16.670	-0.645	-0.645	0.000	0.000	0.000	0.000
47	D	83	ARG	1	0.913	0.967	17.077	14.786	14.786	0.000	0.000	0.000	0.000
48	D	84	SER	0	0.096	0.034	13.983	0.486	0.486	0.000	0.000	0.000	0.000
49	D	85	ALA	0	0.060	0.032	12.707	-0.402	-0.402	0.000	0.000	0.000	0.000
50	D	86	ALA	0	0.069	0.040	9.717	-2.038	-2.038	0.000	0.000	0.000	0.000
51	D	87	GLN	0	-0.062	-0.060	9.550	-2.431	-2.431	0.000	0.000	0.000	0.000
52	D	88	ILE	0	0.030	0.029	12.187	0.256	0.256	0.000	0.000	0.000	0.000
53	D	89	ARG	1	0.831	0.908	7.902	29.789	29.789	0.000	0.000	0.000	0.000
54	D	90	VAL	0	0.051	0.013	8.776	2.954	2.954	0.000	0.000	0.000	0.000
55	D	91	TRP	0	-0.015	-0.055	6.893	-5.198	-5.198	0.000	0.000	0.000	0.000
56	D	92	ARG	1	0.955	0.984	3.485	42.157	42.551	0.002	-0.087	-0.309	0.000
57	D	93	ASP	-1	-0.923	-0.968	7.809	-21.516	-21.516	0.000	0.000	0.000	0.000
58	D	94	GLY	0	0.040	0.018	10.790	1.918	1.918	0.000	0.000	0.000	0.000
59	D	95	ALA	0	-0.039	0.004	11.541	1.523	1.523	0.000	0.000	0.000	0.000
60	D	96	VAL	0	0.041	0.026	11.368	-2.027	-2.027	0.000	0.000	0.000	0.000
61	D	97	THR	0	0.010	0.050	12.003	1.099	1.099	0.000	0.000	0.000	0.000
62	D	98	LEU	0	-0.002	-0.008	13.304	-1.080	-1.080	0.000	0.000	0.000	0.000
63	D	99	ALA	0	-0.034	-0.002	11.594	1.005	1.005	0.000	0.000	0.000	0.000
64	D	100	PRO	0	0.027	0.025	13.727	0.940	0.940	0.000	0.000	0.000	0.000
65	D	101	ALA	0	0.008	0.005	14.207	-1.063	-1.063	0.000	0.000	0.000	0.000
66	D	119	GLN	0	-0.005	-0.013	28.881	-0.006	-0.006	0.000	0.000	0.000	0.000
67	D	120	CYS	0	0.003	-0.001	26.944	-0.237	-0.237	0.000	0.000	0.000	0.000
68	D	121	MET	0	-0.017	0.007	29.031	0.041	0.041	0.000	0.000	0.000	0.000
69	D	122	GLU	-1	-0.892	-0.972	27.714	-11.195	-11.195	0.000	0.000	0.000	0.000
70	D	123	THR	0	0.052	0.006	27.699	-0.340	-0.340	0.000	0.000	0.000	0.000
71	D	124	GLU	-1	-0.856	-0.938	27.539	-10.789	-10.789	0.000	0.000	0.000	0.000
72	D	125	VAL	0	-0.065	-0.011	22.204	-0.387	-0.387	0.000	0.000	0.000	0.000
73	D	126	ILE	0	0.010	0.015	23.596	-0.520	-0.520	0.000	0.000	0.000	0.000
74	D	127	GLU	-1	-0.912	-0.935	24.836	-12.193	-12.193	0.000	0.000	0.000	0.000
75	D	128	SER	0	-0.014	-0.027	21.824	-0.485	-0.485	0.000	0.000	0.000	0.000
76	D	129	LEU	0	-0.028	-0.038	18.545	-0.612	-0.612	0.000	0.000	0.000	0.000
77	D	130	GLY	0	0.077	0.058	21.112	-0.520	-0.520	0.000	0.000	0.000	0.000
78	D	131	ILE	0	0.052	0.032	21.768	-0.420	-0.420	0.000	0.000	0.000	0.000
79	D	132	ILE	0	-0.095	-0.057	16.353	-0.447	-0.447	0.000	0.000	0.000	0.000
80	D	133	ILE	0	0.009	-0.004	18.083	-0.938	-0.938	0.000	0.000	0.000	0.000
81	D	134	TYR	0	0.075	0.046	19.955	-0.271	-0.271	0.000	0.000	0.000	0.000
82	D	135	LYS	1	0.941	0.966	18.512	15.154	15.154	0.000	0.000	0.000	0.000
83	D	136	ALA	0	-0.051	-0.018	16.334	-0.515	-0.515	0.000	0.000	0.000	0.000
84	D	137	LEU	0	-0.043	-0.033	17.454	-0.526	-0.526	0.000	0.000	0.000	0.000
85	D	138	ASP	-1	-0.909	-0.960	20.407	-13.159	-13.159	0.000	0.000	0.000	0.000
86	D	139	TYR	0	-0.037	0.004	13.800	-0.370	-0.370	0.000	0.000	0.000	0.000
87	D	140	GLY	0	-0.021	-0.030	18.764	0.176	0.176	0.000	0.000	0.000	0.000
88	D	141	LEU	0	-0.001	0.021	20.055	0.392	0.392	0.000	0.000	0.000	0.000
89	D	142	LYS	1	0.825	0.902	23.417	12.150	12.150	0.000	0.000	0.000	0.000
90	D	143	GLU	-1	-0.926	-0.960	25.983	-10.805	-10.805	0.000	0.000	0.000	0.000
91	D	144	ASN	0	-0.053	-0.042	28.423	-0.110	-0.110	0.000	0.000	0.000	0.000
92	D	145	GLU	-1	-0.924	-0.943	26.512	-11.383	-11.383	0.000	0.000	0.000	0.000
93	D	146	GLU	-1	-0.882	-0.931	27.817	-10.421	-10.421	0.000	0.000	0.000	0.000
94	D	147	ARG	1	0.799	0.887	20.919	14.306	14.306	0.000	0.000	0.000	0.000
95	D	148	GLU	-1	-0.929	-0.956	27.582	-9.696	-9.696	0.000	0.000	0.000	0.000
96	D	149	LEU	0	-0.035	-0.025	25.397	-0.435	-0.435	0.000	0.000	0.000	0.000
97	D	150	SER	0	0.014	0.001	29.211	0.429	0.429	0.000	0.000	0.000	0.000
98	D	151	PRO	0	0.067	0.013	31.574	-0.098	-0.098	0.000	0.000	0.000	0.000
99	D	152	PRO	0	-0.059	-0.033	31.040	-0.005	-0.005	0.000	0.000	0.000	0.000
100	D	153	LEU	0	-0.015	-0.018	24.945	-0.162	-0.162	0.000	0.000	0.000	0.000
101	D	154	GLU	-1	-0.909	-0.948	28.648	-10.076	-10.076	0.000	0.000	0.000	0.000
102	D	155	GLN	0	-0.002	0.000	30.601	0.037	0.037	0.000	0.000	0.000	0.000
103	D	156	LEU	0	-0.028	-0.008	25.672	-0.006	-0.006	0.000	0.000	0.000	0.000
104	D	157	ILE	0	0.023	0.002	24.027	-0.297	-0.297	0.000	0.000	0.000	0.000
105	D	158	ASP	-1	-0.883	-0.931	27.794	-10.256	-10.256	0.000	0.000	0.000	0.000
106	D	159	HIS	0	-0.045	-0.044	31.044	0.075	0.075	0.000	0.000	0.000	0.000
107	D	160	MET	0	-0.146	-0.065	23.493	0.060	0.060	0.000	0.000	0.000	0.000
108	D	161	ALA	0	0.061	0.031	27.385	-0.434	-0.434	0.000	0.000	0.000	0.000
109	D	162	ASN	0	-0.071	-0.021	29.697	0.145	0.145	0.000	0.000	0.000	0.000
110	D	192	ALA	0	-0.006	-0.014	36.282	-0.050	-0.050	0.000	0.000	0.000	0.000
111	D	193	ILE	0	0.010	0.014	29.713	0.050	0.050	0.000	0.000	0.000	0.000
112	D	194	ARG	1	0.903	0.938	31.996	8.703	8.703	0.000	0.000	0.000	0.000
113	D	195	SER	0	-0.004	0.007	29.885	-0.009	-0.009	0.000	0.000	0.000	0.000
114	D	196	TYR	0	0.073	0.018	24.357	0.062	0.062	0.000	0.000	0.000	0.000
115	D	197	ARG	1	0.911	0.949	26.271	9.668	9.668	0.000	0.000	0.000	0.000
116	D	198	ASP	-1	-0.857	-0.915	28.448	-9.695	-9.695	0.000	0.000	0.000	0.000
117	D	199	VAL	0	0.104	0.047	25.158	0.153	0.153	0.000	0.000	0.000	0.000
118	D	200	MET	0	-0.045	-0.029	23.742	-0.141	-0.141	0.000	0.000	0.000	0.000
119	D	201	LYS	1	0.913	0.954	26.160	9.701	9.701	0.000	0.000	0.000	0.000
120	D	202	LEU	0	0.066	0.045	29.027	0.237	0.237	0.000	0.000	0.000	0.000
121	D	203	CYS	0	-0.037	-0.001	24.479	-0.141	-0.141	0.000	0.000	0.000	0.000
122	D	204	ALA	0	-0.030	-0.017	26.549	-0.172	-0.172	0.000	0.000	0.000	0.000
123	D	205	ALA	0	0.058	0.037	27.916	0.122	0.122	0.000	0.000	0.000	0.000
124	D	206	HIS	1	0.806	0.923	25.998	12.262	12.262	0.000	0.000	0.000	0.000
125	D	207	LEU	0	-0.016	0.000	25.653	-0.158	-0.158	0.000	0.000	0.000	0.000
126	D	208	PRO	0	0.002	-0.002	29.781	0.289	0.289	0.000	0.000	0.000	0.000
127	D	209	THR	0	-0.018	-0.002	31.213	0.477	0.477	0.000	0.000	0.000	0.000
128	D	210	GLU	-1	-0.906	-0.949	30.254	-9.927	-9.927	0.000	0.000	0.000	0.000
129	D	211	SER	0	-0.037	-0.040	29.468	-0.231	-0.231	0.000	0.000	0.000	0.000
130	D	212	ASP	-1	-0.925	-0.960	26.589	-11.243	-11.243	0.000	0.000	0.000	0.000
131	D	213	ALA	0	0.076	0.038	24.724	-0.479	-0.479	0.000	0.000	0.000	0.000
132	D	214	PRO	0	-0.077	-0.035	22.001	-0.648	-0.648	0.000	0.000	0.000	0.000
133	D	215	ASN	0	-0.002	-0.019	20.629	-1.038	-1.038	0.000	0.000	0.000	0.000
134	D	216	HIS	0	0.004	0.017	20.810	-0.636	-0.636	0.000	0.000	0.000	0.000
135	D	217	TYR	0	0.036	-0.004	19.436	-0.745	-0.745	0.000	0.000	0.000	0.000
136	D	218	GLN	0	-0.017	-0.003	15.075	-0.866	-0.866	0.000	0.000	0.000	0.000
137	D	219	ALA	0	0.006	-0.007	15.675	-1.389	-1.389	0.000	0.000	0.000	0.000
138	D	220	VAL	0	0.008	0.026	16.555	-0.741	-0.741	0.000	0.000	0.000	0.000
139	D	221	CYS	0	-0.051	-0.016	13.285	-0.912	-0.912	0.000	0.000	0.000	0.000
140	D	222	ARG	1	0.928	0.963	12.076	16.948	16.948	0.000	0.000	0.000	0.000
141	D	223	ALA	0	-0.035	0.005	11.967	-1.418	-1.418	0.000	0.000	0.000	0.000
142	D	224	LEU	0	0.053	0.026	11.269	-1.218	-1.218	0.000	0.000	0.000	0.000
143	D	225	PHE	0	-0.059	-0.013	4.251	-3.778	-3.528	-0.001	-0.026	-0.223	0.000
144	D	226	ALA	0	0.021	-0.005	7.942	-3.154	-3.154	0.000	0.000	0.000	0.000
145	D	227	GLU	-1	-0.917	-0.963	9.906	-21.210	-21.210	0.000	0.000	0.000	0.000
146	D	228	THR	0	0.005	-0.016	6.562	0.186	0.186	0.000	0.000	0.000	0.000
147	D	229	MET	0	-0.112	-0.063	2.563	-10.274	-8.851	0.283	-0.553	-1.154	-0.005
148	D	230	GLU	-1	-0.997	-0.961	6.891	-24.081	-24.081	0.000	0.000	0.000	0.000
149	D	231	LEU	0	-0.082	-0.029	6.363	-2.115	-2.115	0.000	0.000	0.000	0.000

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