FMO DATABASE

FMODB ID: 82YGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1473532.459684
FMO2-HF: Nuclear repulsion	1412130.783497
FMO2-HF: Total energy	-61401.676187
FMO2-MP2: Total energy	-61575.397615

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.
-127.788	-129.402	28.22	-13.752	-12.854	-0.125

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 : 0.902 / q_NPA : 0.939

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	-0.016	-0.013	2.590	3.401	7.567	0.110	-2.239	-2.037	0.005
4	D	40	LEU	0	0.013	0.022	2.459	-18.444	-16.387	2.106	-1.431	-2.732	-0.011
5	D	41	SER	0	-0.069	-0.060	4.267	12.878	13.017	-0.001	-0.014	-0.124	0.000
6	D	42	LEU	0	0.046	0.012	6.346	-1.394	-1.394	0.000	0.000	0.000	0.000
7	D	43	GLU	-1	-0.755	-0.867	8.301	-24.806	-24.806	0.000	0.000	0.000	0.000
8	D	44	GLU	-1	-0.802	-0.843	1.726	-124.288	-133.966	25.937	-9.591	-6.668	-0.117
9	D	45	ILE	0	0.009	0.008	5.896	2.299	2.299	0.000	0.000	0.000	0.000
10	D	46	LEU	0	-0.017	0.004	7.894	1.974	1.974	0.000	0.000	0.000	0.000
11	D	47	ARG	1	0.823	0.895	8.290	30.195	30.195	0.000	0.000	0.000	0.000
12	D	48	LEU	0	-0.057	-0.027	4.580	1.336	1.392	-0.001	-0.001	-0.054	0.000
13	D	49	TYR	0	0.010	-0.017	9.066	2.522	2.522	0.000	0.000	0.000	0.000
14	D	50	ASN	0	-0.040	0.002	11.920	1.533	1.533	0.000	0.000	0.000	0.000
15	D	51	GLN	0	-0.044	-0.026	13.877	2.231	2.231	0.000	0.000	0.000	0.000
16	D	52	PRO	0	0.002	0.016	14.573	-1.456	-1.456	0.000	0.000	0.000	0.000
17	D	53	ILE	0	-0.010	0.012	13.708	-0.030	-0.030	0.000	0.000	0.000	0.000
18	D	54	ASN	0	0.071	0.029	16.264	1.500	1.500	0.000	0.000	0.000	0.000
19	D	55	GLU	-1	-0.739	-0.858	19.261	-12.572	-12.572	0.000	0.000	0.000	0.000
20	D	56	GLU	-1	-0.800	-0.889	21.250	-13.432	-13.432	0.000	0.000	0.000	0.000
21	D	57	GLN	0	0.015	-0.006	15.413	0.004	0.004	0.000	0.000	0.000	0.000
22	D	58	ALA	0	0.022	0.014	17.189	-0.789	-0.789	0.000	0.000	0.000	0.000
23	D	59	TRP	0	0.023	0.002	18.801	-0.149	-0.149	0.000	0.000	0.000	0.000
24	D	60	ALA	0	-0.017	-0.006	17.705	0.073	0.073	0.000	0.000	0.000	0.000
25	D	61	VAL	0	0.024	-0.001	13.894	-0.293	-0.293	0.000	0.000	0.000	0.000
26	D	62	CYS	0	0.008	0.016	16.547	0.032	0.032	0.000	0.000	0.000	0.000
27	D	63	TYR	0	0.013	0.011	19.671	0.332	0.332	0.000	0.000	0.000	0.000
28	D	64	GLN	0	-0.004	-0.029	15.890	1.294	1.294	0.000	0.000	0.000	0.000
29	D	65	CYS	0	-0.017	0.009	16.524	-0.298	-0.298	0.000	0.000	0.000	0.000
30	D	66	CYS	0	-0.049	-0.018	17.855	0.558	0.558	0.000	0.000	0.000	0.000
31	D	67	GLY	0	0.028	-0.005	20.744	0.624	0.624	0.000	0.000	0.000	0.000
32	D	68	SER	0	-0.024	-0.039	16.078	0.654	0.654	0.000	0.000	0.000	0.000
33	D	69	LEU	0	-0.015	-0.002	18.834	0.426	0.426	0.000	0.000	0.000	0.000
34	D	70	ARG	0	0.083	0.064	21.278	1.144	1.144	0.000	0.000	0.000	0.000
35	D	71	ALA	0	-0.012	-0.008	20.680	0.580	0.580	0.000	0.000	0.000	0.000
36	D	72	ALA	0	0.008	0.022	20.183	0.139	0.139	0.000	0.000	0.000	0.000
37	D	73	ALA	0	0.044	0.020	22.197	0.454	0.454	0.000	0.000	0.000	0.000
38	D	74	ARG	1	0.795	0.861	25.748	11.496	11.496	0.000	0.000	0.000	0.000
39	D	75	ARG	1	0.869	0.929	19.674	14.562	14.562	0.000	0.000	0.000	0.000
40	D	76	ARG	1	0.898	0.950	25.628	10.120	10.120	0.000	0.000	0.000	0.000
41	D	77	GLN	0	0.056	0.040	20.276	0.406	0.406	0.000	0.000	0.000	0.000
42	D	78	PRO	0	-0.029	-0.006	21.381	0.275	0.275	0.000	0.000	0.000	0.000
43	D	79	ARG	1	0.831	0.903	21.612	11.051	11.051	0.000	0.000	0.000	0.000
44	D	80	HIS	0	0.027	0.009	18.319	-0.089	-0.089	0.000	0.000	0.000	0.000
45	D	81	ARG	1	0.789	0.875	20.127	12.105	12.105	0.000	0.000	0.000	0.000
46	D	82	VAL	0	-0.004	-0.003	15.671	-0.732	-0.732	0.000	0.000	0.000	0.000
47	D	83	ARG	1	0.939	0.964	16.299	15.081	15.081	0.000	0.000	0.000	0.000
48	D	84	SER	0	0.020	-0.016	12.339	0.476	0.476	0.000	0.000	0.000	0.000
49	D	85	ALA	0	0.084	0.036	11.651	-0.345	-0.345	0.000	0.000	0.000	0.000
50	D	86	ALA	0	0.021	0.028	8.525	-2.462	-2.462	0.000	0.000	0.000	0.000
51	D	87	GLN	0	-0.040	-0.025	8.919	-1.843	-1.843	0.000	0.000	0.000	0.000
52	D	88	ILE	0	0.026	0.023	11.439	-0.051	-0.051	0.000	0.000	0.000	0.000
53	D	89	ARG	1	0.856	0.921	6.743	31.903	31.903	0.000	0.000	0.000	0.000
54	D	90	VAL	0	0.039	0.018	8.399	3.874	3.874	0.000	0.000	0.000	0.000
55	D	91	TRP	0	-0.032	-0.034	6.815	-6.387	-6.387	0.000	0.000	0.000	0.000
56	D	92	ARG	1	0.900	0.925	3.252	40.698	41.180	0.003	-0.175	-0.310	0.000
57	D	93	ASP	-1	-0.857	-0.936	8.120	-21.343	-21.343	0.000	0.000	0.000	0.000
58	D	94	GLY	0	0.036	0.039	10.985	1.971	1.971	0.000	0.000	0.000	0.000
59	D	95	ALA	0	-0.039	-0.006	12.005	1.412	1.412	0.000	0.000	0.000	0.000
60	D	96	VAL	0	0.019	0.000	11.619	-2.079	-2.079	0.000	0.000	0.000	0.000
61	D	97	THR	0	-0.031	0.011	11.945	1.608	1.608	0.000	0.000	0.000	0.000
62	D	98	LEU	0	0.003	0.006	12.579	-1.710	-1.710	0.000	0.000	0.000	0.000
63	D	99	ALA	0	-0.017	0.001	10.861	0.863	0.863	0.000	0.000	0.000	0.000
64	D	100	PRO	0	0.017	0.000	12.965	0.926	0.926	0.000	0.000	0.000	0.000
65	D	101	ALA	0	-0.007	0.006	13.522	-1.209	-1.209	0.000	0.000	0.000	0.000
66	D	119	GLN	0	-0.006	-0.017	28.534	0.005	0.005	0.000	0.000	0.000	0.000
67	D	120	CYS	0	-0.058	-0.031	26.037	-0.313	-0.313	0.000	0.000	0.000	0.000
68	D	121	MET	0	0.004	0.001	28.222	0.165	0.165	0.000	0.000	0.000	0.000
69	D	122	GLU	-1	-0.821	-0.913	26.781	-11.830	-11.830	0.000	0.000	0.000	0.000
70	D	123	THR	0	0.072	0.015	26.419	-0.482	-0.482	0.000	0.000	0.000	0.000
71	D	124	GLU	-1	-0.726	-0.823	26.158	-11.213	-11.213	0.000	0.000	0.000	0.000
72	D	125	VAL	0	-0.029	-0.008	20.847	-0.425	-0.425	0.000	0.000	0.000	0.000
73	D	126	ILE	0	-0.018	-0.004	22.098	-0.584	-0.584	0.000	0.000	0.000	0.000
74	D	127	GLU	-1	-0.803	-0.897	23.851	-12.845	-12.845	0.000	0.000	0.000	0.000
75	D	128	SER	0	-0.014	-0.001	20.574	-0.509	-0.509	0.000	0.000	0.000	0.000
76	D	129	LEU	0	-0.026	-0.028	17.830	-0.709	-0.709	0.000	0.000	0.000	0.000
77	D	130	GLY	0	0.049	0.038	20.039	-0.541	-0.541	0.000	0.000	0.000	0.000
78	D	131	ILE	0	0.033	0.011	21.142	-0.304	-0.304	0.000	0.000	0.000	0.000
79	D	132	ILE	0	-0.087	-0.035	15.324	-0.448	-0.448	0.000	0.000	0.000	0.000
80	D	133	ILE	0	0.000	-0.013	16.952	-0.863	-0.863	0.000	0.000	0.000	0.000
81	D	134	TYR	0	0.037	0.024	18.917	-0.268	-0.268	0.000	0.000	0.000	0.000
82	D	135	LYS	1	0.908	0.943	18.145	15.359	15.359	0.000	0.000	0.000	0.000
83	D	136	ALA	0	-0.050	-0.021	15.154	-0.568	-0.568	0.000	0.000	0.000	0.000
84	D	137	LEU	0	-0.030	-0.014	16.491	-0.417	-0.417	0.000	0.000	0.000	0.000
85	D	138	ASP	-1	-0.788	-0.906	19.593	-12.939	-12.939	0.000	0.000	0.000	0.000
86	D	139	TYR	0	-0.083	-0.040	13.670	-0.318	-0.318	0.000	0.000	0.000	0.000
87	D	140	GLY	0	0.019	0.004	18.023	-0.016	-0.016	0.000	0.000	0.000	0.000
88	D	141	LEU	0	-0.025	0.018	19.752	0.525	0.525	0.000	0.000	0.000	0.000
89	D	142	LYS	1	0.733	0.842	23.166	12.339	12.339	0.000	0.000	0.000	0.000
90	D	143	GLU	-1	-0.896	-0.959	25.969	-10.875	-10.875	0.000	0.000	0.000	0.000
91	D	144	ASN	0	-0.117	-0.057	28.316	0.147	0.147	0.000	0.000	0.000	0.000
92	D	145	GLU	-1	-0.846	-0.906	26.250	-11.302	-11.302	0.000	0.000	0.000	0.000
93	D	146	GLU	-1	-0.892	-0.939	27.106	-10.393	-10.393	0.000	0.000	0.000	0.000
94	D	147	ARG	1	0.779	0.877	19.721	14.551	14.551	0.000	0.000	0.000	0.000
95	D	148	GLU	-1	-0.910	-0.943	26.386	-9.734	-9.734	0.000	0.000	0.000	0.000
96	D	149	LEU	0	-0.047	-0.035	24.127	-0.584	-0.584	0.000	0.000	0.000	0.000
97	D	150	SER	0	-0.034	-0.048	27.609	0.556	0.556	0.000	0.000	0.000	0.000
98	D	151	PRO	0	0.082	0.031	29.745	-0.185	-0.185	0.000	0.000	0.000	0.000
99	D	152	PRO	0	-0.069	-0.026	29.666	0.035	0.035	0.000	0.000	0.000	0.000
100	D	153	LEU	0	-0.012	-0.014	23.104	-0.220	-0.220	0.000	0.000	0.000	0.000
101	D	154	GLU	-1	-0.894	-0.951	27.195	-9.995	-9.995	0.000	0.000	0.000	0.000
102	D	155	GLN	0	-0.031	-0.030	29.301	0.120	0.120	0.000	0.000	0.000	0.000
103	D	156	LEU	0	-0.025	-0.006	24.256	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	157	ILE	0	0.006	0.000	23.534	-0.359	-0.359	0.000	0.000	0.000	0.000
105	D	158	ASP	-1	-0.847	-0.918	26.803	-10.320	-10.320	0.000	0.000	0.000	0.000
106	D	159	HIS	0	-0.068	-0.053	29.830	-0.030	-0.030	0.000	0.000	0.000	0.000
107	D	160	MET	0	-0.125	-0.059	22.498	-0.037	-0.037	0.000	0.000	0.000	0.000
108	D	161	ALA	0	0.063	0.043	26.143	-0.432	-0.432	0.000	0.000	0.000	0.000
109	D	162	ASN	0	-0.126	-0.056	28.461	0.537	0.537	0.000	0.000	0.000	0.000
110	D	192	ALA	0	0.020	-0.002	35.140	-0.059	-0.059	0.000	0.000	0.000	0.000
111	D	193	ILE	0	0.017	0.010	28.528	0.088	0.088	0.000	0.000	0.000	0.000
112	D	194	ARG	1	0.897	0.951	31.366	8.993	8.993	0.000	0.000	0.000	0.000
113	D	195	SER	0	-0.056	-0.035	29.283	-0.022	-0.022	0.000	0.000	0.000	0.000
114	D	196	TYR	0	0.073	0.016	23.676	0.024	0.024	0.000	0.000	0.000	0.000
115	D	197	ARG	1	0.854	0.914	26.311	9.755	9.755	0.000	0.000	0.000	0.000
116	D	198	ASP	-1	-0.761	-0.857	28.391	-10.050	-10.050	0.000	0.000	0.000	0.000
117	D	199	VAL	0	0.095	0.046	24.118	0.176	0.176	0.000	0.000	0.000	0.000
118	D	200	MET	0	-0.052	0.001	22.826	0.028	0.028	0.000	0.000	0.000	0.000
119	D	201	LYS	1	0.858	0.908	26.169	9.846	9.846	0.000	0.000	0.000	0.000
120	D	202	LEU	0	0.038	0.027	28.695	0.116	0.116	0.000	0.000	0.000	0.000
121	D	203	CYS	0	0.009	0.002	24.413	-0.123	-0.123	0.000	0.000	0.000	0.000
122	D	204	ALA	0	-0.041	-0.008	26.472	-0.123	-0.123	0.000	0.000	0.000	0.000
123	D	205	ALA	0	0.009	0.000	27.929	0.109	0.109	0.000	0.000	0.000	0.000
124	D	206	HIS	1	0.823	0.932	24.663	12.685	12.685	0.000	0.000	0.000	0.000
125	D	207	LEU	0	-0.034	0.002	25.636	-0.087	-0.087	0.000	0.000	0.000	0.000
126	D	208	PRO	0	-0.008	-0.013	29.775	0.285	0.285	0.000	0.000	0.000	0.000
127	D	209	THR	0	-0.015	-0.031	30.537	0.458	0.458	0.000	0.000	0.000	0.000
128	D	210	GLU	-1	-0.881	-0.920	30.074	-10.150	-10.150	0.000	0.000	0.000	0.000
129	D	211	SER	0	-0.050	-0.055	29.276	-0.232	-0.232	0.000	0.000	0.000	0.000
130	D	212	ASP	-1	-0.805	-0.868	27.020	-10.937	-10.937	0.000	0.000	0.000	0.000
131	D	213	ALA	0	0.044	0.038	24.840	-0.578	-0.578	0.000	0.000	0.000	0.000
132	D	214	PRO	0	-0.051	-0.026	22.234	-0.661	-0.661	0.000	0.000	0.000	0.000
133	D	215	ASN	0	-0.032	-0.019	21.162	-0.817	-0.817	0.000	0.000	0.000	0.000
134	D	216	HIS	0	-0.020	-0.019	20.704	-0.765	-0.765	0.000	0.000	0.000	0.000
135	D	217	TYR	0	0.019	-0.016	19.653	-0.742	-0.742	0.000	0.000	0.000	0.000
136	D	218	GLN	0	0.021	0.024	15.123	-0.744	-0.744	0.000	0.000	0.000	0.000
137	D	219	ALA	0	0.000	-0.001	15.877	-1.311	-1.311	0.000	0.000	0.000	0.000
138	D	220	VAL	0	0.011	0.009	16.576	-0.909	-0.909	0.000	0.000	0.000	0.000
139	D	221	CYS	0	-0.053	-0.010	13.379	-0.972	-0.972	0.000	0.000	0.000	0.000
140	D	222	ARG	1	0.882	0.917	11.960	16.841	16.841	0.000	0.000	0.000	0.000
141	D	223	ALA	0	-0.046	-0.004	12.242	-1.360	-1.360	0.000	0.000	0.000	0.000
142	D	224	LEU	0	0.074	0.039	10.872	-1.170	-1.170	0.000	0.000	0.000	0.000
143	D	225	PHE	0	-0.043	-0.011	4.572	-2.962	-2.763	-0.001	-0.023	-0.175	0.000
144	D	226	ALA	0	-0.001	-0.008	8.086	-3.011	-3.011	0.000	0.000	0.000	0.000
145	D	227	GLU	-1	-0.850	-0.945	10.120	-21.315	-21.315	0.000	0.000	0.000	0.000
146	D	228	THR	0	-0.025	-0.007	5.952	0.573	0.573	0.000	0.000	0.000	0.000
147	D	229	MET	0	-0.080	-0.048	3.273	-8.292	-7.327	0.067	-0.278	-0.754	-0.002
148	D	230	GLU	-1	-0.952	-0.952	6.886	-22.353	-22.353	0.000	0.000	0.000	0.000
149	D	231	LEU	0	-0.114	-0.039	6.750	-1.103	-1.103	0.000	0.000	0.000	0.000

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