FMO DATABASE

FMODB ID: 76V7K

Calculation Name: 2RFR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RFR

Chain ID: A

ChEMBL ID:

UniProt ID: A4XF70

Base Structure: X-ray

Registration Date: 2023-09-23

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1349573.472591
FMO2-HF: Nuclear repulsion	1291053.498315
FMO2-HF: Total energy	-58519.974276
FMO2-MP2: Total energy	-58690.245199

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(A:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-11.356	-13.478	11.755	-5.44	-4.192	-0.048

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.015

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	A	2	ASP	-1	-0.815	-0.902	3.805	-2.114	-1.124	-0.001	-0.384	-0.604	0.002
4	A	3	ASP	-1	-0.827	-0.887	1.829	-13.365	-16.762	11.757	-4.999	-3.361	-0.050
5	A	4	LEU	0	0.040	0.002	4.825	0.827	0.855	-0.001	-0.005	-0.021	0.000
6	A	5	THR	0	0.021	0.009	4.844	0.816	0.816	0.000	0.000	0.000	0.000
7	A	6	ASN	0	0.010	0.011	3.651	0.342	0.599	0.000	-0.052	-0.206	0.000
8	A	7	LEU	0	-0.007	-0.007	5.674	0.577	0.577	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.038	0.024	8.800	0.278	0.278	0.000	0.000	0.000	0.000
10	A	9	ALA	0	-0.022	-0.008	8.669	0.164	0.164	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.783	0.859	7.562	1.061	1.061	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.004	0.005	11.591	0.057	0.057	0.000	0.000	0.000	0.000
13	A	12	ARG	1	1.000	1.008	13.599	0.082	0.082	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.017	0.006	14.459	0.037	0.037	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.049	-0.038	16.015	0.025	0.025	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.864	-0.942	17.494	-0.195	-0.195	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.718	-0.811	18.617	0.000	0.000	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.820	0.892	19.283	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.909	-0.947	22.131	-0.068	-0.068	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.844	-0.918	23.643	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.020	-0.021	23.565	0.008	0.008	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.864	0.914	24.093	0.026	0.026	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.854	-0.917	28.057	-0.049	-0.049	0.000	0.000	0.000	0.000
24	A	23	LEU	0	-0.066	-0.030	28.936	0.004	0.004	0.000	0.000	0.000	0.000
25	A	24	ILE	0	-0.072	-0.043	30.132	0.004	0.004	0.000	0.000	0.000	0.000
26	A	25	ALA	0	-0.023	-0.012	32.480	0.002	0.002	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.993	0.998	32.349	0.039	0.039	0.000	0.000	0.000	0.000
28	A	27	TYR	0	0.031	0.021	36.034	0.003	0.003	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.012	-0.002	38.117	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	PRO	0	0.042	0.021	38.436	0.001	0.001	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.017	0.032	37.881	0.000	0.000	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.012	-0.008	41.784	0.001	0.001	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.739	-0.845	44.066	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	33	SER	0	-0.038	-0.025	43.943	0.000	0.000	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.027	-0.022	46.541	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.836	-0.914	42.614	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	36	ALA	0	0.005	-0.012	43.261	0.000	0.000	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.919	-0.955	42.404	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.077	0.050	39.347	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	LEU	0	-0.063	-0.028	38.604	0.001	0.001	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.068	-0.049	38.750	0.002	0.002	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.856	-0.933	36.823	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.072	-0.026	34.072	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	43	TRP	0	-0.101	-0.041	33.477	0.002	0.002	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.013	-0.010	32.036	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.829	-0.919	34.776	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.873	-0.948	36.376	0.018	0.018	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.008	0.003	37.011	0.003	0.003	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.804	-0.885	37.742	0.026	0.026	0.000	0.000	0.000	0.000
50	A	49	TYR	0	-0.017	-0.011	38.633	0.001	0.001	0.000	0.000	0.000	0.000
51	A	50	ALA	0	-0.018	-0.004	40.983	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	51	VAL	0	0.028	0.002	42.299	0.000	0.000	0.000	0.000	0.000	0.000
53	A	52	VAL	0	-0.001	-0.005	44.751	0.000	0.000	0.000	0.000	0.000	0.000
54	A	53	GLY	0	-0.006	-0.006	47.010	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	PHE	0	-0.033	-0.004	48.098	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	55	ALA	0	-0.004	0.002	48.701	0.002	0.002	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.040	-0.024	43.170	0.000	0.000	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.012	0.019	44.119	0.000	0.000	0.000	0.000	0.000	0.000
59	A	58	LYS	1	0.864	0.902	42.522	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	59	GLY	0	0.046	0.024	41.318	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.819	0.919	35.828	0.011	0.011	0.000	0.000	0.000	0.000
62	A	61	ALA	0	0.034	0.022	42.000	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.009	-0.007	45.279	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.018	-0.015	39.913	0.000	0.000	0.000	0.000	0.000	0.000
65	A	64	ALA	0	0.017	0.009	44.010	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.034	0.018	45.499	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.091	-0.046	44.529	0.000	0.000	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.065	-0.023	44.319	0.000	0.000	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.803	-0.897	47.883	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.025	0.017	50.816	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	GLN	0	0.042	-0.016	52.832	0.000	0.000	0.000	0.000	0.000	0.000
72	A	71	THR	0	-0.010	0.004	53.005	0.000	0.000	0.000	0.000	0.000	0.000
73	A	72	HIS	0	-0.029	-0.013	46.830	0.001	0.001	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.867	0.901	49.221	0.011	0.011	0.000	0.000	0.000	0.000
75	A	74	ALA	0	-0.019	-0.005	53.645	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	LEU	0	-0.023	-0.016	49.649	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	MET	0	-0.009	-0.015	49.704	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	ALA	0	-0.054	-0.013	52.365	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.824	-0.877	55.210	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.004	0.022	52.757	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	80	CYS	0	-0.078	-0.051	48.344	0.002	0.002	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.002	0.021	45.238	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	82	HIS	1	0.744	0.838	42.823	0.010	0.010	0.000	0.000	0.000	0.000
84	A	83	PHE	0	0.040	0.022	39.490	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	84	LEU	0	-0.019	-0.016	36.468	0.004	0.004	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.004	0.014	36.537	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	86	PRO	0	0.021	-0.002	31.582	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.016	0.020	29.926	0.005	0.005	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.046	-0.011	27.688	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	89	VAL	0	0.074	0.017	23.962	0.002	0.002	0.000	0.000	0.000	0.000
91	A	90	THR	0	-0.073	-0.030	22.488	0.005	0.005	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.025	0.005	19.557	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.942	-0.964	19.104	0.251	0.251	0.000	0.000	0.000	0.000
94	A	93	GLY	0	0.057	0.032	18.198	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	94	ASP	-1	-0.839	-0.901	19.241	0.041	0.041	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.047	-0.023	22.041	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.056	0.021	23.103	0.007	0.007	0.000	0.000	0.000	0.000
98	A	97	THR	0	-0.025	-0.013	25.251	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.006	0.007	27.196	0.000	0.000	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.855	0.927	28.675	-0.053	-0.053	0.000	0.000	0.000	0.000
101	A	100	CYS	0	-0.011	0.002	32.219	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	101	HIS	0	0.079	0.046	34.859	0.001	0.001	0.000	0.000	0.000	0.000
103	A	102	SER	0	-0.013	-0.007	38.295	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	103	VAL	0	-0.021	-0.009	40.880	0.003	0.003	0.000	0.000	0.000	0.000
105	A	104	VAL	0	-0.016	0.005	44.249	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	105	PHE	0	0.023	-0.004	44.419	0.001	0.001	0.000	0.000	0.000	0.000
107	A	106	ARG	1	0.811	0.881	48.976	0.002	0.002	0.000	0.000	0.000	0.000
108	A	107	CYS	0	-0.038	-0.004	52.393	0.000	0.000	0.000	0.000	0.000	0.000
109	A	108	VAL	0	0.025	0.003	55.226	0.001	0.001	0.000	0.000	0.000	0.000
110	A	109	SER	0	-0.003	-0.011	58.569	0.000	0.000	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.030	0.021	59.523	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.059	-0.014	57.487	0.000	0.000	0.000	0.000	0.000	0.000
113	A	112	PHE	0	0.046	0.010	52.216	0.000	0.000	0.000	0.000	0.000	0.000
114	A	113	GLY	0	0.023	0.013	53.032	0.001	0.001	0.000	0.000	0.000	0.000
115	A	114	SER	0	-0.036	-0.015	48.429	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	115	HIS	0	0.006	0.009	50.374	0.001	0.001	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.948	0.974	46.420	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	117	VAL	0	0.055	0.029	44.327	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	118	SER	0	-0.047	-0.021	42.656	0.001	0.001	0.000	0.000	0.000	0.000
120	A	119	ALA	0	0.017	0.025	39.143	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	120	ASN	0	-0.005	-0.009	36.700	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.865	0.935	32.240	-0.052	-0.052	0.000	0.000	0.000	0.000
123	A	122	TRP	0	0.042	0.013	31.873	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	123	THR	0	0.013	0.003	30.046	0.005	0.005	0.000	0.000	0.000	0.000
125	A	124	PHE	0	0.028	0.006	27.195	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.914	0.954	26.275	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	126	ARG	1	0.760	0.840	19.073	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	127	THR	0	-0.057	-0.048	25.021	0.006	0.006	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.032	-0.004	26.028	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	129	ALA	0	0.003	0.018	26.887	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	130	GLY	0	0.058	0.037	25.529	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	131	TRP	0	-0.127	-0.060	21.041	0.021	0.021	0.000	0.000	0.000	0.000
133	A	132	ARG	1	0.863	0.943	26.840	0.024	0.024	0.000	0.000	0.000	0.000
134	A	133	ALA	0	0.010	-0.001	30.002	0.008	0.008	0.000	0.000	0.000	0.000
135	A	134	VAL	0	-0.043	-0.022	30.778	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	135	ARG	1	0.825	0.874	33.490	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	136	ARG	1	0.828	0.933	34.694	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.824	-0.896	37.079	0.037	0.037	0.000	0.000	0.000	0.000
139	A	138	ASN	0	0.012	-0.021	38.808	0.000	0.000	0.000	0.000	0.000	0.000
140	A	139	ALA	0	0.027	0.005	41.485	0.001	0.001	0.000	0.000	0.000	0.000
141	A	140	LEU	0	-0.009	0.007	43.735	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	141	LEU	0	-0.055	-0.034	41.357	0.003	0.003	0.000	0.000	0.000	0.000
143	A	142	ASP	-1	-0.795	-0.903	45.789	0.016	0.016	0.000	0.000	0.000	0.000
144	A	143	GLY	0	0.013	0.009	47.912	0.000	0.000	0.000	0.000	0.000	0.000
145	A	144	SER	0	-0.029	0.002	46.664	0.003	0.003	0.000	0.000	0.000	0.000
146	A	145	ALA	0	0.007	-0.012	45.417	0.001	0.001	0.000	0.000	0.000	0.000
147	A	146	ALA	0	0.024	0.008	43.086	0.002	0.002	0.000	0.000	0.000	0.000
148	A	147	ALA	0	0.035	0.018	41.531	0.002	0.002	0.000	0.000	0.000	0.000
149	A	148	ARG	1	0.936	0.942	40.396	-0.030	-0.030	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.001	0.010	38.827	0.003	0.003	0.000	0.000	0.000	0.000
151	A	150	LEU	0	-0.021	-0.002	37.136	0.005	0.005	0.000	0.000	0.000	0.000
152	A	151	LEU	0	0.015	-0.005	35.455	0.001	0.001	0.000	0.000	0.000	0.000
153	A	152	GLN	0	-0.009	0.041	34.256	0.001	0.001	0.000	0.000	0.000	0.000
154	A	153	PHE	0	0.025	0.004	25.241	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)