FMO DATABASE

FMODB ID: MN1YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1348964.903839
FMO2-HF: Nuclear repulsion	1290445.432922
FMO2-HF: Total energy	-58519.470917
FMO2-MP2: Total energy	-58689.707604

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.
-11.834	-10.114	6.007	-3.796	-3.93	-0.037

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 : -0.002 / q_NPA : -0.008

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	-0.865	-0.939	3.799	-2.473	-1.474	0.002	-0.390	-0.611	0.002
4	A	3	ASP	-1	-0.851	-0.909	2.059	-13.850	-13.384	6.006	-3.357	-3.115	-0.039
5	A	4	LEU	0	0.033	-0.002	4.820	0.877	0.901	-0.001	-0.005	-0.018	0.000
6	A	5	THR	0	0.016	0.003	4.806	0.578	0.578	0.000	0.000	0.000	0.000
7	A	6	ASN	0	0.038	0.037	3.712	0.613	0.844	0.000	-0.044	-0.186	0.000
8	A	7	LEU	0	-0.017	-0.014	5.605	0.683	0.683	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.041	0.027	8.750	0.314	0.314	0.000	0.000	0.000	0.000
10	A	9	ALA	0	-0.022	-0.010	8.649	0.191	0.191	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.839	0.900	8.026	1.128	1.128	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.010	0.012	11.509	0.072	0.072	0.000	0.000	0.000	0.000
13	A	12	ARG	1	1.000	1.004	13.534	0.140	0.140	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.015	0.012	14.380	0.045	0.045	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.038	-0.036	16.012	0.032	0.032	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.879	-0.946	17.770	-0.232	-0.232	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.715	-0.831	18.427	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.815	0.893	19.452	0.032	0.032	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.927	-0.957	22.054	-0.088	-0.088	0.000	0.000	0.000	0.000
20	A	19	GLU	-1	-0.830	-0.923	23.566	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.047	-0.026	23.497	0.011	0.011	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.864	0.912	23.724	0.044	0.044	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.851	-0.910	27.976	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	23	LEU	0	-0.070	-0.035	29.211	0.005	0.005	0.000	0.000	0.000	0.000
25	A	24	ILE	0	-0.064	-0.040	30.229	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	ALA	0	-0.021	-0.013	32.396	0.003	0.003	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.983	0.995	32.037	0.050	0.050	0.000	0.000	0.000	0.000
28	A	27	TYR	0	0.030	0.020	35.957	0.003	0.003	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.015	-0.003	38.038	0.002	0.002	0.000	0.000	0.000	0.000
30	A	29	PRO	0	0.036	0.017	38.455	0.001	0.001	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.019	0.023	37.753	0.000	0.000	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.009	-0.006	41.709	0.002	0.002	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.745	-0.851	43.988	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	33	SER	0	-0.046	-0.018	43.889	0.000	0.000	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.022	-0.015	46.467	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.848	-0.926	42.847	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.001	-0.013	43.191	0.000	0.000	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.920	-0.951	42.216	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.104	0.064	39.269	0.000	0.000	0.000	0.000	0.000	0.000
40	A	39	LEU	0	-0.080	-0.036	38.536	0.000	0.000	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.069	-0.051	38.678	0.002	0.002	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.925	-0.970	36.887	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.068	-0.027	34.057	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	43	TRP	0	-0.079	-0.021	33.406	0.001	0.001	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.008	-0.008	31.915	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.897	-0.954	34.713	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.908	-0.962	36.683	0.015	0.015	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.010	0.003	36.943	0.003	0.003	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.852	-0.922	37.673	0.023	0.023	0.000	0.000	0.000	0.000
50	A	49	TYR	0	-0.013	-0.015	38.556	0.001	0.001	0.000	0.000	0.000	0.000
51	A	50	ALA	0	-0.029	-0.010	40.899	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	VAL	0	0.032	0.009	42.215	0.000	0.000	0.000	0.000	0.000	0.000
53	A	52	VAL	0	-0.001	-0.008	44.665	0.001	0.001	0.000	0.000	0.000	0.000
54	A	53	GLY	0	-0.007	-0.005	46.924	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	54	PHE	0	-0.034	0.000	47.954	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	55	ALA	0	-0.007	0.001	48.620	0.002	0.002	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.038	-0.031	43.196	0.000	0.000	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.011	0.021	43.998	0.000	0.000	0.000	0.000	0.000	0.000
59	A	58	LYS	1	0.913	0.944	42.450	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	59	GLY	0	0.057	0.034	41.252	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.902	0.951	35.326	0.016	0.016	0.000	0.000	0.000	0.000
62	A	61	ALA	0	0.053	0.035	41.934	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.009	-0.010	45.313	0.000	0.000	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.026	-0.018	39.791	0.000	0.000	0.000	0.000	0.000	0.000
65	A	64	ALA	0	0.025	0.012	43.937	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.041	0.021	45.429	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.100	-0.052	44.410	0.001	0.001	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.061	-0.021	44.368	0.000	0.000	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.816	-0.912	47.808	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.026	0.017	50.741	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	GLN	0	0.050	-0.012	52.756	0.000	0.000	0.000	0.000	0.000	0.000
72	A	71	THR	0	-0.023	-0.002	52.996	0.000	0.000	0.000	0.000	0.000	0.000
73	A	72	HIS	0	-0.037	-0.015	46.982	0.001	0.001	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.883	0.919	49.286	0.015	0.015	0.000	0.000	0.000	0.000
75	A	74	ALA	0	-0.023	-0.007	53.567	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	LEU	0	-0.013	-0.015	49.825	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	MET	0	-0.017	-0.020	49.419	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	ALA	0	-0.055	-0.013	52.284	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.841	-0.901	55.045	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.008	0.021	52.675	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	80	CYS	0	-0.069	-0.043	48.390	0.002	0.002	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.009	0.025	45.127	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	82	HIS	1	0.748	0.843	42.642	0.016	0.016	0.000	0.000	0.000	0.000
84	A	83	PHE	0	0.048	0.026	39.107	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	84	LEU	0	-0.019	-0.019	36.387	0.005	0.005	0.000	0.000	0.000	0.000
86	A	85	GLY	0	-0.002	0.012	36.447	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	86	PRO	0	0.021	-0.001	31.561	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.017	0.020	29.776	0.006	0.006	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.064	-0.024	27.635	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	89	VAL	0	0.068	0.012	23.659	0.003	0.003	0.000	0.000	0.000	0.000
91	A	90	THR	0	-0.058	-0.023	22.284	0.004	0.004	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.026	0.008	19.276	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.942	-0.958	19.122	0.243	0.243	0.000	0.000	0.000	0.000
94	A	93	GLY	0	0.055	0.026	18.127	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	94	ASP	-1	-0.851	-0.906	19.170	0.028	0.028	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.053	-0.029	21.974	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.057	0.025	23.024	0.006	0.006	0.000	0.000	0.000	0.000
98	A	97	THR	0	-0.027	-0.013	25.169	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.003	0.008	27.107	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.870	0.937	28.493	-0.045	-0.045	0.000	0.000	0.000	0.000
101	A	100	CYS	0	-0.010	0.000	32.126	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	101	HIS	0	0.066	0.041	34.767	0.001	0.001	0.000	0.000	0.000	0.000
103	A	102	SER	0	-0.011	-0.008	38.204	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	103	VAL	0	0.001	0.004	40.789	0.003	0.003	0.000	0.000	0.000	0.000
105	A	104	VAL	0	-0.025	0.002	44.159	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	105	PHE	0	0.017	-0.003	44.367	0.002	0.002	0.000	0.000	0.000	0.000
107	A	106	ARG	1	0.830	0.909	48.888	0.006	0.006	0.000	0.000	0.000	0.000
108	A	107	CYS	0	-0.041	-0.011	52.306	0.000	0.000	0.000	0.000	0.000	0.000
109	A	108	VAL	0	0.034	0.001	55.140	0.001	0.001	0.000	0.000	0.000	0.000
110	A	109	SER	0	-0.002	-0.007	58.482	0.000	0.000	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.025	0.020	59.440	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.055	-0.018	57.365	0.000	0.000	0.000	0.000	0.000	0.000
113	A	112	PHE	0	0.044	0.021	52.118	0.000	0.000	0.000	0.000	0.000	0.000
114	A	113	GLY	0	0.017	0.006	52.945	0.001	0.001	0.000	0.000	0.000	0.000
115	A	114	SER	0	-0.029	-0.015	48.958	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	115	HIS	0	0.001	0.008	50.059	0.001	0.001	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.959	0.973	47.069	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	117	VAL	0	0.063	0.036	44.219	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	118	SER	0	-0.046	-0.023	42.679	0.002	0.002	0.000	0.000	0.000	0.000
120	A	119	ALA	0	0.016	0.023	39.060	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	120	ASN	0	0.004	-0.004	36.587	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.874	0.949	32.432	-0.050	-0.050	0.000	0.000	0.000	0.000
123	A	122	TRP	0	0.033	0.011	31.795	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	123	THR	0	0.026	0.003	29.963	0.003	0.003	0.000	0.000	0.000	0.000
125	A	124	PHE	0	0.029	0.014	27.068	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.969	0.974	26.202	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	126	ARG	1	0.766	0.868	18.794	0.002	0.002	0.000	0.000	0.000	0.000
128	A	127	THR	0	-0.069	-0.055	24.958	0.007	0.007	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.031	-0.008	25.976	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	129	ALA	0	-0.001	0.015	26.843	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	130	GLY	0	0.050	0.031	25.472	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	131	TRP	0	-0.102	-0.039	20.991	0.026	0.026	0.000	0.000	0.000	0.000
133	A	132	ARG	1	0.878	0.954	26.773	0.034	0.034	0.000	0.000	0.000	0.000
134	A	133	ALA	0	0.018	0.004	29.930	0.008	0.008	0.000	0.000	0.000	0.000
135	A	134	VAL	0	-0.053	-0.028	30.722	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	135	ARG	1	0.856	0.889	33.417	-0.029	-0.029	0.000	0.000	0.000	0.000
137	A	136	ARG	1	0.828	0.937	34.613	0.002	0.002	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.847	-0.910	36.996	0.034	0.034	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.012	-0.023	38.720	0.000	0.000	0.000	0.000	0.000	0.000
140	A	139	ALA	0	0.043	0.011	41.397	0.001	0.001	0.000	0.000	0.000	0.000
141	A	140	LEU	0	-0.014	0.005	43.644	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	141	LEU	0	-0.048	-0.033	41.243	0.003	0.003	0.000	0.000	0.000	0.000
143	A	142	ASP	-1	-0.810	-0.910	45.696	0.013	0.013	0.000	0.000	0.000	0.000
144	A	143	GLY	0	0.005	0.007	47.840	0.000	0.000	0.000	0.000	0.000	0.000
145	A	144	SER	0	-0.027	-0.003	46.599	0.003	0.003	0.000	0.000	0.000	0.000
146	A	145	ALA	0	0.013	-0.008	45.378	0.001	0.001	0.000	0.000	0.000	0.000
147	A	146	ALA	0	0.022	0.008	43.054	0.002	0.002	0.000	0.000	0.000	0.000
148	A	147	ALA	0	0.032	0.017	41.469	0.002	0.002	0.000	0.000	0.000	0.000
149	A	148	ARG	1	0.936	0.948	40.324	-0.028	-0.028	0.000	0.000	0.000	0.000
150	A	149	ALA	0	-0.004	0.008	38.827	0.003	0.003	0.000	0.000	0.000	0.000
151	A	150	LEU	0	-0.014	-0.005	37.133	0.004	0.004	0.000	0.000	0.000	0.000
152	A	151	LEU	0	0.011	-0.006	35.363	0.001	0.001	0.000	0.000	0.000	0.000
153	A	152	GLN	0	-0.006	0.035	34.238	0.000	0.000	0.000	0.000	0.000	0.000
154	A	153	PHE	0	0.009	-0.011	25.295	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)