FMO DATABASE

FMODB ID: 3JVZL

Calculation Name: 2FR2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FR2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WFG7

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1515278.408064
FMO2-HF: Nuclear repulsion	1454589.205285
FMO2-HF: Total energy	-60689.202779
FMO2-MP2: Total energy	-60868.61296

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:4:ASP)

Summations of interaction energy for fragment #1(A:4: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.
-19.772	-14.984	0.91	-2.797	-2.901	0.029

Interaction energy analysis for fragmet #1(A:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.929 / q_NPA : -0.979

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	6	ALA	0	0.014	0.009	3.844	-6.705	-5.408	-0.006	-0.611	-0.680	0.002
4	A	7	PRO	0	0.065	0.012	5.697	-1.678	-1.678	0.000	0.000	0.000	0.000
5	A	8	ALA	0	-0.043	-0.022	7.896	-1.170	-1.170	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.010	0.005	8.057	-1.808	-1.808	0.000	0.000	0.000	0.000
7	A	10	GLN	0	0.027	0.020	7.682	2.415	2.415	0.000	0.000	0.000	0.000
8	A	11	ALA	0	-0.019	-0.013	9.916	-0.094	-0.094	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.025	0.014	12.321	-0.844	-0.844	0.000	0.000	0.000	0.000
10	A	13	SER	0	-0.007	0.000	8.637	0.303	0.303	0.000	0.000	0.000	0.000
11	A	14	PRO	0	0.030	0.018	10.347	1.317	1.317	0.000	0.000	0.000	0.000
12	A	15	LEU	0	0.041	0.013	13.182	-1.007	-1.007	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.059	-0.004	6.841	0.115	0.115	0.000	0.000	0.000	0.000
14	A	17	GLY	0	0.009	0.002	10.940	-0.529	-0.529	0.000	0.000	0.000	0.000
15	A	18	SER	0	-0.005	-0.001	12.487	-0.888	-0.888	0.000	0.000	0.000	0.000
16	A	19	TRP	0	-0.042	-0.019	15.151	-0.830	-0.830	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.021	0.000	19.184	-0.213	-0.213	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.007	0.009	22.828	-0.062	-0.062	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.808	0.886	26.181	-9.649	-9.649	0.000	0.000	0.000	0.000
20	A	23	GLY	0	0.054	0.026	29.443	0.170	0.170	0.000	0.000	0.000	0.000
21	A	24	ALA	0	-0.039	-0.012	31.013	-0.302	-0.302	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.051	0.027	33.404	0.247	0.247	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.899	0.945	35.295	-8.639	-8.639	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.043	-0.007	37.722	0.131	0.131	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.011	0.025	40.240	-0.122	-0.122	0.000	0.000	0.000	0.000
26	A	29	THR	0	-0.016	-0.001	41.880	-0.118	-0.118	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.044	-0.014	38.230	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.947	0.969	42.552	-7.068	-7.068	0.000	0.000	0.000	0.000
29	A	32	PRO	0	0.006	-0.005	39.915	0.170	0.170	0.000	0.000	0.000	0.000
30	A	33	PHE	0	-0.055	-0.012	33.359	-0.144	-0.144	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.809	-0.887	34.887	8.958	8.958	0.000	0.000	0.000	0.000
32	A	35	TYR	0	-0.108	-0.066	28.079	-0.345	-0.345	0.000	0.000	0.000	0.000
33	A	36	LEU	0	0.006	0.004	28.641	0.088	0.088	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.751	-0.862	23.721	12.941	12.941	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.961	-0.970	21.475	14.107	14.107	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.018	0.006	17.379	-0.155	-0.155	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.025	-0.007	13.251	0.547	0.547	0.000	0.000	0.000	0.000
38	A	41	PHE	0	0.027	0.016	12.290	-0.522	-0.522	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.005	-0.006	8.968	1.827	1.827	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.037	0.020	2.558	-20.889	-17.528	0.918	-2.139	-2.140	0.027
41	A	44	VAL	0	-0.001	0.003	6.521	1.760	1.760	0.000	0.000	0.000	0.000
42	A	45	GLY	0	0.056	0.029	4.368	-1.545	-1.428	-0.001	-0.045	-0.071	0.000
43	A	46	LYS	1	0.888	0.952	5.132	-28.320	-28.307	-0.001	-0.002	-0.010	0.000
44	A	47	PRO	0	0.003	-0.007	8.646	1.686	1.686	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.024	-0.024	10.428	-2.387	-2.387	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.018	0.028	9.492	3.155	3.155	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.036	-0.038	10.978	-1.822	-1.822	0.000	0.000	0.000	0.000
48	A	51	TYR	0	-0.013	-0.044	12.996	0.953	0.953	0.000	0.000	0.000	0.000
49	A	52	THR	0	-0.044	-0.004	15.913	-0.949	-0.949	0.000	0.000	0.000	0.000
50	A	53	GLN	0	0.067	0.022	18.516	0.187	0.187	0.000	0.000	0.000	0.000
51	A	54	GLN	0	-0.014	-0.017	21.572	-0.256	-0.256	0.000	0.000	0.000	0.000
52	A	55	THR	0	-0.004	-0.006	24.517	-0.133	-0.133	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.934	0.973	26.685	-11.833	-11.833	0.000	0.000	0.000	0.000
54	A	57	ALA	0	-0.010	-0.013	30.664	-0.059	-0.059	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.025	0.011	33.308	0.104	0.104	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.048	-0.015	34.722	0.006	0.006	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.827	-0.929	36.798	8.692	8.692	0.000	0.000	0.000	0.000
58	A	61	GLY	0	-0.004	0.014	32.566	0.152	0.152	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.909	0.951	32.117	-8.437	-8.437	0.000	0.000	0.000	0.000
60	A	63	PRO	0	0.020	-0.001	30.233	0.057	0.057	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.066	-0.028	30.570	-0.428	-0.428	0.000	0.000	0.000	0.000
62	A	65	HIS	0	0.002	0.032	26.911	-0.277	-0.277	0.000	0.000	0.000	0.000
63	A	66	SER	0	0.023	0.017	24.645	0.097	0.097	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.774	-0.838	22.550	12.775	12.775	0.000	0.000	0.000	0.000
65	A	68	THR	0	0.013	-0.001	19.556	0.922	0.922	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.030	0.015	18.477	-0.913	-0.913	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.051	-0.025	14.253	0.964	0.964	0.000	0.000	0.000	0.000
68	A	71	LEU	0	0.035	0.029	14.938	-1.168	-1.168	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.830	0.902	14.406	-14.692	-14.692	0.000	0.000	0.000	0.000
70	A	73	VAL	0	0.035	0.021	13.735	-0.823	-0.823	0.000	0.000	0.000	0.000
71	A	74	CYS	0	-0.053	-0.007	15.310	0.210	0.210	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.945	0.960	16.111	-13.376	-13.376	0.000	0.000	0.000	0.000
73	A	76	PRO	0	0.015	-0.006	13.818	-0.212	-0.212	0.000	0.000	0.000	0.000
74	A	77	GLY	0	0.033	0.016	16.338	-0.840	-0.840	0.000	0.000	0.000	0.000
75	A	78	CYS	0	-0.051	-0.004	18.911	-0.722	-0.722	0.000	0.000	0.000	0.000
76	A	79	VAL	0	-0.002	-0.018	17.517	1.075	1.075	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.791	-0.897	19.192	13.908	13.908	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.009	0.003	19.257	1.124	1.124	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.026	-0.013	19.872	-0.857	-0.857	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.017	-0.004	20.485	0.769	0.769	0.000	0.000	0.000	0.000
81	A	84	ALA	0	0.004	0.001	22.968	-0.698	-0.698	0.000	0.000	0.000	0.000
82	A	85	HIS	1	0.823	0.883	24.769	-11.556	-11.556	0.000	0.000	0.000	0.000
83	A	86	PRO	0	0.010	0.008	27.017	-0.318	-0.318	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.048	-0.024	29.609	-0.241	-0.241	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.007	0.011	31.316	-0.337	-0.337	0.000	0.000	0.000	0.000
86	A	89	ILE	0	-0.002	0.001	30.254	-0.231	-0.231	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.032	-0.022	27.230	0.318	0.318	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.738	-0.847	26.104	11.698	11.698	0.000	0.000	0.000	0.000
89	A	92	ILE	0	-0.043	-0.027	23.925	0.628	0.628	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.763	-0.907	24.306	11.447	11.447	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.006	-0.001	23.714	0.805	0.805	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.031	0.004	23.728	-0.548	-0.548	0.000	0.000	0.000	0.000
93	A	96	THR	0	-0.069	-0.021	22.497	0.365	0.365	0.000	0.000	0.000	0.000
94	A	97	TYR	0	0.039	0.018	15.654	0.357	0.357	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.030	-0.007	21.577	0.064	0.064	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.004	0.002	16.929	0.381	0.381	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.003	-0.002	20.255	-0.535	-0.535	0.000	0.000	0.000	0.000
98	A	101	GLY	0	-0.020	-0.014	20.758	-0.222	-0.222	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.938	-0.969	18.610	16.900	16.900	0.000	0.000	0.000	0.000
100	A	103	VAL	0	0.004	0.001	20.193	0.133	0.133	0.000	0.000	0.000	0.000
101	A	104	ILE	0	-0.047	-0.018	15.880	0.185	0.185	0.000	0.000	0.000	0.000
102	A	105	GLU	-1	-0.925	-0.957	20.372	11.790	11.790	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.039	-0.035	18.282	0.381	0.381	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.826	-0.860	22.782	11.164	11.164	0.000	0.000	0.000	0.000
105	A	108	LEU	0	-0.053	-0.030	21.414	0.320	0.320	0.000	0.000	0.000	0.000
106	A	109	SER	0	0.073	-0.001	25.925	-0.505	-0.505	0.000	0.000	0.000	0.000
107	A	110	THR	0	0.015	0.005	28.446	0.115	0.115	0.000	0.000	0.000	0.000
108	A	111	ARG	1	0.730	0.836	29.894	-9.650	-9.650	0.000	0.000	0.000	0.000
109	A	112	ALA	0	-0.058	-0.013	28.911	-0.340	-0.340	0.000	0.000	0.000	0.000
110	A	113	ASP	-1	-0.936	-0.977	29.014	10.787	10.787	0.000	0.000	0.000	0.000
111	A	114	GLY	0	0.000	0.025	28.081	0.383	0.383	0.000	0.000	0.000	0.000
112	A	115	SER	0	-0.068	-0.038	28.659	-0.487	-0.487	0.000	0.000	0.000	0.000
113	A	116	ILE	0	0.008	0.003	29.393	0.304	0.304	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.022	0.007	30.907	-0.295	-0.295	0.000	0.000	0.000	0.000
115	A	118	LEU	0	-0.035	-0.021	32.367	0.166	0.166	0.000	0.000	0.000	0.000
116	A	119	ALA	0	0.024	0.011	34.141	-0.142	-0.142	0.000	0.000	0.000	0.000
117	A	120	PRO	0	-0.001	-0.021	35.784	-0.138	-0.138	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.014	0.001	38.300	-0.126	-0.126	0.000	0.000	0.000	0.000
119	A	122	ALA	0	-0.029	0.005	35.559	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	123	LYS	1	0.944	0.964	37.271	-8.278	-8.278	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.854	-0.935	37.299	7.925	7.925	0.000	0.000	0.000	0.000
122	A	125	VAL	0	-0.004	-0.004	33.277	-0.155	-0.155	0.000	0.000	0.000	0.000
123	A	126	THR	0	-0.035	-0.028	35.930	0.003	0.003	0.000	0.000	0.000	0.000
124	A	127	ALA	0	-0.049	-0.035	33.559	0.035	0.035	0.000	0.000	0.000	0.000
125	A	128	LEU	0	0.014	0.010	29.220	-0.264	-0.264	0.000	0.000	0.000	0.000
126	A	129	ASP	-1	-0.703	-0.785	29.628	10.075	10.075	0.000	0.000	0.000	0.000
127	A	130	ARG	1	0.705	0.809	23.975	-13.035	-13.035	0.000	0.000	0.000	0.000
128	A	131	SER	0	-0.030	-0.039	26.558	0.189	0.189	0.000	0.000	0.000	0.000
129	A	132	TYR	0	0.011	-0.007	22.025	-0.058	-0.058	0.000	0.000	0.000	0.000
130	A	133	ARG	1	0.963	0.988	23.485	-12.100	-12.100	0.000	0.000	0.000	0.000
131	A	134	ILE	0	-0.040	-0.027	17.406	0.107	0.107	0.000	0.000	0.000	0.000
132	A	135	ASP	-1	-0.887	-0.942	20.842	13.119	13.119	0.000	0.000	0.000	0.000
133	A	136	GLY	0	0.084	0.043	19.524	-0.280	-0.280	0.000	0.000	0.000	0.000
134	A	137	ASP	-1	-0.853	-0.912	18.110	18.130	18.130	0.000	0.000	0.000	0.000
135	A	138	GLU	-1	-0.906	-0.954	19.949	11.911	11.911	0.000	0.000	0.000	0.000
136	A	139	LEU	0	-0.001	0.011	18.749	0.266	0.266	0.000	0.000	0.000	0.000
137	A	140	SER	0	-0.014	-0.012	22.154	-0.594	-0.594	0.000	0.000	0.000	0.000
138	A	141	TYR	0	-0.037	-0.058	24.268	0.128	0.128	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.006	-0.002	26.617	-0.508	-0.508	0.000	0.000	0.000	0.000
140	A	143	LEU	0	0.023	0.021	27.595	0.209	0.209	0.000	0.000	0.000	0.000
141	A	144	GLN	0	-0.040	-0.046	30.184	-0.428	-0.428	0.000	0.000	0.000	0.000
142	A	145	MET	0	0.020	0.008	32.589	0.291	0.291	0.000	0.000	0.000	0.000
143	A	146	ARG	1	0.899	0.973	34.895	-8.822	-8.822	0.000	0.000	0.000	0.000
144	A	147	ALA	0	0.051	0.012	37.088	0.184	0.184	0.000	0.000	0.000	0.000
145	A	148	VAL	0	-0.011	0.006	39.076	-0.166	-0.166	0.000	0.000	0.000	0.000
146	A	149	GLY	0	0.008	0.004	42.225	-0.159	-0.159	0.000	0.000	0.000	0.000
147	A	150	GLN	0	-0.075	-0.022	41.572	-0.222	-0.222	0.000	0.000	0.000	0.000
148	A	151	PRO	0	0.003	-0.009	41.445	0.174	0.174	0.000	0.000	0.000	0.000
149	A	152	LEU	0	-0.011	-0.010	34.482	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	153	GLN	0	-0.031	-0.011	37.483	-0.214	-0.214	0.000	0.000	0.000	0.000
151	A	154	ASP	-1	-0.849	-0.912	35.302	9.264	9.264	0.000	0.000	0.000	0.000
152	A	155	HIS	0	-0.104	-0.062	32.915	-0.120	-0.120	0.000	0.000	0.000	0.000
153	A	156	LEU	0	0.007	-0.001	29.712	-0.145	-0.145	0.000	0.000	0.000	0.000
154	A	157	ALA	0	0.022	0.013	29.819	0.080	0.080	0.000	0.000	0.000	0.000
155	A	158	ALA	0	-0.021	0.000	26.835	-0.280	-0.280	0.000	0.000	0.000	0.000
156	A	159	VAL	0	0.022	0.019	26.440	0.177	0.177	0.000	0.000	0.000	0.000
157	A	160	LEU	0	-0.078	-0.036	21.532	-0.159	-0.159	0.000	0.000	0.000	0.000
158	A	161	HIS	0	0.027	0.013	22.020	0.234	0.234	0.000	0.000	0.000	0.000
159	A	162	ARG	1	0.788	0.896	13.742	-20.590	-20.590	0.000	0.000	0.000	0.000
160	A	163	GLN	0	-0.094	-0.055	17.760	-0.990	-0.990	0.000	0.000	0.000	0.000
161	A	164	ARG	1	0.862	0.923	16.462	-15.091	-15.091	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASP)