FMO DATABASE

FMODB ID: YVRM2

Calculation Name: 3CFU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CFU

Chain ID: A

ChEMBL ID:

UniProt ID: O34725

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	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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1447780.406553
FMO2-HF: Nuclear repulsion	1387901.33382
FMO2-HF: Total energy	-59879.072733
FMO2-MP2: Total energy	-60054.16287

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:63:MET)

Summations of interaction energy for fragment #1(A:63:MET)

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.
-16.586	-8.273	5.984	-4.609	-9.688	-0.019

Interaction energy analysis for fragmet #1(A:63:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.007

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	65	LYS	1	0.807	0.885	3.502	-2.030	0.659	0.033	-1.389	-1.332	0.003
4	A	66	ILE	0	0.048	0.022	6.338	-0.223	-0.223	0.000	0.000	0.000	0.000
5	A	67	GLY	0	-0.033	-0.010	9.660	-0.003	-0.003	0.000	0.000	0.000	0.000
6	A	68	GLU	-1	-0.854	-0.902	6.557	-3.954	-3.954	0.000	0.000	0.000	0.000
7	A	69	THR	0	-0.033	-0.016	10.493	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	70	PHE	0	-0.027	-0.015	7.257	-0.203	-0.203	0.000	0.000	0.000	0.000
9	A	71	LYS	1	0.918	0.957	11.009	0.874	0.874	0.000	0.000	0.000	0.000
10	A	72	ALA	0	0.007	-0.004	10.064	-0.233	-0.233	0.000	0.000	0.000	0.000
11	A	73	GLY	0	0.056	0.055	11.738	0.126	0.126	0.000	0.000	0.000	0.000
12	A	74	HIS	0	-0.092	-0.069	14.748	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	75	THR	0	-0.033	-0.020	14.668	0.042	0.042	0.000	0.000	0.000	0.000
14	A	76	ASN	0	-0.046	-0.027	14.186	-0.147	-0.147	0.000	0.000	0.000	0.000
15	A	77	PHE	0	0.021	-0.008	9.398	0.120	0.120	0.000	0.000	0.000	0.000
16	A	78	THR	0	0.041	0.018	11.185	-0.168	-0.168	0.000	0.000	0.000	0.000
17	A	79	VAL	0	0.045	0.027	8.710	0.137	0.137	0.000	0.000	0.000	0.000
18	A	80	ASN	0	-0.019	-0.006	11.531	0.017	0.017	0.000	0.000	0.000	0.000
19	A	81	LYS	1	0.835	0.885	14.123	0.257	0.257	0.000	0.000	0.000	0.000
20	A	82	VAL	0	-0.019	-0.005	11.444	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	83	ASP	-1	-0.815	-0.883	14.812	-0.112	-0.112	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.843	0.898	15.467	-0.103	-0.103	0.000	0.000	0.000	0.000
23	A	85	VAL	0	-0.013	0.010	19.212	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	86	GLN	0	0.015	-0.004	21.793	0.013	0.013	0.000	0.000	0.000	0.000
25	A	87	LYS	1	0.741	0.860	24.236	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	88	GLY	0	0.016	0.007	26.902	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	89	GLU	-1	-0.825	-0.911	27.742	0.012	0.012	0.000	0.000	0.000	0.000
28	A	90	TYR	0	-0.048	-0.017	22.485	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	91	MET	0	-0.019	-0.006	24.615	0.006	0.006	0.000	0.000	0.000	0.000
30	A	92	ASN	0	0.038	0.005	22.178	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	93	VAL	0	-0.051	-0.014	20.669	0.002	0.002	0.000	0.000	0.000	0.000
32	A	94	GLY	0	-0.002	-0.007	22.803	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	95	GLY	0	-0.036	-0.022	24.747	0.007	0.007	0.000	0.000	0.000	0.000
34	A	96	ALA	0	0.043	0.028	25.778	0.009	0.009	0.000	0.000	0.000	0.000
35	A	97	VAL	0	0.025	0.003	27.897	0.006	0.006	0.000	0.000	0.000	0.000
36	A	98	ASN	0	-0.062	-0.025	30.603	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	99	GLU	-1	-0.820	-0.902	31.391	0.002	0.002	0.000	0.000	0.000	0.000
38	A	100	GLU	-1	-0.888	-0.924	25.632	0.015	0.015	0.000	0.000	0.000	0.000
39	A	101	THR	0	-0.030	-0.021	29.983	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	102	LYS	1	0.789	0.863	32.458	0.005	0.005	0.000	0.000	0.000	0.000
41	A	103	THR	0	-0.034	-0.018	31.010	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	104	ILE	0	0.026	0.035	25.803	0.007	0.007	0.000	0.000	0.000	0.000
43	A	105	LYS	1	0.858	0.918	27.898	-0.060	-0.060	0.000	0.000	0.000	0.000
44	A	106	ASP	-1	-0.782	-0.894	24.945	0.038	0.038	0.000	0.000	0.000	0.000
45	A	107	ASP	-1	-0.915	-0.943	20.609	0.095	0.095	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.802	-0.901	20.176	0.185	0.185	0.000	0.000	0.000	0.000
47	A	109	GLU	-1	-0.828	-0.888	18.130	0.136	0.136	0.000	0.000	0.000	0.000
48	A	110	ARG	1	0.789	0.864	18.324	0.069	0.069	0.000	0.000	0.000	0.000
49	A	111	LEU	0	0.020	0.006	12.256	0.002	0.002	0.000	0.000	0.000	0.000
50	A	112	ILE	0	-0.013	0.006	16.460	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	113	ILE	0	0.012	0.010	10.657	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	114	GLU	-1	-0.810	-0.878	14.365	-0.264	-0.264	0.000	0.000	0.000	0.000
53	A	115	VAL	0	-0.029	-0.021	12.561	-0.060	-0.060	0.000	0.000	0.000	0.000
54	A	116	THR	0	-0.027	-0.029	14.828	0.081	0.081	0.000	0.000	0.000	0.000
55	A	117	MET	0	-0.010	0.018	15.246	-0.093	-0.093	0.000	0.000	0.000	0.000
56	A	118	GLU	-1	-0.817	-0.903	17.161	-0.488	-0.488	0.000	0.000	0.000	0.000
57	A	119	ASN	0	-0.031	-0.019	18.323	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	120	ILE	0	-0.053	-0.026	17.001	0.025	0.025	0.000	0.000	0.000	0.000
59	A	121	GLY	0	0.030	0.020	21.013	0.001	0.001	0.000	0.000	0.000	0.000
60	A	122	GLU	-1	-0.955	-0.962	23.091	-0.224	-0.224	0.000	0.000	0.000	0.000
61	A	123	ASP	-1	-0.776	-0.871	24.858	-0.240	-0.240	0.000	0.000	0.000	0.000
62	A	124	SER	0	-0.091	-0.047	25.667	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	125	ILE	0	0.009	0.021	19.474	0.003	0.003	0.000	0.000	0.000	0.000
64	A	126	SER	0	-0.034	-0.025	23.497	0.018	0.018	0.000	0.000	0.000	0.000
65	A	127	TYR	0	0.020	0.016	20.251	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	128	ASN	0	0.028	0.001	20.230	0.037	0.037	0.000	0.000	0.000	0.000
67	A	129	PHE	0	0.044	0.003	18.064	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	130	ILE	0	-0.033	-0.013	17.015	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	131	GLY	0	0.021	0.030	15.866	0.006	0.006	0.000	0.000	0.000	0.000
70	A	132	PHE	0	-0.060	-0.038	11.885	-0.126	-0.126	0.000	0.000	0.000	0.000
71	A	133	ASP	-1	-0.775	-0.851	10.368	-0.125	-0.125	0.000	0.000	0.000	0.000
72	A	134	LEU	0	-0.053	-0.018	8.281	-0.147	-0.147	0.000	0.000	0.000	0.000
73	A	135	ARG	1	0.786	0.883	6.814	0.357	0.357	0.000	0.000	0.000	0.000
74	A	136	ASP	-1	-0.789	-0.884	7.176	0.312	0.312	0.000	0.000	0.000	0.000
75	A	137	LYS	1	0.902	0.949	7.189	-1.053	-1.053	0.000	0.000	0.000	0.000
76	A	138	ASN	0	-0.078	-0.060	8.254	0.298	0.298	0.000	0.000	0.000	0.000
77	A	139	ASP	-1	-0.823	-0.909	6.561	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	140	GLN	0	-0.044	-0.017	8.907	-0.102	-0.102	0.000	0.000	0.000	0.000
79	A	141	SER	0	0.014	-0.008	11.233	0.016	0.016	0.000	0.000	0.000	0.000
80	A	142	VAL	0	-0.074	-0.039	11.586	0.048	0.048	0.000	0.000	0.000	0.000
81	A	143	ARG	1	0.956	0.976	14.016	-0.109	-0.109	0.000	0.000	0.000	0.000
82	A	144	PRO	0	0.040	0.029	16.807	0.005	0.005	0.000	0.000	0.000	0.000
83	A	145	VAL	0	0.001	-0.005	17.683	0.021	0.021	0.000	0.000	0.000	0.000
84	A	146	PHE	0	-0.035	-0.022	20.041	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	147	SER	0	0.054	0.002	22.686	0.019	0.019	0.000	0.000	0.000	0.000
86	A	148	ILE	0	-0.012	-0.017	25.480	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	149	GLU	-1	-0.794	-0.868	25.832	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	150	GLU	-1	-0.762	-0.852	21.588	-0.116	-0.116	0.000	0.000	0.000	0.000
89	A	151	LYS	1	0.838	0.907	25.257	0.085	0.085	0.000	0.000	0.000	0.000
90	A	152	GLY	0	-0.009	-0.004	27.595	0.000	0.000	0.000	0.000	0.000	0.000
91	A	153	ARG	1	0.835	0.901	20.926	0.173	0.173	0.000	0.000	0.000	0.000
92	A	154	ILE	0	-0.041	-0.010	21.661	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	155	LEU	0	0.003	0.019	17.040	0.003	0.003	0.000	0.000	0.000	0.000
94	A	156	MET	0	-0.029	-0.012	20.695	0.010	0.010	0.000	0.000	0.000	0.000
95	A	157	GLY	0	0.067	0.009	22.384	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	158	GLY	0	-0.048	-0.012	23.968	0.019	0.019	0.000	0.000	0.000	0.000
97	A	159	THR	0	-0.024	-0.008	25.449	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	160	LEU	0	-0.028	-0.006	20.343	0.007	0.007	0.000	0.000	0.000	0.000
99	A	161	VAL	0	0.034	0.009	24.364	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	162	SER	0	0.013	0.002	24.987	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	163	GLY	0	0.028	0.021	24.429	0.019	0.019	0.000	0.000	0.000	0.000
102	A	164	LYS	1	0.834	0.910	23.876	0.305	0.305	0.000	0.000	0.000	0.000
103	A	165	LYS	1	0.872	0.914	19.831	0.472	0.472	0.000	0.000	0.000	0.000
104	A	166	VAL	0	0.006	0.015	20.612	0.042	0.042	0.000	0.000	0.000	0.000
105	A	167	THR	0	0.011	0.004	19.065	-0.067	-0.067	0.000	0.000	0.000	0.000
106	A	168	GLY	0	0.031	0.031	18.907	0.042	0.042	0.000	0.000	0.000	0.000
107	A	169	VAL	0	-0.064	-0.032	17.468	-0.041	-0.041	0.000	0.000	0.000	0.000
108	A	170	LEU	0	0.036	0.035	13.055	0.014	0.014	0.000	0.000	0.000	0.000
109	A	171	SER	0	-0.049	-0.037	16.390	0.023	0.023	0.000	0.000	0.000	0.000
110	A	172	TYR	0	0.068	0.024	13.177	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	173	VAL	0	-0.024	-0.003	16.367	0.006	0.006	0.000	0.000	0.000	0.000
112	A	174	ILE	0	-0.013	0.003	12.725	0.009	0.009	0.000	0.000	0.000	0.000
113	A	175	PRO	0	0.048	0.012	15.137	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	176	LYS	1	0.786	0.867	16.647	-0.117	-0.117	0.000	0.000	0.000	0.000
115	A	177	GLY	0	-0.006	0.008	16.554	0.032	0.032	0.000	0.000	0.000	0.000
116	A	178	GLU	-1	-0.788	-0.871	12.372	0.641	0.641	0.000	0.000	0.000	0.000
117	A	179	GLN	0	-0.019	-0.033	10.867	0.049	0.049	0.000	0.000	0.000	0.000
118	A	180	LYS	1	0.818	0.903	9.182	-0.588	-0.588	0.000	0.000	0.000	0.000
119	A	181	HIS	0	-0.068	-0.054	7.552	0.500	0.500	0.000	0.000	0.000	0.000
120	A	182	TYR	0	-0.011	-0.006	6.677	0.125	0.125	0.000	0.000	0.000	0.000
121	A	183	THR	0	-0.029	-0.019	2.511	-1.286	-0.687	2.096	-0.790	-1.905	-0.009
122	A	184	LEU	0	0.016	0.025	4.502	0.135	0.206	-0.001	-0.010	-0.061	0.000
123	A	185	VAL	0	-0.023	-0.012	5.371	-0.601	-0.601	0.000	0.000	0.000	0.000
124	A	186	TYR	0	0.024	-0.010	7.776	0.223	0.223	0.000	0.000	0.000	0.000
125	A	187	ASN	0	0.024	0.001	9.844	-0.158	-0.158	0.000	0.000	0.000	0.000
126	A	188	PRO	0	-0.015	-0.006	11.789	0.075	0.075	0.000	0.000	0.000	0.000
127	A	189	PHE	0	-0.027	0.000	14.813	0.064	0.064	0.000	0.000	0.000	0.000
128	A	190	LEU	0	0.031	0.016	15.972	0.045	0.045	0.000	0.000	0.000	0.000
129	A	191	ALA	0	-0.020	-0.002	15.842	0.030	0.030	0.000	0.000	0.000	0.000
130	A	192	ASP	-1	-0.789	-0.903	17.864	-0.282	-0.282	0.000	0.000	0.000	0.000
131	A	193	THR	0	-0.019	-0.014	20.697	0.021	0.021	0.000	0.000	0.000	0.000
132	A	194	ASN	0	-0.033	0.011	23.762	0.046	0.046	0.000	0.000	0.000	0.000
133	A	195	SER	0	0.031	0.016	25.673	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	196	SER	0	-0.107	-0.071	28.326	0.010	0.010	0.000	0.000	0.000	0.000
135	A	197	ASN	0	0.043	0.024	24.373	0.011	0.011	0.000	0.000	0.000	0.000
136	A	198	THR	0	0.007	-0.006	23.705	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	199	GLU	-1	-0.897	-0.956	23.720	-0.175	-0.175	0.000	0.000	0.000	0.000
138	A	200	GLU	-1	-0.943	-0.973	24.597	-0.208	-0.208	0.000	0.000	0.000	0.000
139	A	201	ARG	1	0.730	0.840	20.212	0.290	0.290	0.000	0.000	0.000	0.000
140	A	202	VAL	0	0.054	0.030	19.494	-0.039	-0.039	0.000	0.000	0.000	0.000
141	A	203	LYS	1	0.869	0.932	17.980	0.267	0.267	0.000	0.000	0.000	0.000
142	A	204	ASP	-1	-0.829	-0.894	15.119	-0.577	-0.577	0.000	0.000	0.000	0.000
143	A	205	ASP	-1	-0.908	-0.943	14.072	-0.407	-0.407	0.000	0.000	0.000	0.000
144	A	206	ILE	0	-0.034	-0.021	8.815	0.035	0.035	0.000	0.000	0.000	0.000
145	A	207	ASP	-1	-0.796	-0.896	7.973	-0.599	-0.599	0.000	0.000	0.000	0.000
146	A	208	TYR	0	-0.051	-0.028	5.851	-0.201	-0.201	0.000	0.000	0.000	0.000
147	A	209	LEU	0	0.007	0.000	2.448	-1.684	-0.565	1.812	-0.579	-2.352	-0.004
148	A	210	VAL	0	-0.028	-0.023	3.275	-3.726	-1.847	0.150	-1.055	-0.974	-0.008
149	A	211	LYS	1	0.784	0.893	2.473	-3.609	-1.776	1.888	-0.760	-2.961	-0.001
150	A	212	LEU	0	0.025	0.007	3.969	-0.560	-0.437	0.006	-0.026	-0.103	0.000
151	A	213	ASP	-1	-0.805	-0.882	6.980	2.005	2.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:MET)