FMO DATABASE

FMODB ID: J3VL9

Calculation Name: 3CBN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CBN

Chain ID: A

ChEMBL ID:

UniProt ID: O26735

Base Structure: X-ray

Registration Date: 2023-03-14

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	145
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1405113.740881
FMO2-HF: Nuclear repulsion	1347443.076393
FMO2-HF: Total energy	-57670.664488
FMO2-MP2: Total energy	-57838.427476

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:21:LEU)

Summations of interaction energy for fragment #1(A:21:LEU)

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.
-15.993	-8.081	11.048	-7.81	-11.151	-0.055

Interaction energy analysis for fragmet #1(A:21:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.022

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	23	VAL	0	-0.012	-0.026	3.613	-2.044	0.128	-0.008	-1.077	-1.087	0.005
4	A	24	LEU	0	-0.031	0.000	5.956	0.251	0.251	0.000	0.000	0.000	0.000
5	A	25	ARG	1	0.873	0.912	9.529	0.216	0.216	0.000	0.000	0.000	0.000
6	A	26	TYR	0	-0.023	-0.038	12.597	0.032	0.032	0.000	0.000	0.000	0.000
7	A	27	THR	0	-0.065	-0.029	16.108	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.055	0.053	19.320	0.009	0.009	0.000	0.000	0.000	0.000
9	A	29	ARG	1	0.909	0.932	22.384	0.036	0.036	0.000	0.000	0.000	0.000
10	A	30	ALA	0	0.065	0.055	25.802	0.002	0.002	0.000	0.000	0.000	0.000
11	A	31	ARG	1	0.876	0.950	28.330	0.026	0.026	0.000	0.000	0.000	0.000
12	A	32	GLY	0	0.050	0.026	31.258	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	33	HIS	0	-0.024	-0.038	32.678	0.001	0.001	0.000	0.000	0.000	0.000
14	A	34	PRO	0	0.004	-0.005	35.724	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	35	ASN	0	-0.030	-0.011	37.504	0.000	0.000	0.000	0.000	0.000	0.000
16	A	36	VAL	0	-0.014	0.026	31.531	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	37	THR	0	-0.005	-0.020	33.865	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	38	ALA	0	0.016	-0.001	29.193	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	39	GLY	0	0.039	0.024	30.658	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	40	HIS	0	0.028	0.043	28.048	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	41	ARG	1	0.908	0.935	28.294	0.046	0.046	0.000	0.000	0.000	0.000
22	A	42	THR	0	-0.041	-0.028	25.106	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	43	THR	0	-0.022	-0.014	23.482	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	44	PHE	0	0.045	0.009	19.494	0.003	0.003	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.923	-0.964	23.496	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	46	VAL	0	-0.022	-0.003	23.772	0.001	0.001	0.000	0.000	0.000	0.000
27	A	47	THR	0	0.044	0.003	25.885	0.001	0.001	0.000	0.000	0.000	0.000
28	A	48	VAL	0	0.002	0.004	27.656	0.000	0.000	0.000	0.000	0.000	0.000
29	A	49	ASP	-1	-0.911	-0.936	29.902	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	50	PRO	0	-0.068	-0.044	32.871	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	51	GLU	-1	-0.897	-0.937	35.352	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	52	ILE	0	0.036	0.022	32.928	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	53	GLY	0	0.006	0.001	36.318	0.001	0.001	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.925	-0.970	37.727	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	55	THR	0	-0.044	-0.038	37.884	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	ALA	0	0.015	0.028	33.223	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	ASP	-1	-0.862	-0.944	32.739	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	58	CYS	0	-0.008	-0.009	27.845	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	59	ILE	0	0.005	0.012	27.726	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	60	ILE	0	-0.041	-0.029	24.088	0.001	0.001	0.000	0.000	0.000	0.000
41	A	61	GLY	0	-0.012	-0.010	27.860	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	62	VAL	0	0.002	0.018	28.797	0.000	0.000	0.000	0.000	0.000	0.000
43	A	63	SER	0	-0.015	-0.028	30.603	0.000	0.000	0.000	0.000	0.000	0.000
44	A	64	SER	0	-0.027	-0.036	25.327	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	65	SER	0	-0.051	-0.026	24.947	0.002	0.002	0.000	0.000	0.000	0.000
46	A	66	ASP	-1	-0.803	-0.865	22.759	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	67	SER	0	0.052	0.063	24.618	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	68	ILE	0	-0.040	-0.021	18.441	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	69	SER	0	0.006	0.005	20.484	0.002	0.002	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.071	-0.066	22.554	0.008	0.008	0.000	0.000	0.000	0.000
51	A	71	LEU	0	0.003	0.027	17.122	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	72	PRO	0	0.026	0.003	15.913	0.013	0.013	0.000	0.000	0.000	0.000
53	A	73	ASP	-1	-0.830	-0.931	16.288	0.031	0.031	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.902	-0.937	11.273	0.241	0.241	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.033	-0.011	11.716	0.001	0.001	0.000	0.000	0.000	0.000
56	A	76	LYS	1	0.859	0.936	12.508	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	77	ARG	1	0.886	0.935	12.232	-0.153	-0.153	0.000	0.000	0.000	0.000
58	A	78	ALA	0	-0.025	0.003	8.262	0.019	0.019	0.000	0.000	0.000	0.000
59	A	79	ILE	0	0.003	-0.013	8.861	-0.059	-0.059	0.000	0.000	0.000	0.000
60	A	80	ALA	0	0.002	0.012	10.959	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	81	ARG	1	0.809	0.905	6.667	-0.190	-0.190	0.000	0.000	0.000	0.000
62	A	82	GLU	-1	-0.872	-0.951	9.592	-0.072	-0.072	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.074	-0.043	6.802	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	84	SER	0	0.006	0.031	5.431	-0.088	-0.088	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.031	-0.012	5.521	0.087	0.087	0.000	0.000	0.000	0.000
66	A	86	VAL	0	0.037	0.006	7.489	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	87	ARG	1	0.842	0.915	9.912	0.310	0.310	0.000	0.000	0.000	0.000
68	A	88	VAL	0	-0.001	-0.003	12.561	0.003	0.003	0.000	0.000	0.000	0.000
69	A	89	ILE	0	-0.055	-0.017	14.851	0.003	0.003	0.000	0.000	0.000	0.000
70	A	90	LEU	0	0.000	0.007	18.295	0.008	0.008	0.000	0.000	0.000	0.000
71	A	91	ARG	1	0.840	0.891	17.989	0.116	0.116	0.000	0.000	0.000	0.000
72	A	92	THR	0	0.031	0.002	24.560	0.002	0.002	0.000	0.000	0.000	0.000
73	A	93	GLU	-1	-0.872	-0.932	28.182	-0.040	-0.040	0.000	0.000	0.000	0.000
74	A	94	ASN	0	-0.116	-0.077	30.506	0.001	0.001	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.043	0.026	28.125	0.000	0.000	0.000	0.000	0.000	0.000
76	A	96	TYR	0	-0.056	-0.037	18.105	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	97	ASP	-1	-0.745	-0.864	21.833	-0.096	-0.096	0.000	0.000	0.000	0.000
78	A	98	GLU	-1	-0.830	-0.883	14.673	-0.204	-0.204	0.000	0.000	0.000	0.000
79	A	99	ILE	0	-0.015	0.007	17.054	0.005	0.005	0.000	0.000	0.000	0.000
80	A	100	ARG	1	0.825	0.881	10.430	0.210	0.210	0.000	0.000	0.000	0.000
81	A	101	GLY	0	0.081	0.008	12.582	0.024	0.024	0.000	0.000	0.000	0.000
82	A	102	TYR	0	-0.090	-0.036	10.043	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	103	GLY	0	0.077	0.048	10.040	0.030	0.030	0.000	0.000	0.000	0.000
84	A	104	HIS	0	-0.025	-0.032	11.526	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	105	PRO	0	0.004	0.003	12.702	0.008	0.008	0.000	0.000	0.000	0.000
86	A	106	GLU	-1	-0.936	-0.969	14.395	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.081	-0.018	14.120	0.001	0.001	0.000	0.000	0.000	0.000
88	A	108	THR	0	-0.008	-0.046	17.569	0.006	0.006	0.000	0.000	0.000	0.000
89	A	109	LEU	0	-0.081	-0.035	15.636	0.004	0.004	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.807	-0.899	19.876	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	111	HIS	0	-0.003	0.014	23.417	0.003	0.003	0.000	0.000	0.000	0.000
92	A	112	PRO	0	0.001	-0.018	25.373	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	113	THR	0	-0.010	-0.032	27.902	0.002	0.002	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.797	-0.864	26.190	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	115	ILE	0	0.001	0.001	20.054	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	116	VAL	0	-0.023	-0.012	21.773	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	117	CYS	0	-0.033	0.008	18.614	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	118	ARG	1	0.853	0.848	19.246	0.067	0.067	0.000	0.000	0.000	0.000
99	A	119	LYS	1	0.846	0.931	19.071	0.083	0.083	0.000	0.000	0.000	0.000
100	A	120	SER	0	-0.045	-0.015	20.562	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	121	ASP	-1	-0.888	-0.961	19.170	-0.084	-0.084	0.000	0.000	0.000	0.000
102	A	122	TYR	0	-0.015	-0.003	20.128	0.005	0.005	0.000	0.000	0.000	0.000
103	A	123	ILE	0	0.024	0.006	17.723	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	124	CYM	-1	-0.883	-0.783	21.644	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	125	SER	0	0.085	0.030	21.874	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	126	ARG	1	0.929	0.905	22.659	0.033	0.033	0.000	0.000	0.000	0.000
107	A	127	THR	0	-0.062	-0.067	18.208	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	128	LEU	0	0.027	0.019	15.485	0.002	0.002	0.000	0.000	0.000	0.000
109	A	129	MET	0	-0.047	-0.009	14.088	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	130	ILE	0	-0.001	0.021	14.904	0.017	0.017	0.000	0.000	0.000	0.000
111	A	131	ARG	1	0.866	0.929	12.528	0.146	0.146	0.000	0.000	0.000	0.000
112	A	132	ALA	0	0.032	0.008	16.329	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	133	ASP	-1	-0.829	-0.919	16.822	-0.142	-0.142	0.000	0.000	0.000	0.000
114	A	134	LYS	1	0.786	0.876	18.766	0.110	0.110	0.000	0.000	0.000	0.000
115	A	135	ALA	0	-0.035	-0.013	21.192	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	136	ALA	0	-0.006	-0.007	23.995	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	137	PHE	0	-0.022	-0.013	26.645	0.002	0.002	0.000	0.000	0.000	0.000
118	A	138	ASP	-1	-0.825	-0.909	24.479	-0.080	-0.080	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.057	-0.018	23.159	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	140	ASP	-1	-0.782	-0.897	25.732	-0.060	-0.060	0.000	0.000	0.000	0.000
121	A	141	GLU	-1	-0.814	-0.894	27.500	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	142	ASN	0	-0.052	-0.044	30.368	0.006	0.006	0.000	0.000	0.000	0.000
123	A	143	LEU	0	0.011	0.022	25.404	0.002	0.002	0.000	0.000	0.000	0.000
124	A	144	VAL	0	0.021	0.006	29.208	0.004	0.004	0.000	0.000	0.000	0.000
125	A	145	ARG	1	0.761	0.863	31.525	0.049	0.049	0.000	0.000	0.000	0.000
126	A	146	ASP	-1	-0.751	-0.847	31.529	-0.043	-0.043	0.000	0.000	0.000	0.000
127	A	147	LEU	0	-0.006	0.001	28.132	0.003	0.003	0.000	0.000	0.000	0.000
128	A	148	ARG	1	0.875	0.945	32.672	0.043	0.043	0.000	0.000	0.000	0.000
129	A	149	LYS	1	0.875	0.943	35.893	0.038	0.038	0.000	0.000	0.000	0.000
130	A	150	GLY	0	-0.015	-0.005	35.423	0.002	0.002	0.000	0.000	0.000	0.000
131	A	151	ARG	1	0.754	0.888	33.225	0.038	0.038	0.000	0.000	0.000	0.000
132	A	152	GLU	-1	-0.912	-0.958	29.923	-0.037	-0.037	0.000	0.000	0.000	0.000
133	A	153	LEU	0	-0.005	-0.003	25.024	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	154	LYS	1	0.824	0.908	21.437	0.079	0.079	0.000	0.000	0.000	0.000
135	A	155	VAL	0	0.037	0.012	19.650	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	156	GLU	-1	-0.834	-0.887	15.387	-0.152	-0.152	0.000	0.000	0.000	0.000
137	A	157	ILE	0	0.049	0.023	13.191	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	158	ILE	0	-0.042	-0.037	9.060	0.000	0.000	0.000	0.000	0.000	0.000
139	A	159	VAL	0	0.020	0.014	7.368	0.011	0.011	0.000	0.000	0.000	0.000
140	A	160	GLU	-1	-0.948	-0.963	2.743	-2.386	-1.084	0.372	-0.354	-1.320	-0.002
141	A	161	TYR	0	-0.024	-0.023	3.591	-0.702	0.366	0.046	-0.326	-0.789	-0.001
142	A	162	GLU	-1	-0.794	-0.898	2.170	-10.865	-7.130	10.585	-6.643	-7.677	-0.057
143	A	163	GLY	0	-0.002	0.005	3.123	0.273	-0.123	0.054	0.591	-0.249	0.000
144	A	164	HIS	0	-0.032	-0.021	5.355	-0.557	-0.526	-0.001	-0.001	-0.029	0.000
145	A	165	HIS	0	0.030	0.024	7.904	-0.071	-0.071	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:LEU)