FMO DATABASE

FMODB ID: N1L9Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1403791.720578
FMO2-HF: Nuclear repulsion	1346121.666429
FMO2-HF: Total energy	-57670.054149
FMO2-MP2: Total energy	-57837.799445

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.
-14.849	-7.576	11.324	-7.758	-10.839	-0.052

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 : -0.033 / q_NPA : -0.023

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	-0.009	-0.023	3.602	-1.967	0.101	-0.006	-1.008	-1.054	0.004
4	A	24	LEU	0	-0.032	-0.002	5.932	0.250	0.250	0.000	0.000	0.000	0.000
5	A	25	ARG	1	0.868	0.913	9.513	0.280	0.280	0.000	0.000	0.000	0.000
6	A	26	TYR	0	-0.013	-0.030	12.583	0.040	0.040	0.000	0.000	0.000	0.000
7	A	27	THR	0	-0.045	-0.025	16.097	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.037	0.050	19.311	0.012	0.012	0.000	0.000	0.000	0.000
9	A	29	ARG	1	0.896	0.920	22.380	0.047	0.047	0.000	0.000	0.000	0.000
10	A	30	ALA	0	0.073	0.061	25.799	0.004	0.004	0.000	0.000	0.000	0.000
11	A	31	ARG	1	0.909	0.972	28.267	0.032	0.032	0.000	0.000	0.000	0.000
12	A	32	GLY	0	0.051	0.027	31.179	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	33	HIS	0	-0.023	-0.029	32.613	0.001	0.001	0.000	0.000	0.000	0.000
14	A	34	PRO	0	-0.001	-0.010	35.665	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	35	ASN	0	-0.018	-0.003	37.579	0.000	0.000	0.000	0.000	0.000	0.000
16	A	36	VAL	0	-0.013	0.026	31.458	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	37	THR	0	-0.035	-0.034	33.854	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	38	ALA	0	0.022	-0.002	29.228	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	39	GLY	0	0.047	0.027	30.648	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	40	HIS	0	0.030	0.031	28.257	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	41	ARG	1	0.951	0.957	28.303	0.056	0.056	0.000	0.000	0.000	0.000
22	A	42	THR	0	-0.052	-0.034	25.145	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	43	THR	0	-0.013	-0.005	23.490	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	44	PHE	0	0.055	0.009	19.305	0.002	0.002	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.904	-0.967	23.476	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	46	VAL	0	-0.036	-0.001	23.584	0.000	0.000	0.000	0.000	0.000	0.000
27	A	47	THR	0	0.049	0.006	25.834	0.003	0.003	0.000	0.000	0.000	0.000
28	A	48	VAL	0	-0.015	-0.002	27.584	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	49	ASP	-1	-0.912	-0.941	29.832	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	50	PRO	0	-0.066	-0.048	32.807	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	51	GLU	-1	-0.898	-0.940	35.283	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	52	ILE	0	0.034	0.023	32.992	0.000	0.000	0.000	0.000	0.000	0.000
33	A	53	GLY	0	-0.007	-0.008	36.274	0.001	0.001	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.927	-0.970	37.695	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	55	THR	0	-0.048	-0.039	37.870	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	ALA	0	0.022	0.031	33.124	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	ASP	-1	-0.883	-0.949	32.993	-0.054	-0.054	0.000	0.000	0.000	0.000
38	A	58	CYS	0	-0.022	-0.017	27.823	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	59	ILE	0	0.022	0.026	27.704	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	60	ILE	0	-0.040	-0.030	24.047	0.001	0.001	0.000	0.000	0.000	0.000
41	A	61	GLY	0	-0.022	-0.016	27.797	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	62	VAL	0	0.010	0.022	28.737	0.001	0.001	0.000	0.000	0.000	0.000
43	A	63	SER	0	-0.033	-0.040	30.528	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	64	SER	0	-0.038	-0.047	25.241	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	65	SER	0	-0.056	-0.030	25.015	0.002	0.002	0.000	0.000	0.000	0.000
46	A	66	ASP	-1	-0.817	-0.873	22.688	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	67	SER	0	0.060	0.077	24.487	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	68	ILE	0	-0.051	-0.020	18.539	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	69	SER	0	-0.011	-0.011	20.420	0.004	0.004	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.051	-0.056	22.540	0.010	0.010	0.000	0.000	0.000	0.000
51	A	71	LEU	0	0.003	0.027	16.857	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	72	PRO	0	0.022	0.006	15.929	0.016	0.016	0.000	0.000	0.000	0.000
53	A	73	ASP	-1	-0.852	-0.942	16.276	0.063	0.063	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-1.001	-1.010	10.900	0.228	0.228	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.017	0.002	11.708	0.014	0.014	0.000	0.000	0.000	0.000
56	A	76	LYS	1	0.893	0.949	12.439	-0.040	-0.040	0.000	0.000	0.000	0.000
57	A	77	ARG	1	0.936	0.971	12.403	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	78	ALA	0	-0.023	0.003	8.234	0.034	0.034	0.000	0.000	0.000	0.000
59	A	79	ILE	0	0.007	-0.010	8.830	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	80	ALA	0	0.008	0.015	10.926	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	81	ARG	1	0.820	0.909	6.991	-0.395	-0.395	0.000	0.000	0.000	0.000
62	A	82	GLU	-1	-0.869	-0.949	9.745	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.079	-0.040	6.656	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	84	SER	0	-0.008	0.025	5.465	-0.127	-0.127	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.022	-0.011	5.247	0.079	0.079	0.000	0.000	0.000	0.000
66	A	86	VAL	0	0.042	0.009	7.501	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	87	ARG	1	0.884	0.952	9.611	0.428	0.428	0.000	0.000	0.000	0.000
68	A	88	VAL	0	0.018	0.005	12.518	0.007	0.007	0.000	0.000	0.000	0.000
69	A	89	ILE	0	-0.056	-0.018	14.886	0.000	0.000	0.000	0.000	0.000	0.000
70	A	90	LEU	0	0.003	0.003	18.230	0.012	0.012	0.000	0.000	0.000	0.000
71	A	91	ARG	1	0.914	0.951	18.373	0.149	0.149	0.000	0.000	0.000	0.000
72	A	92	THR	0	0.017	-0.015	24.482	0.003	0.003	0.000	0.000	0.000	0.000
73	A	93	GLU	-1	-0.880	-0.937	28.097	-0.055	-0.055	0.000	0.000	0.000	0.000
74	A	94	ASN	0	-0.094	-0.045	30.416	0.000	0.000	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.056	0.030	28.054	0.000	0.000	0.000	0.000	0.000	0.000
76	A	96	TYR	0	-0.079	-0.049	18.194	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	97	ASP	-1	-0.757	-0.885	21.905	-0.127	-0.127	0.000	0.000	0.000	0.000
78	A	98	GLU	-1	-0.954	-0.977	14.294	-0.277	-0.277	0.000	0.000	0.000	0.000
79	A	99	ILE	0	-0.014	0.006	17.010	0.005	0.005	0.000	0.000	0.000	0.000
80	A	100	ARG	1	0.882	0.932	10.061	0.319	0.319	0.000	0.000	0.000	0.000
81	A	101	GLY	0	0.086	0.012	12.589	0.030	0.030	0.000	0.000	0.000	0.000
82	A	102	TYR	0	-0.099	-0.038	9.764	-0.064	-0.064	0.000	0.000	0.000	0.000
83	A	103	GLY	0	0.074	0.045	10.076	0.034	0.034	0.000	0.000	0.000	0.000
84	A	104	HIS	0	-0.025	-0.026	11.549	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	105	PRO	0	-0.004	0.001	12.872	0.011	0.011	0.000	0.000	0.000	0.000
86	A	106	GLU	-1	-0.926	-0.973	14.440	0.003	0.003	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.086	-0.020	14.096	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	108	THR	0	0.000	-0.027	17.565	0.010	0.010	0.000	0.000	0.000	0.000
89	A	109	LEU	0	-0.067	-0.035	15.619	0.005	0.005	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.819	-0.916	19.842	0.008	0.008	0.000	0.000	0.000	0.000
91	A	111	HIS	0	-0.016	0.013	23.378	0.001	0.001	0.000	0.000	0.000	0.000
92	A	112	PRO	0	-0.001	-0.025	25.323	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	113	THR	0	-0.011	-0.035	27.850	0.002	0.002	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.808	-0.879	26.146	-0.039	-0.039	0.000	0.000	0.000	0.000
95	A	115	ILE	0	-0.008	-0.006	20.014	0.001	0.001	0.000	0.000	0.000	0.000
96	A	116	VAL	0	-0.021	-0.007	21.748	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	117	CYS	0	-0.045	-0.002	18.549	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	118	ARG	1	0.867	0.864	19.256	0.072	0.072	0.000	0.000	0.000	0.000
99	A	119	LYS	1	0.965	0.995	19.100	0.098	0.098	0.000	0.000	0.000	0.000
100	A	120	SER	0	-0.058	-0.022	20.617	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	121	ASP	-1	-0.889	-0.963	19.017	-0.087	-0.087	0.000	0.000	0.000	0.000
102	A	122	TYR	0	-0.012	-0.001	20.190	0.008	0.008	0.000	0.000	0.000	0.000
103	A	123	ILE	0	0.026	0.008	17.847	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	124	CYM	-1	-0.884	-0.817	21.675	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	125	SER	0	0.054	0.017	21.875	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	126	ARG	1	0.983	0.951	22.636	0.033	0.033	0.000	0.000	0.000	0.000
107	A	127	THR	0	-0.050	-0.038	18.136	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	128	LEU	0	0.030	0.022	15.342	0.005	0.005	0.000	0.000	0.000	0.000
109	A	129	MET	0	-0.051	-0.012	14.104	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	130	ILE	0	-0.007	0.020	14.932	0.018	0.018	0.000	0.000	0.000	0.000
111	A	131	ARG	1	0.889	0.935	12.351	0.172	0.172	0.000	0.000	0.000	0.000
112	A	132	ALA	0	0.024	0.004	16.379	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	133	ASP	-1	-0.875	-0.950	17.100	-0.184	-0.184	0.000	0.000	0.000	0.000
114	A	134	LYS	1	0.855	0.944	18.798	0.158	0.158	0.000	0.000	0.000	0.000
115	A	135	ALA	0	-0.048	-0.018	21.199	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	136	ALA	0	-0.006	-0.004	24.002	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	137	PHE	0	-0.076	-0.041	26.636	0.002	0.002	0.000	0.000	0.000	0.000
118	A	138	ASP	-1	-0.885	-0.948	24.496	-0.100	-0.100	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.063	-0.018	23.143	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	140	ASP	-1	-0.816	-0.920	25.660	-0.082	-0.082	0.000	0.000	0.000	0.000
121	A	141	GLU	-1	-0.864	-0.928	27.458	-0.059	-0.059	0.000	0.000	0.000	0.000
122	A	142	ASN	0	-0.059	-0.037	29.916	0.007	0.007	0.000	0.000	0.000	0.000
123	A	143	LEU	0	0.017	0.024	25.330	0.003	0.003	0.000	0.000	0.000	0.000
124	A	144	VAL	0	0.025	0.010	29.151	0.005	0.005	0.000	0.000	0.000	0.000
125	A	145	ARG	1	0.818	0.898	31.480	0.064	0.064	0.000	0.000	0.000	0.000
126	A	146	ASP	-1	-0.740	-0.839	31.437	-0.059	-0.059	0.000	0.000	0.000	0.000
127	A	147	LEU	0	-0.005	0.000	28.098	0.004	0.004	0.000	0.000	0.000	0.000
128	A	148	ARG	1	0.903	0.964	32.612	0.055	0.055	0.000	0.000	0.000	0.000
129	A	149	LYS	1	0.863	0.937	35.833	0.048	0.048	0.000	0.000	0.000	0.000
130	A	150	GLY	0	-0.012	-0.002	35.354	0.002	0.002	0.000	0.000	0.000	0.000
131	A	151	ARG	1	0.744	0.865	33.278	0.051	0.051	0.000	0.000	0.000	0.000
132	A	152	GLU	-1	-0.906	-0.953	29.909	-0.048	-0.048	0.000	0.000	0.000	0.000
133	A	153	LEU	0	0.004	0.001	24.988	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	154	LYS	1	0.782	0.894	22.408	0.094	0.094	0.000	0.000	0.000	0.000
135	A	155	VAL	0	0.058	0.022	19.523	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	156	GLU	-1	-0.852	-0.920	15.282	-0.203	-0.203	0.000	0.000	0.000	0.000
137	A	157	ILE	0	0.035	0.015	13.100	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	158	ILE	0	-0.047	-0.042	9.039	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	159	VAL	0	0.018	0.012	7.222	0.008	0.008	0.000	0.000	0.000	0.000
140	A	160	GLU	-1	-0.947	-0.962	2.538	-3.584	-1.720	0.688	-0.779	-1.773	-0.006
141	A	161	TYR	0	-0.031	-0.028	3.502	-0.723	0.393	0.061	-0.342	-0.835	-0.001
142	A	162	GLU	-1	-0.817	-0.905	2.153	-8.082	-5.572	10.537	-6.134	-6.913	-0.049
143	A	163	GLY	0	0.000	-0.001	3.164	-0.148	-0.462	0.045	0.506	-0.238	0.000
144	A	164	HIS	0	-0.018	-0.013	5.378	-0.639	-0.610	-0.001	-0.001	-0.026	0.000
145	A	165	HIS	0	0.037	0.027	7.954	-0.049	-0.049	0.000	0.000	0.000	0.000

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