FMO DATABASE

FMODB ID: 6YNVZ

Calculation Name: 3CNB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CNB

Chain ID: A

ChEMBL ID:

UniProt ID: Q47UF8

Base Structure: X-ray

Registration Date: 2023-09-21

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1070704.549487
FMO2-HF: Nuclear repulsion	1021482.477419
FMO2-HF: Total energy	-49222.072068
FMO2-MP2: Total energy	-49362.128731

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:66:PHE)

Summations of interaction energy for fragment #1(A:66:PHE)

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.
-19.948	-5.44	12.071	-8.676	-17.9	-0.032

Interaction energy analysis for fragmet #1(A:66:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.019

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	68	ILE	0	-0.016	-0.003	2.541	-3.578	0.975	0.954	-2.185	-3.323	0.011
4	A	69	LEU	0	-0.021	-0.006	6.206	-0.211	-0.211	0.000	0.000	0.000	0.000
5	A	70	ILE	0	-0.008	-0.005	9.648	0.021	0.021	0.000	0.000	0.000	0.000
6	A	71	ILE	0	0.015	0.000	11.661	0.020	0.020	0.000	0.000	0.000	0.000
7	A	72	GLU	-1	-0.810	-0.907	14.849	-0.275	-0.275	0.000	0.000	0.000	0.000
8	A	73	ASP	-1	-0.805	-0.906	17.139	-0.221	-0.221	0.000	0.000	0.000	0.000
9	A	74	ASP	-1	-0.870	-0.919	19.862	-0.206	-0.206	0.000	0.000	0.000	0.000
10	A	75	LYS	1	0.785	0.870	19.345	0.258	0.258	0.000	0.000	0.000	0.000
11	A	76	GLU	-1	-0.909	-0.948	19.298	-0.199	-0.199	0.000	0.000	0.000	0.000
12	A	77	PHE	0	-0.006	-0.017	15.077	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	78	ALA	0	0.013	0.003	15.211	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	79	ASP	-1	-0.740	-0.846	14.246	-0.353	-0.353	0.000	0.000	0.000	0.000
15	A	80	MET	0	-0.031	-0.010	14.651	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	81	LEU	0	-0.025	-0.018	10.382	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	82	THR	0	0.011	-0.015	10.313	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	83	GLN	0	-0.005	0.002	9.965	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	84	PHE	0	-0.035	-0.023	9.568	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	85	LEU	0	0.011	-0.012	5.828	-0.058	-0.058	0.000	0.000	0.000	0.000
21	A	86	GLU	-1	-0.923	-0.968	5.954	-0.897	-0.897	0.000	0.000	0.000	0.000
22	A	87	ASN	0	-0.046	-0.025	8.179	0.030	0.030	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.063	-0.018	5.685	0.119	0.119	0.000	0.000	0.000	0.000
24	A	89	PHE	0	-0.038	-0.028	2.845	-4.037	-1.269	1.482	-0.966	-3.283	-0.013
25	A	90	PRO	0	0.039	0.021	5.017	-0.110	-0.079	-0.001	-0.003	-0.026	0.000
26	A	91	TYR	0	-0.060	-0.028	5.056	0.268	0.268	0.000	0.000	0.000	0.000
27	A	92	ALA	0	-0.017	0.008	2.169	-1.614	-1.087	2.150	-0.774	-1.903	0.002
28	A	93	LYS	1	0.849	0.904	3.810	2.609	3.350	0.011	-0.189	-0.562	0.000
29	A	94	ILE	0	0.040	0.036	4.665	0.001	0.158	-0.001	-0.016	-0.139	0.000
30	A	95	LYS	1	0.861	0.921	8.162	0.802	0.802	0.000	0.000	0.000	0.000
31	A	96	ILE	0	0.026	0.020	11.385	0.016	0.016	0.000	0.000	0.000	0.000
32	A	97	ALA	0	-0.002	-0.005	14.196	0.000	0.000	0.000	0.000	0.000	0.000
33	A	98	TYR	0	0.008	-0.008	16.616	0.012	0.012	0.000	0.000	0.000	0.000
34	A	99	ASN	0	-0.013	-0.009	19.582	0.036	0.036	0.000	0.000	0.000	0.000
35	A	100	PRO	0	0.089	0.023	20.324	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	101	PHE	0	-0.032	0.004	20.981	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	102	ASP	-1	-0.844	-0.920	18.375	-0.299	-0.299	0.000	0.000	0.000	0.000
38	A	103	ALA	0	-0.015	-0.014	16.321	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	104	GLY	0	-0.004	0.010	16.379	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	105	ASP	-1	-0.865	-0.921	17.156	-0.343	-0.343	0.000	0.000	0.000	0.000
41	A	106	LEU	0	0.027	0.008	13.317	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	107	LEU	0	-0.050	-0.018	12.330	-0.094	-0.094	0.000	0.000	0.000	0.000
43	A	108	HIS	0	-0.055	-0.032	12.395	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	109	THR	0	-0.043	-0.045	12.776	-0.046	-0.046	0.000	0.000	0.000	0.000
45	A	110	VAL	0	-0.010	-0.002	8.253	-0.060	-0.060	0.000	0.000	0.000	0.000
46	A	111	LYS	1	0.895	0.956	7.848	0.111	0.111	0.000	0.000	0.000	0.000
47	A	112	PRO	0	-0.027	0.003	6.184	-0.364	-0.364	0.000	0.000	0.000	0.000
48	A	113	ASP	-1	-0.800	-0.909	2.381	-8.586	-4.720	3.972	-3.391	-4.447	-0.035
49	A	114	VAL	0	-0.040	-0.027	2.362	-0.859	-0.136	1.096	-0.391	-1.429	0.000
50	A	115	VAL	0	0.008	-0.005	5.140	0.143	0.153	-0.001	-0.002	-0.006	0.000
51	A	116	MET	0	-0.021	0.012	8.182	-0.031	-0.031	0.000	0.000	0.000	0.000
52	A	117	LEU	0	0.006	-0.008	10.372	0.012	0.012	0.000	0.000	0.000	0.000
53	A	118	ASP	-1	-0.770	-0.872	13.953	-0.209	-0.209	0.000	0.000	0.000	0.000
54	A	119	LEU	0	-0.073	-0.045	17.158	0.005	0.005	0.000	0.000	0.000	0.000
55	A	120	MET	0	-0.062	-0.011	20.113	0.024	0.024	0.000	0.000	0.000	0.000
56	A	121	MET	0	-0.021	0.031	18.444	0.009	0.009	0.000	0.000	0.000	0.000
57	A	122	VAL	0	-0.015	-0.022	22.210	0.012	0.012	0.000	0.000	0.000	0.000
58	A	123	GLY	0	-0.021	-0.012	25.779	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	124	MET	0	-0.062	-0.033	17.968	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	125	ASP	-1	-0.805	-0.897	23.699	-0.149	-0.149	0.000	0.000	0.000	0.000
61	A	126	GLY	0	0.059	0.017	19.561	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	127	PHE	0	0.009	-0.008	18.804	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	128	SER	0	-0.012	-0.001	20.228	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	129	ILE	0	-0.010	-0.007	16.563	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	130	CYS	0	-0.024	-0.007	15.561	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	131	HIS	0	0.058	0.034	16.224	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	132	ARG	1	0.845	0.928	15.893	0.258	0.258	0.000	0.000	0.000	0.000
68	A	133	ILE	0	-0.042	-0.013	11.738	0.003	0.003	0.000	0.000	0.000	0.000
69	A	134	LYS	1	0.848	0.920	10.804	0.293	0.293	0.000	0.000	0.000	0.000
70	A	135	SER	0	-0.039	-0.024	15.087	0.029	0.029	0.000	0.000	0.000	0.000
71	A	136	THR	0	-0.017	-0.003	16.966	0.028	0.028	0.000	0.000	0.000	0.000
72	A	137	PRO	0	0.016	-0.011	16.170	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	138	ALA	0	-0.050	-0.026	15.239	0.006	0.006	0.000	0.000	0.000	0.000
74	A	139	THR	0	-0.018	-0.023	12.026	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	140	ALA	0	0.006	0.027	11.719	-0.047	-0.047	0.000	0.000	0.000	0.000
76	A	141	ASN	0	-0.035	-0.032	9.462	0.040	0.040	0.000	0.000	0.000	0.000
77	A	142	ILE	0	-0.013	0.015	7.189	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	143	ILE	0	-0.023	0.008	4.129	0.015	0.146	-0.001	-0.009	-0.121	0.000
79	A	144	VAL	0	-0.010	-0.018	7.528	-0.082	-0.082	0.000	0.000	0.000	0.000
80	A	145	ILE	0	-0.018	-0.015	7.175	0.059	0.059	0.000	0.000	0.000	0.000
81	A	146	ALA	0	0.042	0.024	10.867	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	147	MET	0	-0.049	-0.016	13.569	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	148	THR	0	0.062	0.027	16.286	0.011	0.011	0.000	0.000	0.000	0.000
84	A	149	GLY	0	0.025	-0.007	20.088	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	150	ALA	0	-0.011	-0.014	23.012	0.007	0.007	0.000	0.000	0.000	0.000
86	A	151	LEU	0	-0.013	-0.002	19.916	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	152	THR	0	0.014	0.000	23.919	0.008	0.008	0.000	0.000	0.000	0.000
88	A	153	ASP	-1	-0.842	-0.925	24.808	-0.094	-0.094	0.000	0.000	0.000	0.000
89	A	154	ASP	-1	-0.877	-0.908	25.409	-0.098	-0.098	0.000	0.000	0.000	0.000
90	A	155	ASN	0	0.027	0.011	23.096	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	156	VAL	0	0.013	0.006	19.846	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	157	SER	0	0.000	-0.018	20.869	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	158	ARG	1	0.821	0.897	22.643	0.118	0.118	0.000	0.000	0.000	0.000
94	A	159	ILE	0	-0.014	-0.006	17.308	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	160	VAL	0	-0.009	0.007	17.201	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	161	ALA	0	-0.044	-0.014	18.658	0.004	0.004	0.000	0.000	0.000	0.000
97	A	162	LEU	0	-0.067	-0.028	19.792	0.008	0.008	0.000	0.000	0.000	0.000
98	A	163	GLY	0	0.038	0.010	16.250	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	164	ALA	0	0.015	0.005	13.466	-0.021	-0.021	0.000	0.000	0.000	0.000
100	A	165	GLU	-1	-0.809	-0.894	9.967	-0.280	-0.280	0.000	0.000	0.000	0.000
101	A	166	THR	0	-0.064	-0.035	11.972	0.034	0.034	0.000	0.000	0.000	0.000
102	A	167	CYS	0	0.004	0.002	14.293	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	168	PHE	0	-0.025	-0.002	11.815	0.020	0.020	0.000	0.000	0.000	0.000
104	A	169	GLY	0	0.035	0.008	16.420	0.005	0.005	0.000	0.000	0.000	0.000
105	A	170	LYS	1	0.778	0.862	17.437	0.238	0.238	0.000	0.000	0.000	0.000
106	A	171	PRO	0	0.008	-0.003	20.640	0.012	0.012	0.000	0.000	0.000	0.000
107	A	172	LEU	0	0.027	0.028	13.596	0.009	0.009	0.000	0.000	0.000	0.000
108	A	173	ASN	0	0.005	0.002	17.348	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	174	PHE	0	0.103	0.031	12.810	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	175	THR	0	-0.003	0.005	13.319	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	176	LEU	0	-0.020	-0.007	14.367	0.009	0.009	0.000	0.000	0.000	0.000
112	A	177	LEU	0	0.027	0.028	8.939	0.006	0.006	0.000	0.000	0.000	0.000
113	A	178	GLU	-1	-0.803	-0.878	9.531	-0.278	-0.278	0.000	0.000	0.000	0.000
114	A	179	LYS	1	0.981	0.983	9.310	0.014	0.014	0.000	0.000	0.000	0.000
115	A	180	THR	0	-0.043	-0.038	10.028	0.068	0.068	0.000	0.000	0.000	0.000
116	A	181	ILE	0	0.016	0.008	4.008	-0.107	0.052	-0.001	-0.013	-0.145	0.000
117	A	182	LYS	1	0.824	0.898	5.417	0.132	0.132	0.000	0.000	0.000	0.000
118	A	183	GLN	0	-0.028	-0.009	6.826	0.307	0.307	0.000	0.000	0.000	0.000
119	A	184	LEU	0	0.007	0.000	7.095	0.118	0.118	0.000	0.000	0.000	0.000
120	A	185	VAL	0	0.039	0.018	2.259	-1.277	-0.550	2.412	-0.735	-2.404	0.003
121	A	186	GLU	-1	-0.813	-0.886	5.238	2.083	2.198	-0.001	-0.002	-0.112	0.000
122	A	187	GLN	0	-0.086	-0.041	8.434	0.021	0.021	0.000	0.000	0.000	0.000
123	A	188	LYS	1	0.884	0.950	6.525	0.016	0.016	0.000	0.000	0.000	0.000
124	A	189	LYS	1	0.730	0.868	5.619	-2.722	-2.722	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:66:PHE)