FMO DATABASE

FMODB ID: 2NJ3R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1067712.243234
FMO2-HF: Nuclear repulsion	1018490.341727
FMO2-HF: Total energy	-49221.901506
FMO2-MP2: Total energy	-49361.934092

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.
-20.352	-5.804	13.252	-9.043	-18.756	-0.03

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 : 0.006 / q_NPA : 0.014

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

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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	-0.001	0.013	2.596	-3.860	0.932	1.236	-2.232	-3.797	0.013
4	A	69	LEU	0	-0.021	-0.006	5.982	-0.273	-0.229	-0.001	-0.003	-0.039	0.000
5	A	70	ILE	0	0.003	-0.004	9.319	0.028	0.028	0.000	0.000	0.000	0.000
6	A	71	ILE	0	-0.013	-0.017	11.283	0.018	0.018	0.000	0.000	0.000	0.000
7	A	72	GLU	-1	-0.811	-0.922	14.552	-0.288	-0.288	0.000	0.000	0.000	0.000
8	A	73	ASP	-1	-0.809	-0.906	16.961	-0.230	-0.230	0.000	0.000	0.000	0.000
9	A	74	ASP	-1	-0.868	-0.904	19.890	-0.216	-0.216	0.000	0.000	0.000	0.000
10	A	75	LYS	1	0.800	0.865	18.920	0.277	0.277	0.000	0.000	0.000	0.000
11	A	76	GLU	-1	-0.907	-0.950	19.094	-0.205	-0.205	0.000	0.000	0.000	0.000
12	A	77	PHE	0	-0.009	-0.011	15.165	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	78	ALA	0	0.022	0.005	15.162	-0.033	-0.033	0.000	0.000	0.000	0.000
14	A	79	ASP	-1	-0.780	-0.866	14.157	-0.379	-0.379	0.000	0.000	0.000	0.000
15	A	80	MET	0	-0.014	0.003	14.719	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	81	LEU	0	-0.027	-0.019	10.236	-0.030	-0.030	0.000	0.000	0.000	0.000
17	A	82	THR	0	0.020	-0.015	10.120	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	83	GLN	0	-0.005	0.008	9.862	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	84	PHE	0	-0.023	-0.023	9.477	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	85	LEU	0	-0.001	-0.018	5.638	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	86	GLU	-1	-0.939	-0.966	5.942	-0.975	-0.975	0.000	0.000	0.000	0.000
22	A	87	ASN	0	-0.068	-0.036	8.183	0.041	0.041	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.057	-0.015	5.887	0.126	0.126	0.000	0.000	0.000	0.000
24	A	89	PHE	0	-0.037	-0.030	2.960	-3.472	-0.881	1.028	-0.828	-2.792	-0.012
25	A	90	PRO	0	0.039	0.020	5.096	-0.167	-0.144	-0.001	-0.002	-0.019	0.000
26	A	91	TYR	0	-0.049	-0.026	4.973	0.199	0.199	0.000	0.000	0.000	0.000
27	A	92	ALA	0	-0.024	0.007	2.167	-2.240	-1.217	2.180	-1.026	-2.176	0.000
28	A	93	LYS	1	0.831	0.907	3.535	2.535	3.571	0.022	-0.302	-0.756	0.000
29	A	94	ILE	0	0.061	0.036	4.979	0.129	0.129	0.000	0.000	0.000	0.000
30	A	95	LYS	1	0.855	0.915	8.418	0.945	0.945	0.000	0.000	0.000	0.000
31	A	96	ILE	0	0.038	0.024	11.320	0.014	0.014	0.000	0.000	0.000	0.000
32	A	97	ALA	0	-0.003	0.014	14.141	0.014	0.014	0.000	0.000	0.000	0.000
33	A	98	TYR	0	0.019	-0.006	16.519	0.008	0.008	0.000	0.000	0.000	0.000
34	A	99	ASN	0	0.001	-0.007	19.423	0.032	0.032	0.000	0.000	0.000	0.000
35	A	100	PRO	0	0.104	0.032	20.144	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	101	PHE	0	-0.043	-0.005	20.552	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	102	ASP	-1	-0.828	-0.913	18.536	-0.301	-0.301	0.000	0.000	0.000	0.000
38	A	103	ALA	0	-0.018	-0.006	16.151	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	104	GLY	0	-0.007	-0.004	15.992	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	105	ASP	-1	-0.906	-0.956	17.564	-0.330	-0.330	0.000	0.000	0.000	0.000
41	A	106	LEU	0	0.008	-0.022	13.370	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	107	LEU	0	-0.062	-0.017	11.915	-0.091	-0.091	0.000	0.000	0.000	0.000
43	A	108	HIS	0	-0.063	-0.040	12.231	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	109	THR	0	-0.010	-0.006	12.517	-0.056	-0.056	0.000	0.000	0.000	0.000
45	A	110	VAL	0	-0.031	-0.010	8.097	-0.070	-0.070	0.000	0.000	0.000	0.000
46	A	111	LYS	1	0.911	0.958	7.513	0.042	0.042	0.000	0.000	0.000	0.000
47	A	112	PRO	0	-0.034	0.004	6.271	-0.280	-0.280	0.000	0.000	0.000	0.000
48	A	113	ASP	-1	-0.811	-0.916	2.310	-9.106	-5.246	4.139	-3.450	-4.549	-0.034
49	A	114	VAL	0	-0.021	-0.014	2.281	-0.708	-0.102	1.411	-0.396	-1.621	-0.001
50	A	115	VAL	0	0.000	-0.007	4.910	0.156	0.166	-0.001	-0.004	-0.005	0.000
51	A	116	MET	0	-0.027	0.008	7.784	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	117	LEU	0	0.013	-0.007	10.095	0.015	0.015	0.000	0.000	0.000	0.000
53	A	118	ASP	-1	-0.754	-0.863	13.686	-0.229	-0.229	0.000	0.000	0.000	0.000
54	A	119	LEU	0	-0.100	-0.061	16.758	0.009	0.009	0.000	0.000	0.000	0.000
55	A	120	MET	0	-0.090	-0.024	19.613	0.028	0.028	0.000	0.000	0.000	0.000
56	A	121	MET	0	-0.009	0.040	18.366	0.007	0.007	0.000	0.000	0.000	0.000
57	A	122	VAL	0	-0.017	-0.017	21.728	0.014	0.014	0.000	0.000	0.000	0.000
58	A	123	GLY	0	-0.036	-0.022	24.950	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	124	MET	0	-0.036	-0.029	17.643	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	125	ASP	-1	-0.818	-0.898	23.493	-0.159	-0.159	0.000	0.000	0.000	0.000
61	A	126	GLY	0	0.062	0.011	19.364	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	127	PHE	0	0.019	-0.008	18.812	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	128	SER	0	-0.007	0.004	20.398	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	129	ILE	0	0.005	0.003	16.452	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	130	CYS	0	-0.012	0.000	15.567	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	131	HIS	0	0.054	0.037	16.299	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	132	ARG	1	0.877	0.952	16.089	0.261	0.261	0.000	0.000	0.000	0.000
68	A	133	ILE	0	-0.049	-0.018	11.828	0.003	0.003	0.000	0.000	0.000	0.000
69	A	134	LYS	1	0.873	0.951	10.621	0.323	0.323	0.000	0.000	0.000	0.000
70	A	135	SER	0	-0.045	-0.023	15.184	0.028	0.028	0.000	0.000	0.000	0.000
71	A	136	THR	0	-0.033	-0.011	16.983	0.029	0.029	0.000	0.000	0.000	0.000
72	A	137	PRO	0	0.023	-0.011	16.034	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	138	ALA	0	-0.044	-0.021	15.109	0.000	0.000	0.000	0.000	0.000	0.000
74	A	139	THR	0	-0.007	-0.026	11.996	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	140	ALA	0	0.007	0.028	11.678	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	141	ASN	0	-0.040	-0.036	9.376	0.042	0.042	0.000	0.000	0.000	0.000
77	A	142	ILE	0	0.014	0.026	6.949	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	143	ILE	0	-0.025	-0.003	4.022	0.023	0.172	-0.001	-0.012	-0.136	0.000
79	A	144	VAL	0	0.003	0.005	7.345	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	145	ILE	0	-0.017	-0.013	7.176	0.064	0.064	0.000	0.000	0.000	0.000
81	A	146	ALA	0	0.030	0.023	10.755	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	147	MET	0	-0.028	-0.006	13.222	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	148	THR	0	0.039	0.013	15.860	0.008	0.008	0.000	0.000	0.000	0.000
84	A	149	GLY	0	0.061	0.009	19.676	0.001	0.001	0.000	0.000	0.000	0.000
85	A	150	ALA	0	-0.002	-0.014	22.690	0.004	0.004	0.000	0.000	0.000	0.000
86	A	151	LEU	0	0.008	0.016	19.632	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	152	THR	0	0.001	0.001	23.676	0.008	0.008	0.000	0.000	0.000	0.000
88	A	153	ASP	-1	-0.845	-0.940	24.460	-0.104	-0.104	0.000	0.000	0.000	0.000
89	A	154	ASP	-1	-0.931	-0.949	25.355	-0.102	-0.102	0.000	0.000	0.000	0.000
90	A	155	ASN	0	0.018	-0.008	22.938	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	156	VAL	0	0.026	0.016	19.742	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	157	SER	0	-0.004	-0.019	20.785	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	158	ARG	1	0.871	0.953	22.757	0.129	0.129	0.000	0.000	0.000	0.000
94	A	159	ILE	0	-0.006	-0.008	17.194	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	160	VAL	0	-0.018	-0.002	17.114	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	161	ALA	0	-0.038	-0.008	18.438	0.001	0.001	0.000	0.000	0.000	0.000
97	A	162	LEU	0	-0.064	-0.031	19.607	0.007	0.007	0.000	0.000	0.000	0.000
98	A	163	GLY	0	0.014	0.001	15.993	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	164	ALA	0	-0.001	-0.001	13.360	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	165	GLU	-1	-0.860	-0.943	9.930	-0.288	-0.288	0.000	0.000	0.000	0.000
101	A	166	THR	0	-0.047	-0.033	12.176	0.043	0.043	0.000	0.000	0.000	0.000
102	A	167	CYS	0	-0.013	-0.004	14.249	-0.031	-0.031	0.000	0.000	0.000	0.000
103	A	168	PHE	0	-0.044	-0.008	11.701	0.018	0.018	0.000	0.000	0.000	0.000
104	A	169	GLY	0	0.043	0.003	16.279	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	170	LYS	1	0.749	0.866	17.411	0.254	0.254	0.000	0.000	0.000	0.000
106	A	171	PRO	0	0.001	-0.008	20.521	0.013	0.013	0.000	0.000	0.000	0.000
107	A	172	LEU	0	0.039	0.027	13.102	0.008	0.008	0.000	0.000	0.000	0.000
108	A	173	ASN	0	0.002	0.006	17.144	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	174	PHE	0	0.109	0.023	12.725	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	175	THR	0	-0.006	0.006	13.408	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	176	LEU	0	-0.012	-0.009	14.297	0.005	0.005	0.000	0.000	0.000	0.000
112	A	177	LEU	0	0.018	0.027	8.845	0.006	0.006	0.000	0.000	0.000	0.000
113	A	178	GLU	-1	-0.804	-0.885	9.506	-0.246	-0.246	0.000	0.000	0.000	0.000
114	A	179	LYS	1	0.976	0.979	9.364	0.028	0.028	0.000	0.000	0.000	0.000
115	A	180	THR	0	-0.043	-0.033	9.811	0.066	0.066	0.000	0.000	0.000	0.000
116	A	181	ILE	0	0.023	0.009	3.932	-0.127	0.059	0.000	-0.018	-0.168	0.000
117	A	182	LYS	1	0.840	0.915	5.337	0.142	0.142	0.000	0.000	0.000	0.000
118	A	183	GLN	0	-0.032	-0.014	7.002	0.318	0.318	0.000	0.000	0.000	0.000
119	A	184	LEU	0	-0.006	-0.008	6.758	0.124	0.124	0.000	0.000	0.000	0.000
120	A	185	VAL	0	0.020	0.014	2.323	-0.815	-0.703	3.241	-0.766	-2.588	0.004
121	A	186	GLU	-1	-0.812	-0.894	5.181	1.727	1.843	-0.001	-0.004	-0.110	0.000
122	A	187	GLN	0	-0.078	-0.029	8.567	0.010	0.010	0.000	0.000	0.000	0.000
123	A	188	LYS	1	0.881	0.953	6.492	0.013	0.013	0.000	0.000	0.000	0.000
124	A	189	LYS	1	0.755	0.879	5.557	-2.438	-2.438	0.000	0.000	0.000	0.000

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