FMO DATABASE

FMODB ID: 762VK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1065550.274434
FMO2-HF: Nuclear repulsion	1016328.989152
FMO2-HF: Total energy	-49221.285282
FMO2-MP2: Total energy	-49361.23193

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.
-20.902	-8.236	13.908	-8.474	-18.094	-0.04

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 : -0.040 / 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	68	ILE	0	0.022	0.024	2.597	-3.677	0.228	1.363	-1.599	-3.668	0.005
4	A	69	LEU	0	-0.025	-0.011	5.704	-0.143	-0.087	-0.001	-0.005	-0.050	0.000
5	A	70	ILE	0	-0.003	-0.005	9.073	-0.103	-0.103	0.000	0.000	0.000	0.000
6	A	71	ILE	0	-0.022	-0.027	11.003	0.057	0.057	0.000	0.000	0.000	0.000
7	A	72	GLU	-1	-0.841	-0.956	14.273	-0.217	-0.217	0.000	0.000	0.000	0.000
8	A	73	ASP	-1	-0.821	-0.914	16.698	-0.092	-0.092	0.000	0.000	0.000	0.000
9	A	74	ASP	-1	-0.899	-0.926	19.674	-0.134	-0.134	0.000	0.000	0.000	0.000
10	A	75	LYS	1	0.883	0.925	18.959	0.089	0.089	0.000	0.000	0.000	0.000
11	A	76	GLU	-1	-0.914	-0.952	18.821	-0.141	-0.141	0.000	0.000	0.000	0.000
12	A	77	PHE	0	-0.009	-0.005	15.216	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	78	ALA	0	0.012	0.005	14.923	-0.043	-0.043	0.000	0.000	0.000	0.000
14	A	79	ASP	-1	-0.830	-0.900	13.885	-0.196	-0.196	0.000	0.000	0.000	0.000
15	A	80	MET	0	-0.012	0.000	14.501	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	81	LEU	0	-0.036	-0.024	10.211	-0.061	-0.061	0.000	0.000	0.000	0.000
17	A	82	THR	0	0.014	-0.029	9.870	-0.115	-0.115	0.000	0.000	0.000	0.000
18	A	83	GLN	0	-0.006	0.007	9.661	-0.064	-0.064	0.000	0.000	0.000	0.000
19	A	84	PHE	0	-0.023	-0.021	9.520	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	85	LEU	0	-0.010	-0.023	5.503	-0.128	-0.128	0.000	0.000	0.000	0.000
21	A	86	GLU	-1	-0.930	-0.961	5.859	-0.817	-0.817	0.000	0.000	0.000	0.000
22	A	87	ASN	0	-0.058	-0.030	8.075	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	88	LEU	0	-0.049	-0.019	5.876	0.085	0.085	0.000	0.000	0.000	0.000
24	A	89	PHE	0	-0.055	-0.031	3.022	-3.154	-0.769	0.736	-0.737	-2.383	-0.011
25	A	90	PRO	0	0.039	0.021	5.199	-0.121	-0.102	-0.001	-0.002	-0.016	0.000
26	A	91	TYR	0	-0.048	-0.029	5.069	0.272	0.272	0.000	0.000	0.000	0.000
27	A	92	ALA	0	-0.022	0.006	2.096	-2.092	-1.644	3.072	-1.171	-2.348	0.001
28	A	93	LYS	1	0.874	0.943	3.537	-1.460	-0.478	0.024	-0.257	-0.749	0.000
29	A	94	ILE	0	0.044	0.028	5.172	0.231	0.231	0.000	0.000	0.000	0.000
30	A	95	LYS	1	0.890	0.938	8.116	-0.071	-0.071	0.000	0.000	0.000	0.000
31	A	96	ILE	0	0.039	0.027	11.109	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	97	ALA	0	-0.011	0.003	13.860	0.043	0.043	0.000	0.000	0.000	0.000
33	A	98	TYR	0	0.017	-0.001	16.226	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	99	ASN	0	-0.003	-0.010	19.138	0.003	0.003	0.000	0.000	0.000	0.000
35	A	100	PRO	0	0.105	0.032	19.889	0.006	0.006	0.000	0.000	0.000	0.000
36	A	101	PHE	0	-0.057	-0.008	20.340	0.005	0.005	0.000	0.000	0.000	0.000
37	A	102	ASP	-1	-0.802	-0.907	18.533	0.044	0.044	0.000	0.000	0.000	0.000
38	A	103	ALA	0	-0.025	-0.007	15.935	0.019	0.019	0.000	0.000	0.000	0.000
39	A	104	GLY	0	-0.024	-0.013	15.779	0.010	0.010	0.000	0.000	0.000	0.000
40	A	105	ASP	-1	-0.935	-0.966	17.418	0.174	0.174	0.000	0.000	0.000	0.000
41	A	106	LEU	0	0.020	-0.020	13.417	0.050	0.050	0.000	0.000	0.000	0.000
42	A	107	LEU	0	-0.036	-0.009	11.658	0.058	0.058	0.000	0.000	0.000	0.000
43	A	108	HIS	0	-0.079	-0.036	12.200	0.038	0.038	0.000	0.000	0.000	0.000
44	A	109	THR	0	-0.010	-0.007	12.587	0.108	0.108	0.000	0.000	0.000	0.000
45	A	110	VAL	0	-0.045	-0.021	8.304	0.153	0.153	0.000	0.000	0.000	0.000
46	A	111	LYS	1	0.891	0.943	7.726	-0.704	-0.704	0.000	0.000	0.000	0.000
47	A	112	PRO	0	-0.030	0.009	6.241	0.251	0.251	0.000	0.000	0.000	0.000
48	A	113	ASP	-1	-0.822	-0.925	2.183	-6.917	-3.626	5.177	-3.697	-4.771	-0.036
49	A	114	VAL	0	-0.018	-0.009	2.180	-0.894	-0.548	1.973	-0.457	-1.861	-0.002
50	A	115	VAL	0	0.003	-0.004	4.733	0.352	0.376	-0.001	-0.006	-0.016	0.000
51	A	116	MET	0	-0.028	0.001	7.478	-0.119	-0.119	0.000	0.000	0.000	0.000
52	A	117	LEU	0	0.010	-0.007	9.861	0.065	0.065	0.000	0.000	0.000	0.000
53	A	118	ASP	-1	-0.832	-0.922	13.452	-0.177	-0.177	0.000	0.000	0.000	0.000
54	A	119	LEU	0	-0.100	-0.062	16.530	0.024	0.024	0.000	0.000	0.000	0.000
55	A	120	MET	0	-0.064	-0.029	19.397	0.017	0.017	0.000	0.000	0.000	0.000
56	A	121	MET	0	0.002	0.049	18.291	0.011	0.011	0.000	0.000	0.000	0.000
57	A	122	VAL	0	-0.012	-0.011	21.472	0.009	0.009	0.000	0.000	0.000	0.000
58	A	123	GLY	0	-0.039	-0.023	24.676	0.005	0.005	0.000	0.000	0.000	0.000
59	A	124	MET	0	-0.038	-0.030	17.482	0.015	0.015	0.000	0.000	0.000	0.000
60	A	125	ASP	-1	-0.831	-0.909	23.256	-0.077	-0.077	0.000	0.000	0.000	0.000
61	A	126	GLY	0	0.057	0.009	19.189	0.002	0.002	0.000	0.000	0.000	0.000
62	A	127	PHE	0	-0.005	-0.009	18.652	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	128	SER	0	0.013	0.010	20.253	0.001	0.001	0.000	0.000	0.000	0.000
64	A	129	ILE	0	-0.004	0.005	16.068	0.007	0.007	0.000	0.000	0.000	0.000
65	A	130	CYS	0	-0.015	-0.002	15.417	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	131	HIS	0	0.053	0.036	16.163	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	132	ARG	1	0.920	0.988	16.212	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	133	ILE	0	-0.042	-0.021	11.566	0.023	0.023	0.000	0.000	0.000	0.000
69	A	134	LYS	1	0.890	0.968	10.827	0.266	0.266	0.000	0.000	0.000	0.000
70	A	135	SER	0	-0.046	-0.025	15.075	0.014	0.014	0.000	0.000	0.000	0.000
71	A	136	THR	0	-0.042	-0.017	16.898	0.024	0.024	0.000	0.000	0.000	0.000
72	A	137	PRO	0	0.021	-0.010	15.924	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	138	ALA	0	-0.039	-0.020	15.044	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	139	THR	0	-0.008	-0.031	11.868	0.041	0.041	0.000	0.000	0.000	0.000
75	A	140	ALA	0	0.029	0.037	11.559	-0.063	-0.063	0.000	0.000	0.000	0.000
76	A	141	ASN	0	-0.057	-0.046	9.449	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	142	ILE	0	0.024	0.033	6.976	-0.098	-0.098	0.000	0.000	0.000	0.000
78	A	143	ILE	0	-0.029	-0.014	4.145	-0.010	0.122	-0.001	-0.009	-0.122	0.000
79	A	144	VAL	0	0.022	0.013	7.222	-0.084	-0.084	0.000	0.000	0.000	0.000
80	A	145	ILE	0	-0.014	-0.008	7.112	0.025	0.025	0.000	0.000	0.000	0.000
81	A	146	ALA	0	0.031	0.023	10.618	0.014	0.014	0.000	0.000	0.000	0.000
82	A	147	MET	0	-0.023	-0.005	12.938	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	148	THR	0	0.030	0.010	15.695	0.026	0.026	0.000	0.000	0.000	0.000
84	A	149	GLY	0	0.046	0.020	19.507	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	150	ALA	0	0.003	-0.010	22.527	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	151	LEU	0	0.010	0.003	19.564	0.003	0.003	0.000	0.000	0.000	0.000
87	A	152	THR	0	-0.004	0.003	23.562	0.007	0.007	0.000	0.000	0.000	0.000
88	A	153	ASP	-1	-0.842	-0.942	24.359	-0.122	-0.122	0.000	0.000	0.000	0.000
89	A	154	ASP	-1	-0.956	-0.964	25.274	-0.081	-0.081	0.000	0.000	0.000	0.000
90	A	155	ASN	0	0.011	-0.009	22.725	0.004	0.004	0.000	0.000	0.000	0.000
91	A	156	VAL	0	0.020	0.012	19.647	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	157	SER	0	0.013	-0.002	20.697	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	158	ARG	1	0.931	0.972	22.671	0.083	0.083	0.000	0.000	0.000	0.000
94	A	159	ILE	0	-0.017	-0.013	17.029	0.002	0.002	0.000	0.000	0.000	0.000
95	A	160	VAL	0	-0.006	0.003	17.012	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	161	ALA	0	-0.031	-0.007	18.379	0.001	0.001	0.000	0.000	0.000	0.000
97	A	162	LEU	0	-0.072	-0.037	19.340	0.012	0.012	0.000	0.000	0.000	0.000
98	A	163	GLY	0	0.010	-0.005	15.921	0.007	0.007	0.000	0.000	0.000	0.000
99	A	164	ALA	0	-0.010	-0.006	13.275	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	165	GLU	-1	-0.935	-0.973	10.068	-0.308	-0.308	0.000	0.000	0.000	0.000
101	A	166	THR	0	-0.057	-0.037	12.137	0.039	0.039	0.000	0.000	0.000	0.000
102	A	167	CYS	0	-0.030	-0.013	14.156	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	168	PHE	0	-0.028	-0.001	11.674	0.005	0.005	0.000	0.000	0.000	0.000
104	A	169	GLY	0	0.046	0.015	16.190	0.012	0.012	0.000	0.000	0.000	0.000
105	A	170	LYS	1	0.853	0.956	17.240	0.178	0.178	0.000	0.000	0.000	0.000
106	A	171	PRO	0	0.011	-0.003	20.396	0.015	0.015	0.000	0.000	0.000	0.000
107	A	172	LEU	0	0.042	0.026	13.099	0.003	0.003	0.000	0.000	0.000	0.000
108	A	173	ASN	0	0.002	-0.001	17.083	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	174	PHE	0	0.096	0.018	12.592	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	175	THR	0	0.000	0.013	13.428	-0.040	-0.040	0.000	0.000	0.000	0.000
111	A	176	LEU	0	-0.016	-0.008	14.385	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	177	LEU	0	0.025	0.027	8.764	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	178	GLU	-1	-0.911	-0.954	9.565	-0.545	-0.545	0.000	0.000	0.000	0.000
114	A	179	LYS	1	0.981	0.989	9.502	0.188	0.188	0.000	0.000	0.000	0.000
115	A	180	THR	0	-0.048	-0.043	9.841	0.038	0.038	0.000	0.000	0.000	0.000
116	A	181	ILE	0	0.019	0.010	3.700	-0.187	0.045	0.002	-0.029	-0.205	0.000
117	A	182	LYS	1	0.941	0.977	5.512	0.425	0.425	0.000	0.000	0.000	0.000
118	A	183	GLN	0	-0.026	-0.005	7.227	0.230	0.230	0.000	0.000	0.000	0.000
119	A	184	LEU	0	-0.001	-0.011	6.893	0.088	0.088	0.000	0.000	0.000	0.000
120	A	185	VAL	0	0.017	0.014	2.599	-1.064	-0.218	1.565	-0.505	-1.905	0.003
121	A	186	GLU	-1	-0.920	-0.976	5.406	0.450	0.450	0.000	0.000	0.000	0.000
122	A	187	GLN	0	-0.061	-0.022	8.764	0.052	0.052	0.000	0.000	0.000	0.000
123	A	188	LYS	1	0.912	0.971	6.439	0.202	0.202	0.000	0.000	0.000	0.000
124	A	189	LYS	1	0.856	0.952	5.543	-0.790	-0.790	0.000	0.000	0.000	0.000

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