FMO DATABASE

FMODB ID: 3QM9L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1406101.222762
FMO2-HF: Nuclear repulsion	1348430.242309
FMO2-HF: Total energy	-57670.980453
FMO2-MP2: Total energy	-57838.74611

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.
-19.118	-13.833	14.096	-8.015	-11.365	-0.071

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 : -0.049 / q_NPA : -0.034

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	-0.014	-0.022	3.842	-2.042	0.087	-0.013	-1.090	-1.025	0.005
4	A	24	LEU	0	-0.020	0.000	6.070	0.229	0.229	0.000	0.000	0.000	0.000
5	A	25	ARG	1	0.856	0.902	9.786	0.145	0.145	0.000	0.000	0.000	0.000
6	A	26	TYR	0	-0.008	-0.018	13.003	0.028	0.028	0.000	0.000	0.000	0.000
7	A	27	THR	0	-0.030	-0.015	16.566	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.053	0.049	19.770	0.007	0.007	0.000	0.000	0.000	0.000
9	A	29	ARG	1	0.919	0.942	22.970	0.021	0.021	0.000	0.000	0.000	0.000
10	A	30	ALA	0	0.058	0.052	26.375	0.002	0.002	0.000	0.000	0.000	0.000
11	A	31	ARG	1	0.806	0.906	28.605	0.015	0.015	0.000	0.000	0.000	0.000
12	A	32	GLY	0	0.049	0.024	31.429	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	33	HIS	0	-0.014	-0.025	32.773	0.001	0.001	0.000	0.000	0.000	0.000
14	A	34	PRO	0	0.012	0.002	35.964	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	35	ASN	0	-0.017	-0.010	37.706	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	36	VAL	0	-0.007	0.016	31.343	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	37	THR	0	0.007	-0.006	34.303	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	38	ALA	0	-0.004	0.000	29.797	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	39	GLY	0	0.024	0.018	30.971	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	40	HIS	0	0.041	0.052	28.249	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	41	ARG	1	0.882	0.932	28.325	0.032	0.032	0.000	0.000	0.000	0.000
22	A	42	THR	0	-0.025	-0.022	25.085	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	43	THR	0	-0.016	-0.009	23.637	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	44	PHE	0	0.034	0.007	19.836	0.001	0.001	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.873	-0.931	23.593	-0.029	-0.029	0.000	0.000	0.000	0.000
26	A	46	VAL	0	-0.036	-0.012	24.305	0.000	0.000	0.000	0.000	0.000	0.000
27	A	47	THR	0	0.027	-0.005	26.078	0.002	0.002	0.000	0.000	0.000	0.000
28	A	48	VAL	0	0.004	0.000	27.978	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	49	ASP	-1	-0.893	-0.934	30.178	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	50	PRO	0	-0.049	-0.025	33.228	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	51	GLU	-1	-0.840	-0.919	35.703	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	52	ILE	0	0.031	0.019	33.358	0.000	0.000	0.000	0.000	0.000	0.000
33	A	53	GLY	0	0.014	0.009	36.782	0.001	0.001	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.920	-0.975	37.791	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	55	THR	0	-0.049	-0.030	37.972	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	ALA	0	0.011	0.025	33.644	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	ASP	-1	-0.870	-0.947	32.715	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	58	CYS	0	-0.046	-0.033	27.871	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	59	ILE	0	-0.005	0.000	27.886	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	60	ILE	0	-0.035	-0.028	24.286	0.001	0.001	0.000	0.000	0.000	0.000
41	A	61	GLY	0	-0.013	-0.015	28.112	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	62	VAL	0	0.013	0.017	29.021	0.001	0.001	0.000	0.000	0.000	0.000
43	A	63	SER	0	-0.024	-0.022	31.230	0.000	0.000	0.000	0.000	0.000	0.000
44	A	64	SER	0	-0.055	-0.037	25.733	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	65	SER	0	-0.052	-0.055	25.144	0.001	0.001	0.000	0.000	0.000	0.000
46	A	66	ASP	-1	-0.816	-0.865	23.117	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	67	SER	0	0.032	0.035	24.851	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	68	ILE	0	-0.055	-0.026	18.562	0.000	0.000	0.000	0.000	0.000	0.000
49	A	69	SER	0	-0.020	0.005	20.665	0.004	0.004	0.000	0.000	0.000	0.000
50	A	70	THR	0	-0.018	-0.030	22.486	0.007	0.007	0.000	0.000	0.000	0.000
51	A	71	LEU	0	-0.006	0.020	17.562	0.000	0.000	0.000	0.000	0.000	0.000
52	A	72	PRO	0	0.028	0.009	16.130	0.011	0.011	0.000	0.000	0.000	0.000
53	A	73	ASP	-1	-0.834	-0.921	16.114	0.051	0.051	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.857	-0.895	11.116	0.255	0.255	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.020	-0.003	11.674	0.003	0.003	0.000	0.000	0.000	0.000
56	A	76	LYS	1	0.806	0.895	12.703	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	77	ARG	1	0.865	0.899	11.958	-0.184	-0.184	0.000	0.000	0.000	0.000
58	A	78	ALA	0	-0.018	0.015	8.413	0.035	0.035	0.000	0.000	0.000	0.000
59	A	79	ILE	0	0.006	-0.004	9.067	-0.049	-0.049	0.000	0.000	0.000	0.000
60	A	80	ALA	0	0.017	0.023	11.484	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	81	ARG	1	0.758	0.865	6.783	-0.317	-0.317	0.000	0.000	0.000	0.000
62	A	82	GLU	-1	-0.829	-0.935	9.522	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.082	-0.049	7.242	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	84	SER	0	0.012	0.021	5.657	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.029	-0.006	5.735	0.058	0.058	0.000	0.000	0.000	0.000
66	A	86	VAL	0	0.033	0.002	7.657	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	87	ARG	1	0.839	0.909	10.562	0.226	0.226	0.000	0.000	0.000	0.000
68	A	88	VAL	0	0.003	0.002	12.853	0.003	0.003	0.000	0.000	0.000	0.000
69	A	89	ILE	0	-0.058	-0.023	15.290	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	90	LEU	0	0.006	0.009	18.697	0.007	0.007	0.000	0.000	0.000	0.000
71	A	91	ARG	1	0.869	0.894	18.523	0.082	0.082	0.000	0.000	0.000	0.000
72	A	92	THR	0	0.007	-0.007	25.206	0.002	0.002	0.000	0.000	0.000	0.000
73	A	93	GLU	-1	-0.841	-0.913	28.853	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	94	ASN	0	-0.105	-0.070	31.470	0.000	0.000	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.037	0.031	28.673	0.000	0.000	0.000	0.000	0.000	0.000
76	A	96	TYR	0	-0.045	-0.026	18.398	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	97	ASP	-1	-0.767	-0.865	22.479	-0.068	-0.068	0.000	0.000	0.000	0.000
78	A	98	GLU	-1	-0.821	-0.889	15.057	-0.150	-0.150	0.000	0.000	0.000	0.000
79	A	99	ILE	0	0.001	0.018	17.242	0.006	0.006	0.000	0.000	0.000	0.000
80	A	100	ARG	1	0.828	0.881	11.533	0.146	0.146	0.000	0.000	0.000	0.000
81	A	101	GLY	0	0.076	0.020	12.781	0.018	0.018	0.000	0.000	0.000	0.000
82	A	102	TYR	0	-0.087	-0.032	10.034	-0.035	-0.035	0.000	0.000	0.000	0.000
83	A	103	GLY	0	0.074	0.040	10.252	0.020	0.020	0.000	0.000	0.000	0.000
84	A	104	HIS	0	-0.024	-0.024	11.682	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	105	PRO	0	-0.004	0.007	12.810	0.008	0.008	0.000	0.000	0.000	0.000
86	A	106	GLU	-1	-0.933	-0.969	14.589	0.000	0.000	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.084	-0.032	14.204	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	108	THR	0	-0.020	-0.042	17.308	0.007	0.007	0.000	0.000	0.000	0.000
89	A	109	LEU	0	-0.075	-0.038	15.710	0.005	0.005	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.801	-0.892	19.921	0.008	0.008	0.000	0.000	0.000	0.000
91	A	111	HIS	0	0.008	0.010	23.586	0.001	0.001	0.000	0.000	0.000	0.000
92	A	112	PRO	0	0.015	-0.001	25.573	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	113	THR	0	-0.003	-0.023	28.260	0.001	0.001	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.786	-0.849	26.367	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	115	ILE	0	-0.003	-0.001	20.247	0.001	0.001	0.000	0.000	0.000	0.000
96	A	116	VAL	0	-0.011	-0.002	21.745	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	117	CYS	0	-0.039	0.008	18.663	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	118	ARG	1	0.864	0.844	19.181	0.042	0.042	0.000	0.000	0.000	0.000
99	A	119	LYS	1	0.824	0.905	19.227	0.058	0.058	0.000	0.000	0.000	0.000
100	A	120	SER	0	-0.054	-0.022	20.874	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	121	ASP	-1	-0.875	-0.962	19.002	-0.055	-0.055	0.000	0.000	0.000	0.000
102	A	122	TYR	0	-0.016	-0.002	20.008	0.003	0.003	0.000	0.000	0.000	0.000
103	A	123	ILE	0	0.027	0.014	18.114	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	124	CYM	-1	-0.922	-0.798	21.827	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	125	SER	0	0.107	0.047	22.086	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	126	ARG	1	0.941	0.917	22.775	0.018	0.018	0.000	0.000	0.000	0.000
107	A	127	THR	0	-0.056	-0.065	18.419	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	128	LEU	0	0.016	0.005	15.670	0.003	0.003	0.000	0.000	0.000	0.000
109	A	129	MET	0	-0.039	-0.011	14.062	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	130	ILE	0	-0.002	0.020	15.152	0.010	0.010	0.000	0.000	0.000	0.000
111	A	131	ARG	1	0.862	0.926	12.459	0.098	0.098	0.000	0.000	0.000	0.000
112	A	132	ALA	0	0.026	0.004	16.440	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	133	ASP	-1	-0.826	-0.920	17.104	-0.100	-0.100	0.000	0.000	0.000	0.000
114	A	134	LYS	1	0.750	0.848	18.947	0.078	0.078	0.000	0.000	0.000	0.000
115	A	135	ALA	0	-0.026	-0.006	21.250	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	136	ALA	0	0.005	-0.008	24.167	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	137	PHE	0	0.026	0.009	27.006	0.001	0.001	0.000	0.000	0.000	0.000
118	A	138	ASP	-1	-0.816	-0.889	24.423	-0.057	-0.057	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.026	-0.004	23.546	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	140	ASP	-1	-0.795	-0.896	26.062	-0.044	-0.044	0.000	0.000	0.000	0.000
121	A	141	GLU	-1	-0.802	-0.888	27.838	-0.032	-0.032	0.000	0.000	0.000	0.000
122	A	142	ASN	0	-0.043	-0.038	30.709	0.005	0.005	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.006	0.010	25.759	0.002	0.002	0.000	0.000	0.000	0.000
124	A	144	VAL	0	0.023	0.012	29.632	0.003	0.003	0.000	0.000	0.000	0.000
125	A	145	ARG	1	0.761	0.853	31.725	0.035	0.035	0.000	0.000	0.000	0.000
126	A	146	ASP	-1	-0.731	-0.835	32.046	-0.029	-0.029	0.000	0.000	0.000	0.000
127	A	147	LEU	0	-0.004	0.005	28.370	0.002	0.002	0.000	0.000	0.000	0.000
128	A	148	ARG	1	0.860	0.921	32.891	0.030	0.030	0.000	0.000	0.000	0.000
129	A	149	LYS	1	0.814	0.909	36.242	0.028	0.028	0.000	0.000	0.000	0.000
130	A	150	GLY	0	-0.014	0.001	35.883	0.001	0.001	0.000	0.000	0.000	0.000
131	A	151	ARG	1	0.749	0.874	33.658	0.026	0.026	0.000	0.000	0.000	0.000
132	A	152	GLU	-1	-0.903	-0.956	30.312	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	153	LEU	0	-0.005	0.002	25.438	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	154	LYS	1	0.752	0.863	21.465	0.055	0.055	0.000	0.000	0.000	0.000
135	A	155	VAL	0	0.033	0.022	20.030	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	156	GLU	-1	-0.826	-0.885	16.185	-0.111	-0.111	0.000	0.000	0.000	0.000
137	A	157	ILE	0	0.047	0.025	13.571	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	158	ILE	0	-0.029	-0.028	9.793	0.001	0.001	0.000	0.000	0.000	0.000
139	A	159	VAL	0	0.004	0.009	7.734	0.015	0.015	0.000	0.000	0.000	0.000
140	A	160	GLU	-1	-0.940	-0.965	3.236	-1.478	-0.855	0.041	-0.134	-0.531	-0.001
141	A	161	TYR	0	0.008	-0.005	3.565	-0.751	0.193	0.042	-0.292	-0.694	-0.001
142	A	162	GLU	-1	-0.779	-0.885	1.896	-15.124	-12.711	13.953	-7.635	-8.731	-0.074
143	A	163	GLY	0	-0.006	0.009	2.988	0.906	0.028	0.074	1.138	-0.334	0.000
144	A	164	HIS	0	-0.041	-0.027	5.087	-0.788	-0.734	-0.001	-0.002	-0.050	0.000
145	A	165	HIS	0	-0.002	0.017	7.992	-0.093	-0.093	0.000	0.000	0.000	0.000

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