FMO DATABASE

FMODB ID: NN1YQ

Calculation Name: 2A4C-A-Xray372

Preferred Name: Cadherin-11

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A4C

Chain ID: A

ChEMBL ID: CHEMBL2163173

UniProt ID: P55288

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-691789.204875
FMO2-HF: Nuclear repulsion	653421.379608
FMO2-HF: Total energy	-38367.825267
FMO2-MP2: Total energy	-38481.607896

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-11.063	-5.152	1.816	-3.514	-4.214	0.022

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.010

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	2	TRP	0	-0.035	-0.003	2.474	-7.945	-2.024	1.817	-3.484	-4.254	0.022
4	A	3	VAL	0	0.010	0.007	4.499	-2.039	-2.049	-0.001	-0.030	0.040	0.000
5	A	4	TRP	0	0.015	-0.006	4.881	0.043	0.043	0.000	0.000	0.000	0.000
6	A	5	ASN	0	-0.051	-0.034	9.320	0.027	0.027	0.000	0.000	0.000	0.000
7	A	6	GLN	0	0.027	0.006	11.602	-0.150	-0.150	0.000	0.000	0.000	0.000
8	A	7	PHE	0	-0.004	0.013	14.671	0.077	0.077	0.000	0.000	0.000	0.000
9	A	8	PHE	0	-0.018	-0.016	17.622	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.012	0.007	20.544	0.008	0.008	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.013	0.008	24.232	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.777	-0.885	26.583	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.982	-0.977	29.536	0.055	0.055	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.025	-0.010	27.715	0.010	0.010	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.096	-0.046	28.998	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.014	-0.007	31.508	0.004	0.004	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.069	-0.032	34.380	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.917	-0.945	35.052	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	PRO	0	-0.036	-0.035	31.301	0.000	0.000	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.028	0.033	27.624	0.010	0.010	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.040	-0.028	23.475	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.041	-0.014	20.918	0.009	0.009	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.033	0.007	19.325	0.017	0.017	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.901	0.973	18.118	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.031	-0.020	16.811	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	25	HIS	0	-0.044	-0.055	16.297	0.049	0.049	0.000	0.000	0.000	0.000
27	A	26	SER	0	0.009	0.023	15.225	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.942	-0.977	13.472	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.011	-0.014	16.448	0.033	0.033	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.894	-0.923	19.068	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.029	-0.016	21.223	0.027	0.027	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.036	-0.025	24.025	0.014	0.014	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.859	-0.941	25.628	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	33	GLY	0	-0.104	-0.058	27.171	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	34	ASN	0	0.035	0.012	27.416	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.014	0.037	19.962	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.799	0.916	24.599	0.144	0.144	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.041	-0.035	18.831	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.022	-0.024	21.942	0.017	0.017	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.008	0.025	20.953	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.047	-0.035	21.727	0.010	0.010	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.063	0.029	22.012	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.867	-0.930	23.024	-0.213	-0.213	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.044	0.014	24.608	0.004	0.004	0.000	0.000	0.000	0.000
45	A	44	ALA	0	-0.016	-0.001	24.562	0.016	0.016	0.000	0.000	0.000	0.000
46	A	45	GLY	0	-0.017	-0.009	26.337	0.001	0.001	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.036	-0.019	29.319	0.009	0.009	0.000	0.000	0.000	0.000
48	A	47	ILE	0	-0.017	0.030	27.449	0.010	0.010	0.000	0.000	0.000	0.000
49	A	48	PHE	0	0.031	0.017	24.622	0.012	0.012	0.000	0.000	0.000	0.000
50	A	49	VAL	0	0.012	0.017	26.773	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.010	-0.001	22.136	0.005	0.005	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.836	-0.904	26.204	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.855	-0.917	25.556	-0.090	-0.090	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.986	0.995	25.707	0.021	0.021	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.057	-0.034	25.291	0.003	0.003	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.064	0.033	21.929	0.006	0.006	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.056	-0.025	21.794	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.011	0.002	19.889	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	58	HIS	0	0.009	-0.008	23.941	0.022	0.022	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.017	0.011	26.674	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	60	THR	0	-0.061	-0.073	28.128	0.012	0.012	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.919	0.988	31.259	0.062	0.062	0.000	0.000	0.000	0.000
63	A	62	THR	0	0.080	0.024	31.825	0.003	0.003	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.110	-0.074	26.857	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.743	-0.877	30.722	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.844	0.915	23.635	0.012	0.012	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-1.015	-0.982	28.689	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.988	-0.988	31.556	-0.063	-0.063	0.000	0.000	0.000	0.000
69	A	68	ARG	1	0.823	0.895	25.461	0.140	0.140	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.024	0.033	24.232	0.006	0.006	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.051	-0.041	19.085	0.024	0.024	0.000	0.000	0.000	0.000
72	A	71	TYR	0	0.007	0.011	21.577	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	72	THR	0	0.014	0.007	17.624	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.060	-0.037	18.529	0.026	0.026	0.000	0.000	0.000	0.000
75	A	74	MET	0	0.005	0.025	16.357	-0.076	-0.076	0.000	0.000	0.000	0.000
76	A	75	ALA	0	-0.004	-0.004	15.760	0.068	0.068	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.018	-0.034	17.198	-0.067	-0.067	0.000	0.000	0.000	0.000
78	A	77	ALA	0	0.069	0.034	19.065	0.037	0.037	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.049	-0.005	20.719	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.804	-0.904	23.812	-0.102	-0.102	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.788	0.871	26.148	0.081	0.081	0.000	0.000	0.000	0.000
82	A	81	ASP	-1	-0.904	-0.956	28.787	-0.083	-0.083	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.097	-0.041	28.573	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	83	ASN	0	0.025	-0.010	27.797	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.891	0.959	25.503	0.143	0.143	0.000	0.000	0.000	0.000
86	A	85	PRO	0	0.008	-0.010	21.172	0.008	0.008	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.018	-0.014	20.478	0.007	0.007	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.813	-0.895	15.001	-0.408	-0.408	0.000	0.000	0.000	0.000
89	A	88	PRO	0	-0.081	-0.026	13.156	0.028	0.028	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.020	-0.021	15.097	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	90	SER	0	-0.003	0.009	11.048	-0.162	-0.162	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.879	-0.953	13.220	-0.547	-0.547	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.049	-0.010	12.842	-0.083	-0.083	0.000	0.000	0.000	0.000
94	A	93	ILE	0	0.010	0.010	14.658	0.048	0.048	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.018	-0.002	17.081	0.041	0.041	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.900	0.943	16.520	0.122	0.122	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.031	0.017	21.119	0.024	0.024	0.000	0.000	0.000	0.000
98	A	97	GLN	0	-0.076	-0.041	21.503	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.856	-0.936	24.713	0.033	0.033	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)