FMO DATABASE

FMODB ID: JQ359

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

Total energy (hartree)

FMO2-HF: Electronic energy	-691315.101349
FMO2-HF: Nuclear repulsion	652946.568561
FMO2-HF: Total energy	-38368.532788
FMO2-MP2: Total energy	-38482.270291

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.
-11.171	-5.103	1.724	-3.629	-4.163	0.023

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 : 0.014 / q_NPA : 0.002

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	-0.041	-0.007	2.421	-8.448	-2.351	1.725	-3.606	-4.216	0.023
4	A	3	VAL	0	0.011	0.006	4.618	-1.758	-1.787	-0.001	-0.023	0.053	0.000
5	A	4	TRP	0	0.017	-0.003	4.900	0.283	0.283	0.000	0.000	0.000	0.000
6	A	5	ASN	0	-0.042	-0.018	9.535	0.019	0.019	0.000	0.000	0.000	0.000
7	A	6	GLN	0	0.023	-0.006	11.629	-0.102	-0.102	0.000	0.000	0.000	0.000
8	A	7	PHE	0	0.015	0.023	14.697	0.061	0.061	0.000	0.000	0.000	0.000
9	A	8	PHE	0	-0.016	-0.016	17.748	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.013	0.010	20.644	0.007	0.007	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.020	0.011	24.027	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.739	-0.863	26.680	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.961	-0.973	29.638	0.010	0.010	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.044	-0.023	27.740	0.008	0.008	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.088	-0.035	29.033	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.015	-0.004	31.672	0.005	0.005	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.058	-0.024	34.390	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.935	-0.955	35.300	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	18	PRO	0	-0.027	-0.033	31.110	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.001	0.027	27.285	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.022	-0.019	23.738	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.035	-0.015	20.959	0.006	0.006	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.035	0.009	19.411	0.006	0.006	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.843	0.951	18.633	0.047	0.047	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.024	-0.009	16.870	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	25	HIS	0	-0.020	-0.046	16.174	0.044	0.044	0.000	0.000	0.000	0.000
27	A	26	SER	0	0.001	-0.015	15.106	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.942	-0.978	13.510	-0.137	-0.137	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.013	-0.010	16.254	0.041	0.041	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.868	-0.908	18.939	-0.080	-0.080	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.047	-0.025	21.073	0.021	0.021	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.031	-0.014	23.820	0.014	0.014	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.841	-0.922	25.525	-0.055	-0.055	0.000	0.000	0.000	0.000
34	A	33	GLY	0	-0.108	-0.065	27.021	0.000	0.000	0.000	0.000	0.000	0.000
35	A	34	ASN	0	0.018	-0.002	27.383	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.023	0.044	19.970	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.749	0.876	24.567	0.140	0.140	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.052	-0.053	18.849	-0.036	-0.036	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.020	-0.024	22.029	0.018	0.018	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.007	0.028	21.000	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.037	-0.038	21.920	0.013	0.013	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.054	0.023	22.240	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.783	-0.865	23.468	-0.210	-0.210	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.057	0.020	24.804	0.000	0.000	0.000	0.000	0.000	0.000
45	A	44	ALA	0	-0.027	-0.008	24.717	0.013	0.013	0.000	0.000	0.000	0.000
46	A	45	GLY	0	-0.017	-0.009	26.505	0.004	0.004	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.037	-0.021	29.462	0.011	0.011	0.000	0.000	0.000	0.000
48	A	47	ILE	0	-0.002	0.032	27.751	0.008	0.008	0.000	0.000	0.000	0.000
49	A	48	PHE	0	0.027	0.018	24.720	0.008	0.008	0.000	0.000	0.000	0.000
50	A	49	VAL	0	0.012	0.015	26.848	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.002	-0.004	22.184	0.001	0.001	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.780	-0.844	26.212	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.828	-0.894	25.566	-0.113	-0.113	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.981	0.989	25.679	0.049	0.049	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.071	-0.072	25.126	0.000	0.000	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.061	0.033	21.842	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.074	-0.038	21.719	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.010	0.002	19.664	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	58	HIS	0	0.013	-0.007	23.902	0.018	0.018	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.016	0.009	26.637	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	60	THR	0	-0.058	-0.065	28.131	0.012	0.012	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.876	0.962	31.290	0.085	0.085	0.000	0.000	0.000	0.000
63	A	62	THR	0	0.081	0.026	31.843	0.001	0.001	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.097	-0.063	26.935	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.776	-0.895	30.780	-0.048	-0.048	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.792	0.872	24.134	0.048	0.048	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.981	-0.968	28.803	-0.065	-0.065	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.996	-0.990	31.728	-0.085	-0.085	0.000	0.000	0.000	0.000
69	A	68	ARG	1	0.725	0.799	24.929	0.171	0.171	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.037	0.040	24.426	0.003	0.003	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.008	-0.011	19.014	0.009	0.009	0.000	0.000	0.000	0.000
72	A	71	TYR	0	0.041	0.034	21.746	0.002	0.002	0.000	0.000	0.000	0.000
73	A	72	THR	0	0.017	0.010	17.919	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.060	-0.031	18.765	0.030	0.030	0.000	0.000	0.000	0.000
75	A	74	MET	0	0.012	0.025	16.223	-0.070	-0.070	0.000	0.000	0.000	0.000
76	A	75	ALA	0	-0.009	-0.003	15.849	0.063	0.063	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.016	-0.028	17.387	-0.047	-0.047	0.000	0.000	0.000	0.000
78	A	77	ALA	0	0.070	0.036	19.207	0.029	0.029	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.043	-0.008	20.807	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.753	-0.852	23.913	-0.106	-0.106	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.761	0.856	26.203	0.101	0.101	0.000	0.000	0.000	0.000
82	A	81	ASP	-1	-0.917	-0.964	28.818	-0.085	-0.085	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.039	-0.045	28.957	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.044	-0.025	27.901	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.910	0.966	25.706	0.125	0.125	0.000	0.000	0.000	0.000
86	A	85	PRO	0	0.012	-0.007	21.315	0.004	0.004	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.022	-0.014	20.604	0.011	0.011	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.808	-0.861	14.782	-0.426	-0.426	0.000	0.000	0.000	0.000
89	A	88	PRO	0	-0.085	-0.025	13.147	0.031	0.031	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.011	-0.022	15.313	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	90	SER	0	0.016	0.017	11.862	-0.163	-0.163	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.937	-0.978	13.572	-0.542	-0.542	0.000	0.000	0.000	0.000
93	A	92	PHE	0	-0.047	-0.020	13.069	-0.104	-0.104	0.000	0.000	0.000	0.000
94	A	93	ILE	0	-0.004	0.006	14.577	0.053	0.053	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.013	-0.002	17.167	0.024	0.024	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.859	0.926	16.133	0.246	0.246	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.019	0.013	21.185	0.019	0.019	0.000	0.000	0.000	0.000
98	A	97	GLN	0	-0.058	-0.028	21.953	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	98	ASP	-1	-0.865	-0.929	24.822	-0.009	-0.009	0.000	0.000	0.000	0.000

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