FMO DATABASE

FMODB ID: QVZ9Y

Calculation Name: 1U2H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1U2H

Chain ID: A

ChEMBL ID:

UniProt ID: Q15772

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-690417.425351
FMO2-HF: Nuclear repulsion	651795.971803
FMO2-HF: Total energy	-38621.453548
FMO2-MP2: Total energy	-38732.037814

3D Structure Molmil

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:17:LYS)

Summations of interaction energy for fragment #1(A:17:LYS)

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.
6.588	15.783	5.36	-6.031	-8.525	-0.043

Interaction energy analysis for fragmet #1(A:17:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 1.007

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	19	PRO	0	0.027	0.036	3.784	1.443	4.134	-0.030	-1.385	-1.276	0.006
4	A	20	PRO	0	-0.009	0.000	6.741	1.028	1.028	0.000	0.000	0.000	0.000
5	A	21	THR	0	-0.066	-0.037	9.469	1.142	1.142	0.000	0.000	0.000	0.000
6	A	22	PHE	0	0.033	0.007	11.815	0.177	0.177	0.000	0.000	0.000	0.000
7	A	23	LYS	1	0.870	0.936	12.233	19.890	19.890	0.000	0.000	0.000	0.000
8	A	24	VAL	0	0.008	0.014	16.038	0.653	0.653	0.000	0.000	0.000	0.000
9	A	25	SER	0	0.019	-0.001	18.775	-0.591	-0.591	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.006	-0.005	20.745	0.410	0.410	0.000	0.000	0.000	0.000
11	A	27	MET	0	0.000	-0.001	23.808	-0.136	-0.136	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.821	-0.907	27.218	-9.758	-9.758	0.000	0.000	0.000	0.000
13	A	29	GLN	0	-0.076	-0.037	28.739	0.311	0.311	0.000	0.000	0.000	0.000
14	A	30	SER	0	0.057	0.024	32.915	0.140	0.140	0.000	0.000	0.000	0.000
15	A	31	VAL	0	0.025	0.043	34.927	0.114	0.114	0.000	0.000	0.000	0.000
16	A	32	ARG	1	0.867	0.922	37.810	6.785	6.785	0.000	0.000	0.000	0.000
17	A	33	GLU	-1	-0.792	-0.902	40.259	-6.988	-6.988	0.000	0.000	0.000	0.000
18	A	34	GLY	0	-0.015	0.001	40.941	0.148	0.148	0.000	0.000	0.000	0.000
19	A	35	GLN	0	-0.029	-0.010	38.052	-0.090	-0.090	0.000	0.000	0.000	0.000
20	A	36	ASP	-1	-0.799	-0.889	34.167	-8.101	-8.101	0.000	0.000	0.000	0.000
21	A	37	VAL	0	-0.038	-0.020	30.710	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	38	ILE	0	-0.018	-0.011	26.588	-0.156	-0.156	0.000	0.000	0.000	0.000
23	A	39	MET	0	-0.019	0.018	25.595	-0.110	-0.110	0.000	0.000	0.000	0.000
24	A	40	SER	0	0.025	-0.002	21.823	-0.102	-0.102	0.000	0.000	0.000	0.000
25	A	41	ILE	0	-0.020	-0.003	16.519	-0.055	-0.055	0.000	0.000	0.000	0.000
26	A	42	ARG	1	0.883	0.948	13.009	17.221	17.221	0.000	0.000	0.000	0.000
27	A	43	VAL	0	-0.005	0.002	11.562	-0.400	-0.400	0.000	0.000	0.000	0.000
28	A	44	GLN	0	0.008	-0.010	8.898	1.844	1.844	0.000	0.000	0.000	0.000
29	A	45	GLY	0	0.044	0.005	6.015	0.321	0.321	0.000	0.000	0.000	0.000
30	A	46	GLU	-1	-0.918	-0.939	2.495	-28.343	-27.524	0.767	-0.633	-0.953	-0.002
31	A	47	PRO	0	0.096	0.017	2.668	-10.567	-8.060	0.822	-1.736	-1.594	-0.019
32	A	48	LYS	1	0.832	0.931	5.744	17.121	17.121	0.000	0.000	0.000	0.000
33	A	49	PRO	0	-0.072	-0.029	8.202	0.685	0.685	0.000	0.000	0.000	0.000
34	A	50	VAL	0	0.041	0.025	10.365	1.359	1.359	0.000	0.000	0.000	0.000
35	A	51	VAL	0	-0.006	-0.020	13.789	-0.263	-0.263	0.000	0.000	0.000	0.000
36	A	52	SER	0	-0.029	-0.009	16.348	0.786	0.786	0.000	0.000	0.000	0.000
37	A	53	TRP	0	0.069	0.019	19.819	-0.145	-0.145	0.000	0.000	0.000	0.000
38	A	54	LEU	0	-0.042	-0.023	22.507	0.197	0.197	0.000	0.000	0.000	0.000
39	A	55	ARG	1	0.935	0.977	25.708	8.764	8.764	0.000	0.000	0.000	0.000
40	A	56	ASN	0	-0.013	-0.017	29.176	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	57	ARG	1	0.814	0.876	26.614	11.084	11.084	0.000	0.000	0.000	0.000
42	A	58	GLN	0	0.021	0.029	28.016	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	59	PRO	0	0.010	-0.003	26.024	-0.112	-0.112	0.000	0.000	0.000	0.000
44	A	60	VAL	0	0.015	0.012	26.303	0.416	0.416	0.000	0.000	0.000	0.000
45	A	61	ARG	1	0.918	0.969	27.347	8.494	8.494	0.000	0.000	0.000	0.000
46	A	62	PRO	0	-0.003	-0.001	27.435	0.187	0.187	0.000	0.000	0.000	0.000
47	A	63	ASP	-1	-0.848	-0.937	29.940	-8.393	-8.393	0.000	0.000	0.000	0.000
48	A	64	GLN	0	0.062	0.018	32.455	-0.322	-0.322	0.000	0.000	0.000	0.000
49	A	65	ARG	1	0.779	0.875	34.358	8.058	8.058	0.000	0.000	0.000	0.000
50	A	66	ARG	1	0.914	0.957	30.010	8.859	8.859	0.000	0.000	0.000	0.000
51	A	67	PHE	0	-0.005	0.004	27.240	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	68	ALA	0	-0.002	0.001	22.562	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	69	GLU	-1	-0.758	-0.850	22.697	-10.774	-10.774	0.000	0.000	0.000	0.000
54	A	70	GLU	-1	-0.845	-0.926	16.255	-16.133	-16.133	0.000	0.000	0.000	0.000
55	A	71	ALA	0	-0.022	-0.008	19.172	0.422	0.422	0.000	0.000	0.000	0.000
56	A	72	GLU	-1	-0.883	-0.940	17.257	-13.437	-13.437	0.000	0.000	0.000	0.000
57	A	73	GLY	0	0.015	-0.010	14.574	0.178	0.178	0.000	0.000	0.000	0.000
58	A	74	GLY	0	0.034	0.010	13.814	-0.514	-0.514	0.000	0.000	0.000	0.000
59	A	75	LEU	0	-0.064	-0.025	14.527	-0.079	-0.079	0.000	0.000	0.000	0.000
60	A	76	CYS	0	-0.011	0.008	16.478	-0.097	-0.097	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.875	0.918	19.317	11.781	11.781	0.000	0.000	0.000	0.000
62	A	78	LEU	0	-0.011	0.009	23.027	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	79	ARG	1	0.840	0.897	25.649	10.091	10.091	0.000	0.000	0.000	0.000
64	A	80	ILE	0	-0.012	-0.006	29.035	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	81	LEU	0	-0.014	-0.004	32.382	0.046	0.046	0.000	0.000	0.000	0.000
66	A	82	ALA	0	-0.004	-0.009	35.495	0.096	0.096	0.000	0.000	0.000	0.000
67	A	83	ALA	0	-0.023	0.003	36.518	0.028	0.028	0.000	0.000	0.000	0.000
68	A	84	GLU	-1	-0.853	-0.937	37.872	-7.147	-7.147	0.000	0.000	0.000	0.000
69	A	85	ARG	1	0.873	0.906	38.729	6.580	6.580	0.000	0.000	0.000	0.000
70	A	86	GLY	0	-0.018	-0.003	39.053	-0.118	-0.118	0.000	0.000	0.000	0.000
71	A	87	ASP	-1	-0.756	-0.850	34.422	-8.476	-8.476	0.000	0.000	0.000	0.000
72	A	88	ALA	0	-0.015	0.016	34.013	-0.324	-0.324	0.000	0.000	0.000	0.000
73	A	89	GLY	0	-0.009	-0.012	33.299	0.074	0.074	0.000	0.000	0.000	0.000
74	A	90	PHE	0	-0.001	0.000	29.345	-0.039	-0.039	0.000	0.000	0.000	0.000
75	A	91	TYR	0	-0.004	-0.029	26.380	-0.111	-0.111	0.000	0.000	0.000	0.000
76	A	92	THR	0	-0.049	-0.035	21.872	-0.148	-0.148	0.000	0.000	0.000	0.000
77	A	93	CYS	0	-0.030	0.007	19.103	-0.105	-0.105	0.000	0.000	0.000	0.000
78	A	94	LYS	1	0.904	0.938	17.972	13.874	13.874	0.000	0.000	0.000	0.000
79	A	95	ALA	0	0.035	0.018	12.801	0.191	0.191	0.000	0.000	0.000	0.000
80	A	96	VAL	0	0.006	-0.015	12.074	-0.491	-0.491	0.000	0.000	0.000	0.000
81	A	97	ASN	0	0.017	-0.008	5.397	0.051	0.051	0.000	0.000	0.000	0.000
82	A	98	GLU	-1	-0.828	-0.927	6.222	-27.503	-27.503	0.000	0.000	0.000	0.000
83	A	99	TYR	0	-0.040	-0.014	2.650	-12.380	-9.202	3.801	-2.277	-4.702	-0.028
84	A	100	GLY	0	-0.003	-0.002	6.318	-0.312	-0.312	0.000	0.000	0.000	0.000
85	A	101	ALA	0	0.012	0.008	9.611	0.914	0.914	0.000	0.000	0.000	0.000
86	A	102	ARG	1	0.890	0.947	12.541	20.571	20.571	0.000	0.000	0.000	0.000
87	A	103	GLN	0	0.050	0.032	14.885	0.153	0.153	0.000	0.000	0.000	0.000
88	A	104	CYS	0	-0.051	-0.002	18.244	0.090	0.090	0.000	0.000	0.000	0.000
89	A	105	GLU	-1	-0.788	-0.881	20.885	-11.353	-11.353	0.000	0.000	0.000	0.000
90	A	106	ALA	0	0.014	0.028	24.513	-0.053	-0.053	0.000	0.000	0.000	0.000
91	A	107	ARG	1	0.819	0.902	27.568	8.551	8.551	0.000	0.000	0.000	0.000
92	A	108	LEU	0	0.008	0.017	31.112	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	109	GLU	-1	-0.871	-0.934	32.894	-7.871	-7.871	0.000	0.000	0.000	0.000
94	A	110	VAL	0	0.012	-0.002	36.666	-0.045	-0.045	0.000	0.000	0.000	0.000
95	A	111	ARG	1	0.857	0.912	39.154	7.633	7.633	0.000	0.000	0.000	0.000
96	A	112	GLY	0	0.060	0.040	42.576	0.030	0.030	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:LYS)