FMO DATABASE

FMODB ID: LZ479

Calculation Name: 4U3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3H

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-671980.100851
FMO2-HF: Nuclear repulsion	634650.41601
FMO2-HF: Total energy	-37329.684841
FMO2-MP2: Total energy	-37440.343762

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:1:MET)

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

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.
-5.689	-2.555	1.822	-1.28	-3.676	-0.013

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.016

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	3	HIS	0	-0.006	-0.017	2.571	-6.526	-3.556	1.817	-1.390	-3.398	-0.013
4	A	4	HIS	0	0.010	0.009	3.596	0.588	0.752	0.005	0.110	-0.278	0.000
5	A	5	HIS	0	0.012	0.009	6.235	0.190	0.190	0.000	0.000	0.000	0.000
6	A	6	HIS	0	0.011	0.013	8.623	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.024	0.001	11.906	0.091	0.091	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.030	-0.011	15.207	0.009	0.009	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.025	0.016	17.742	0.014	0.014	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.018	0.014	20.927	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.917	0.954	19.450	0.169	0.169	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.045	0.024	24.966	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.054	-0.014	23.831	0.001	0.001	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.011	0.000	25.285	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.005	-0.005	22.350	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.001	-0.007	19.249	0.013	0.013	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.022	0.005	22.334	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.009	0.021	23.729	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.048	-0.054	24.935	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.018	0.001	22.684	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.911	0.957	24.765	0.107	0.107	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.028	0.003	26.243	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.083	-0.042	28.677	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.901	-0.945	32.239	-0.054	-0.054	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.006	0.009	29.906	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.038	0.055	33.136	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.019	-0.028	34.097	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.002	-0.011	35.087	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.039	-0.038	34.392	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.059	0.032	28.479	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.018	-0.010	31.935	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.022	-0.009	26.937	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.013	-0.019	29.565	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.066	-0.033	27.720	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.879	-0.923	28.545	-0.114	-0.114	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.006	-0.005	28.598	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.021	0.010	25.972	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.013	-0.006	26.865	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.019	-0.002	29.471	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.016	-0.008	31.679	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.044	0.014	29.484	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.060	-0.052	32.273	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.018	0.004	32.277	0.007	0.007	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.011	0.004	27.970	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.914	0.966	26.413	0.102	0.102	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.001	-0.001	26.665	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.879	-0.948	22.672	-0.126	-0.126	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.001	-0.014	24.377	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.823	0.924	17.211	0.087	0.087	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.827	-0.906	24.086	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.018	-0.003	20.102	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.024	-0.018	18.900	0.017	0.017	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.033	-0.009	19.952	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.901	-0.948	22.145	-0.035	-0.035	0.000	0.000	0.000	0.000
55	A	55	TRP	0	-0.061	-0.044	18.826	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.924	0.971	24.986	0.036	0.036	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.908	-0.983	27.167	-0.090	-0.090	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.012	0.013	29.139	0.008	0.008	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.008	-0.004	30.735	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.019	-0.003	32.018	0.006	0.006	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.039	0.002	34.003	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.044	0.025	33.794	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.029	-0.018	34.634	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.966	-0.971	34.327	-0.068	-0.068	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.002	-0.008	32.839	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.001	-0.010	32.847	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.027	0.022	31.816	0.004	0.004	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.036	0.023	32.868	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.006	0.030	30.352	0.004	0.004	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.005	-0.018	33.550	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.001	0.001	35.323	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.047	-0.009	30.528	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.863	0.935	29.446	0.012	0.012	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.031	0.018	32.370	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.041	-0.025	31.674	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.036	-0.009	27.683	0.009	0.009	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.898	-0.942	23.267	-0.066	-0.066	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.008	-0.017	24.675	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.823	-0.909	17.619	-0.178	-0.178	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.019	-0.009	22.111	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.817	0.913	17.279	0.179	0.179	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.031	0.027	22.361	0.016	0.016	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.919	0.963	19.773	0.159	0.159	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.053	0.038	24.397	0.015	0.015	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.005	0.001	26.198	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.030	0.008	28.839	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.009	-0.012	30.918	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.032	-0.002	28.416	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.010	0.000	27.175	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.893	-0.952	23.508	-0.128	-0.128	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.026	0.017	22.648	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.062	-0.039	17.674	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	PRO	0	0.010	0.014	17.426	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.010	0.003	18.574	-0.036	-0.036	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.005	-0.029	17.749	0.023	0.023	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.010	0.023	19.735	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.006	0.001	19.508	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.017	0.000	21.870	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	THR	0	0.056	0.036	25.354	0.007	0.007	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.049	-0.023	27.614	0.000	0.000	0.000	0.000	0.000	0.000

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