FMO DATABASE

FMODB ID: YZNY2

Calculation Name: 3H3M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H3M

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-06-22

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-564136.775643
FMO2-HF: Nuclear repulsion	529156.770466
FMO2-HF: Total energy	-34980.005177
FMO2-MP2: Total energy	-35081.889557

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:18:ALA)

Summations of interaction energy for fragment #1(A:18:ALA)

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.
-2.253	1.315	0.134	-1.325	-2.378	-0.001

Interaction energy analysis for fragmet #1(A:18:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.006

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	20	VAL	0	0.058	0.036	3.372	-1.066	0.953	-0.003	-0.989	-1.027	-0.001
4	A	21	LEU	0	-0.036	-0.026	2.773	0.048	0.982	0.139	-0.257	-0.816	0.000
5	A	22	GLU	-1	-0.930	-0.950	5.054	-1.372	-1.207	-0.001	-0.016	-0.148	0.000
6	A	23	ILE	0	0.032	0.013	6.745	0.591	0.591	0.000	0.000	0.000	0.000
7	A	24	TYR	0	-0.034	-0.025	7.316	0.365	0.365	0.000	0.000	0.000	0.000
8	A	25	GLN	0	-0.013	0.004	8.784	0.213	0.213	0.000	0.000	0.000	0.000
9	A	26	ASP	-1	-0.877	-0.941	10.591	-0.711	-0.711	0.000	0.000	0.000	0.000
10	A	27	ILE	0	0.014	0.005	12.910	0.151	0.151	0.000	0.000	0.000	0.000
11	A	28	ALA	0	0.030	0.029	13.749	0.115	0.115	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.030	-0.028	13.164	0.114	0.114	0.000	0.000	0.000	0.000
13	A	30	LEU	0	-0.050	-0.009	16.445	0.073	0.073	0.000	0.000	0.000	0.000
14	A	31	THR	0	0.014	-0.010	17.931	0.055	0.055	0.000	0.000	0.000	0.000
15	A	32	SER	0	0.008	0.009	18.663	0.048	0.048	0.000	0.000	0.000	0.000
16	A	33	ARG	1	0.875	0.942	17.596	0.403	0.403	0.000	0.000	0.000	0.000
17	A	34	MET	0	-0.055	-0.023	21.608	0.034	0.034	0.000	0.000	0.000	0.000
18	A	35	LEU	0	0.032	0.016	23.917	0.025	0.025	0.000	0.000	0.000	0.000
19	A	36	ALA	0	-0.003	-0.001	25.196	0.021	0.021	0.000	0.000	0.000	0.000
20	A	37	ALA	0	-0.020	-0.011	27.094	0.017	0.017	0.000	0.000	0.000	0.000
21	A	38	ALA	0	0.034	0.010	28.559	0.014	0.014	0.000	0.000	0.000	0.000
22	A	39	ASN	0	-0.047	-0.017	29.573	0.019	0.019	0.000	0.000	0.000	0.000
23	A	40	ALA	0	-0.065	-0.008	31.392	0.010	0.010	0.000	0.000	0.000	0.000
24	A	41	SER	0	-0.019	-0.024	33.440	0.009	0.009	0.000	0.000	0.000	0.000
25	A	42	ASN	0	-0.039	-0.012	31.785	0.006	0.006	0.000	0.000	0.000	0.000
26	A	43	TRP	0	0.063	0.009	31.644	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	44	ASP	-1	-0.827	-0.918	31.828	-0.130	-0.130	0.000	0.000	0.000	0.000
28	A	45	LEU	0	-0.066	-0.014	27.488	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	46	VAL	0	-0.025	-0.014	27.189	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	47	LEU	0	0.031	-0.003	27.011	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	48	ASN	0	-0.045	-0.011	26.966	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	49	HIS	0	0.003	-0.013	23.395	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	50	GLY	0	0.045	0.018	22.989	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	51	GLN	0	-0.063	-0.031	23.592	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	52	GLU	-1	-0.883	-0.943	18.436	-0.372	-0.372	0.000	0.000	0.000	0.000
36	A	53	TYR	0	-0.033	-0.023	19.117	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	54	VAL	0	0.010	0.003	18.718	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	55	CYS	0	-0.024	-0.013	18.559	0.005	0.005	0.000	0.000	0.000	0.000
39	A	56	LEU	0	0.021	0.012	14.319	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.010	0.005	14.263	-0.075	-0.075	0.000	0.000	0.000	0.000
41	A	58	GLU	-1	-0.924	-0.949	15.335	-0.290	-0.290	0.000	0.000	0.000	0.000
42	A	59	ARG	1	0.861	0.919	10.778	0.464	0.464	0.000	0.000	0.000	0.000
43	A	60	LEU	0	-0.024	-0.026	9.796	-0.046	-0.046	0.000	0.000	0.000	0.000
44	A	61	ARG	1	0.930	0.953	11.220	0.304	0.304	0.000	0.000	0.000	0.000
45	A	62	GLU	-1	-0.935	-0.939	12.595	-0.261	-0.261	0.000	0.000	0.000	0.000
46	A	63	LEU	0	-0.109	-0.054	6.676	0.031	0.031	0.000	0.000	0.000	0.000
47	A	64	GLU	-1	-0.832	-0.873	8.325	-0.830	-0.830	0.000	0.000	0.000	0.000
48	A	65	PRO	0	-0.067	-0.067	10.225	0.065	0.065	0.000	0.000	0.000	0.000
49	A	66	GLY	0	-0.041	0.001	9.151	0.069	0.069	0.000	0.000	0.000	0.000
50	A	67	GLU	-1	-0.883	-0.960	6.457	0.019	0.019	0.000	0.000	0.000	0.000
51	A	68	PRO	0	-0.068	-0.035	7.330	-0.134	-0.134	0.000	0.000	0.000	0.000
52	A	69	LEU	0	0.034	0.004	3.910	-0.166	-0.011	0.001	-0.020	-0.136	0.000
53	A	70	ASP	-1	-0.883	-0.958	4.189	-0.453	-0.226	-0.001	-0.034	-0.193	0.000
54	A	71	GLU	-1	-0.979	-1.001	7.300	-0.116	-0.116	0.000	0.000	0.000	0.000
55	A	72	ALA	0	0.027	0.013	7.738	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	73	ALA	0	0.026	0.000	4.320	-0.161	-0.093	-0.001	-0.009	-0.058	0.000
57	A	74	ARG	1	0.863	0.957	6.409	0.141	0.141	0.000	0.000	0.000	0.000
58	A	75	GLY	0	0.040	0.012	8.911	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	76	MET	0	0.053	0.047	6.889	-0.191	-0.191	0.000	0.000	0.000	0.000
60	A	77	LYS	1	0.966	0.999	7.289	0.834	0.834	0.000	0.000	0.000	0.000
61	A	78	PHE	0	-0.044	-0.026	9.157	0.115	0.115	0.000	0.000	0.000	0.000
62	A	79	ASP	-1	-0.878	-0.934	12.610	-0.433	-0.433	0.000	0.000	0.000	0.000
63	A	80	LEU	0	-0.029	-0.015	8.930	0.066	0.066	0.000	0.000	0.000	0.000
64	A	81	LEU	0	-0.009	-0.012	12.136	0.077	0.077	0.000	0.000	0.000	0.000
65	A	82	VAL	0	0.009	0.017	14.513	0.061	0.061	0.000	0.000	0.000	0.000
66	A	83	ARG	1	0.953	0.981	16.009	0.415	0.415	0.000	0.000	0.000	0.000
67	A	84	ILE	0	-0.023	-0.006	13.349	0.039	0.039	0.000	0.000	0.000	0.000
68	A	85	LEU	0	-0.006	-0.015	17.713	0.049	0.049	0.000	0.000	0.000	0.000
69	A	86	GLU	-1	-0.956	-0.975	20.170	-0.254	-0.254	0.000	0.000	0.000	0.000
70	A	87	ASN	0	-0.052	-0.033	19.486	0.055	0.055	0.000	0.000	0.000	0.000
71	A	88	ASP	-1	-0.886	-0.938	21.526	-0.305	-0.305	0.000	0.000	0.000	0.000
72	A	89	ALA	0	-0.066	-0.041	23.537	0.027	0.027	0.000	0.000	0.000	0.000
73	A	90	ALA	0	0.060	0.034	25.597	0.019	0.019	0.000	0.000	0.000	0.000
74	A	91	VAL	0	0.008	0.002	25.667	0.018	0.018	0.000	0.000	0.000	0.000
75	A	92	ARG	1	0.908	0.951	25.912	0.223	0.223	0.000	0.000	0.000	0.000
76	A	93	ASP	-1	-0.907	-0.958	29.913	-0.149	-0.149	0.000	0.000	0.000	0.000
77	A	94	LEU	0	-0.056	-0.015	29.813	0.011	0.011	0.000	0.000	0.000	0.000
78	A	95	ALA	0	0.003	0.002	32.494	0.011	0.011	0.000	0.000	0.000	0.000
79	A	96	LEU	0	-0.005	-0.010	32.772	0.010	0.010	0.000	0.000	0.000	0.000
80	A	97	PRO	0	-0.015	0.003	35.117	0.009	0.009	0.000	0.000	0.000	0.000
81	A	98	GLN	0	-0.008	-0.014	36.518	0.011	0.011	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.017	0.020	36.475	0.005	0.005	0.000	0.000	0.000	0.000
83	A	100	ALA	0	0.020	0.010	39.424	0.006	0.006	0.000	0.000	0.000	0.000
84	A	101	ARG	1	0.958	0.981	41.315	0.079	0.079	0.000	0.000	0.000	0.000
85	A	102	LEU	0	-0.008	-0.016	41.466	0.005	0.005	0.000	0.000	0.000	0.000
86	A	103	SER	0	-0.055	-0.044	42.217	0.003	0.003	0.000	0.000	0.000	0.000
87	A	104	ASP	-1	-0.996	-0.988	44.794	-0.067	-0.067	0.000	0.000	0.000	0.000
88	A	105	LEU	0	-0.091	-0.033	47.360	0.003	0.003	0.000	0.000	0.000	0.000
89	A	106	LEU	0	-0.031	0.004	46.556	0.004	0.004	0.000	0.000	0.000	0.000
90	B	127	HOH	0	-0.019	-0.015	25.725	0.006	0.006	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ALA)