FMO DATABASE

FMODB ID: 5NYGZ

Calculation Name: 1A92-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A92

Chain ID: A

ChEMBL ID:

UniProt ID: P25989

Base Structure: X-ray

Registration Date: 2025-07-07

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	OptAll
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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-220009.769294
FMO2-HF: Nuclear repulsion	199647.8573
FMO2-HF: Total energy	-20361.911994
FMO2-MP2: Total energy	-20423.020375

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-10.113	-6.392	6.615	-5.573	-4.765	-0.049

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : 0.027

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	13	ARG	1	0.882	1.041	4.418	1.495	1.702	-0.001	-0.083	-0.123	0.000
4	A	14	GLU	0	0.125	-0.092	3.616	-1.520	0.463	0.006	-1.077	-0.912	0.005
5	A	14	GLU	-1	-1.006	-0.832	4.549	-0.743	-0.619	-0.001	-0.005	-0.117	0.000
6	A	15	ASP	0	0.120	-0.063	3.348	1.233	1.521	0.026	-0.040	-0.274	-0.001
7	A	15	ASP	-1	-0.878	-0.811	1.980	-16.779	-16.312	6.567	-4.095	-2.940	-0.053
8	A	16	ILE	0	0.093	-0.093	3.636	1.632	1.922	-0.001	-0.120	-0.170	0.000
9	A	16	ILE	0	-0.116	0.083	3.273	-0.035	0.327	0.019	-0.153	-0.229	0.000
10	A	17	LEU	0	0.096	-0.096	5.454	1.103	1.103	0.000	0.000	0.000	0.000
11	A	17	LEU	0	-0.082	0.105	8.072	0.065	0.065	0.000	0.000	0.000	0.000
12	A	18	GLU	0	0.069	-0.144	7.519	0.531	0.531	0.000	0.000	0.000	0.000
13	A	18	GLU	-1	-0.947	-0.815	7.632	-1.259	-1.259	0.000	0.000	0.000	0.000
14	A	19	GLN	0	0.058	-0.103	7.666	0.594	0.594	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.116	0.078	5.228	0.588	0.588	0.000	0.000	0.000	0.000
16	A	20	TRP	0	0.115	-0.072	9.265	0.391	0.391	0.000	0.000	0.000	0.000
17	A	20	TRP	0	-0.092	0.085	10.385	0.061	0.061	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.042	-0.124	11.401	0.229	0.229	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.073	0.115	12.487	0.027	0.027	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.006	-0.125	12.405	0.188	0.188	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.035	0.082	11.959	0.069	0.069	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.025	-0.107	13.281	0.140	0.140	0.000	0.000	0.000	0.000
23	A	24	ARG	0	0.052	-0.017	15.046	0.114	0.114	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.745	1.013	15.798	0.592	0.592	0.000	0.000	0.000	0.000
25	A	25	LYS	0	0.189	-0.053	16.980	0.081	0.081	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.805	1.033	17.491	0.412	0.412	0.000	0.000	0.000	0.000
27	A	26	LYS	0	0.066	-0.133	17.835	0.074	0.074	0.000	0.000	0.000	0.000
28	A	26	LYS	1	0.779	1.044	18.004	0.348	0.348	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.101	-0.119	19.059	0.066	0.066	0.000	0.000	0.000	0.000
30	A	27	LEU	0	-0.062	0.130	19.521	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	28	GLU	0	0.097	-0.118	20.922	0.050	0.050	0.000	0.000	0.000	0.000
32	A	28	GLU	-1	-0.882	-0.755	20.885	-0.471	-0.471	0.000	0.000	0.000	0.000
33	A	29	GLU	0	0.024	-0.142	22.479	0.043	0.043	0.000	0.000	0.000	0.000
34	A	29	GLU	-1	-0.890	-0.781	22.147	-0.356	-0.356	0.000	0.000	0.000	0.000
35	A	30	LEU	0	0.067	-0.119	23.470	0.038	0.038	0.000	0.000	0.000	0.000
36	A	30	LEU	0	-0.065	0.119	21.792	0.003	0.003	0.000	0.000	0.000	0.000
37	A	31	GLU	0	0.098	-0.120	24.958	0.034	0.034	0.000	0.000	0.000	0.000
38	A	31	GLU	-1	-0.904	-0.748	25.151	-0.302	-0.302	0.000	0.000	0.000	0.000
39	A	32	ARG	0	0.063	-0.115	26.740	0.026	0.026	0.000	0.000	0.000	0.000
40	A	32	ARG	1	0.755	1.013	25.991	0.252	0.252	0.000	0.000	0.000	0.000
41	A	33	ASP	0	0.027	-0.126	28.068	0.022	0.022	0.000	0.000	0.000	0.000
42	A	33	ASP	-1	-0.841	-0.745	27.940	-0.220	-0.220	0.000	0.000	0.000	0.000
43	A	34	LEU	0	0.117	-0.108	29.172	0.022	0.022	0.000	0.000	0.000	0.000
44	A	34	LEU	0	-0.064	0.115	29.176	0.001	0.001	0.000	0.000	0.000	0.000
45	A	35	ARG	0	0.050	-0.110	30.782	0.017	0.017	0.000	0.000	0.000	0.000
46	A	35	ARG	1	0.740	0.993	28.269	0.243	0.243	0.000	0.000	0.000	0.000
47	A	36	LYS	0	0.054	-0.111	32.737	0.011	0.011	0.000	0.000	0.000	0.000
48	A	36	LYS	1	0.778	1.003	31.733	0.183	0.183	0.000	0.000	0.000	0.000
49	A	37	LEU	0	0.107	-0.096	33.723	0.013	0.013	0.000	0.000	0.000	0.000
50	A	37	LEU	0	-0.092	0.116	33.141	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	38	LYS	0	0.083	-0.102	34.937	0.011	0.011	0.000	0.000	0.000	0.000
52	A	38	LYS	1	0.873	1.072	32.399	0.184	0.184	0.000	0.000	0.000	0.000
53	A	39	LYS	0	0.074	-0.072	36.787	0.008	0.008	0.000	0.000	0.000	0.000
54	A	39	LYS	1	0.902	1.066	37.119	0.147	0.147	0.000	0.000	0.000	0.000
55	A	40	LYS	0	0.138	-0.038	38.441	0.008	0.008	0.000	0.000	0.000	0.000
56	A	40	LYS	1	0.853	1.051	38.407	0.112	0.112	0.000	0.000	0.000	0.000
57	A	41	ILE	0	0.031	-0.118	39.246	0.008	0.008	0.000	0.000	0.000	0.000
58	A	41	ILE	0	-0.083	0.096	38.290	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	42	LYS	0	0.175	-0.038	40.826	0.007	0.007	0.000	0.000	0.000	0.000
60	A	42	LYS	1	0.684	0.945	41.517	0.103	0.103	0.000	0.000	0.000	0.000
61	A	43	LYS	0	0.117	-0.063	42.832	0.005	0.005	0.000	0.000	0.000	0.000
62	A	43	LYS	1	0.760	0.976	43.725	0.088	0.088	0.000	0.000	0.000	0.000
63	A	44	LEU	0	0.064	-0.089	43.860	0.005	0.005	0.000	0.000	0.000	0.000
64	A	44	LEU	0	-0.113	0.063	42.380	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	45	GLU	0	0.111	-0.086	45.207	0.005	0.005	0.000	0.000	0.000	0.000
66	A	45	GLU	-1	-0.869	-0.794	44.030	-0.097	-0.097	0.000	0.000	0.000	0.000
67	A	46	GLU	0	0.055	-0.088	47.046	0.004	0.004	0.000	0.000	0.000	0.000
68	A	46	GLU	-1	-0.880	-0.792	46.255	-0.098	-0.098	0.000	0.000	0.000	0.000
69	A	47	ASP	0	0.113	-0.081	48.578	0.004	0.004	0.000	0.000	0.000	0.000
70	A	47	ASP	-1	-0.969	-0.824	48.304	-0.084	-0.084	0.000	0.000	0.000	0.000
71	A	48	ASN	0	-0.036	-0.089	49.702	0.004	0.004	0.000	0.000	0.000	0.000
72	A	48	ASN	0	-0.120	0.038	48.554	0.003	0.003	0.000	0.000	0.000	0.000
73	A	49	PRO	0	0.145	-0.058	50.358	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	50	TRP	0	0.102	0.015	52.103	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	50	TRP	0	-0.064	0.112	49.936	0.000	0.000	0.000	0.000	0.000	0.000
76	A	51	LEU	0	0.015	-0.142	48.121	0.003	0.003	0.000	0.000	0.000	0.000
77	A	51	LEU	0	-0.049	0.125	45.978	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	52	GLY	0	0.022	-0.097	48.472	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	53	ASN	0	0.093	0.021	49.953	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	53	ASN	0	-0.074	0.080	53.280	0.000	0.000	0.000	0.000	0.000	0.000
81	A	54	ILE	0	0.069	-0.087	48.951	0.002	0.002	0.000	0.000	0.000	0.000
82	A	54	ILE	0	-0.091	0.098	47.182	0.000	0.000	0.000	0.000	0.000	0.000
83	A	55	LYS	0	0.089	-0.099	46.293	0.000	0.000	0.000	0.000	0.000	0.000
84	A	55	LYS	1	0.729	0.978	43.971	0.095	0.095	0.000	0.000	0.000	0.000
85	A	56	GLY	0	0.038	-0.088	47.149	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	57	ILE	0	0.110	0.024	50.224	0.001	0.001	0.000	0.000	0.000	0.000
87	A	57	ILE	0	-0.103	0.092	49.913	0.000	0.000	0.000	0.000	0.000	0.000
88	A	58	ILE	0	0.029	-0.110	45.645	0.003	0.003	0.000	0.000	0.000	0.000
89	A	58	ILE	0	-0.113	0.082	43.474	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	59	GLY	0	-0.030	-0.137	45.885	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	60	LYS	0	0.025	0.029	46.742	0.000	0.000	0.000	0.000	0.000	0.000
92	A	60	LYS	1	0.860	1.049	47.411	0.064	0.064	0.000	0.000	0.000	0.000
93	A	61	TYR	0	-0.028	-0.128	50.242	0.003	0.003	0.000	0.000	0.000	0.000
94	A	61	TYR	0	0.013	0.025	47.132	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)