FMO DATABASE

FMODB ID: Y9Y32

Calculation Name: 5GNJ-G-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5GNJ

Chain ID: G

ChEMBL ID:

UniProt ID: Q39204

Base Structure: X-ray

Registration Date: 2025-07-11

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-357428.244307
FMO2-HF: Nuclear repulsion	328483.121205
FMO2-HF: Total energy	-28945.123103
FMO2-MP2: Total energy	-29030.415321

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(G:452:ASN)

Summations of interaction energy for fragment #1(G:452:ASN)

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.
-13.237	-26.838	18.565	3.557	-8.522	0.03

Interaction energy analysis for fragmet #1(G:452:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.171 / q_NPA : 0.069

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].
4	G	453	HIS	0	-0.058	0.112	4.026	-0.450	0.273	0.004	-0.442	-0.286	0.001
5	G	454	VAL	0	0.074	-0.125	2.709	11.161	5.742	0.360	6.591	-1.533	-0.002
6	G	454	VAL	0	-0.052	0.116	5.075	-0.327	-0.327	0.000	0.000	0.000	0.000
7	G	455	GLU	0	0.040	-0.134	2.333	-1.925	-6.125	4.008	2.032	-1.839	0.013
8	G	455	GLU	-1	-0.850	-0.781	2.112	0.325	-0.467	4.461	-2.112	-1.557	0.000
9	G	456	ALA	0	0.122	-0.093	2.047	-8.407	-12.850	9.046	-1.952	-2.651	0.016
10	G	456	ALA	0	-0.055	0.121	2.519	-0.453	-0.090	0.633	-0.532	-0.464	0.001
11	G	457	GLU	0	0.093	-0.094	3.416	-3.108	-3.013	0.054	-0.025	-0.124	0.001
12	G	457	GLU	-1	-0.848	-0.743	6.481	2.248	2.248	0.000	0.000	0.000	0.000
13	G	458	ARG	0	0.054	-0.112	6.030	-1.370	-1.370	0.000	0.000	0.000	0.000
14	G	458	ARG	1	0.759	1.002	5.531	-3.068	-3.068	0.000	0.000	0.000	0.000
15	G	459	GLN	0	0.097	-0.104	6.164	-0.844	-0.844	0.000	0.000	0.000	0.000
16	G	459	GLN	0	-0.077	0.114	4.603	-0.131	-0.059	-0.001	-0.003	-0.068	0.000
17	G	460	ARG	0	0.085	-0.089	7.516	-0.660	-0.660	0.000	0.000	0.000	0.000
18	G	460	ARG	1	0.783	1.017	8.694	-1.658	-1.658	0.000	0.000	0.000	0.000
19	G	461	ARG	0	0.104	-0.092	9.573	-0.428	-0.428	0.000	0.000	0.000	0.000
20	G	461	ARG	1	0.755	1.002	10.914	-1.823	-1.823	0.000	0.000	0.000	0.000
21	G	462	GLU	0	0.085	-0.111	10.948	-0.247	-0.247	0.000	0.000	0.000	0.000
22	G	462	GLU	-1	-0.936	-0.801	11.074	0.831	0.831	0.000	0.000	0.000	0.000
23	G	463	LYS	0	0.106	-0.093	11.744	-0.200	-0.200	0.000	0.000	0.000	0.000
24	G	463	LYS	1	0.874	1.078	11.900	-0.621	-0.621	0.000	0.000	0.000	0.000
25	G	464	LEU	0	0.111	-0.092	13.520	-0.176	-0.176	0.000	0.000	0.000	0.000
26	G	464	LEU	0	-0.097	0.109	14.663	0.011	0.011	0.000	0.000	0.000	0.000
27	G	465	ASN	0	0.039	-0.107	15.414	-0.111	-0.111	0.000	0.000	0.000	0.000
28	G	465	ASN	0	-0.044	0.099	15.542	-0.057	-0.057	0.000	0.000	0.000	0.000
29	G	466	GLN	0	0.155	-0.095	16.652	-0.068	-0.068	0.000	0.000	0.000	0.000
30	G	466	GLN	0	-0.095	0.087	14.576	-0.042	-0.042	0.000	0.000	0.000	0.000
31	G	467	ARG	0	0.091	-0.052	18.506	-0.063	-0.063	0.000	0.000	0.000	0.000
32	G	467	ARG	1	0.764	1.001	16.418	-0.485	-0.485	0.000	0.000	0.000	0.000
33	G	468	PHE	0	0.066	-0.083	20.057	-0.049	-0.049	0.000	0.000	0.000	0.000
34	G	468	PHE	0	-0.102	0.062	19.250	0.013	0.013	0.000	0.000	0.000	0.000
35	G	469	TYR	0	0.172	-0.068	21.376	-0.035	-0.035	0.000	0.000	0.000	0.000
36	G	469	TYR	0	-0.099	0.093	21.846	0.008	0.008	0.000	0.000	0.000	0.000
37	G	470	ALA	0	0.117	-0.099	22.690	-0.031	-0.031	0.000	0.000	0.000	0.000
38	G	470	ALA	0	-0.105	0.098	23.057	0.001	0.001	0.000	0.000	0.000	0.000
39	G	471	LEU	0	0.103	-0.089	24.471	-0.032	-0.032	0.000	0.000	0.000	0.000
40	G	471	LEU	0	-0.115	0.096	25.171	0.004	0.004	0.000	0.000	0.000	0.000
41	G	472	ARG	0	0.045	-0.129	26.478	-0.021	-0.021	0.000	0.000	0.000	0.000
42	G	472	ARG	1	0.777	0.990	25.953	-0.318	-0.318	0.000	0.000	0.000	0.000
43	G	473	ALA	0	0.067	-0.072	27.864	-0.015	-0.015	0.000	0.000	0.000	0.000
44	G	473	ALA	0	-0.092	0.094	28.030	0.001	0.001	0.000	0.000	0.000	0.000
45	G	474	VAL	0	-0.048	-0.120	29.591	-0.015	-0.015	0.000	0.000	0.000	0.000
46	G	474	VAL	0	-0.084	0.095	28.723	0.000	0.000	0.000	0.000	0.000	0.000
47	G	475	VAL	0	0.098	-0.115	31.309	-0.015	-0.015	0.000	0.000	0.000	0.000
48	G	475	VAL	0	-0.062	0.113	30.717	0.001	0.001	0.000	0.000	0.000	0.000
49	G	476	PRO	0	0.053	-0.086	33.126	0.006	0.006	0.000	0.000	0.000	0.000
50	G	477	ASN	0	0.032	0.032	35.675	0.007	0.007	0.000	0.000	0.000	0.000
51	G	477	ASN	0	-0.059	0.079	37.562	-0.002	-0.002	0.000	0.000	0.000	0.000
52	G	478	VAL	0	0.064	-0.109	32.059	-0.004	-0.004	0.000	0.000	0.000	0.000
53	G	478	VAL	0	-0.045	0.131	30.598	0.003	0.003	0.000	0.000	0.000	0.000
54	G	479	SER	0	0.068	-0.089	30.974	0.026	0.026	0.000	0.000	0.000	0.000
55	G	479	SER	0	-0.017	0.071	32.826	-0.003	-0.003	0.000	0.000	0.000	0.000
56	G	480	LYS	0	0.015	-0.087	30.444	0.016	0.016	0.000	0.000	0.000	0.000
57	G	480	LYS	1	0.911	1.057	31.747	-0.211	-0.211	0.000	0.000	0.000	0.000
58	G	481	MET	0	0.099	-0.069	31.178	0.005	0.005	0.000	0.000	0.000	0.000
59	G	481	MET	0	-0.049	0.119	31.157	-0.003	-0.003	0.000	0.000	0.000	0.000
60	G	482	ASP	0	0.077	-0.070	27.812	0.020	0.020	0.000	0.000	0.000	0.000
61	G	482	ASP	-1	-0.830	-0.772	27.723	0.325	0.325	0.000	0.000	0.000	0.000
62	G	483	LYS	0	0.116	-0.079	24.309	-0.022	-0.022	0.000	0.000	0.000	0.000
63	G	483	LYS	1	0.767	1.001	19.007	-0.630	-0.630	0.000	0.000	0.000	0.000
64	G	484	ALA	0	0.084	-0.102	25.764	0.004	0.004	0.000	0.000	0.000	0.000
65	G	484	ALA	0	-0.053	0.112	27.473	-0.001	-0.001	0.000	0.000	0.000	0.000
66	G	485	SER	0	0.014	-0.091	27.947	-0.010	-0.010	0.000	0.000	0.000	0.000
67	G	485	SER	0	-0.039	0.036	31.123	-0.007	-0.007	0.000	0.000	0.000	0.000
68	G	486	LEU	0	0.102	-0.067	28.183	-0.022	-0.022	0.000	0.000	0.000	0.000
69	G	486	LEU	0	-0.161	0.080	25.640	0.006	0.006	0.000	0.000	0.000	0.000
70	G	487	LEU	0	0.080	-0.100	27.650	-0.015	-0.015	0.000	0.000	0.000	0.000
71	G	487	LEU	0	-0.099	0.081	24.269	0.005	0.005	0.000	0.000	0.000	0.000
72	G	488	GLY	0	-0.005	-0.100	28.632	-0.014	-0.014	0.000	0.000	0.000	0.000
73	G	489	ASP	0	0.107	0.010	32.184	-0.015	-0.015	0.000	0.000	0.000	0.000
74	G	489	ASP	-1	-0.943	-0.846	33.089	0.201	0.201	0.000	0.000	0.000	0.000
75	G	490	ALA	0	0.106	-0.094	30.496	-0.019	-0.019	0.000	0.000	0.000	0.000
76	G	490	ALA	0	-0.082	0.100	30.004	0.004	0.004	0.000	0.000	0.000	0.000
77	G	491	ILE	0	0.044	-0.092	32.009	-0.012	-0.012	0.000	0.000	0.000	0.000
78	G	491	ILE	0	-0.087	0.082	29.984	0.000	0.000	0.000	0.000	0.000	0.000
79	G	492	ALA	0	0.073	-0.124	33.319	-0.012	-0.012	0.000	0.000	0.000	0.000
80	G	492	ALA	0	-0.067	0.123	36.659	0.000	0.000	0.000	0.000	0.000	0.000
81	G	493	TYR	0	0.095	-0.092	35.709	-0.014	-0.014	0.000	0.000	0.000	0.000
82	G	493	TYR	0	-0.086	0.098	33.909	-0.002	-0.002	0.000	0.000	0.000	0.000
83	G	494	ILE	0	0.115	-0.082	34.434	-0.012	-0.012	0.000	0.000	0.000	0.000
84	G	494	ILE	0	-0.120	0.077	31.111	0.000	0.000	0.000	0.000	0.000	0.000
85	G	495	ASN	0	0.034	-0.098	35.731	-0.009	-0.009	0.000	0.000	0.000	0.000
86	G	495	ASN	0	-0.085	0.079	36.915	-0.003	-0.003	0.000	0.000	0.000	0.000
87	G	496	GLU	0	0.157	-0.083	38.744	-0.008	-0.008	0.000	0.000	0.000	0.000
88	G	496	GLU	-1	-0.966	-0.846	40.320	0.111	0.111	0.000	0.000	0.000	0.000
89	G	497	LEU	0	0.095	-0.107	38.632	-0.009	-0.009	0.000	0.000	0.000	0.000
90	G	497	LEU	0	-0.111	0.109	36.435	0.001	0.001	0.000	0.000	0.000	0.000
91	G	498	LYS	0	0.071	-0.099	39.690	-0.007	-0.007	0.000	0.000	0.000	0.000
92	G	498	LYS	1	0.791	1.014	36.651	-0.137	-0.137	0.000	0.000	0.000	0.000
93	G	499	SER	0	0.053	-0.073	41.112	-0.007	-0.007	0.000	0.000	0.000	0.000
94	G	499	SER	0	-0.070	0.082	43.585	-0.001	-0.001	0.000	0.000	0.000	0.000
95	G	500	LYS	0	0.104	-0.071	43.991	-0.006	-0.006	0.000	0.000	0.000	0.000
96	G	500	LYS	1	0.867	1.052	44.361	-0.083	-0.083	0.000	0.000	0.000	0.000
97	G	501	VAL	0	0.050	-0.082	43.475	-0.006	-0.006	0.000	0.000	0.000	0.000
98	G	501	VAL	0	-0.073	0.106	41.650	0.000	0.000	0.000	0.000	0.000	0.000
99	G	502	VAL	0	0.100	-0.099	44.810	-0.005	-0.005	0.000	0.000	0.000	0.000
100	G	502	VAL	0	-0.069	0.102	44.532	0.000	0.000	0.000	0.000	0.000	0.000
101	G	503	LYS	0	0.108	-0.089	46.942	-0.005	-0.005	0.000	0.000	0.000	0.000
102	G	503	LYS	1	0.756	1.001	49.076	-0.073	-0.073	0.000	0.000	0.000	0.000
103	G	504	THR	0	0.045	-0.069	48.433	-0.004	-0.004	0.000	0.000	0.000	0.000
104	G	504	THR	0	-0.089	0.026	47.697	0.001	0.001	0.000	0.000	0.000	0.000
105	G	505	GLU	0	0.104	-0.085	48.828	-0.004	-0.004	0.000	0.000	0.000	0.000
106	G	505	GLU	-1	-0.882	-0.779	47.414	0.065	0.065	0.000	0.000	0.000	0.000
107	G	506	SER	0	0.052	-0.078	50.228	-0.004	-0.004	0.000	0.000	0.000	0.000
108	G	506	SER	0	-0.013	0.085	52.421	0.000	0.000	0.000	0.000	0.000	0.000
109	G	507	GLU	0	0.032	-0.091	52.944	-0.004	-0.004	0.000	0.000	0.000	0.000
110	G	507	GLU	-1	-0.916	-0.824	51.943	0.071	0.071	0.000	0.000	0.000	0.000
111	G	508	LYS	0	0.138	-0.094	52.932	-0.003	-0.003	0.000	0.000	0.000	0.000
112	G	508	LYS	1	0.671	0.984	49.172	-0.060	-0.060	0.000	0.000	0.000	0.000
113	G	509	LEU	0	0.100	-0.101	54.306	-0.003	-0.003	0.000	0.000	0.000	0.000
114	G	509	LEU	0	-0.093	0.101	54.467	0.000	0.000	0.000	0.000	0.000	0.000
115	G	510	GLN	0	0.082	-0.110	55.993	-0.003	-0.003	0.000	0.000	0.000	0.000
116	G	510	GLN	0	-0.127	0.093	58.258	0.002	0.002	0.000	0.000	0.000	0.000
117	G	511	ILE	0	0.083	-0.087	58.109	-0.003	-0.003	0.000	0.000	0.000	0.000
118	G	511	ILE	0	-0.087	0.089	56.543	0.000	0.000	0.000	0.000	0.000	0.000
119	G	512	LYS	0	0.110	-0.082	57.931	-0.002	-0.002	0.000	0.000	0.000	0.000
120	G	512	LYS	1	0.716	0.990	57.105	-0.038	-0.038	0.000	0.000	0.000	0.000
121	G	513	ASN	0	0.073	-0.087	59.177	-0.002	-0.002	0.000	0.000	0.000	0.000
122	G	513	ASN	0	-0.080	0.072	59.543	-0.001	-0.001	0.000	0.000	0.000	0.000
123	G	514	GLN	0	0.136	-0.059	62.011	-0.002	-0.002	0.000	0.000	0.000	0.000
124	G	514	GLN	0	-0.089	0.072	62.852	0.001	0.001	0.000	0.000	0.000	0.000
125	G	515	LEU	0	0.107	-0.087	62.565	-0.001	-0.001	0.000	0.000	0.000	0.000
126	G	515	LEU	0	-0.126	0.088	60.769	0.000	0.000	0.000	0.000	0.000	0.000
127	G	516	GLU	0	0.076	-0.098	63.669	-0.001	-0.001	0.000	0.000	0.000	0.000
128	G	516	GLU	-1	-0.908	-0.809	62.737	0.034	0.034	0.000	0.000	0.000	0.000
129	G	517	GLU	0	0.106	-0.101	65.072	-0.002	-0.002	0.000	0.000	0.000	0.000
130	G	517	GLU	-1	-0.989	-0.840	67.804	0.031	0.031	0.000	0.000	0.000	0.000
131	G	518	VAL	0	0.097	-0.083	67.880	-0.001	-0.001	0.000	0.000	0.000	0.000
132	G	518	VAL	0	-0.080	0.095	66.831	0.000	0.000	0.000	0.000	0.000	0.000
133	G	519	LYS	0	0.123	-0.072	67.572	-0.001	-0.001	0.000	0.000	0.000	0.000
134	G	519	LYS	1	0.737	0.997	64.214	-0.030	-0.030	0.000	0.000	0.000	0.000
135	G	520	LEU	0	0.011	-0.122	68.903	-0.001	-0.001	0.000	0.000	0.000	0.000
136	G	520	LEU	0	-0.089	0.087	68.812	0.000	0.000	0.000	0.000	0.000	0.000
137	G	521	GLU	0	0.068	-0.119	71.289	-0.001	-0.001	0.000	0.000	0.000	0.000
138	G	521	GLU	-1	-0.998	-0.859	72.490	0.030	0.030	0.000	0.000	0.000	0.000
139	G	522	LEU	0	0.071	-0.073	72.319	-0.001	-0.001	0.000	0.000	0.000	0.000
140	G	522	LEU	0	-0.122	0.079	70.424	0.000	0.000	0.000	0.000	0.000	0.000
141	G	523	ALA	0	0.039	-0.111	73.181	-0.001	-0.001	0.000	0.000	0.000	0.000
142	G	523	ALA	0	-0.095	0.094	72.390	0.000	0.000	0.000	0.000	0.000	0.000
143	G	524	GLY	0	-0.083	-0.132	74.372	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:452:ASN)