FMO DATABASE

FMODB ID: RYGL8

Calculation Name: 3Q6C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3Q6C

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-07-09

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-403442.000173
FMO2-HF: Nuclear repulsion	376467.418733
FMO2-HF: Total energy	-26974.58144
FMO2-MP2: Total energy	-27053.320962

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:38:LEU)

Summations of interaction energy for fragment #1(A:38:LEU)

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.
-42.772	-45.507	20.736	-8.864	-9.137	0.041

Interaction energy analysis for fragmet #1(A:38:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.155 / q_NPA : 0.077

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	A	39	LEU	0	-0.057	0.114	2.845	-0.344	0.469	0.117	-0.331	-0.598	-0.001
5	A	40	GLN	0	0.098	-0.117	3.859	0.150	1.673	-0.012	-0.845	-0.666	0.002
6	A	40	GLN	0	-0.043	0.113	5.361	0.456	0.456	0.000	0.000	0.000	0.000
7	A	41	LYS	0	0.088	-0.078	6.597	-0.109	-0.109	0.000	0.000	0.000	0.000
8	A	41	LYS	1	0.795	1.031	9.883	0.539	0.539	0.000	0.000	0.000	0.000
9	A	42	ARG	0	0.133	-0.083	10.208	0.115	0.115	0.000	0.000	0.000	0.000
10	A	42	ARG	1	0.754	0.993	13.883	0.402	0.402	0.000	0.000	0.000	0.000
11	A	43	VAL	0	-0.052	-0.132	13.554	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	43	VAL	0	-0.041	0.109	12.521	0.009	0.009	0.000	0.000	0.000	0.000
13	A	44	ILE	0	0.174	-0.053	15.170	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	44	ILE	0	-0.111	0.081	18.928	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	45	VAL	0	0.045	-0.139	17.271	0.009	0.009	0.000	0.000	0.000	0.000
16	A	45	VAL	0	-0.091	0.133	16.350	0.004	0.004	0.000	0.000	0.000	0.000
17	A	46	SER	0	0.087	-0.057	18.165	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.116	0.010	18.755	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	47	ASN	0	0.017	-0.074	19.636	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	47	ASN	0	-0.084	0.045	20.817	0.024	0.024	0.000	0.000	0.000	0.000
21	A	48	LYS	0	0.141	-0.106	19.683	0.020	0.020	0.000	0.000	0.000	0.000
22	A	48	LYS	1	0.753	1.027	20.017	-0.185	-0.185	0.000	0.000	0.000	0.000
23	A	49	ARG	0	0.103	-0.073	21.275	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	49	ARG	1	0.766	1.011	21.468	-0.235	-0.235	0.000	0.000	0.000	0.000
25	A	50	GLU	0	0.134	-0.112	22.115	0.041	0.041	0.000	0.000	0.000	0.000
26	A	50	GLU	-1	-0.925	-0.775	24.537	0.212	0.212	0.000	0.000	0.000	0.000
27	A	51	LYS	0	0.098	-0.095	24.662	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	51	LYS	1	0.670	0.970	22.052	-0.299	-0.299	0.000	0.000	0.000	0.000
29	A	52	VAL	0	0.148	-0.066	25.956	0.028	0.028	0.000	0.000	0.000	0.000
30	A	52	VAL	0	-0.067	0.117	30.218	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	53	ILE	0	-0.018	-0.107	26.813	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	53	ILE	0	-0.116	0.038	24.092	0.010	0.010	0.000	0.000	0.000	0.000
33	A	54	ASN	0	0.006	-0.077	28.117	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	54	ASN	0	0.044	0.013	30.929	0.001	0.001	0.000	0.000	0.000	0.000
35	A	69	GLU	0	0.103	-0.016	27.031	0.013	0.013	0.000	0.000	0.000	0.000
36	A	69	GLU	-1	-0.955	-0.819	29.714	0.239	0.239	0.000	0.000	0.000	0.000
37	A	70	MET	0	0.058	-0.145	26.075	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	70	MET	0	-0.088	0.131	25.924	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	71	ARG	0	0.099	-0.085	22.086	0.035	0.035	0.000	0.000	0.000	0.000
40	A	71	ARG	1	0.756	0.993	18.273	-0.459	-0.459	0.000	0.000	0.000	0.000
41	A	72	TYR	0	0.071	-0.106	20.260	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	72	TYR	0	-0.118	0.068	19.554	0.010	0.010	0.000	0.000	0.000	0.000
43	A	73	GLU	0	0.075	-0.092	17.535	0.085	0.085	0.000	0.000	0.000	0.000
44	A	73	GLU	-1	-0.815	-0.764	18.082	0.339	0.339	0.000	0.000	0.000	0.000
45	A	74	ALA	0	0.116	-0.081	16.539	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	74	ALA	0	-0.030	0.117	15.981	0.001	0.001	0.000	0.000	0.000	0.000
47	A	75	SER	0	-0.041	-0.115	15.490	0.064	0.064	0.000	0.000	0.000	0.000
48	A	75	SER	0	-0.041	0.049	18.094	0.009	0.009	0.000	0.000	0.000	0.000
49	A	76	PHE	0	0.088	-0.068	13.734	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	76	PHE	0	-0.086	0.102	13.007	0.003	0.003	0.000	0.000	0.000	0.000
51	A	77	ARG	0	0.137	-0.084	15.003	0.005	0.005	0.000	0.000	0.000	0.000
52	A	77	ARG	1	0.773	1.025	18.343	0.026	0.026	0.000	0.000	0.000	0.000
53	A	78	PRO	0	-0.039	-0.124	14.996	-0.041	-0.041	0.000	0.000	0.000	0.000
54	A	79	GLU	0	0.054	0.039	16.619	0.047	0.047	0.000	0.000	0.000	0.000
55	A	79	GLU	-1	-0.877	-0.818	17.128	-0.410	-0.410	0.000	0.000	0.000	0.000
56	A	80	ASN	0	0.059	-0.101	18.678	0.041	0.041	0.000	0.000	0.000	0.000
57	A	80	ASN	0	-0.137	0.069	18.780	0.016	0.016	0.000	0.000	0.000	0.000
58	A	81	GLY	0	0.020	-0.113	18.700	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	82	GLY	0	0.000	0.006	19.183	0.027	0.027	0.000	0.000	0.000	0.000
60	A	83	DLE	0	0.011	0.005	17.219	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	84	GLU	0	0.054	-0.032	16.639	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	84	GLU	-1	-0.790	-0.718	17.688	0.076	0.076	0.000	0.000	0.000	0.000
63	A	85	VAL	0	0.042	-0.117	12.501	0.010	0.010	0.000	0.000	0.000	0.000
64	A	85	VAL	0	-0.072	0.120	10.529	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	86	VAL	0	0.103	-0.097	13.920	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	86	VAL	0	-0.079	0.094	16.279	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	87	PHE	0	0.072	-0.099	12.222	0.062	0.062	0.000	0.000	0.000	0.000
68	A	87	PHE	0	-0.101	0.115	7.766	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	88	ARG	0	0.163	-0.073	13.154	-0.100	-0.100	0.000	0.000	0.000	0.000
70	A	88	ARG	1	0.740	1.003	14.766	-0.652	-0.652	0.000	0.000	0.000	0.000
71	A	89	LEU	0	-0.050	-0.130	13.801	0.167	0.167	0.000	0.000	0.000	0.000
72	A	89	LEU	0	-0.044	0.120	13.270	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	90	ASP	0	0.074	-0.101	15.942	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	90	ASP	-1	-0.840	-0.800	16.162	0.603	0.603	0.000	0.000	0.000	0.000
75	A	91	ALA	0	0.161	-0.081	18.553	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	91	ALA	0	-0.067	0.112	22.964	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	92	PRO	0	-0.036	-0.126	19.291	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	93	GLN	0	0.153	0.023	15.840	-0.065	-0.065	0.000	0.000	0.000	0.000
79	A	93	GLN	0	-0.101	0.098	13.757	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	94	TYR	0	0.123	-0.080	16.997	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	94	TYR	0	-0.120	0.084	18.947	0.000	0.000	0.000	0.000	0.000	0.000
82	A	95	HIS	0	0.029	-0.103	18.834	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	95	HIS	0	-0.101	0.087	22.517	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	96	ALA	0	0.111	-0.100	18.672	-0.040	-0.040	0.000	0.000	0.000	0.000
85	A	96	ALA	0	-0.090	0.108	17.798	0.007	0.007	0.000	0.000	0.000	0.000
86	A	97	LEU	0	-0.003	-0.115	18.040	-0.033	-0.033	0.000	0.000	0.000	0.000
87	A	97	LEU	0	-0.069	0.103	14.826	0.000	0.000	0.000	0.000	0.000	0.000
88	A	98	SER	0	0.012	-0.118	19.015	0.020	0.020	0.000	0.000	0.000	0.000
89	A	98	SER	0	-0.016	0.085	21.522	0.003	0.003	0.000	0.000	0.000	0.000
90	A	99	VAL	0	0.096	-0.115	20.849	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	99	VAL	0	-0.088	0.115	21.968	0.003	0.003	0.000	0.000	0.000	0.000
92	A	100	GLY	0	-0.015	-0.093	21.641	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	101	ASP	0	0.120	-0.002	19.807	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	101	ASP	-1	-0.879	-0.773	19.020	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	102	ARG	0	-0.021	-0.110	17.649	0.018	0.018	0.000	0.000	0.000	0.000
96	A	102	ARG	1	0.806	1.023	18.597	0.117	0.117	0.000	0.000	0.000	0.000
97	A	103	GLY	0	0.048	-0.083	15.483	0.017	0.017	0.000	0.000	0.000	0.000
98	A	104	MET	0	0.127	-0.002	11.432	0.017	0.017	0.000	0.000	0.000	0.000
99	A	104	MET	0	-0.122	0.122	9.398	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	105	LEU	0	0.093	-0.087	9.606	0.092	0.092	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.085	0.098	8.339	0.002	0.002	0.000	0.000	0.000	0.000
102	A	106	SER	0	0.009	-0.114	5.511	-0.594	-0.594	0.000	0.000	0.000	0.000
103	A	106	SER	0	-0.017	0.085	4.924	-0.103	-0.103	0.000	0.000	0.000	0.000
104	A	107	TYR	0	0.048	-0.068	4.131	0.732	0.918	-0.001	-0.076	-0.109	0.000
105	A	107	TYR	0	-0.083	0.084	5.543	-0.440	-0.440	0.000	0.000	0.000	0.000
106	A	108	LYS	0	0.088	-0.097	2.186	-6.566	-6.300	4.031	-1.798	-2.500	-0.034
107	A	108	LYS	1	0.790	1.009	1.885	-36.412	-41.507	16.500	-6.377	-5.029	0.073
108	A	109	GLY	0	0.040	-0.093	3.038	0.154	-0.388	0.101	0.589	-0.148	0.001
109	A	110	THR	0	0.052	0.024	6.294	-0.166	-0.166	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.037	0.065	10.423	0.078	0.078	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.153	-0.074	7.180	-0.606	-0.606	0.000	0.000	0.000	0.000
112	A	111	ALA	0	-0.100	0.103	6.308	0.149	0.149	0.000	0.000	0.000	0.000
113	A	112	PHE	0	0.099	-0.098	6.167	0.650	0.650	0.000	0.000	0.000	0.000
114	A	112	PHE	0	-0.043	0.106	9.972	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	113	VAL	0	-0.034	-0.096	5.582	0.254	0.254	0.000	0.000	0.000	0.000
116	A	113	VAL	0	-0.131	0.059	3.955	0.151	0.265	0.000	-0.026	-0.087	0.000
117	A	114	ALA	0	0.176	-0.085	7.062	-0.137	-0.137	0.000	0.000	0.000	0.000
118	A	114	ALA	0	-0.043	0.100	8.369	-0.047	-0.047	0.000	0.000	0.000	0.000
119	A	115	PHE	0	0.050	-0.104	9.030	-0.056	-0.056	0.000	0.000	0.000	0.000
120	A	115	PHE	0	-0.073	0.098	11.872	0.011	0.011	0.000	0.000	0.000	0.000
121	A	116	THR	0	0.017	-0.086	11.555	0.075	0.075	0.000	0.000	0.000	0.000
122	A	116	THR	0	-0.043	0.086	11.292	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	117	PRO	0	-0.001	-0.095	13.476	-0.074	-0.074	0.000	0.000	0.000	0.000
124	A	118	ASP	0	0.105	0.003	16.737	-0.030	-0.030	0.000	0.000	0.000	0.000
125	A	118	ASP	-1	-0.901	-0.806	17.831	-0.299	-0.299	0.000	0.000	0.000	0.000
126	A	119	PRO	0	-0.041	-0.106	18.346	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:LEU)