FMO DATABASE

FMODB ID: ZN9LN

Calculation Name: 3MQK-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MQK

Chain ID: C

ChEMBL ID:

UniProt ID: Q8U1R4

Base Structure: X-ray

Registration Date: 2025-07-08

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	OptH
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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502456.123308
FMO2-HF: Nuclear repulsion	472667.959399
FMO2-HF: Total energy	-29788.163908
FMO2-MP2: Total energy	-29876.207309

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(C:1:MET)

Summations of interaction energy for fragment #1(C: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.
-5.248	-4.272	13.386	-7.966	-6.398	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.212 / q_NPA : 0.007

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	C	2	LYS	1	0.772	1.047	3.110	0.965	1.919	0.052	-0.411	-0.595	0.002
5	C	3	ARG	0	0.165	-0.087	3.767	-1.285	1.288	-0.024	-1.481	-1.068	0.011
6	C	3	ARG	1	0.835	1.070	6.490	0.927	0.927	0.000	0.000	0.000	0.000
7	C	4	LEU	0	0.082	-0.113	6.164	-0.010	-0.010	0.000	0.000	0.000	0.000
8	C	4	LEU	0	-0.143	0.112	7.678	0.015	0.015	0.000	0.000	0.000	0.000
9	C	5	GLY	0	0.044	-0.094	8.792	-0.025	-0.025	0.000	0.000	0.000	0.000
10	C	6	LYS	0	0.037	-0.009	11.555	0.030	0.030	0.000	0.000	0.000	0.000
11	C	6	LYS	1	0.891	1.068	15.180	0.237	0.237	0.000	0.000	0.000	0.000
12	C	7	VAL	0	0.097	-0.103	14.265	-0.012	-0.012	0.000	0.000	0.000	0.000
13	C	7	VAL	0	-0.086	0.122	13.802	0.007	0.007	0.000	0.000	0.000	0.000
14	C	8	LEU	0	0.060	-0.116	15.799	0.000	0.000	0.000	0.000	0.000	0.000
15	C	8	LEU	0	-0.098	0.099	17.950	-0.001	-0.001	0.000	0.000	0.000	0.000
16	C	9	HIS	0	0.091	-0.065	19.159	0.003	0.003	0.000	0.000	0.000	0.000
17	C	9	HIS	0	-0.071	0.079	22.056	-0.006	-0.006	0.000	0.000	0.000	0.000
18	C	10	TYR	0	0.136	-0.127	19.844	-0.001	-0.001	0.000	0.000	0.000	0.000
19	C	10	TYR	0	-0.048	0.148	20.290	0.006	0.006	0.000	0.000	0.000	0.000
20	C	11	ALA	0	0.088	-0.125	21.722	-0.005	-0.005	0.000	0.000	0.000	0.000
21	C	11	ALA	0	-0.093	0.122	22.877	-0.001	-0.001	0.000	0.000	0.000	0.000
22	C	12	LYS	0	0.091	-0.092	23.832	0.010	0.010	0.000	0.000	0.000	0.000
23	C	12	LYS	1	0.910	1.093	27.162	0.006	0.006	0.000	0.000	0.000	0.000
24	C	13	GLN	0	-0.019	-0.120	26.049	0.007	0.007	0.000	0.000	0.000	0.000
25	C	13	GLN	0	-0.030	0.110	25.219	-0.003	-0.003	0.000	0.000	0.000	0.000
26	C	14	GLY	0	-0.002	-0.111	23.497	0.008	0.008	0.000	0.000	0.000	0.000
27	C	15	PHE	0	0.048	-0.050	19.592	0.020	0.020	0.000	0.000	0.000	0.000
28	C	15	PHE	0	-0.062	0.104	18.864	0.000	0.000	0.000	0.000	0.000	0.000
29	C	16	LEU	0	0.088	-0.081	16.547	-0.018	-0.018	0.000	0.000	0.000	0.000
30	C	16	LEU	0	-0.042	0.130	15.108	0.002	0.002	0.000	0.000	0.000	0.000
31	C	17	ILE	0	0.078	-0.100	16.815	0.010	0.010	0.000	0.000	0.000	0.000
32	C	17	ILE	0	-0.113	0.103	18.892	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	18	VAL	0	0.072	-0.142	13.759	0.001	0.001	0.000	0.000	0.000	0.000
34	C	18	VAL	0	-0.021	0.144	12.185	0.000	0.000	0.000	0.000	0.000	0.000
35	C	19	ARG	0	0.129	-0.066	15.281	0.013	0.013	0.000	0.000	0.000	0.000
36	C	19	ARG	1	0.773	1.038	17.335	0.196	0.196	0.000	0.000	0.000	0.000
37	C	20	THR	0	-0.050	-0.113	12.683	-0.024	-0.024	0.000	0.000	0.000	0.000
38	C	20	THR	0	-0.062	0.064	11.223	-0.022	-0.022	0.000	0.000	0.000	0.000
39	C	21	ASN	0	0.091	-0.081	12.852	0.067	0.067	0.000	0.000	0.000	0.000
40	C	21	ASN	0	-0.080	0.073	12.287	-0.043	-0.043	0.000	0.000	0.000	0.000
41	C	22	TRP	0	0.062	-0.076	12.153	-0.004	-0.004	0.000	0.000	0.000	0.000
42	C	22	TRP	0	-0.104	0.081	6.740	-0.107	-0.107	0.000	0.000	0.000	0.000
43	C	23	VAL	0	0.149	-0.142	13.302	0.016	0.016	0.000	0.000	0.000	0.000
44	C	23	VAL	0	-0.087	0.140	14.813	0.003	0.003	0.000	0.000	0.000	0.000
45	C	24	PRO	0	-0.037	-0.111	10.394	-0.008	-0.008	0.000	0.000	0.000	0.000
46	C	25	SER	0	0.088	0.024	11.058	0.003	0.003	0.000	0.000	0.000	0.000
47	C	25	SER	0	-0.037	0.091	11.006	-0.008	-0.008	0.000	0.000	0.000	0.000
48	C	26	LEU	0	0.175	-0.115	12.830	0.028	0.028	0.000	0.000	0.000	0.000
49	C	26	LEU	0	-0.159	0.115	16.845	0.001	0.001	0.000	0.000	0.000	0.000
50	C	27	ASN	0	-0.051	-0.097	14.255	0.008	0.008	0.000	0.000	0.000	0.000
51	C	27	ASN	0	-0.083	0.046	14.881	0.004	0.004	0.000	0.000	0.000	0.000
52	C	28	ASP	0	0.213	-0.085	9.688	0.088	0.088	0.000	0.000	0.000	0.000
53	C	28	ASP	-1	-0.937	-0.811	8.689	0.021	0.021	0.000	0.000	0.000	0.000
54	C	29	ARG	0	0.055	-0.085	9.034	-0.108	-0.108	0.000	0.000	0.000	0.000
55	C	29	ARG	1	0.797	1.049	7.644	-1.290	-1.290	0.000	0.000	0.000	0.000
56	C	30	VAL	0	0.117	-0.098	7.392	0.202	0.202	0.000	0.000	0.000	0.000
57	C	30	VAL	0	-0.119	0.094	8.629	-0.042	-0.042	0.000	0.000	0.000	0.000
58	C	31	VAL	0	0.045	-0.126	6.929	-0.153	-0.153	0.000	0.000	0.000	0.000
59	C	31	VAL	0	-0.030	0.132	5.189	0.024	0.024	0.000	0.000	0.000	0.000
60	C	32	ASP	0	0.139	-0.052	7.730	-0.153	-0.153	0.000	0.000	0.000	0.000
61	C	32	ASP	-1	-0.876	-0.834	10.899	0.271	0.271	0.000	0.000	0.000	0.000
62	C	33	LYS	0	0.096	-0.074	7.978	0.131	0.131	0.000	0.000	0.000	0.000
63	C	33	LYS	1	0.833	1.037	9.527	0.086	0.086	0.000	0.000	0.000	0.000
64	C	34	ARG	0	0.002	-0.094	8.611	-0.074	-0.074	0.000	0.000	0.000	0.000
65	C	34	ARG	1	0.869	1.037	12.450	-0.060	-0.060	0.000	0.000	0.000	0.000
66	C	35	LEU	0	0.085	-0.097	7.826	-0.019	-0.019	0.000	0.000	0.000	0.000
67	C	35	LEU	0	-0.057	0.128	5.369	-0.078	-0.048	-0.001	-0.002	-0.026	0.000
68	C	36	GLN	0	0.087	-0.116	8.776	0.272	0.272	0.000	0.000	0.000	0.000
69	C	36	GLN	0	-0.104	0.089	12.698	-0.031	-0.031	0.000	0.000	0.000	0.000
70	C	37	PHE	0	0.186	-0.082	10.539	0.029	0.029	0.000	0.000	0.000	0.000
71	C	37	PHE	0	-0.178	0.063	12.156	0.019	0.019	0.000	0.000	0.000	0.000
72	C	38	VAL	0	0.046	-0.139	11.175	-0.069	-0.069	0.000	0.000	0.000	0.000
73	C	38	VAL	0	-0.075	0.156	10.783	-0.012	-0.012	0.000	0.000	0.000	0.000
74	C	39	GLY	0	-0.001	-0.116	12.070	-0.080	-0.080	0.000	0.000	0.000	0.000
75	C	40	ILE	0	0.011	0.008	11.984	0.100	0.100	0.000	0.000	0.000	0.000
76	C	40	ILE	0	-0.095	0.076	13.111	-0.005	-0.005	0.000	0.000	0.000	0.000
77	C	41	VAL	0	0.128	-0.105	12.441	-0.033	-0.033	0.000	0.000	0.000	0.000
78	C	41	VAL	0	-0.047	0.142	11.037	-0.001	-0.001	0.000	0.000	0.000	0.000
79	C	42	LYS	0	0.004	-0.147	13.773	0.018	0.018	0.000	0.000	0.000	0.000
80	C	42	LYS	1	0.838	1.061	17.391	-0.127	-0.127	0.000	0.000	0.000	0.000
81	C	43	ASP	0	0.152	-0.100	17.059	0.004	0.004	0.000	0.000	0.000	0.000
82	C	43	ASP	-1	-1.011	-0.828	19.651	-0.025	-0.025	0.000	0.000	0.000	0.000
83	C	44	VAL	0	0.091	-0.143	16.861	0.000	0.000	0.000	0.000	0.000	0.000
84	C	44	VAL	0	-0.082	0.147	14.996	-0.003	-0.003	0.000	0.000	0.000	0.000
85	C	45	PHE	0	0.030	-0.077	17.705	0.007	0.007	0.000	0.000	0.000	0.000
86	C	45	PHE	0	-0.038	0.116	19.653	-0.001	-0.001	0.000	0.000	0.000	0.000
87	C	46	GLY	0	0.024	-0.086	19.902	-0.017	-0.017	0.000	0.000	0.000	0.000
88	C	47	PRO	0	-0.015	-0.025	21.714	0.002	0.002	0.000	0.000	0.000	0.000
89	C	48	VAL	0	0.099	0.011	19.918	-0.015	-0.015	0.000	0.000	0.000	0.000
90	C	48	VAL	0	0.007	0.124	20.586	0.000	0.000	0.000	0.000	0.000	0.000
91	C	49	LYS	0	0.088	-0.063	18.504	-0.025	-0.025	0.000	0.000	0.000	0.000
92	C	49	LYS	1	0.859	1.047	20.503	0.208	0.208	0.000	0.000	0.000	0.000
93	C	50	MET	0	0.092	-0.082	17.568	-0.044	-0.044	0.000	0.000	0.000	0.000
94	C	50	MET	0	-0.174	0.053	17.860	-0.003	-0.003	0.000	0.000	0.000	0.000
95	C	51	PRO	0	0.027	-0.066	15.660	0.031	0.031	0.000	0.000	0.000	0.000
96	C	52	TYR	0	0.071	0.000	16.602	-0.036	-0.036	0.000	0.000	0.000	0.000
97	C	52	TYR	0	-0.046	0.066	19.177	0.000	0.000	0.000	0.000	0.000	0.000
98	C	53	VAL	0	0.051	-0.097	14.192	0.006	0.006	0.000	0.000	0.000	0.000
99	C	53	VAL	0	-0.079	0.118	12.618	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	54	ALA	0	0.154	-0.114	15.708	-0.003	-0.003	0.000	0.000	0.000	0.000
101	C	54	ALA	0	-0.102	0.126	18.552	0.001	0.001	0.000	0.000	0.000	0.000
102	C	55	ILE	0	0.083	-0.115	14.309	0.011	0.011	0.000	0.000	0.000	0.000
103	C	55	ILE	0	-0.092	0.111	11.449	0.004	0.004	0.000	0.000	0.000	0.000
104	C	56	LYS	0	0.101	-0.108	15.505	-0.019	-0.019	0.000	0.000	0.000	0.000
105	C	56	LYS	1	0.843	1.069	17.612	-0.083	-0.083	0.000	0.000	0.000	0.000
106	C	57	PRO	0	-0.011	-0.088	16.320	0.041	0.041	0.000	0.000	0.000	0.000
107	C	58	LYS	0	0.033	-0.006	16.217	-0.029	-0.029	0.000	0.000	0.000	0.000
108	C	58	LYS	1	0.873	1.052	15.998	-0.214	-0.214	0.000	0.000	0.000	0.000
109	C	59	VAL	0	0.075	-0.105	17.712	0.028	0.028	0.000	0.000	0.000	0.000
110	C	59	VAL	0	-0.026	0.121	16.771	0.001	0.001	0.000	0.000	0.000	0.000
111	C	60	SER	0	0.055	-0.038	18.742	-0.017	-0.017	0.000	0.000	0.000	0.000
112	C	60	SER	0	-0.058	0.045	22.215	0.000	0.000	0.000	0.000	0.000	0.000
113	C	61	ASN	0	0.144	-0.082	21.646	-0.007	-0.007	0.000	0.000	0.000	0.000
114	C	61	ASN	0	-0.096	0.092	23.046	-0.005	-0.005	0.000	0.000	0.000	0.000
115	C	62	PRO	0	0.022	-0.094	18.842	0.004	0.004	0.000	0.000	0.000	0.000
116	C	63	GLU	0	0.091	-0.018	19.318	-0.011	-0.011	0.000	0.000	0.000	0.000
117	C	63	GLU	-1	-0.989	-0.834	23.426	0.021	0.021	0.000	0.000	0.000	0.000
118	C	64	ILE	0	0.010	-0.119	20.660	-0.020	-0.020	0.000	0.000	0.000	0.000
119	C	64	ILE	0	-0.069	0.099	18.825	0.001	0.001	0.000	0.000	0.000	0.000
120	C	65	TYR	0	0.062	-0.083	16.258	-0.010	-0.010	0.000	0.000	0.000	0.000
121	C	65	TYR	0	-0.116	0.066	13.784	0.009	0.009	0.000	0.000	0.000	0.000
122	C	66	VAL	0	0.109	-0.133	16.323	-0.025	-0.025	0.000	0.000	0.000	0.000
123	C	66	VAL	0	-0.068	0.150	19.936	0.000	0.000	0.000	0.000	0.000	0.000
124	C	67	GLY	0	-0.066	-0.118	17.990	0.003	0.003	0.000	0.000	0.000	0.000
125	C	68	GLU	0	0.074	-0.045	14.550	-0.060	-0.060	0.000	0.000	0.000	0.000
126	C	68	GLU	-1	-0.961	-0.812	13.398	-0.085	-0.085	0.000	0.000	0.000	0.000
127	C	69	VAL	0	0.058	-0.111	11.036	0.041	0.041	0.000	0.000	0.000	0.000
128	C	69	VAL	0	-0.107	0.074	8.924	-0.028	-0.028	0.000	0.000	0.000	0.000
129	C	70	LEU	0	0.028	-0.130	8.766	0.003	0.003	0.000	0.000	0.000	0.000
130	C	70	LEU	0	-0.043	0.133	9.217	0.016	0.016	0.000	0.000	0.000	0.000
131	C	71	TYR	0	0.032	-0.128	4.467	-0.502	-0.502	-0.002	-0.005	0.006	0.000
132	C	71	TYR	0	-0.038	0.113	3.392	-0.526	-0.250	0.014	-0.086	-0.204	0.000
133	C	72	VAL	0	0.121	-0.062	4.505	0.324	0.406	-0.002	-0.017	-0.064	0.000
134	C	72	VAL	0	-0.099	0.087	5.275	-0.089	-0.089	0.000	0.000	0.000	0.000
135	C	73	ASP	0	0.148	-0.115	2.681	-0.935	0.521	1.014	-1.252	-1.219	-0.011
136	C	73	ASP	-1	-0.953	-0.798	4.379	4.544	4.630	-0.001	-0.028	-0.057	0.000
137	C	74	GLU	0	-0.009	-0.124	3.116	-0.715	-0.126	0.009	-0.373	-0.225	0.001
138	C	74	GLU	-1	-0.884	-0.825	1.849	-5.726	-10.872	12.328	-4.308	-2.875	-0.037
139	C	75	ARG	0	-0.053	-0.125	4.452	-0.291	-0.215	-0.001	-0.003	-0.071	0.000
140	C	75	ARG	1	0.976	0.988	7.357	-0.922	-0.922	0.000	0.000	0.000	0.000

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