FMO DATABASE

FMODB ID: MNYJZ

Calculation Name: 3U6G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U6G

Chain ID: A

ChEMBL ID:

UniProt ID: A6L6K5

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-962912.133187
FMO2-HF: Nuclear repulsion	915052.679449
FMO2-HF: Total energy	-47859.453738
FMO2-MP2: Total energy	-47996.879244

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:30:ALA)

Summations of interaction energy for fragment #1(A:30: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.
-2.496	0.349	0.942	-1.538	-2.248	-0.005

Interaction energy analysis for fragmet #1(A:30:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.025

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

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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	32	ASP	-1	-0.882	-0.896	3.065	-3.269	-1.118	0.016	-0.964	-1.202	-0.002
4	A	33	PHE	0	-0.016	-0.018	2.419	0.277	0.971	0.926	-0.574	-1.046	-0.003
5	A	34	GLN	0	0.007	0.014	5.638	-0.181	-0.181	0.000	0.000	0.000	0.000
6	A	35	THR	0	-0.059	-0.043	8.569	0.047	0.047	0.000	0.000	0.000	0.000
7	A	36	GLY	0	0.054	0.030	10.054	0.032	0.032	0.000	0.000	0.000	0.000
8	A	37	ILE	0	-0.046	-0.022	13.779	0.003	0.003	0.000	0.000	0.000	0.000
9	A	38	HIS	0	-0.007	0.033	9.967	0.031	0.031	0.000	0.000	0.000	0.000
10	A	39	LYS	1	0.811	0.870	15.425	0.228	0.228	0.000	0.000	0.000	0.000
11	A	40	ILE	0	0.015	0.004	16.775	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	41	VAL	0	-0.007	-0.007	19.992	0.020	0.020	0.000	0.000	0.000	0.000
13	A	42	ILE	0	0.005	-0.001	23.283	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	43	GLN	0	-0.040	-0.036	25.766	0.006	0.006	0.000	0.000	0.000	0.000
15	A	44	GLN	0	-0.019	-0.013	29.144	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	45	SER	0	-0.024	-0.014	31.907	0.005	0.005	0.000	0.000	0.000	0.000
17	A	46	GLY	0	0.007	-0.009	35.314	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	47	ASP	-1	-0.829	-0.896	38.151	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	48	THR	0	-0.019	-0.038	35.769	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	49	ASP	-1	-0.924	-0.951	37.976	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	50	SER	0	-0.056	-0.017	40.102	0.003	0.003	0.000	0.000	0.000	0.000
22	A	51	PHE	0	-0.008	0.006	35.115	0.000	0.000	0.000	0.000	0.000	0.000
23	A	52	GLU	-1	-0.866	-0.889	34.766	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	53	VAL	0	0.030	0.014	29.420	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	54	SER	0	-0.041	-0.022	29.159	0.002	0.002	0.000	0.000	0.000	0.000
26	A	55	VAL	0	0.001	0.001	23.860	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	56	SER	0	-0.034	-0.031	22.407	0.013	0.013	0.000	0.000	0.000	0.000
28	A	57	ILE	0	-0.005	-0.003	19.111	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	58	GLY	0	0.051	0.021	17.591	0.023	0.023	0.000	0.000	0.000	0.000
30	A	59	GLY	0	0.035	0.017	13.475	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	60	ALA	0	-0.027	0.006	10.367	0.044	0.044	0.000	0.000	0.000	0.000
32	A	61	ASP	-1	-0.755	-0.882	11.199	-0.267	-0.267	0.000	0.000	0.000	0.000
33	A	62	LYS	1	0.864	0.918	5.850	0.515	0.515	0.000	0.000	0.000	0.000
34	A	63	GLY	0	-0.006	0.011	11.051	0.038	0.038	0.000	0.000	0.000	0.000
35	A	64	GLY	0	-0.005	0.002	14.233	0.023	0.023	0.000	0.000	0.000	0.000
36	A	65	PRO	0	0.002	-0.002	14.514	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	66	ALA	0	-0.035	-0.004	14.259	0.012	0.012	0.000	0.000	0.000	0.000
38	A	67	LYS	1	0.798	0.880	16.177	0.128	0.128	0.000	0.000	0.000	0.000
39	A	68	LEU	0	0.009	0.002	18.268	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	69	TYR	0	-0.029	-0.020	21.078	0.017	0.017	0.000	0.000	0.000	0.000
41	A	70	ASN	0	0.042	0.009	23.665	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.805	-0.892	26.250	-0.104	-0.104	0.000	0.000	0.000	0.000
43	A	72	LYS	1	0.782	0.879	27.712	0.096	0.096	0.000	0.000	0.000	0.000
44	A	73	GLY	0	0.004	0.009	26.259	0.004	0.004	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.922	-0.939	27.340	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	75	TYR	0	-0.067	-0.058	23.229	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	76	ILE	0	-0.031	-0.027	24.239	0.008	0.008	0.000	0.000	0.000	0.000
48	A	77	GLY	0	0.015	0.021	24.817	0.005	0.005	0.000	0.000	0.000	0.000
49	A	78	ASP	-1	-0.794	-0.868	20.497	-0.136	-0.136	0.000	0.000	0.000	0.000
50	A	79	SER	0	-0.017	-0.012	19.810	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	80	TYR	0	0.002	0.004	21.763	0.013	0.013	0.000	0.000	0.000	0.000
52	A	81	SER	0	0.024	0.008	23.398	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	82	ALA	0	-0.032	-0.004	26.095	0.009	0.009	0.000	0.000	0.000	0.000
54	A	83	GLN	0	0.043	0.028	28.704	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	84	ILE	0	-0.014	-0.016	27.044	0.001	0.001	0.000	0.000	0.000	0.000
56	A	85	ARG	1	0.966	0.988	31.187	0.076	0.076	0.000	0.000	0.000	0.000
57	A	86	THR	0	-0.024	-0.017	32.237	0.004	0.004	0.000	0.000	0.000	0.000
58	A	87	ALA	0	0.090	0.044	33.474	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	88	THR	0	-0.025	-0.021	28.735	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	89	MET	0	-0.038	0.023	25.013	0.003	0.003	0.000	0.000	0.000	0.000
61	A	90	SER	0	0.026	-0.001	24.082	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	91	CYS	0	-0.043	-0.017	21.929	0.007	0.007	0.000	0.000	0.000	0.000
63	A	92	CYS	0	0.022	0.012	19.417	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	93	THR	0	0.017	-0.006	15.226	0.003	0.003	0.000	0.000	0.000	0.000
65	A	94	ASN	0	0.004	-0.001	16.318	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	95	GLY	0	0.028	0.013	16.563	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	96	ASN	0	-0.050	-0.014	13.682	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	97	ALA	0	-0.017	-0.012	11.708	-0.038	-0.038	0.000	0.000	0.000	0.000
69	A	98	PHE	0	-0.005	-0.010	5.860	0.013	0.013	0.000	0.000	0.000	0.000
70	A	99	PHE	0	-0.004	-0.014	7.836	-0.221	-0.221	0.000	0.000	0.000	0.000
71	A	100	MET	0	0.021	0.030	9.712	0.098	0.098	0.000	0.000	0.000	0.000
72	A	101	THR	0	-0.051	-0.029	13.092	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	102	CYS	0	0.004	0.002	15.343	0.036	0.036	0.000	0.000	0.000	0.000
74	A	103	ALA	0	0.012	0.013	18.955	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	104	GLY	0	0.032	0.002	20.817	0.009	0.009	0.000	0.000	0.000	0.000
76	A	105	SER	0	-0.038	-0.009	24.590	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	106	VAL	0	-0.018	-0.010	27.894	0.001	0.001	0.000	0.000	0.000	0.000
78	A	107	SER	0	-0.032	-0.053	30.931	0.000	0.000	0.000	0.000	0.000	0.000
79	A	108	SER	0	0.026	-0.011	34.386	0.001	0.001	0.000	0.000	0.000	0.000
80	A	109	ILE	0	-0.016	-0.007	38.087	0.001	0.001	0.000	0.000	0.000	0.000
81	A	110	SER	0	-0.024	-0.005	41.344	0.004	0.004	0.000	0.000	0.000	0.000
82	A	111	GLU	-1	-0.885	-0.931	43.312	-0.040	-0.040	0.000	0.000	0.000	0.000
83	A	112	ALA	0	0.009	0.010	43.222	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	113	GLY	0	-0.033	-0.019	42.520	0.002	0.002	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.845	0.945	40.991	0.045	0.045	0.000	0.000	0.000	0.000
86	A	115	ARG	1	0.833	0.884	35.432	0.067	0.067	0.000	0.000	0.000	0.000
87	A	116	LEU	0	-0.020	-0.010	32.771	0.000	0.000	0.000	0.000	0.000	0.000
88	A	117	HIS	0	-0.035	-0.021	29.631	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	118	ILE	0	-0.025	-0.017	26.462	0.000	0.000	0.000	0.000	0.000	0.000
90	A	119	THR	0	0.046	0.018	25.621	0.000	0.000	0.000	0.000	0.000	0.000
91	A	120	VAL	0	-0.029	-0.022	20.635	0.002	0.002	0.000	0.000	0.000	0.000
92	A	121	ILE	0	-0.018	0.000	20.392	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.019	0.012	16.711	0.005	0.005	0.000	0.000	0.000	0.000
94	A	123	TYR	0	-0.008	-0.021	16.662	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	124	ILE	0	-0.015	-0.013	10.556	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	125	ASP	-1	-0.815	-0.900	14.807	-0.319	-0.319	0.000	0.000	0.000	0.000
97	A	126	ASP	-1	-0.850	-0.915	17.487	-0.161	-0.161	0.000	0.000	0.000	0.000
98	A	127	LYS	1	0.825	0.938	12.982	0.461	0.461	0.000	0.000	0.000	0.000
99	A	128	GLU	-1	-0.823	-0.895	16.893	-0.219	-0.219	0.000	0.000	0.000	0.000
100	A	129	VAL	0	-0.068	-0.034	12.696	0.002	0.002	0.000	0.000	0.000	0.000
101	A	130	ASN	0	-0.065	-0.038	12.573	0.022	0.022	0.000	0.000	0.000	0.000
102	A	131	ARG	1	0.798	0.861	16.672	0.173	0.173	0.000	0.000	0.000	0.000
103	A	132	LEU	0	-0.044	-0.013	20.113	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	133	GLU	-1	-0.866	-0.918	22.087	-0.126	-0.126	0.000	0.000	0.000	0.000
105	A	134	LYS	1	0.825	0.902	24.671	0.121	0.121	0.000	0.000	0.000	0.000
106	A	135	GLU	-1	-0.773	-0.844	28.124	-0.073	-0.073	0.000	0.000	0.000	0.000
107	A	136	TYR	0	-0.053	-0.056	28.017	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	137	ILE	0	0.017	-0.012	33.785	0.002	0.002	0.000	0.000	0.000	0.000
109	A	138	THR	0	-0.027	-0.019	37.462	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	139	ASP	-1	-0.817	-0.901	39.614	-0.048	-0.048	0.000	0.000	0.000	0.000
111	A	140	GLY	0	-0.022	-0.014	41.399	0.003	0.003	0.000	0.000	0.000	0.000
112	A	141	ASN	0	-0.124	-0.062	40.297	0.003	0.003	0.000	0.000	0.000	0.000
113	A	142	THR	0	-0.018	-0.020	37.641	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	143	LEU	0	0.001	0.029	33.677	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	144	ILE	0	-0.012	-0.024	31.114	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	145	GLU	-1	-0.822	-0.865	28.035	-0.106	-0.106	0.000	0.000	0.000	0.000
117	A	146	THR	0	-0.018	-0.016	24.824	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	147	PHE	0	0.011	0.004	22.096	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	148	SER	0	-0.015	-0.018	17.455	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	149	VAL	0	0.021	0.025	16.529	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	150	SER	0	-0.021	-0.017	12.040	-0.035	-0.035	0.000	0.000	0.000	0.000
122	A	151	THR	0	0.021	-0.026	11.614	0.004	0.004	0.000	0.000	0.000	0.000
123	A	152	LYS	1	0.810	0.908	5.354	1.218	1.218	0.000	0.000	0.000	0.000
124	A	153	GLU	-1	-0.759	-0.873	8.059	-0.426	-0.426	0.000	0.000	0.000	0.000
125	A	154	ILE	0	-0.036	-0.009	8.561	-0.087	-0.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:ALA)