FMO DATABASE

FMODB ID: R8QV8

Calculation Name: 3LMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LMB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptH
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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1646530.659993
FMO2-HF: Nuclear repulsion	1580674.439309
FMO2-HF: Total energy	-65856.220684
FMO2-MP2: Total energy	-66043.774441

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-5.644	-0.374	2.639	-3.048	-4.86	-0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.014

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	3	ALA	0	0.024	0.013	3.655	0.308	3.837	0.576	-1.854	-2.252	-0.003
4	A	4	SER	0	0.034	0.014	6.282	0.410	0.410	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.081	-0.026	7.306	-0.065	-0.065	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.044	0.016	9.945	-0.074	-0.074	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.103	0.031	13.482	0.011	0.011	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.872	-0.936	15.820	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.085	-0.050	12.222	0.037	0.037	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.025	0.014	11.028	0.028	0.028	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.034	0.032	13.600	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.903	0.943	16.848	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.966	0.996	9.607	-0.334	-0.334	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.024	0.030	15.579	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.933	0.967	17.382	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.095	-0.069	18.117	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.060	0.033	16.613	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.009	-0.018	19.120	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.002	-0.004	22.402	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.931	-0.930	19.816	0.073	0.073	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.002	-0.011	18.543	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.036	-0.010	22.256	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.057	0.025	25.399	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.013	-0.012	27.940	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.001	0.005	26.161	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.014	0.001	26.149	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.030	-0.009	30.030	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.072	-0.025	30.670	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.051	0.014	31.632	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.081	-0.044	25.276	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.952	-0.962	26.220	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.020	-0.026	20.051	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.870	-0.900	24.272	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.000	-0.011	23.790	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.084	-0.098	14.250	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.857	-0.914	19.991	-0.074	-0.074	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.008	-0.009	16.246	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.868	-0.914	17.008	-0.147	-0.147	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.027	-0.022	19.812	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.052	-0.008	19.269	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.021	-0.008	21.845	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.017	0.013	22.467	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.036	-0.003	26.240	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.018	-0.005	29.592	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.026	-0.006	32.152	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.020	0.000	35.764	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.976	-0.982	38.481	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.059	0.036	35.779	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.061	-0.020	33.995	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.036	0.053	37.517	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.004	-0.018	41.103	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.833	-0.936	43.511	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.818	0.909	45.516	0.016	0.016	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.007	-0.007	45.512	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.018	0.015	42.651	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.034	0.005	37.278	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.004	-0.008	37.606	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.024	-0.008	37.174	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.037	0.019	35.165	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.017	0.000	33.379	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.023	-0.015	32.266	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.004	-0.008	29.268	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.009	-0.020	29.026	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.030	0.018	27.541	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.012	0.006	26.648	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.010	0.001	24.826	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.012	0.000	23.082	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.036	0.026	21.957	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	CYS	0	-0.008	-0.004	21.136	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.046	-0.013	17.083	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.033	0.003	17.577	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	72	MET	0	0.024	0.025	16.566	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.020	-0.002	14.487	-0.029	-0.029	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.022	0.006	13.085	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.025	-0.028	11.962	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.837	0.917	11.251	0.212	0.212	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.006	-0.005	8.855	-0.156	-0.156	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.022	-0.027	7.098	-0.133	-0.133	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.812	-0.850	7.197	-0.090	-0.090	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.856	-0.939	5.263	-0.557	-0.557	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.163	-0.077	2.155	-2.937	-1.953	1.973	-0.869	-2.087	-0.004
82	A	82	ILE	0	-0.002	0.015	3.347	-1.580	-0.823	0.090	-0.325	-0.521	-0.002
83	A	83	ALA	0	-0.029	-0.011	5.554	0.546	0.546	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.062	-0.038	7.767	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.010	-0.007	11.115	0.072	0.072	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.038	0.008	14.769	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.027	0.001	16.533	0.026	0.026	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.069	0.025	20.260	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.198	-0.096	22.782	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.860	-0.925	24.695	-0.057	-0.057	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.042	0.015	26.198	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.078	-0.028	28.545	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.008	0.020	31.302	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.916	0.979	33.620	0.036	0.036	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.033	-0.032	35.688	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.075	-0.041	37.476	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.008	-0.010	40.063	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	PRO	0	0.008	0.015	40.339	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.031	0.015	36.462	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.015	-0.018	39.728	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.044	0.026	39.854	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.894	0.958	32.612	0.019	0.019	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.013	0.017	31.733	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.793	0.846	30.413	0.039	0.039	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.026	-0.010	27.587	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.011	0.012	26.316	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	CYS	0	-0.005	0.013	21.975	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	HIS	0	0.051	0.027	22.153	0.009	0.009	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.013	-0.002	17.233	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.022	-0.012	16.929	0.009	0.009	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.869	-0.935	18.243	-0.159	-0.159	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.917	-0.963	16.155	-0.215	-0.215	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.968	-0.988	15.795	-0.231	-0.231	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.874	-0.950	17.158	-0.215	-0.215	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.031	-0.013	13.017	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.001	0.012	12.486	-0.082	-0.082	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.001	-0.005	13.196	-0.067	-0.067	0.000	0.000	0.000	0.000
118	A	118	PHE	0	-0.039	-0.011	12.653	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	PHE	0	0.055	-0.002	8.816	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.790	-0.887	10.535	-0.466	-0.466	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.107	-0.071	12.394	0.083	0.083	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.036	-0.024	8.253	0.098	0.098	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.933	-0.955	8.377	-0.782	-0.782	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.858	0.927	10.679	0.397	0.397	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.838	0.917	14.051	0.239	0.239	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.054	-0.012	13.033	0.050	0.050	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.942	0.962	14.094	0.148	0.148	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.024	0.027	14.571	-0.015	-0.015	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.872	0.941	16.495	0.121	0.121	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.085	0.060	16.380	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.009	-0.017	19.272	0.016	0.016	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.027	0.010	18.960	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.923	-0.956	22.999	-0.076	-0.076	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.002	-0.006	25.222	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.056	-0.022	27.321	0.004	0.004	0.000	0.000	0.000	0.000
136	A	136	ILE	0	-0.001	0.008	30.242	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	TYR	0	0.064	0.019	31.213	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.001	-0.022	35.496	0.002	0.002	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.893	-0.947	37.673	-0.032	-0.032	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.008	0.002	35.902	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	141	CYS	0	-0.020	-0.008	34.907	0.000	0.000	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.010	0.021	31.879	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	143	MET	0	0.018	0.013	28.968	0.000	0.000	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.955	0.971	27.671	0.056	0.056	0.000	0.000	0.000	0.000
145	A	145	ILE	0	-0.031	-0.017	27.080	0.005	0.005	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.914	-0.963	30.067	-0.051	-0.051	0.000	0.000	0.000	0.000
147	A	147	PRO	0	-0.060	-0.037	33.091	0.003	0.003	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.917	-0.977	35.333	-0.047	-0.047	0.000	0.000	0.000	0.000
149	A	149	THR	0	-0.020	0.007	36.176	0.004	0.004	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.921	0.949	36.739	0.037	0.037	0.000	0.000	0.000	0.000
151	A	151	PRO	0	-0.004	0.023	34.456	0.002	0.002	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.005	0.000	36.563	0.001	0.001	0.000	0.000	0.000	0.000
153	A	153	VAL	0	-0.019	-0.012	33.201	0.002	0.002	0.000	0.000	0.000	0.000
154	A	154	LYS	1	0.954	0.988	32.349	0.048	0.048	0.000	0.000	0.000	0.000
155	A	155	PHE	0	0.018	-0.001	25.241	0.005	0.005	0.000	0.000	0.000	0.000
156	A	156	ASN	0	0.036	0.031	27.537	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.030	0.007	24.957	0.007	0.007	0.000	0.000	0.000	0.000
158	A	158	GLN	0	0.054	0.030	22.507	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	159	TYR	0	0.006	-0.021	18.690	0.016	0.016	0.000	0.000	0.000	0.000
160	A	160	ALA	0	-0.033	-0.021	18.118	-0.014	-0.014	0.000	0.000	0.000	0.000
161	A	161	ILE	0	0.020	0.024	11.176	0.028	0.028	0.000	0.000	0.000	0.000
162	A	162	LEU	0	-0.023	-0.040	14.665	-0.004	-0.004	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.984	1.006	9.731	0.278	0.278	0.000	0.000	0.000	0.000
164	A	164	ASN	0	-0.028	0.003	11.443	0.069	0.069	0.000	0.000	0.000	0.000

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