FMO DATABASE

FMODB ID: 2NLMR

Calculation Name: 3B7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B7H

Chain ID: A

ChEMBL ID:

UniProt ID: F9UL97

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-476159.329826
FMO2-HF: Nuclear repulsion	445764.281684
FMO2-HF: Total energy	-30395.048142
FMO2-MP2: Total energy	-30482.093816

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.
-0.211	1.159	-0.018	-0.631	-0.721	0

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 : -0.024 / q_NPA : -0.036

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].
3	A	3	THR	0	-0.038	-0.010	3.846	0.869	2.239	-0.018	-0.631	-0.721
4	A	4	ASP	-1	-0.785	-0.864	6.081	0.191	0.191	0.000	0.000	0.000
5	A	5	GLY	0	-0.008	-0.005	9.139	0.042	0.042	0.000	0.000	0.000
6	A	6	GLU	-1	-0.837	-0.906	6.233	-1.981	-1.981	0.000	0.000	0.000
7	A	7	PHE	0	0.039	0.019	5.482	-0.007	-0.007	0.000	0.000	0.000
8	A	8	VAL	0	-0.023	-0.013	9.817	0.031	0.031	0.000	0.000	0.000
9	A	9	SER	0	-0.029	-0.047	12.513	0.030	0.030	0.000	0.000	0.000
10	A	10	GLU	-1	-0.864	-0.934	9.113	-0.472	-0.472	0.000	0.000	0.000
11	A	11	HIS	1	0.914	0.984	13.138	0.052	0.052	0.000	0.000	0.000
12	A	12	LEU	0	0.010	-0.009	14.912	0.016	0.016	0.000	0.000	0.000
13	A	13	MET	0	-0.035	-0.022	16.328	0.020	0.020	0.000	0.000	0.000
14	A	14	GLU	-1	-0.901	-0.944	14.346	-0.014	-0.014	0.000	0.000	0.000
15	A	15	LEU	0	0.011	0.002	18.230	0.011	0.011	0.000	0.000	0.000
16	A	16	ILE	0	-0.051	-0.032	20.926	0.004	0.004	0.000	0.000	0.000
17	A	17	THR	0	-0.045	-0.033	20.504	0.005	0.005	0.000	0.000	0.000
18	A	18	GLN	0	-0.026	-0.011	20.566	0.007	0.007	0.000	0.000	0.000
19	A	19	GLN	0	-0.056	-0.036	24.195	0.003	0.003	0.000	0.000	0.000
20	A	20	ASN	0	-0.042	-0.011	26.459	0.000	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.034	0.003	26.160	-0.001	-0.001	0.000	0.000	0.000
22	A	22	THR	0	0.045	0.004	24.730	-0.004	-0.004	0.000	0.000	0.000
23	A	23	ILE	0	0.083	0.026	20.481	0.003	0.003	0.000	0.000	0.000
24	A	24	ASN	0	0.007	0.007	23.546	-0.006	-0.006	0.000	0.000	0.000
25	A	25	ARG	1	0.957	0.991	26.556	0.044	0.044	0.000	0.000	0.000
26	A	26	VAL	0	0.058	0.038	24.371	0.003	0.003	0.000	0.000	0.000
27	A	27	ALA	0	0.018	-0.038	25.204	0.001	0.001	0.000	0.000	0.000
28	A	28	THR	0	-0.067	-0.050	26.866	0.005	0.005	0.000	0.000	0.000
29	A	29	LEU	0	-0.017	-0.015	30.319	0.002	0.002	0.000	0.000	0.000
30	A	30	ALA	0	-0.016	0.000	27.255	0.002	0.002	0.000	0.000	0.000
31	A	31	GLY	0	-0.022	0.002	29.202	-0.001	-0.001	0.000	0.000	0.000
32	A	32	LEU	0	-0.114	0.010	24.135	-0.005	-0.005	0.000	0.000	0.000
33	A	33	ASN	0	0.075	0.034	26.639	-0.004	-0.004	0.000	0.000	0.000
34	A	34	GLN	0	0.084	0.021	24.111	-0.002	-0.002	0.000	0.000	0.000
35	A	35	SER	0	-0.054	-0.023	23.770	-0.011	-0.011	0.000	0.000	0.000
36	A	36	THR	0	-0.042	-0.028	21.901	-0.018	-0.018	0.000	0.000	0.000
37	A	37	VAL	0	0.009	0.003	20.578	-0.015	-0.015	0.000	0.000	0.000
38	A	38	ASN	0	0.045	-0.003	19.578	-0.013	-0.013	0.000	0.000	0.000
39	A	39	ALA	0	-0.033	-0.012	18.013	-0.024	-0.024	0.000	0.000	0.000
40	A	40	MET	0	-0.086	-0.022	15.992	-0.032	-0.032	0.000	0.000	0.000
41	A	41	PHE	0	0.055	0.013	14.266	-0.020	-0.020	0.000	0.000	0.000
42	A	42	GLU	-1	-0.973	-0.959	14.085	-0.321	-0.321	0.000	0.000	0.000
43	A	43	GLY	0	0.108	0.049	10.321	-0.017	-0.017	0.000	0.000	0.000
44	A	44	ARG	1	0.902	0.939	10.237	0.533	0.533	0.000	0.000	0.000
45	A	45	SER	0	-0.042	-0.004	12.350	0.076	0.076	0.000	0.000	0.000
46	A	46	LYS	1	0.993	0.984	12.592	0.255	0.255	0.000	0.000	0.000
47	A	47	ARG	1	0.856	0.954	14.234	0.235	0.235	0.000	0.000	0.000
48	A	48	PRO	0	0.108	0.050	14.233	-0.033	-0.033	0.000	0.000	0.000
49	A	49	THR	0	0.023	0.011	16.335	0.003	0.003	0.000	0.000	0.000
50	A	50	ILE	0	0.133	0.048	19.060	0.003	0.003	0.000	0.000	0.000
51	A	51	THR	0	-0.058	-0.032	20.698	0.009	0.009	0.000	0.000	0.000
52	A	52	THR	0	-0.014	-0.004	20.577	0.008	0.008	0.000	0.000	0.000
53	A	53	ILE	0	0.075	0.045	16.729	0.004	0.004	0.000	0.000	0.000
54	A	54	ARG	1	0.990	0.989	21.080	0.065	0.065	0.000	0.000	0.000
55	A	55	LYS	1	0.890	0.946	24.482	0.083	0.083	0.000	0.000	0.000
56	A	56	VAL	0	0.037	0.019	22.219	0.004	0.004	0.000	0.000	0.000
57	A	57	CYS	0	-0.038	-0.005	22.543	0.006	0.006	0.000	0.000	0.000
58	A	58	GLY	0	0.014	0.010	25.181	0.005	0.005	0.000	0.000	0.000
59	A	59	THR	0	-0.057	-0.031	27.358	0.003	0.003	0.000	0.000	0.000
60	A	60	LEU	0	-0.015	-0.009	22.727	0.002	0.002	0.000	0.000	0.000
61	A	61	GLY	0	0.006	0.043	27.157	0.005	0.005	0.000	0.000	0.000
62	A	62	ILE	0	0.013	0.012	22.601	0.004	0.004	0.000	0.000	0.000
63	A	63	SER	0	0.008	0.002	26.308	-0.005	-0.005	0.000	0.000	0.000
64	A	64	VAL	0	0.011	-0.021	21.322	0.000	0.000	0.000	0.000	0.000
65	A	65	HIS	0	0.004	-0.007	21.749	0.000	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.810	-0.904	21.889	0.011	0.011	0.000	0.000	0.000
67	A	67	PHE	0	-0.112	-0.054	16.629	0.002	0.002	0.000	0.000	0.000
68	A	68	PHE	0	-0.048	-0.054	15.031	-0.011	-0.011	0.000	0.000	0.000
69	A	69	ASP	-1	-0.863	-0.896	17.448	0.070	0.070	0.000	0.000	0.000
70	A	70	PHE	0	-0.073	-0.046	11.691	-0.011	-0.011	0.000	0.000	0.000
71	A	71	PRO	0	0.030	0.033	11.319	0.010	0.010	0.000	0.000	0.000
72	A	72	PRO	0	-0.039	-0.036	8.853	-0.019	-0.019	0.000	0.000	0.000
73	A	73	TYR	0	-0.081	-0.097	10.397	-0.033	-0.033	0.000	0.000	0.000
74	A	74	ASN	0	-0.052	-0.022	14.360	-0.001	-0.001	0.000	0.000	0.000
75	A	75	GLU	-1	-0.931	-0.952	14.270	0.120	0.120	0.000	0.000	0.000
76	A	76	VAL	0	-0.063	-0.027	14.818	0.013	0.013	0.000	0.000	0.000

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