FMO DATABASE

FMODB ID: 1NJRZ

Calculation Name: 4LMQ-D-Xray372

Preferred Name: Stromal cell-derived factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4LMQ

Chain ID: D

ChEMBL ID: CHEMBL3286074

UniProt ID: P48061

Base Structure: X-ray

Registration Date: 2023-09-20

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-329121.953962
FMO2-HF: Nuclear repulsion	305088.019191
FMO2-HF: Total energy	-24033.934771
FMO2-MP2: Total energy	-24103.341496

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(D:11:CYS)

Summations of interaction energy for fragment #1(D:11:CYS)

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.
-46.181	-31.099	22.572	-13.195	-24.458	0.032

Interaction energy analysis for fragmet #1(D:11:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.050

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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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	D	13	PHE	0	0.073	0.043	3.824	-0.648	2.405	0.440	-1.367	-2.126	0.003
4	D	14	PHE	0	0.011	-0.001	2.338	-5.921	-2.882	3.413	-1.958	-4.495	-0.016
5	D	15	GLU	-1	-0.789	-0.878	3.700	-8.991	-8.312	0.002	-0.134	-0.546	0.000
6	D	16	SER	0	0.014	-0.006	6.089	1.483	1.483	0.000	0.000	0.000	0.000
7	D	17	HIS	0	-0.013	-0.002	9.375	-0.048	-0.048	0.000	0.000	0.000	0.000
8	D	18	VAL	0	0.003	0.011	5.644	-0.070	-0.070	0.000	0.000	0.000	0.000
9	D	19	ALA	0	0.036	0.020	8.885	0.526	0.526	0.000	0.000	0.000	0.000
10	D	20	ARG	1	0.955	0.977	10.411	-1.685	-1.685	0.000	0.000	0.000	0.000
11	D	21	ALA	0	0.043	0.026	11.421	0.166	0.166	0.000	0.000	0.000	0.000
12	D	22	ASN	0	0.033	0.007	9.153	0.011	0.011	0.000	0.000	0.000	0.000
13	D	23	VAL	0	-0.006	0.000	6.858	-0.008	-0.008	0.000	0.000	0.000	0.000
14	D	24	LYS	1	0.914	0.962	8.946	-1.486	-1.486	0.000	0.000	0.000	0.000
15	D	25	HIS	0	0.005	-0.006	8.809	0.157	0.157	0.000	0.000	0.000	0.000
16	D	26	LEU	0	0.007	0.015	5.936	1.374	1.374	0.000	0.000	0.000	0.000
17	D	27	LYS	1	0.925	0.969	6.471	-6.174	-6.174	0.000	0.000	0.000	0.000
18	D	28	ILE	0	0.030	0.010	6.582	2.123	2.123	0.000	0.000	0.000	0.000
19	D	29	LEU	0	-0.050	-0.022	3.268	-2.454	-1.245	0.137	-0.496	-0.851	0.004
20	D	30	ASN	0	0.015	-0.004	6.357	-0.211	-0.211	0.000	0.000	0.000	0.000
21	D	31	THR	0	0.030	0.012	5.885	0.042	0.042	0.000	0.000	0.000	0.000
22	D	32	PRO	0	0.023	0.039	2.989	-0.934	-0.288	0.193	-0.286	-0.553	0.002
23	D	33	ASN	0	-0.011	-0.018	4.024	-1.906	-1.724	-0.001	-0.059	-0.123	0.000
24	D	34	CYS	0	-0.066	-0.033	3.284	0.415	1.016	0.026	-0.108	-0.518	-0.001
25	D	35	ALA	0	0.071	0.033	5.157	0.668	0.668	0.000	0.000	0.000	0.000
26	D	36	LEU	0	0.011	0.015	6.142	0.593	0.593	0.000	0.000	0.000	0.000
27	D	37	GLN	0	0.014	-0.002	2.274	-2.774	-2.883	4.608	-1.347	-3.153	0.000
28	D	38	ILE	0	0.026	0.015	3.173	1.207	0.984	-0.002	0.657	-0.432	0.000
29	D	39	VAL	0	-0.004	-0.015	2.437	-4.071	0.094	6.119	-4.398	-5.886	0.008
30	D	40	ALA	0	0.028	0.022	1.913	-12.952	-16.405	7.636	-1.387	-2.796	0.031
31	D	41	ARG	1	0.846	0.934	3.560	-4.692	-4.198	0.050	-0.106	-0.438	0.000
32	D	42	LEU	0	-0.001	-0.007	4.773	0.168	0.253	-0.002	-0.003	-0.080	0.000
33	D	43	LYS	1	0.810	0.894	7.449	-1.393	-1.393	0.000	0.000	0.000	0.000
34	D	44	ASN	0	0.049	0.020	10.248	-0.215	-0.215	0.000	0.000	0.000	0.000
35	D	45	ASN	0	0.058	0.028	7.984	-0.219	-0.219	0.000	0.000	0.000	0.000
36	D	46	ASN	0	0.012	0.009	9.760	0.018	0.018	0.000	0.000	0.000	0.000
37	D	47	ARG	1	0.999	1.014	5.335	2.923	2.950	-0.002	-0.001	-0.024	0.000
38	D	48	GLN	0	-0.007	0.000	3.836	1.025	3.356	-0.027	-1.135	-1.168	-0.003
41	D	52	ASP	-1	-0.764	-0.877	3.850	-0.978	1.253	-0.016	-1.061	-1.153	0.004
42	D	53	PRO	0	0.005	-0.014	5.659	0.208	0.333	-0.002	-0.006	-0.116	0.000
43	D	54	LYS	1	0.880	0.943	8.534	-0.512	-0.512	0.000	0.000	0.000	0.000
44	D	55	LEU	0	-0.006	0.009	8.591	-0.303	-0.303	0.000	0.000	0.000	0.000
45	D	56	LYS	1	1.031	1.006	11.980	-0.451	-0.451	0.000	0.000	0.000	0.000
46	D	57	TRP	0	0.014	-0.004	7.897	0.157	0.157	0.000	0.000	0.000	0.000
47	D	58	ILE	0	0.046	0.016	7.704	0.139	0.139	0.000	0.000	0.000	0.000
48	D	59	GLN	0	0.032	0.012	11.039	0.007	0.007	0.000	0.000	0.000	0.000
49	D	60	GLU	-1	-0.837	-0.908	14.242	1.041	1.041	0.000	0.000	0.000	0.000
50	D	61	TYR	0	-0.081	-0.052	11.691	0.085	0.085	0.000	0.000	0.000	0.000
51	D	62	LEU	0	0.013	-0.003	10.491	-0.053	-0.053	0.000	0.000	0.000	0.000
52	D	63	GLU	-1	-0.882	-0.945	14.326	0.966	0.966	0.000	0.000	0.000	0.000
53	D	64	LYS	1	0.857	0.928	17.373	-1.223	-1.223	0.000	0.000	0.000	0.000
54	D	65	ALA	0	-0.022	-0.007	15.162	-0.083	-0.083	0.000	0.000	0.000	0.000
55	D	66	LEU	0	-0.057	-0.022	16.119	-0.080	-0.080	0.000	0.000	0.000	0.000
56	D	67	ASN	0	-0.043	-0.013	19.587	-0.148	-0.148	0.000	0.000	0.000	0.000
57	D	68	LYS	1	0.946	0.986	21.315	-1.000	-1.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:11:CYS)