FMO DATABASE

FMODB ID: JKG89

Calculation Name: 1MKC-A-Other549

Preferred Name: Midkine

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MKC

Chain ID: A

ChEMBL ID: CHEMBL1949490

UniProt ID: P21741

Base Structure: SolutionNMR

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	41
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-193418.65957
FMO2-HF: Nuclear repulsion	175669.826328
FMO2-HF: Total energy	-17748.833242
FMO2-MP2: Total energy	-17797.832023

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(A:62:CYS)

Summations of interaction energy for fragment #1(A:62: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.
8.837	18.832	29.453	-13.744	-25.705	-0.148

Interaction energy analysis for fragmet #1(A:62:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.676 / q_NPA : 0.874

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	64	TYR	0	0.012	-0.013	3.862	-1.082	0.594	-0.016	-0.758	-0.901	0.003
24	A	85	LEU	0	0.008	0.030	3.070	0.613	1.709	0.357	-0.351	-1.103	0.001
25	A	86	LYS	1	0.946	0.965	2.345	18.567	22.826	3.268	-3.087	-4.441	-0.032
26	A	87	LYS	1	0.998	0.970	2.358	36.687	33.540	12.737	-3.089	-6.502	-0.001
27	A	88	ALA	0	-0.016	-0.018	3.481	5.729	1.173	0.125	5.081	-0.650	0.004
30	A	91	ASN	0	0.064	0.014	2.424	-9.164	-7.007	3.107	-2.140	-3.123	-0.022
31	A	92	ALA	0	0.002	0.019	3.362	-7.344	-3.812	0.041	-1.834	-1.739	-0.011
34	A	96	GLU	-1	-0.814	-0.908	1.835	-116.522	-111.902	9.832	-7.559	-6.893	-0.090
35	A	97	THR	0	0.010	-0.011	4.158	1.468	1.650	0.002	0.015	-0.198	0.000
36	A	98	ILE	0	0.019	0.016	3.824	3.036	3.212	0.000	-0.022	-0.155	0.000
4	A	65	LYS	1	0.965	0.991	6.746	25.414	25.414	0.000	0.000	0.000	0.000
5	A	66	PHE	0	-0.011	0.017	7.674	-1.385	-1.385	0.000	0.000	0.000	0.000
6	A	67	GLU	-1	-0.829	-0.896	11.476	-16.769	-16.769	0.000	0.000	0.000	0.000
7	A	68	ASN	0	-0.020	-0.024	11.596	-2.971	-2.971	0.000	0.000	0.000	0.000
8	A	69	TRP	0	-0.002	-0.012	8.764	-0.177	-0.177	0.000	0.000	0.000	0.000
9	A	70	GLY	0	0.080	0.048	14.883	0.288	0.288	0.000	0.000	0.000	0.000
10	A	71	ALA	0	0.023	0.033	17.472	-0.522	-0.522	0.000	0.000	0.000	0.000
11	A	104	CYS	-1	-0.789	-0.891	15.561	-15.643	-15.643	0.000	0.000	0.000	0.000
12	A	73	ASP	-1	-0.760	-0.881	18.502	-12.063	-12.063	0.000	0.000	0.000	0.000
13	A	74	GLY	0	-0.097	-0.048	19.151	-0.673	-0.673	0.000	0.000	0.000	0.000
14	A	75	GLY	0	-0.014	0.003	21.233	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	76	THR	0	-0.064	-0.035	17.263	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	77	GLY	0	0.089	0.056	19.430	0.154	0.154	0.000	0.000	0.000	0.000
17	A	78	THR	0	0.003	0.000	13.544	-0.597	-0.597	0.000	0.000	0.000	0.000
18	A	79	LYS	1	0.803	0.909	12.809	18.040	18.040	0.000	0.000	0.000	0.000
19	A	80	VAL	0	0.015	-0.018	11.518	-1.415	-1.415	0.000	0.000	0.000	0.000
20	A	81	ARG	1	0.858	0.952	9.238	27.019	27.019	0.000	0.000	0.000	0.000
21	A	82	GLN	0	0.084	0.030	9.872	-3.318	-3.318	0.000	0.000	0.000	0.000
22	A	83	GLY	0	0.001	-0.002	9.626	0.978	0.978	0.000	0.000	0.000	0.000
23	A	84	THR	0	-0.070	-0.058	4.870	-1.338	-1.338	0.000	0.000	0.000	0.000
28	A	89	ARG	1	0.942	0.969	4.895	24.346	24.346	0.000	0.000	0.000	0.000
29	A	90	TYR	0	0.033	0.022	5.961	1.815	1.815	0.000	0.000	0.000	0.000
37	A	99	ARG	1	0.970	0.994	7.746	18.005	18.005	0.000	0.000	0.000	0.000
38	A	100	VAL	0	-0.090	-0.027	4.931	0.486	0.486	0.000	0.000	0.000	0.000
39	A	101	THR	0	0.054	0.015	7.965	0.981	0.981	0.000	0.000	0.000	0.000
40	A	102	LYS	1	0.914	0.931	9.380	15.981	15.981	0.000	0.000	0.000	0.000
41	A	103	PRO	0	-0.132	-0.059	11.791	0.253	0.253	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:62:CYS)