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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZVGYN

Calculation Name: 1KF9-C-Xray372

Preferred Name: Growth hormone receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1KF9

Chain ID: C

ChEMBL ID: CHEMBL1976

UniProt ID: P10912

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1940046.990641
FMO2-HF: Nuclear repulsion 1863989.658737
FMO2-HF: Total energy -76057.331904
FMO2-MP2: Total energy -76277.205692


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:533:PRO)


Summations of interaction energy for fragment #1(C:533:PRO)
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.
-4.224-0.1865.44-3.227-6.251-0.015
Interaction energy analysis for fragmet #1(C:533:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.013
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   
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].
3C535PHE00.0610.0393.452-0.7931.340-0.032-0.977-1.1240.000
4C536THR0-0.136-0.0495.659-0.249-0.2490.0000.0000.0000.000
5C537LYS10.9570.9627.9960.1320.1320.0000.0000.0000.000
6C538CYS0-0.103-0.04110.214-0.010-0.0100.0000.0000.0000.000
7C539ARG10.7950.84813.415-0.016-0.0160.0000.0000.0000.000
8C540SER0-0.084-0.12017.0050.0220.0220.0000.0000.0000.000
9C541PRO0-0.013-0.01120.241-0.016-0.0160.0000.0000.0000.000
10C542GLU-1-0.720-0.88722.6700.0430.0430.0000.0000.0000.000
11C543ARG10.7760.88624.148-0.021-0.0210.0000.0000.0000.000
12C544GLU-1-0.924-0.95525.2110.0480.0480.0000.0000.0000.000
13C545THR0-0.016-0.02221.5460.0150.0150.0000.0000.0000.000
14C546PHE00.0140.05915.467-0.018-0.0180.0000.0000.0000.000
15C547SER00.0200.03014.8090.0230.0230.0000.0000.0000.000
16C549HIS00.1150.0808.9140.0780.0780.0000.0000.0000.000
17C550TRP00.038-0.0213.448-0.1910.2110.005-0.070-0.3370.000
18C551THR00.0010.0252.178-1.696-2.2074.854-1.445-2.898-0.019
19C564ILE0-0.042-0.0292.926-0.9620.0180.426-0.373-1.0330.002
20C565GLN0-0.001-0.0016.394-0.172-0.1720.0000.0000.0000.000
21C566LEU0-0.014-0.0198.3630.3860.3860.0000.0000.0000.000
22C567PHE0-0.0030.00610.347-0.198-0.1980.0000.0000.0000.000
23C568TYR0-0.013-0.02312.671-0.004-0.0040.0000.0000.0000.000
24C569THR00.0210.01715.386-0.031-0.0310.0000.0000.0000.000
25C570ARG10.9820.97718.433-0.162-0.1620.0000.0000.0000.000
26C571ARG10.9480.96218.832-0.110-0.1100.0000.0000.0000.000
27C572ASN00.0450.01824.322-0.013-0.0130.0000.0000.0000.000
28C573THR0-0.037-0.01127.009-0.001-0.0010.0000.0000.0000.000
29C574GLN00.0310.00825.1640.0170.0170.0000.0000.0000.000
30C575GLU-1-0.843-0.90128.3860.0710.0710.0000.0000.0000.000
31C576TRP0-0.049-0.05427.7080.0100.0100.0000.0000.0000.000
32C577THR0-0.081-0.04522.6340.0080.0080.0000.0000.0000.000
33C578GLN0-0.020-0.00318.7580.0250.0250.0000.0000.0000.000
34C579GLU-1-0.893-0.92720.8050.2380.2380.0000.0000.0000.000
35C580TRP0-0.092-0.05313.5300.0330.0330.0000.0000.0000.000
36C581LYS10.9740.99417.508-0.265-0.2650.0000.0000.0000.000
37C582GLU-1-0.767-0.85114.0110.7070.7070.0000.0000.0000.000
38C583CYS0-0.127-0.01510.655-0.062-0.0620.0000.0000.0000.000
39C584PRO0-0.034-0.01915.089-0.010-0.0100.0000.0000.0000.000
40C585ASP-1-0.795-0.90616.7620.1820.1820.0000.0000.0000.000
41C586TYR0-0.034-0.08210.6270.1040.1040.0000.0000.0000.000
42C587VAL00.0490.05314.112-0.002-0.0020.0000.0000.0000.000
43C588SER0-0.017-0.00716.921-0.035-0.0350.0000.0000.0000.000
44C589ALA0-0.060-0.01514.990-0.029-0.0290.0000.0000.0000.000
45C590GLY0-0.0450.00914.734-0.026-0.0260.0000.0000.0000.000
46C591GLU-1-0.840-0.93510.9550.3090.3090.0000.0000.0000.000
47C592ASN0-0.147-0.0685.659-0.141-0.1410.0000.0000.0000.000
48C593SER00.011-0.0538.496-0.051-0.0510.0000.0000.0000.000
49C595TYR00.034-0.00812.749-0.060-0.0600.0000.0000.0000.000
50C596PHE0-0.026-0.02214.0430.0280.0280.0000.0000.0000.000
51C597ASN00.1140.05318.972-0.017-0.0170.0000.0000.0000.000
52C598SER00.0820.04922.6040.0030.0030.0000.0000.0000.000
53C599SER0-0.077-0.02224.239-0.003-0.0030.0000.0000.0000.000
54C600PHE00.0120.00820.9170.0050.0050.0000.0000.0000.000
55C601THR0-0.0490.02021.9080.0120.0120.0000.0000.0000.000
56C602SER0-0.028-0.01223.268-0.014-0.0140.0000.0000.0000.000
57C603ILE00.0340.00324.2310.0050.0050.0000.0000.0000.000
58C604TRP0-0.0040.00726.312-0.006-0.0060.0000.0000.0000.000
59C605ILE0-0.061-0.01824.562-0.003-0.0030.0000.0000.0000.000
60C606PRO00.0250.00121.1660.0080.0080.0000.0000.0000.000
61C607TYR0-0.059-0.09017.1250.0130.0130.0000.0000.0000.000
62C608CYS0-0.174-0.08611.7940.0310.0310.0000.0000.0000.000
63C609ILE0-0.026-0.01810.1200.0200.0200.0000.0000.0000.000
64C610LYS10.9710.9719.051-0.452-0.4520.0000.0000.0000.000
65C611LEU00.0090.0343.262-0.7740.2600.187-0.362-0.8590.002
66C621LYS10.9521.00010.611-0.039-0.0390.0000.0000.0000.000
67C623PHE00.0510.02914.004-0.038-0.0380.0000.0000.0000.000
68C624SER00.0490.03017.9950.0200.0200.0000.0000.0000.000
69C625VAL00.0640.02720.321-0.012-0.0120.0000.0000.0000.000
70C626ASP-1-0.741-0.87021.3310.0110.0110.0000.0000.0000.000
71C627GLU-1-0.952-0.99319.503-0.010-0.0100.0000.0000.0000.000
72C628ILE0-0.110-0.03316.155-0.016-0.0160.0000.0000.0000.000
73C629VAL00.0480.04118.9490.0090.0090.0000.0000.0000.000
74C630GLN0-0.042-0.02817.459-0.015-0.0150.0000.0000.0000.000
75C631PRO00.0370.05822.1280.0090.0090.0000.0000.0000.000
76C632ASP-1-0.842-0.90823.469-0.017-0.0170.0000.0000.0000.000
77C633PRO00.003-0.00524.7540.0010.0010.0000.0000.0000.000
78C634PRO0-0.052-0.01227.6470.0050.0050.0000.0000.0000.000
79C635ILE00.018-0.00131.103-0.003-0.0030.0000.0000.0000.000
80C636ALA0-0.009-0.01933.3590.0000.0000.0000.0000.0000.000
81C637LEU00.0050.01634.2170.0010.0010.0000.0000.0000.000
82C638ASN0-0.028-0.02137.6020.0000.0000.0000.0000.0000.000
83C639TRP00.0590.02541.0760.0010.0010.0000.0000.0000.000
84C640THR00.0050.01043.9780.0020.0020.0000.0000.0000.000
85C641LEU00.0230.01747.677-0.001-0.0010.0000.0000.0000.000
86C642LEU0-0.0680.00248.6470.0010.0010.0000.0000.0000.000
87C643ASN00.021-0.02251.9610.0020.0020.0000.0000.0000.000
88C644VAL00.0110.00453.689-0.001-0.0010.0000.0000.0000.000
89C645SER0-0.047-0.00655.2130.0010.0010.0000.0000.0000.000
90C646LEU00.1140.02757.1450.0000.0000.0000.0000.0000.000
91C647THR0-0.072-0.02558.8000.0000.0000.0000.0000.0000.000
92C648GLY00.0220.00757.422-0.001-0.0010.0000.0000.0000.000
93C649ILE00.002-0.00853.630-0.001-0.0010.0000.0000.0000.000
94C650HIS0-0.0320.00150.362-0.003-0.0030.0000.0000.0000.000
95C651ALA00.0280.01750.0460.0020.0020.0000.0000.0000.000
96C652ASP-1-0.829-0.88348.928-0.025-0.0250.0000.0000.0000.000
97C653ILE00.004-0.01743.4980.0010.0010.0000.0000.0000.000
98C654GLN00.006-0.02044.978-0.001-0.0010.0000.0000.0000.000
99C655VAL0-0.027-0.00439.0730.0000.0000.0000.0000.0000.000
100C656ARG10.8920.93941.2850.0160.0160.0000.0000.0000.000
101C657TRP0-0.028-0.01735.439-0.002-0.0020.0000.0000.0000.000
102C658GLU-1-0.887-0.95035.841-0.006-0.0060.0000.0000.0000.000
103C659ALA0-0.003-0.00133.352-0.003-0.0030.0000.0000.0000.000
104C660PRO00.0030.00228.5660.0020.0020.0000.0000.0000.000
105C661ARG11.0241.01230.6540.0020.0020.0000.0000.0000.000
106C662ASN0-0.0340.00325.412-0.001-0.0010.0000.0000.0000.000
107C663ALA0-0.034-0.03529.4040.0040.0040.0000.0000.0000.000
108C664ASP-1-0.846-0.90530.7390.0250.0250.0000.0000.0000.000
109C665ILE00.0400.01033.2640.0000.0000.0000.0000.0000.000
110C666GLN0-0.060-0.05236.812-0.001-0.0010.0000.0000.0000.000
111C667LYS10.7720.92031.450-0.034-0.0340.0000.0000.0000.000
112C668GLY00.0620.04835.1300.0010.0010.0000.0000.0000.000
113C669TRP0-0.056-0.05930.422-0.003-0.0030.0000.0000.0000.000
114C670MET00.0620.05626.173-0.001-0.0010.0000.0000.0000.000
115C671VAL0-0.029-0.01031.017-0.002-0.0020.0000.0000.0000.000
116C672LEU0-0.010-0.02828.908-0.002-0.0020.0000.0000.0000.000
117C673GLU-1-0.920-0.94531.609-0.026-0.0260.0000.0000.0000.000
118C674TYR0-0.008-0.04031.909-0.002-0.0020.0000.0000.0000.000
119C675GLU-1-0.820-0.89930.747-0.059-0.0590.0000.0000.0000.000
120C676LEU00.0050.01032.630-0.002-0.0020.0000.0000.0000.000
121C677GLN0-0.008-0.01830.772-0.005-0.0050.0000.0000.0000.000
122C678TYR00.024-0.00834.8650.0010.0010.0000.0000.0000.000
123C679LYS10.8370.93234.3240.0610.0610.0000.0000.0000.000
124C680GLU-1-0.752-0.85438.368-0.045-0.0450.0000.0000.0000.000
125C681VAL00.0380.00038.455-0.004-0.0040.0000.0000.0000.000
126C682ASN0-0.069-0.04437.913-0.006-0.0060.0000.0000.0000.000
127C683GLU-1-0.921-0.94638.491-0.052-0.0520.0000.0000.0000.000
128C684THR00.015-0.00333.580-0.004-0.0040.0000.0000.0000.000
129C685LYS10.8930.93030.7390.0880.0880.0000.0000.0000.000
130C686TRP0-0.0020.00231.6320.0040.0040.0000.0000.0000.000
131C687LYS10.9030.97635.0030.0440.0440.0000.0000.0000.000
132C688MET0-0.046-0.02732.442-0.001-0.0010.0000.0000.0000.000
133C689MET0-0.0050.00435.5970.0020.0020.0000.0000.0000.000
134C690ASP-1-0.904-0.94835.986-0.038-0.0380.0000.0000.0000.000
135C691PRO0-0.048-0.02833.5690.0020.0020.0000.0000.0000.000
136C692ILE00.0120.03635.6800.0030.0030.0000.0000.0000.000
137C693LEU00.030-0.01036.4110.0000.0000.0000.0000.0000.000
138C694THR0-0.084-0.04238.2040.0020.0020.0000.0000.0000.000
139C695THR00.0010.00136.988-0.002-0.0020.0000.0000.0000.000
140C696SER00.002-0.01539.1540.0000.0000.0000.0000.0000.000
141C697VAL00.0050.02739.6720.0010.0010.0000.0000.0000.000
142C698PRO0-0.005-0.00242.648-0.001-0.0010.0000.0000.0000.000
143C699VAL00.0100.02241.773-0.001-0.0010.0000.0000.0000.000
144C700TYR00.007-0.01544.3610.0020.0020.0000.0000.0000.000
145C701SER0-0.020-0.01846.602-0.002-0.0020.0000.0000.0000.000
146C702LEU0-0.0020.02043.789-0.002-0.0020.0000.0000.0000.000
147C703LYS10.8760.91147.4290.0340.0340.0000.0000.0000.000
148C704VAL00.0330.00548.462-0.001-0.0010.0000.0000.0000.000
149C705ASP-1-0.894-0.93550.306-0.029-0.0290.0000.0000.0000.000
150C706LYS10.7090.84844.2940.0400.0400.0000.0000.0000.000
151C707GLU-1-0.871-0.92241.580-0.037-0.0370.0000.0000.0000.000
152C708TYR0-0.031-0.02040.960-0.002-0.0020.0000.0000.0000.000
153C709GLU-1-0.829-0.91434.625-0.059-0.0590.0000.0000.0000.000
154C710VAL0-0.020-0.03236.461-0.002-0.0020.0000.0000.0000.000
155C711ARG10.9090.98228.2530.0760.0760.0000.0000.0000.000
156C712VAL00.0350.01332.236-0.001-0.0010.0000.0000.0000.000
157C713ARG10.8880.96525.9050.0740.0740.0000.0000.0000.000
158C714SER00.0280.00327.9090.0050.0050.0000.0000.0000.000
159C715LYS10.8350.89926.5610.0270.0270.0000.0000.0000.000
160C716GLN00.0800.05626.9370.0040.0040.0000.0000.0000.000
161C717ARG10.9841.00028.891-0.004-0.0040.0000.0000.0000.000
162C718ASN0-0.045-0.04930.3700.0030.0030.0000.0000.0000.000
163C719SER0-0.0280.00925.9260.0020.0020.0000.0000.0000.000
164C720GLY00.1020.07422.742-0.001-0.0010.0000.0000.0000.000
165C721ASN0-0.072-0.04720.898-0.003-0.0030.0000.0000.0000.000
166C722TYR00.003-0.00723.6310.0090.0090.0000.0000.0000.000
167C723GLY0-0.0040.00922.738-0.007-0.0070.0000.0000.0000.000
168C724GLU-1-0.949-0.97720.745-0.121-0.1210.0000.0000.0000.000
169C725PHE0-0.072-0.04923.9980.0090.0090.0000.0000.0000.000
170C726SER00.0090.00027.245-0.001-0.0010.0000.0000.0000.000
171C727GLU-1-0.944-0.96829.772-0.044-0.0440.0000.0000.0000.000
172C728VAL0-0.047-0.02031.1920.0020.0020.0000.0000.0000.000
173C729LEU00.0040.01333.5580.0020.0020.0000.0000.0000.000
174C730TYR00.0200.00534.742-0.002-0.0020.0000.0000.0000.000
175C731VAL0-0.041-0.03339.6230.0030.0030.0000.0000.0000.000
176C732THR00.046-0.02442.940-0.001-0.0010.0000.0000.0000.000
177C733LEU0-0.0500.03246.1670.0020.0020.0000.0000.0000.000
178C734PRO00.0220.01949.2160.0000.0000.0000.0000.0000.000