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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: QV41Y

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1936502.800408
FMO2-HF: Nuclear repulsion 1860441.950367
FMO2-HF: Total energy -76060.85004
FMO2-MP2: Total energy -76280.323294


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.
-14.185-23.20324.386-8.485-6.8830.024
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 : 0.036 / q_NPA : 0.023
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].
3C535PHE00.0730.0363.8730.6772.420-0.021-0.844-0.8780.001
4C536THR0-0.074-0.0327.014-0.651-0.6510.0000.0000.0000.000
5C537LYS10.8760.9229.071-0.779-0.7790.0000.0000.0000.000
6C538CYS0-0.070-0.02811.4060.0670.0670.0000.0000.0000.000
7C539ARG10.7630.84814.694-0.403-0.4030.0000.0000.0000.000
8C540SER00.010-0.00318.4490.0170.0170.0000.0000.0000.000
9C541PRO0-0.0250.00421.738-0.015-0.0150.0000.0000.0000.000
10C542GLU-1-0.694-0.84724.2440.2330.2330.0000.0000.0000.000
11C543ARG10.8020.90125.695-0.145-0.1450.0000.0000.0000.000
12C544GLU-1-0.919-0.94926.3480.1440.1440.0000.0000.0000.000
13C545THR0-0.116-0.08923.0780.0100.0100.0000.0000.0000.000
14C546PHE00.003-0.00916.059-0.006-0.0060.0000.0000.0000.000
15C547SER00.0130.02315.9930.0290.0290.0000.0000.0000.000
16C549HIS00.0810.03610.4130.1530.1530.0000.0000.0000.000
17C550TRP0-0.036-0.0184.818-1.011-0.835-0.001-0.029-0.1450.000
18C551THR00.011-0.0121.749-14.061-26.08523.345-7.169-4.1530.027
19C564ILE00.0080.0082.474-1.066-0.5520.861-0.281-1.094-0.004
20C565GLN0-0.025-0.0286.0890.3000.3000.0000.0000.0000.000
21C566LEU0-0.0120.0177.8550.0850.0850.0000.0000.0000.000
22C567PHE00.0140.0059.909-0.108-0.1080.0000.0000.0000.000
23C568TYR0-0.032-0.03212.2590.0050.0050.0000.0000.0000.000
24C569THR00.0300.00115.061-0.035-0.0350.0000.0000.0000.000
25C570ARG10.9200.94318.333-0.144-0.1440.0000.0000.0000.000
26C571ARG10.9100.95319.136-0.070-0.0700.0000.0000.0000.000
27C572ASN00.0460.00624.2700.0030.0030.0000.0000.0000.000
28C573THR0-0.0210.01527.037-0.003-0.0030.0000.0000.0000.000
29C574GLN00.026-0.00825.138-0.003-0.0030.0000.0000.0000.000
30C575GLU-1-0.823-0.89528.8590.0050.0050.0000.0000.0000.000
31C576TRP0-0.027-0.03627.7440.0030.0030.0000.0000.0000.000
32C577THR0-0.112-0.05623.128-0.001-0.0010.0000.0000.0000.000
33C578GLN0-0.007-0.00219.017-0.014-0.0140.0000.0000.0000.000
34C579GLU-1-0.809-0.87721.0880.0830.0830.0000.0000.0000.000
35C580TRP0-0.027-0.00113.4880.0070.0070.0000.0000.0000.000
36C581LYS10.8140.89317.335-0.133-0.1330.0000.0000.0000.000
37C582GLU-1-0.764-0.84013.5550.3810.3810.0000.0000.0000.000
38C583CYS0-0.081-0.02111.592-0.151-0.1510.0000.0000.0000.000
39C584PRO0-0.032-0.01115.079-0.020-0.0200.0000.0000.0000.000
40C585ASP-1-0.779-0.85917.2330.3940.3940.0000.0000.0000.000
41C586TYR0-0.009-0.05410.6480.0900.0900.0000.0000.0000.000
42C587VAL00.0060.02514.5220.0730.0730.0000.0000.0000.000
43C588SER0-0.041-0.06117.258-0.009-0.0090.0000.0000.0000.000
44C589ALA0-0.057-0.02115.696-0.030-0.0300.0000.0000.0000.000
45C590GLY0-0.037-0.01215.8090.0710.0710.0000.0000.0000.000
46C591GLU-1-0.822-0.92011.2131.0321.0320.0000.0000.0000.000
47C592ASN0-0.113-0.0636.4891.0091.0090.0000.0000.0000.000
48C593SER0-0.014-0.0109.1730.3190.3190.0000.0000.0000.000
49C595TYR0-0.003-0.01413.907-0.023-0.0230.0000.0000.0000.000
50C596PHE0-0.014-0.01114.543-0.027-0.0270.0000.0000.0000.000
51C597ASN00.1220.07019.773-0.032-0.0320.0000.0000.0000.000
52C598SER00.0810.02923.4520.0010.0010.0000.0000.0000.000
53C599SER0-0.059-0.02425.462-0.012-0.0120.0000.0000.0000.000
54C600PHE00.002-0.00720.974-0.009-0.0090.0000.0000.0000.000
55C601THR0-0.0400.01821.9650.0160.0160.0000.0000.0000.000
56C602SER0-0.0070.00023.670-0.017-0.0170.0000.0000.0000.000
57C603ILE0-0.006-0.00624.8620.0030.0030.0000.0000.0000.000
58C604TRP00.0190.01026.720-0.004-0.0040.0000.0000.0000.000
59C605ILE0-0.0340.00124.284-0.012-0.0120.0000.0000.0000.000
60C606PRO0-0.019-0.00321.3900.0170.0170.0000.0000.0000.000
61C607TYR00.015-0.03717.414-0.021-0.0210.0000.0000.0000.000
62C608CYS0-0.156-0.08312.194-0.019-0.0190.0000.0000.0000.000
63C609ILE00.0090.01010.4340.0110.0110.0000.0000.0000.000
64C610LYS10.8810.9399.026-0.061-0.0610.0000.0000.0000.000
65C611LEU0-0.021-0.0142.770-0.893-0.3200.202-0.162-0.6130.000
66C621LYS10.9390.97810.801-0.199-0.1990.0000.0000.0000.000
67C623PHE00.0020.00214.1780.0010.0010.0000.0000.0000.000
68C624SER00.0230.00818.282-0.003-0.0030.0000.0000.0000.000
69C625VAL00.0580.01220.9490.0140.0140.0000.0000.0000.000
70C626ASP-1-0.699-0.84022.1430.1490.1490.0000.0000.0000.000
71C627GLU-1-0.856-0.91319.2970.1280.1280.0000.0000.0000.000
72C628ILE0-0.051-0.01817.0450.0050.0050.0000.0000.0000.000
73C629VAL00.0090.02020.1920.0300.0300.0000.0000.0000.000
74C630GLN00.0200.00818.9530.0280.0280.0000.0000.0000.000
75C631PRO00.0550.05023.3250.0270.0270.0000.0000.0000.000
76C632ASP-1-0.788-0.86924.0510.3030.3030.0000.0000.0000.000
77C633PRO00.0190.00625.500-0.016-0.0160.0000.0000.0000.000
78C634PRO0-0.048-0.00528.578-0.001-0.0010.0000.0000.0000.000
79C635ILE00.006-0.00731.8820.0040.0040.0000.0000.0000.000
80C636ALA00.0280.00734.346-0.007-0.0070.0000.0000.0000.000
81C637LEU0-0.0090.01334.627-0.007-0.0070.0000.0000.0000.000
82C638ASN0-0.008-0.00338.188-0.007-0.0070.0000.0000.0000.000
83C639TRP00.0410.01341.886-0.002-0.0020.0000.0000.0000.000
84C640THR0-0.042-0.01944.6920.0000.0000.0000.0000.0000.000
85C641LEU00.0230.02348.4820.0000.0000.0000.0000.0000.000
86C642LEU0-0.057-0.01049.8010.0000.0000.0000.0000.0000.000
87C643ASN0-0.009-0.01752.783-0.002-0.0020.0000.0000.0000.000
88C644VAL00.0080.00253.8810.0010.0010.0000.0000.0000.000
89C645SER0-0.005-0.00655.821-0.001-0.0010.0000.0000.0000.000
90C646LEU00.0480.01557.8320.0000.0000.0000.0000.0000.000
91C647THR0-0.033-0.00858.7520.0000.0000.0000.0000.0000.000
92C648GLY00.0210.02257.795-0.001-0.0010.0000.0000.0000.000
93C649ILE0-0.010-0.03054.0000.0020.0020.0000.0000.0000.000
94C650HIS00.0090.02751.4050.0010.0010.0000.0000.0000.000
95C651ALA00.0340.01950.783-0.001-0.0010.0000.0000.0000.000
96C652ASP-1-0.828-0.89749.6390.0410.0410.0000.0000.0000.000
97C653ILE00.005-0.00743.9170.0000.0000.0000.0000.0000.000
98C654GLN00.0180.02245.8840.0020.0020.0000.0000.0000.000
99C655VAL00.0200.00639.7670.0010.0010.0000.0000.0000.000
100C656ARG10.8930.92141.883-0.070-0.0700.0000.0000.0000.000
101C657TRP0-0.025-0.00336.2330.0010.0010.0000.0000.0000.000
102C658GLU-1-0.798-0.88337.0470.1100.1100.0000.0000.0000.000
103C659ALA00.0300.00634.8320.0040.0040.0000.0000.0000.000
104C660PRO00.0230.01229.686-0.001-0.0010.0000.0000.0000.000
105C661ARG10.8420.89431.704-0.132-0.1320.0000.0000.0000.000
106C662ASN0-0.035-0.02226.434-0.015-0.0150.0000.0000.0000.000
107C663ALA0-0.016-0.00930.7510.0020.0020.0000.0000.0000.000
108C664ASP-1-0.839-0.92432.1480.1180.1180.0000.0000.0000.000
109C665ILE00.0240.00834.561-0.004-0.0040.0000.0000.0000.000
110C666GLN0-0.024-0.01237.954-0.006-0.0060.0000.0000.0000.000
111C667LYS10.7500.87132.565-0.148-0.1480.0000.0000.0000.000
112C668GLY00.0000.01336.641-0.004-0.0040.0000.0000.0000.000
113C669TRP0-0.027-0.03529.852-0.008-0.0080.0000.0000.0000.000
114C670MET00.0080.03027.8810.0020.0020.0000.0000.0000.000
115C671VAL0-0.020-0.00232.385-0.003-0.0030.0000.0000.0000.000
116C672LEU0-0.001-0.00630.3170.0010.0010.0000.0000.0000.000
117C673GLU-1-0.844-0.91432.3630.0830.0830.0000.0000.0000.000
118C674TYR00.012-0.01732.6770.0150.0150.0000.0000.0000.000
119C675GLU-1-0.716-0.81531.8610.0840.0840.0000.0000.0000.000
120C676LEU0-0.0010.00833.2900.0080.0080.0000.0000.0000.000
121C677GLN0-0.007-0.01830.538-0.002-0.0020.0000.0000.0000.000
122C678TYR00.0300.00535.1860.0030.0030.0000.0000.0000.000
123C679LYS10.7830.89734.395-0.072-0.0720.0000.0000.0000.000
124C680GLU-1-0.750-0.84938.8470.0480.0480.0000.0000.0000.000
125C681VAL00.0460.03138.2780.0010.0010.0000.0000.0000.000
126C682ASN0-0.064-0.05637.8460.0020.0020.0000.0000.0000.000
127C683GLU-1-0.835-0.88338.2920.0440.0440.0000.0000.0000.000
128C684THR00.017-0.00233.3660.0030.0030.0000.0000.0000.000
129C685LYS10.8760.93030.694-0.048-0.0480.0000.0000.0000.000
130C686TRP00.0620.02631.6550.0000.0000.0000.0000.0000.000
131C687LYS10.8060.89935.152-0.051-0.0510.0000.0000.0000.000
132C688MET0-0.033-0.01833.0460.0050.0050.0000.0000.0000.000
133C689MET0-0.029-0.00236.064-0.006-0.0060.0000.0000.0000.000
134C690ASP-1-0.896-0.94636.8820.0560.0560.0000.0000.0000.000
135C691PRO0-0.040-0.00934.3600.0020.0020.0000.0000.0000.000
136C692ILE00.0000.00136.503-0.004-0.0040.0000.0000.0000.000
137C693LEU00.032-0.01037.4240.0060.0060.0000.0000.0000.000
138C694THR0-0.058-0.01839.1650.0020.0020.0000.0000.0000.000
139C695THR0-0.012-0.01237.8860.0020.0020.0000.0000.0000.000
140C696SER0-0.002-0.03240.0770.0010.0010.0000.0000.0000.000
141C697VAL0-0.0180.01040.503-0.001-0.0010.0000.0000.0000.000
142C698PRO0-0.0090.00943.5200.0010.0010.0000.0000.0000.000
143C699VAL00.005-0.00342.0140.0010.0010.0000.0000.0000.000
144C700TYR00.0140.00045.2480.0000.0000.0000.0000.0000.000
145C701SER0-0.052-0.03647.297-0.001-0.0010.0000.0000.0000.000
146C702LEU0-0.0180.01044.310-0.001-0.0010.0000.0000.0000.000
147C703LYS10.8900.91647.732-0.034-0.0340.0000.0000.0000.000
148C704VAL00.0450.01748.8890.0020.0020.0000.0000.0000.000
149C705ASP-1-0.947-0.96550.7480.0340.0340.0000.0000.0000.000
150C706LYS10.7850.88045.359-0.039-0.0390.0000.0000.0000.000
151C707GLU-1-0.863-0.92742.1730.0640.0640.0000.0000.0000.000
152C708TYR0-0.027-0.02241.491-0.002-0.0020.0000.0000.0000.000
153C709GLU-1-0.817-0.89735.3310.0850.0850.0000.0000.0000.000
154C710VAL0-0.015-0.02237.080-0.002-0.0020.0000.0000.0000.000
155C711ARG10.8550.95328.571-0.109-0.1090.0000.0000.0000.000
156C712VAL00.0110.00633.073-0.006-0.0060.0000.0000.0000.000
157C713ARG10.7880.88827.011-0.109-0.1090.0000.0000.0000.000
158C714SER00.0150.00328.937-0.011-0.0110.0000.0000.0000.000
159C715LYS10.8450.91327.980-0.095-0.0950.0000.0000.0000.000
160C716GLN00.0830.02928.469-0.010-0.0100.0000.0000.0000.000
161C717ARG10.9540.98330.359-0.082-0.0820.0000.0000.0000.000
162C718ASN0-0.062-0.03831.863-0.001-0.0010.0000.0000.0000.000
163C719SER0-0.077-0.04327.511-0.006-0.0060.0000.0000.0000.000
164C720GLY00.0600.04024.0890.0020.0020.0000.0000.0000.000
165C721ASN0-0.085-0.04720.9920.0100.0100.0000.0000.0000.000
166C722TYR0-0.051-0.04524.5610.0040.0040.0000.0000.0000.000
167C723GLY00.0220.02323.6130.0190.0190.0000.0000.0000.000
168C724GLU-1-0.888-0.96121.9640.2170.2170.0000.0000.0000.000
169C725PHE0-0.058-0.04524.811-0.018-0.0180.0000.0000.0000.000
170C726SER0-0.014-0.00627.9380.0090.0090.0000.0000.0000.000
171C727GLU-1-0.936-0.96530.5250.1390.1390.0000.0000.0000.000
172C728VAL0-0.044-0.01832.004-0.005-0.0050.0000.0000.0000.000
173C729LEU00.0040.01234.233-0.002-0.0020.0000.0000.0000.000
174C730TYR0-0.009-0.01835.295-0.002-0.0020.0000.0000.0000.000
175C731VAL0-0.047-0.02940.131-0.001-0.0010.0000.0000.0000.000
176C732THR00.0410.02443.460-0.002-0.0020.0000.0000.0000.000
177C733LEU0-0.027-0.00746.3940.0000.0000.0000.0000.0000.000
178C734PRO0-0.0030.00549.409-0.002-0.0020.0000.0000.0000.000