Manual

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: 2LK4R

Calculation Name: 1HWG-B-Xray372

Preferred Name: Growth hormone receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1HWG

Chain ID: B

ChEMBL ID: CHEMBL1976

UniProt ID: P10912

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2133569.864102
FMO2-HF: Nuclear repulsion 2052790.230961
FMO2-HF: Total energy -80779.633141
FMO2-MP2: Total energy -81012.892302


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(B:32:GLU)


Summations of interaction energy for fragment #1(B:32:GLU)
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.
73.59778.7729.872-6.529-8.5160.03
Interaction energy analysis for fragmet #1(B:32:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.963
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].
3B34LYS10.8250.8913.799-41.368-39.307-0.009-0.959-1.0930.006
4B35PHE00.009-0.0015.926-2.616-2.6160.0000.0000.0000.000
5B36THR0-0.036-0.0169.618-0.423-0.4230.0000.0000.0000.000
6B37LYS10.9030.94312.111-15.294-15.2940.0000.0000.0000.000
7B38CYS0-0.093-0.03514.6210.2510.2510.0000.0000.0000.000
8B39ARG10.8110.87417.675-12.079-12.0790.0000.0000.0000.000
9B40SER0-0.013-0.01221.355-0.047-0.0470.0000.0000.0000.000
10B41PRO0-0.039-0.02124.755-0.177-0.1770.0000.0000.0000.000
11B42GLU-1-0.720-0.88427.26010.45910.4590.0000.0000.0000.000
12B43ARG10.8730.93228.628-9.609-9.6090.0000.0000.0000.000
13B44GLU-1-0.961-0.97529.1858.9658.9650.0000.0000.0000.000
14B45THR0-0.114-0.06426.5280.2240.2240.0000.0000.0000.000
15B46PHE00.014-0.00219.4440.0040.0040.0000.0000.0000.000
16B47SER00.0200.02419.5670.1120.1120.0000.0000.0000.000
17B49HIS00.0320.01714.0540.3180.3180.0000.0000.0000.000
18B50TRP0-0.012-0.0068.5530.1490.1490.0000.0000.0000.000
19B51THR00.0020.0005.661-1.275-1.2750.0000.0000.0000.000
20B52ASP-1-0.916-0.9606.75129.35829.3580.0000.0000.0000.000
21B53GLU-1-0.993-0.9871.99630.40128.9397.018-2.386-3.169-0.017
22B63PRO0-0.013-0.0109.8060.9920.9920.0000.0000.0000.000
23B64ILE00.0590.0236.4033.0013.0010.0000.0000.0000.000
24B65GLN0-0.097-0.0449.116-1.954-1.9540.0000.0000.0000.000
25B66LEU0-0.0010.00010.9852.0402.0400.0000.0000.0000.000
26B67PHE00.0140.00512.634-2.097-2.0970.0000.0000.0000.000
27B68TYR0-0.021-0.02215.5320.2990.2990.0000.0000.0000.000
28B69THR0-0.029-0.02518.240-1.032-1.0320.0000.0000.0000.000
29B70ARG10.9580.97921.138-11.620-11.6200.0000.0000.0000.000
30B71ARG10.8980.96523.903-11.784-11.7840.0000.0000.0000.000
31B72ASN0-0.032-0.03826.581-0.073-0.0730.0000.0000.0000.000
32B73THR0-0.003-0.01827.548-0.552-0.5520.0000.0000.0000.000
33B74GLN00.0540.03827.3170.1970.1970.0000.0000.0000.000
34B75GLU-1-0.873-0.91426.89211.83911.8390.0000.0000.0000.000
35B76TRP00.023-0.00721.5040.1490.1490.0000.0000.0000.000
36B77THR0-0.044-0.01520.8740.4880.4880.0000.0000.0000.000
37B78GLN00.024-0.00119.7491.3141.3140.0000.0000.0000.000
38B79GLU-1-0.931-0.94721.25213.21813.2180.0000.0000.0000.000
39B80TRP0-0.070-0.04215.7170.0800.0800.0000.0000.0000.000
40B81LYS10.8720.94519.807-14.299-14.2990.0000.0000.0000.000
41B82GLU-1-0.784-0.85116.20620.15520.1550.0000.0000.0000.000
42B83CYS0-0.068-0.01715.465-1.261-1.2610.0000.0000.0000.000
43B84PRO0-0.049-0.01318.625-0.230-0.2300.0000.0000.0000.000
44B85ASP-1-0.808-0.88420.57312.66712.6670.0000.0000.0000.000
45B86TYR00.008-0.04813.9910.7620.7620.0000.0000.0000.000
46B87VAL0-0.0220.01017.6710.3720.3720.0000.0000.0000.000
47B88SER0-0.009-0.03920.383-0.233-0.2330.0000.0000.0000.000
48B89ALA0-0.098-0.03719.738-0.432-0.4320.0000.0000.0000.000
49B90GLY00.009-0.00119.4820.2540.2540.0000.0000.0000.000
50B91GLU-1-0.959-0.97214.01817.35017.3500.0000.0000.0000.000
51B92ASN0-0.018-0.00510.9141.1401.1400.0000.0000.0000.000
52B93SER00.0310.00913.2940.3420.3420.0000.0000.0000.000
53B95TYR0-0.015-0.01917.480-0.368-0.3680.0000.0000.0000.000
54B96PHE00.000-0.00518.339-0.085-0.0850.0000.0000.0000.000
55B97ASN00.0730.02323.545-0.463-0.4630.0000.0000.0000.000
56B98SER00.1240.04127.1950.2150.2150.0000.0000.0000.000
57B99SER0-0.038-0.00429.852-0.141-0.1410.0000.0000.0000.000
58B100PHE0-0.062-0.02824.8390.0550.0550.0000.0000.0000.000
59B101THR0-0.0200.01725.4350.7330.7330.0000.0000.0000.000
60B102SER0-0.028-0.00426.902-0.457-0.4570.0000.0000.0000.000
61B103ILE0-0.007-0.00627.2420.4250.4250.0000.0000.0000.000
62B104TRP0-0.020-0.02028.676-0.319-0.3190.0000.0000.0000.000
63B105ILE0-0.0300.00226.068-0.084-0.0840.0000.0000.0000.000
64B106PRO0-0.024-0.00923.3310.2680.2680.0000.0000.0000.000
65B107TYR0-0.003-0.02620.146-0.335-0.3350.0000.0000.0000.000
66B108CYS0-0.066-0.03213.978-0.232-0.2320.0000.0000.0000.000
67B109ILE0-0.031-0.03013.469-0.544-0.5440.0000.0000.0000.000
68B110LYS10.9710.98911.103-22.296-22.2960.0000.0000.0000.000
69B111LEU00.0060.0126.466-2.090-2.0900.0000.0000.0000.000
70B112THR0-0.002-0.0137.4753.0463.0460.0000.0000.0000.000
71B113SER00.0480.0343.392-11.612-10.6960.014-0.440-0.4900.003
72B114ASN0-0.008-0.0275.775-0.226-0.187-0.0010.000-0.0380.000
73B115GLY0-0.007-0.0018.423-0.672-0.6720.0000.0000.0000.000
74B116GLY0-0.018-0.0046.981-2.944-2.9440.0000.0000.0000.000
75B117THR0-0.053-0.0306.3433.5503.5500.0000.0000.0000.000
76B118VAL00.0450.0392.564-5.649-2.1212.851-2.719-3.6590.038
77B119ASP-1-0.810-0.8974.57930.78930.882-0.001-0.025-0.0670.000
78B120GLU-1-0.954-0.9727.33221.07421.0740.0000.0000.0000.000
79B121LYS10.9090.96711.153-18.849-18.8490.0000.0000.0000.000
80B123PHE0-0.033-0.00816.6860.1040.1040.0000.0000.0000.000
81B124SER00.0330.00720.523-0.086-0.0860.0000.0000.0000.000
82B125VAL00.011-0.00723.5150.1060.1060.0000.0000.0000.000
83B126ASP-1-0.845-0.93824.73010.88610.8860.0000.0000.0000.000
84B127GLU-1-0.873-0.92022.62812.91412.9140.0000.0000.0000.000
85B128ILE0-0.056-0.01319.1640.2390.2390.0000.0000.0000.000
86B129VAL00.0260.01923.1130.0340.0340.0000.0000.0000.000
87B130GLN00.003-0.00222.7900.3800.3800.0000.0000.0000.000
88B131PRO0-0.0050.01526.3690.2120.2120.0000.0000.0000.000
89B132ASP-1-0.778-0.85827.89410.87410.8740.0000.0000.0000.000
90B133PRO00.0210.01129.338-0.187-0.1870.0000.0000.0000.000
91B134PRO0-0.070-0.03432.061-0.107-0.1070.0000.0000.0000.000
92B135ILE00.017-0.00634.3780.0580.0580.0000.0000.0000.000
93B136ALA00.018-0.00737.704-0.140-0.1400.0000.0000.0000.000
94B137LEU00.0270.02837.358-0.190-0.1900.0000.0000.0000.000
95B138ASN0-0.064-0.04441.096-0.204-0.2040.0000.0000.0000.000
96B139TRP00.0430.00544.6300.0110.0110.0000.0000.0000.000
97B140THR0-0.0140.00747.200-0.106-0.1060.0000.0000.0000.000
98B141LEU00.0150.00751.0010.0560.0560.0000.0000.0000.000
99B142LEU0-0.044-0.02051.975-0.055-0.0550.0000.0000.0000.000
100B143ASN0-0.060-0.04354.880-0.180-0.1800.0000.0000.0000.000
101B144VAL00.0450.01155.7500.0960.0960.0000.0000.0000.000
102B145SER0-0.0200.01357.942-0.119-0.1190.0000.0000.0000.000
103B146LEU00.0480.00359.8570.0000.0000.0000.0000.0000.000
104B147THR0-0.046-0.03059.805-0.020-0.0200.0000.0000.0000.000
105B148GLY00.0050.00359.637-0.001-0.0010.0000.0000.0000.000
106B149ILE0-0.028-0.00555.0320.0700.0700.0000.0000.0000.000
107B150HIS0-0.0040.00053.2930.1700.1700.0000.0000.0000.000
108B151ALA00.0380.01253.064-0.126-0.1260.0000.0000.0000.000
109B152ASP-1-0.820-0.87051.5105.8335.8330.0000.0000.0000.000
110B153ILE00.0090.00145.792-0.079-0.0790.0000.0000.0000.000
111B154GLN00.0490.01748.8870.0460.0460.0000.0000.0000.000
112B155VAL0-0.007-0.00842.2370.0030.0030.0000.0000.0000.000
113B156ARG10.8750.92444.582-6.718-6.7180.0000.0000.0000.000
114B157TRP0-0.031-0.00439.6580.0500.0500.0000.0000.0000.000
115B158GLU-1-0.867-0.91340.3456.9196.9190.0000.0000.0000.000
116B159ALA00.0470.04037.6640.1790.1790.0000.0000.0000.000
117B160PRO00.0510.02733.051-0.146-0.1460.0000.0000.0000.000
118B161ARG10.8250.88435.193-7.865-7.8650.0000.0000.0000.000
119B162ASN0-0.010-0.01030.097-0.366-0.3660.0000.0000.0000.000
120B163ALA00.0420.03633.9960.1220.1220.0000.0000.0000.000
121B164ASP-1-0.784-0.89034.9567.6367.6360.0000.0000.0000.000
122B165ILE0-0.011-0.01337.643-0.038-0.0380.0000.0000.0000.000
123B166GLN0-0.018-0.01039.684-0.084-0.0840.0000.0000.0000.000
124B167LYS10.8090.89240.218-7.907-7.9070.0000.0000.0000.000
125B168GLY0-0.0010.00241.0920.0360.0360.0000.0000.0000.000
126B169TRP0-0.0090.01632.719-0.069-0.0690.0000.0000.0000.000
127B170MET0-0.0310.01831.3390.3250.3250.0000.0000.0000.000
128B171VAL0-0.022-0.02235.888-0.280-0.2800.0000.0000.0000.000
129B172LEU0-0.013-0.00433.5700.2260.2260.0000.0000.0000.000
130B173GLU-1-0.866-0.91235.3228.2448.2440.0000.0000.0000.000
131B174TYR0-0.005-0.02735.5530.3100.3100.0000.0000.0000.000
132B175GLU-1-0.742-0.82233.4208.9268.9260.0000.0000.0000.000
133B176LEU00.0100.01236.1200.1080.1080.0000.0000.0000.000
134B177GLN0-0.011-0.03332.424-0.017-0.0170.0000.0000.0000.000
135B178TYR00.0170.00637.5670.0150.0150.0000.0000.0000.000
136B179LYS10.8000.89635.636-7.870-7.8700.0000.0000.0000.000
137B180GLU-1-0.732-0.85040.5196.4586.4580.0000.0000.0000.000
138B181VAL00.0200.01639.4620.1740.1740.0000.0000.0000.000
139B182ASN0-0.013-0.00239.3490.1700.1700.0000.0000.0000.000
140B183GLU-1-0.793-0.84739.7127.0047.0040.0000.0000.0000.000
141B184THR00.009-0.00435.4430.0990.0990.0000.0000.0000.000
142B185LYS10.8580.91534.993-7.021-7.0210.0000.0000.0000.000
143B186TRP00.0610.01533.111-0.184-0.1840.0000.0000.0000.000
144B187LYS10.7690.89636.919-6.933-6.9330.0000.0000.0000.000
145B188MET00.010-0.00534.1520.1190.1190.0000.0000.0000.000
146B189MET0-0.038-0.01238.396-0.139-0.1390.0000.0000.0000.000
147B190ASP-1-0.909-0.94839.2257.2637.2630.0000.0000.0000.000
148B191PRO0-0.024-0.02336.853-0.066-0.0660.0000.0000.0000.000
149B192ILE00.0110.02539.181-0.195-0.1950.0000.0000.0000.000
150B193LEU00.013-0.01340.0090.1740.1740.0000.0000.0000.000
151B194THR0-0.038-0.01141.990-0.013-0.0130.0000.0000.0000.000
152B195THR00.006-0.00441.1770.1240.1240.0000.0000.0000.000
153B196SER0-0.052-0.03143.363-0.109-0.1090.0000.0000.0000.000
154B197VAL00.0100.00143.1690.0260.0260.0000.0000.0000.000
155B198PRO00.0330.04046.3560.0280.0280.0000.0000.0000.000
156B199VAL00.0000.00843.7400.0620.0620.0000.0000.0000.000
157B200TYR0-0.020-0.02746.987-0.084-0.0840.0000.0000.0000.000
158B201SER0-0.077-0.05049.0150.0500.0500.0000.0000.0000.000
159B202LEU0-0.0010.01945.9460.0610.0610.0000.0000.0000.000
160B203LYS10.9450.95949.404-5.997-5.9970.0000.0000.0000.000
161B204VAL00.002-0.01550.3510.0880.0880.0000.0000.0000.000
162B205ASP-1-0.906-0.94751.6645.8275.8270.0000.0000.0000.000
163B206LYS10.7680.88046.719-6.207-6.2070.0000.0000.0000.000
164B207GLU-1-0.846-0.89443.7066.6066.6060.0000.0000.0000.000
165B208TYR0-0.090-0.07142.7510.0890.0890.0000.0000.0000.000
166B209GLU-1-0.775-0.86936.8927.9197.9190.0000.0000.0000.000
167B210VAL0-0.033-0.03139.0160.0150.0150.0000.0000.0000.000
168B211ARG10.9340.98029.841-9.076-9.0760.0000.0000.0000.000
169B212VAL00.005-0.00535.284-0.108-0.1080.0000.0000.0000.000
170B213ARG10.9020.94328.516-9.559-9.5590.0000.0000.0000.000
171B214SER00.0340.01132.314-0.239-0.2390.0000.0000.0000.000
172B215LYS10.8600.92330.471-8.824-8.8240.0000.0000.0000.000
173B216GLN00.0420.03230.841-0.324-0.3240.0000.0000.0000.000
174B217ARG10.9360.96032.524-7.635-7.6350.0000.0000.0000.000
175B218ASN0-0.033-0.01533.2550.0270.0270.0000.0000.0000.000
176B219SER00.004-0.01228.5310.1720.1720.0000.0000.0000.000
177B220GLY00.0250.02325.753-0.209-0.2090.0000.0000.0000.000
178B221ASN0-0.057-0.03425.2390.0300.0300.0000.0000.0000.000
179B222TYR0-0.023-0.02827.035-0.088-0.0880.0000.0000.0000.000
180B223GLY0-0.023-0.01526.4500.4260.4260.0000.0000.0000.000
181B224GLU-1-0.936-0.95923.78511.60811.6080.0000.0000.0000.000
182B225PHE0-0.059-0.05127.679-0.314-0.3140.0000.0000.0000.000
183B226SER0-0.008-0.00630.5000.1170.1170.0000.0000.0000.000
184B227GLU-1-0.924-0.95031.8239.1289.1280.0000.0000.0000.000
185B228VAL0-0.057-0.03433.530-0.155-0.1550.0000.0000.0000.000
186B229LEU0-0.0230.00336.094-0.119-0.1190.0000.0000.0000.000
187B230TYR00.005-0.02336.6620.0500.0500.0000.0000.0000.000
188B231VAL0-0.052-0.03041.942-0.105-0.1050.0000.0000.0000.000
189B232THR00.017-0.01545.3100.0430.0430.0000.0000.0000.000
190B233LEU0-0.063-0.02748.103-0.057-0.0570.0000.0000.0000.000
191B234PRO00.0010.01551.219-0.062-0.0620.0000.0000.0000.000